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Sample records for microsatellite enriched genomic

  1. Development of microsatellite markers from an enriched genomic library for genetic analysis of melon (Cucumis melo L.)

    PubMed Central

    Ritschel, Patricia Silva; Lins, Tulio Cesar de Lima; Tristan, Rodrigo Lourenço; Buso, Gláucia Salles Cortopassi; Buso, José Amauri; Ferreira, Márcio Elias

    2004-01-01

    Background Despite the great advances in genomic technology observed in several crop species, the availability of molecular tools such as microsatellite markers has been limited in melon (Cucumis melo L.) and cucurbit species. The development of microsatellite markers will have a major impact on genetic analysis and breeding of melon, especially on the generation of marker saturated genetic maps and implementation of marker assisted breeding programs. Genomic microsatellite enriched libraries can be an efficient alternative for marker development in such species. Results Seven hundred clones containing microsatellite sequences from a Tsp-AG/TC microsatellite enriched library were identified and one-hundred and forty-four primer pairs designed and synthesized. When 67 microsatellite markers were tested on a panel of melon and other cucurbit accessions, 65 revealed DNA polymorphisms among the melon accessions. For some cucurbit species, such as Cucumis sativus, up to 50% of the melon microsatellite markers could be readily used for DNA polymophism assessment, representing a significant reduction of marker development costs. A random sample of 25 microsatellite markers was extracted from the new microsatellite marker set and characterized on 40 accessions of melon, generating an allelic frequency database for the species. The average expected heterozygosity was 0.52, varying from 0.45 to 0.70, indicating that a small set of selected markers should be sufficient to solve questions regarding genotype identity and variety protection. Genetic distances based on microsatellite polymorphism were congruent with data obtained from RAPD marker analysis. Mapping analysis was initiated with 55 newly developed markers and most primers showed segregation according to Mendelian expectations. Linkage analysis detected linkage between 56% of the markers, distributed in nine linkage groups. Conclusions Genomic library microsatellite enrichment is an efficient procedure for marker

  2. Microsatellite markers isolated from Cabomba aquatica s.l. (Cabombaceae) from an enriched genomic library1

    PubMed Central

    Barbosa, Tiago D. M.; Trad, Rafaela J.; Bajay, Miklos M.; Amaral, Maria C. E.

    2015-01-01

    Premise of the study: Microsatellite primers were designed for the submersed aquatic plant Cabomba aquatica s.l. (Cabombaceae) and characterized to estimate genetic diversity parameters. Methods and Results: Using a selective hybridization method, we designed and tested 30 simple sequence repeat loci using two natural populations of C. aquatica s.l., resulting in 13 amplifiable loci. Twelve loci were polymorphic, and alleles per locus ranged from two to four across the 49 C. aquatica s.l. individuals. Observed heterozygosity, expected heterozygosity, and fixation index varied from 0.0 to 1.0, 0.0 to 0.5, and −1.0 to −0.0667, respectively, for the Manaus population and from 0.0 to 1.0, 0.0 to 0.6, and −1.0 to 0.4643 for the Viruá population. Conclusions: The developed markers will be used in further taxonomic and population studies within Cabomba. This set of microsatellite primers represents the first report on rapid molecular markers in the genus. PMID:26649271

  3. Development of microsatellite markers for common bean (Phaseolus vulgaris L.) based on screening of non-enriched, small-insert genomic libraries.

    PubMed

    Blair, Matthew W; Torres, Monica Muñoz; Pedraza, Fabio; Giraldo, Martha C; Buendía, Hector F; Hurtado, Natalia

    2009-09-01

    Microsatellite markers are useful genetic tools for a wide array of genomic analyses although their development is time-consuming and requires the identification of simple sequence repeats (SSRs) from genomic sequences. Screening of non-enriched, small-insert libraries is an effective method of SSR isolation that can give an unbiased picture of motif frequency. Here we adapt high-throughput protocols for the screening of plasmid-based libraries using robotic colony picking and filter preparation. Seven non-enriched genomic libraries from common bean genomic DNA were made by digestion with four frequently cutting restriction enzymes, double digestion with a frequently cutting restriction enzyme and a less frequently cutting restriction enzyme, or sonication. Library quality was compared and three of the small-insert libraries were selected for further analysis. Each library was plated and picked into 384-well plates that were used to create high-density filter arrays of over 18 000 clones each, which were screened with oligonucleotide probes for various SSR motifs. Positive clones were found to have low redundancy. One hundred SSR markers were developed and 80 were tested for polymorphism in a standard parental survey. These microsatellite markers derived from non-SSR-enriched libraries should be useful additions to previous markers developed from enriched libraries. PMID:19935925

  4. Optimized construction of microsatellite-enriched libraries

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The construction of simple sequence repeat (SSR) libraries is an indispensable tool to search for molecular markers as complete genome sequences are still not available for the majority of species of interest. Numerous protocols are available in the literature for the construction of SSR-enriched l...

  5. Microsatellites in Pursuit of Microbial Genome Evolution

    PubMed Central

    Saeed, Abdullah F.; Wang, Rongzhi; Wang, Shihua

    2016-01-01

    Microsatellites or short sequence repeats are widespread genetic markers which are hypermutable 1–6 bp long short nucleotide motifs. Significantly, their applications in genetics are extensive due to their ceaseless mutational degree, widespread length variations and hypermutability skills. These features make them useful in determining the driving forces of evolution by using powerful molecular techniques. Consequently, revealing important questions, for example, what is the significance of these abundant sequences in DNA, what are their roles in genomic evolution? The answers of these important questions are hidden in the ways these short motifs contributed in altering the microbial genomes since the origin of life. Even though their size ranges from 1 –to- 6 bases, these repeats are becoming one of the most popular genetic probes in determining their associations and phylogenetic relationships in closely related genomes. Currently, they have been widely used in molecular genetics, biotechnology and evolutionary biology. However, due to limited knowledge; there is a significant gap in research and lack of information concerning hypermutational mechanisms. These mechanisms play a key role in microsatellite loci point mutations and phase variations. This review will extend the understandings of impacts and contributions of microsatellite in genomic evolution and their universal applications in microbiology. PMID:26779133

  6. The physical and genomic organization of microsatellites in sugar beet.

    PubMed

    Schmidt, T; Heslop-Harrison, J S

    1996-08-01

    Microsatellites, tandem arrays of short (2-5 bp) nucleotide motifs, are present in high numbers in most eukaryotic genomes. We have characterized the physical distribution of microsatellites on chromosomes of sugar beet (Beta vulgaris L.). Each microsatellite sequence shows a characteristic genomic distribution and motif-dependent dispersion, with site-specific amplification on one to seven pairs of centromeres or intercalary chromosomal regions and weaker, dispersed hybridization along chromosomes. Exclusion of some microsatellites from 18S-5.8S-25S rRNA gene sites, centromeres, and intercalary sites was observed. In-gel and in situ hybridization patterns are correlated, with highly repeated restriction fragments indicating major centromeric sites of microsatellite arrays. The results have implications for genome evolution and the suitability of particular microsatellite markers for genetic mapping and genome analysis. PMID:8710945

  7. Microsatellites in the Genome of the Edible Mushroom, Volvariella volvacea

    PubMed Central

    Chen, Mingjie; Wang, Hong; Bao, Dapeng

    2014-01-01

    Using bioinformatics software and database, we have characterized the microsatellite pattern in the V. volvacea genome and compared it with microsatellite patterns found in the genomes of four other edible fungi: Coprinopsis cinerea, Schizophyllum commune, Agaricus bisporus, and Pleurotus ostreatus. A total of 1346 microsatellites have been identified, with mono-nucleotides being the most frequent motif. The relative abundance of microsatellites was lower in coding regions with 21 No./Mb. However, the microsatellites in the V. volvacea gene models showed a greater tendency to be located in the CDS regions. There was also a higher preponderance of trinucleotide repeats, especially in the kinase genes, which implied a possible role in phenotypic variation. Among the five fungal genomes, microsatellite abundance appeared to be unrelated to genome size. Furthermore, the short motifs (mono- to tri-nucleotides) outnumbered other categories although these differed in proportion. Data analysis indicated a possible relationship between the most frequent microsatellite types and the genetic distance between the five fungal genomes. PMID:24575404

  8. Microsatellites in the genome of the edible mushroom, Volvariella volvacea.

    PubMed

    Wang, Ying; Chen, Mingjie; Wang, Hong; Wang, Jing-Fang; Bao, Dapeng

    2014-01-01

    Using bioinformatics software and database, we have characterized the microsatellite pattern in the V. volvacea genome and compared it with microsatellite patterns found in the genomes of four other edible fungi: Coprinopsis cinerea, Schizophyllum commune, Agaricus bisporus, and Pleurotus ostreatus. A total of 1346 microsatellites have been identified, with mono-nucleotides being the most frequent motif. The relative abundance of microsatellites was lower in coding regions with 21 No./Mb. However, the microsatellites in the V. volvacea gene models showed a greater tendency to be located in the CDS regions. There was also a higher preponderance of trinucleotide repeats, especially in the kinase genes, which implied a possible role in phenotypic variation. Among the five fungal genomes, microsatellite abundance appeared to be unrelated to genome size. Furthermore, the short motifs (mono- to tri-nucleotides) outnumbered other categories although these differed in proportion. Data analysis indicated a possible relationship between the most frequent microsatellite types and the genetic distance between the five fungal genomes. PMID:24575404

  9. Genomic leftovers: identifying novel microsatellites, over-represented motifs and functional elements in the human genome.

    PubMed

    Fonville, Natalie C; Velmurugan, Karthik Raja; Tae, Hongseok; Vaksman, Zalman; McIver, Lauren J; Garner, Harold R

    2016-01-01

    The human genome is 99% complete. This study contributes to filling the 1% gap by enriching previously unknown repeat regions called microsatellites (MST). We devised a Global MST Enrichment (GME) kit to enrich and nextgen sequence 2 colorectal cell lines and 16 normal human samples to illustrate its utility in identifying contigs from reads that do not map to the genome reference. The analysis of these samples yielded 790 novel extra-referential concordant contigs that are observed in more than one sample. We searched for evidence of functional elements in the concordant contigs in two ways: (1) BLAST-ing each contig against normal RNA-Seq samples, (2) Checking for predicted functional elements using GlimmerHMM. Of the 790 concordant contigs, 37 had an exact match to at least one RNA-Seq read; 15 aligned to more than 100 RNA-Seq reads. Of the 249 concordant contigs predicted by GlimmerHMM to have functional elements, 6 had at least one exact RNA-Seq match. BLAST-ing these novel contigs against all publically available sequences confirmed that they were found in human and chimpanzee BAC and FOSMID clones sequenced as part of the original human genome project. These extra-referential contigs predominantly contained pentameric repeats, especially two motifs: AATGG and GTGGA. PMID:27278669

  10. Genomic leftovers: identifying novel microsatellites, over-represented motifs and functional elements in the human genome

    PubMed Central

    Fonville, Natalie C.; Velmurugan, Karthik Raja; Tae, Hongseok; Vaksman, Zalman; McIver, Lauren J.; Garner, Harold R.

    2016-01-01

    The human genome is 99% complete. This study contributes to filling the 1% gap by enriching previously unknown repeat regions called microsatellites (MST). We devised a Global MST Enrichment (GME) kit to enrich and nextgen sequence 2 colorectal cell lines and 16 normal human samples to illustrate its utility in identifying contigs from reads that do not map to the genome reference. The analysis of these samples yielded 790 novel extra-referential concordant contigs that are observed in more than one sample. We searched for evidence of functional elements in the concordant contigs in two ways: (1) BLAST-ing each contig against normal RNA-Seq samples, (2) Checking for predicted functional elements using GlimmerHMM. Of the 790 concordant contigs, 37 had an exact match to at least one RNA-Seq read; 15 aligned to more than 100 RNA-Seq reads. Of the 249 concordant contigs predicted by GlimmerHMM to have functional elements, 6 had at least one exact RNA-Seq match. BLAST-ing these novel contigs against all publically available sequences confirmed that they were found in human and chimpanzee BAC and FOSMID clones sequenced as part of the original human genome project. These extra-referential contigs predominantly contained pentameric repeats, especially two motifs: AATGG and GTGGA. PMID:27278669

  11. Genomic microsatellites as evolutionary chronometers: a test in wild cats.

    PubMed

    Driscoll, Carlos A; Menotti-Raymond, Marilyn; Nelson, George; Goldstein, David; O'Brien, Stephen J

    2002-03-01

    Nuclear microsatellite loci (2- to 5-bp tandem repeats) would seem to be ideal markers for population genetic monitoring because of their abundant polymorphism, wide dispersal in vertebrate genomes, near selective neutrality, and ease of assessment; however, questions about their mode of generation, mutation rates and ascertainment bias have limited interpretation considerably. We have assessed the patterns of genomic diversity for ninety feline microsatellite loci among previously characterized populations of cheetahs, lions and pumas in recapitulating demographic history. The results imply that the microsatellite diversity measures (heterozygosity, allele reconstitution and microsatellite allele variance) offer proportionate indicators, albeit with large variance, of historic population bottlenecks and founder effects. The observed rate of reconstruction of new alleles plus the growth in the breadth of microsatellite allele size (variance) was used here to develop genomic estimates of time intervals following historic founder events in cheetahs (12,000 yr ago), in North American pumas (10,000-17,000 yr ago), and in Asiatic lions of the Gir Forest (1000-4000 yr ago). PMID:11875029

  12. Microsatellite landscape evolutionary dynamics across 450 million years of vertebrate genome evolution.

    PubMed

    Adams, Richard H; Blackmon, Heath; Reyes-Velasco, Jacobo; Schield, Drew R; Card, Daren C; Andrew, Audra L; Waynewood, Nyimah; Castoe, Todd A

    2016-05-01

    The evolutionary dynamics of simple sequence repeats (SSRs or microsatellites) across the vertebrate tree of life remain largely undocumented and poorly understood. In this study, we analyzed patterns of genomic microsatellite abundance and evolution across 71 vertebrate genomes. The highest abundances of microsatellites exist in the genomes of ray-finned fishes, squamate reptiles, and mammals, while crocodilian, turtle, and avian genomes exhibit reduced microsatellite landscapes. We used comparative methods to infer evolutionary rates of change in microsatellite abundance across vertebrates and to highlight particular lineages that have experienced unusually high or low rates of change in genomic microsatellite abundance. Overall, most variation in microsatellite content, abundance, and evolutionary rate is observed among major lineages of reptiles, yet we found that several deeply divergent clades (i.e., squamate reptiles and mammals) contained relatively similar genomic microsatellite compositions. Archosauromorph reptiles (turtles, crocodilians, and birds) exhibit reduced genomic microsatellite content and the slowest rates of microsatellite evolution, in contrast to squamate reptile genomes that have among the highest rates of microsatellite evolution. Substantial branch-specific shifts in SSR content in primates, monotremes, rodents, snakes, and fish are also evident. Collectively, our results support multiple major shifts in microsatellite genomic landscapes among vertebrates. PMID:27064176

  13. Development of microsatellite loci in Artocarpus altilis (Moraceae) and cross-amplification in congeneric species

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Microsatellite loci were isolated and characterized from enriched genomic libraries of Artocarpus altilis (breadfruit) and tested in three other Artocarpus species and one hybrid. The microsatellite markers provide new tools for further studies in Artocarpus. Nineteen microsatellite primers were tes...

  14. Isolation and characterization of novel microsatellite markers from the sika deer (Cervus nippon) genome.

    PubMed

    Li, Y M; Bai, C Y; Niu, W P; Yu, H; Yang, R J; Yan, S Q; Zhang, J Y; Zhang, M J; Zhao, Z H

    2015-01-01

    Microsatellite markers are widely and evenly distributed, and are highly polymorphic. Rapid and convenient detection through automated analysis means that microsatellite markers are widely used in the construction of plant and animal genetic maps, in quantitative trait loci localization, marker-assisted selection, identification of genetic relationships, and genetic diversity and phylogenetic tree construction. However, few microsatellite markers remain to be isolated. We used streptavidin magnetic beads to affinity-capture and construct a (CA)n microsatellite DNA-enriched library from sika deer. We selected sequences containing more than six repeats to design primers. Clear bands were selected, which were amplified using non-specific primers following PCR amplification to screen polymorphisms in a group of 65 unrelated sika deer. The positive clone rate reached 82.9% by constructing the enriched library, and we then selected positive clones for sequencing. There were 395 sequences with CA repeats, and the CA repeat number was 4-105. We selected sequences containing more than six repeats to design primers, of which 297 pairs were designed. We next selected clear bands and used non-specific primers to amplify following PCR amplification. In total, 245 pairs of primers were screened. We then selected 50 pairs of primers to randomly screen for polymorphisms. We detected 47 polymorphic and 3 monomorphic loci in 65 unrelated sika deer. These newly isolated and characterized microsatellite loci can be used to construct genetic maps and for lineage testing in deer. In addition, they can be used for comparative genomics between Cervidae species. PMID:26436393

  15. Low abundance of microsatellite repeats in the genome of the Brown-headed Cowbird (Molothrus ater)

    USGS Publications Warehouse

    Longmire, J.L.; Hahn, D.C.; Roach, J.L.

    1999-01-01

    A cosmid library made from brown-headed cowbird (Molothrus ater) DNA was examined for representation of 17 distinct microsatellite motifs including all possible mono-, di-, and trinucleotide microsatellites, and the tetranucleotide repeat (GATA)n. The overall density of microsatellites within cowbird DNA was found to be one repeat per 89 kb and the frequency of the most abundant motif, (AGC)n, was once every 382 kb. The abundance of microsatellites within the cowbird genome is estimated to be reduced approximately 15-fold compared to humans. The reduced frequency of microsatellites seen in this study is consistent with previous observations indicating reduced numbers of microsatellites and other interspersed repeats in avian DNA. In addition to providing new information concerning the abundance of microsatellites within an avian genome, these results provide useful insights for selecting cloning strategies that might be used in the development of locus-specific microsatellite markers for avian studies.

  16. Genome-Wide Mining, Characterization, and Development of Microsatellite Markers in Gossypium Species

    PubMed Central

    Wang, Qiong; Fang, Lei; Chen, Jiedan; Hu, Yan; Si, Zhanfeng; Wang, Sen; Chang, Lijing; Guo, Wangzhen; Zhang, Tianzhen

    2015-01-01

    Although much research has been conducted to characterize microsatellites and develop markers, the distribution of microsatellites remains ambiguous and the use of microsatellite markers in genomic studies and marker-assisted selection is limited. To identify microsatellites for cotton research, we mined 100,290, 83,160, and 56,937 microsatellites with frequencies of 41.2, 49.1, and 74.8 microsatellites per Mb in the recently sequenced Gossypium species: G. hirsutum, G. arboreum, and G. raimondii, respectively. The distributions of microsatellites in their genomes were non-random and were positively and negatively correlated with genes and transposable elements, respectively. Of the 77,996 developed microsatellite markers, 65,498 were physically anchored to the 26 chromosomes of G. hirsutum with an average marker density of 34 markers per Mb. We confirmed 67,880 (87%) universal and 7,705 (9.9%) new genic microsatellite markers. The polymorphism was estimated in above three species by in silico PCR and validated with 505 markers in G. hirsutum. We further predicted 8,825 polymorphic microsatellite markers within G. hirsutum acc. TM-1 and G. barbadense cv. Hai7124. In our study, genome-wide mining and characterization of microsatellites, and marker development were very useful for the saturation of the allotetraploid genetic linkage map, genome evolution studies and comparative genome mapping. PMID:26030481

  17. Genome Variability and Gene Content in Chordopoxviruses: Dependence on Microsatellites

    PubMed Central

    Hatcher, Eneida L.; Wang, Chunlin; Lefkowitz, Elliot J.

    2015-01-01

    To investigate gene loss in poxviruses belonging to the Chordopoxvirinae subfamily, we assessed the gene content of representative members of the subfamily, and determined whether individual genes present in each genome were intact, truncated, or fragmented. When nonintact genes were identified, the early stop mutations (ESMs) leading to gene truncation or fragmentation were analyzed. Of all the ESMs present in these poxvirus genomes, over 65% co-localized with microsatellites—simple sequence nucleotide repeats. On average, microsatellites comprise 24% of the nucleotide sequence of these poxvirus genomes. These simple repeats have been shown to exhibit high rates of variation, and represent a target for poxvirus protein variation, gene truncation, and reductive evolution. PMID:25912716

  18. Genetic Variation Between Two Cucumber Genotypes Inferred from Genome-wide Microsatellite Polymorphism Analysis

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Variability at microsatellite loci has been used widely to infer the extent of genetic diversity among related plant taxa. However, typically, only the most polymorphic loci in the genome were analyzed that may result in a biased, and generally overestimated picture of genome-wide microsatellite div...

  19. REEF: searching REgionally Enriched Features in genomes

    PubMed Central

    Coppe, Alessandro; Danieli, Gian Antonio; Bortoluzzi, Stefania

    2006-01-01

    Background In Eukaryotic genomes, different features including genes are not uniformly distributed. The integration of annotation information and genomic position of functional DNA elements in the Eukaryotic genomes opened the way to test novel hypotheses of higher order genome organization and regulation of expression. Results REEF is a new tool, aimed at identifying genomic regions enriched in specific features, such as a class or group of genes homogeneous for expression and/or functional characteristics. The method for the calculation of local feature enrichment uses test statistic based on the Hypergeometric Distribution applied genome-wide by using a sliding window approach and adopting the False Discovery Rate for controlling multiplicity. REEF software, source code and documentation are freely available at . Conclusion REEF can aid to shed light on the role of organization of specific genomic regions in the determination of their functional role. PMID:17042935

  20. Genome-Wide Microsatellite Identification in the Fungus Anisogramma anomala Using Illumina Sequencing and Genome Assembly

    PubMed Central

    Cai, Guohong; Leadbetter, Clayton W.; Muehlbauer, Megan F.; Molnar, Thomas J.; Hillman, Bradley I.

    2013-01-01

    High-throughput sequencing has been dramatically accelerating the discovery of microsatellite markers (also known as Simple Sequence Repeats). Both 454 and Illumina reads have been used directly in microsatellite discovery and primer design (the “Seq-to-SSR” approach). However, constraints of this approach include: 1) many microsatellite-containing reads do not have sufficient flanking sequences to allow primer design, and 2) difficulties in removing microsatellite loci residing in longer, repetitive regions. In the current study, we applied the novel “Seq-Assembly-SSR” approach to overcome these constraints in Anisogramma anomala. In our approach, Illumina reads were first assembled into a draft genome, and the latter was then used in microsatellite discovery. A. anomala is an obligate biotrophic ascomycete that causes eastern filbert blight disease of commercial European hazelnut. Little is known about its population structure or diversity. Approximately 26 M 146 bp Illumina reads were generated from a paired-end library of a fungal strain from Oregon. The reads were assembled into a draft genome of 333 Mb (excluding gaps), with contig N50 of 10,384 bp and scaffold N50 of 32,987 bp. A bioinformatics pipeline identified 46,677 microsatellite motifs at 44,247 loci, including 2,430 compound loci. Primers were successfully designed for 42,923 loci (97%). After removing 2,886 loci close to assembly gaps and 676 loci in repetitive regions, a genome-wide microsatellite database of 39,361 loci was generated for the fungus. In experimental screening of 236 loci using four geographically representative strains, 228 (96.6%) were successfully amplified and 214 (90.7%) produced single PCR products. Twenty-three (9.7%) were found to be perfect polymorphic loci. A small-scale population study using 11 polymorphic loci revealed considerable gene diversity. Clustering analysis grouped isolates of this fungus into two clades in accordance with their geographic origins

  1. Genomic characterization of EmsB microsatellite loci in Echinococcus multilocularis.

    PubMed

    Valot, Benoît; Knapp, Jenny; Umhang, Gérald; Grenouillet, Frédéric; Millon, Laurence

    2015-06-01

    EmsB is a molecular marker applied to Echinococcus multilocularis genotyping studies. This marker has largely been used to investigate the epidemiology of the parasite in different endemic foci. The present study has lifted the veil on the genetic structure of this microsatellite. By in silico analysis on the E. multilocularis genome the microsatellite was described in about 40 copies on the chromosome 5 of the parasite. Similar structure was found in the relative parasite Echinococcus granulosus, where the microsatellite was firstly described. The present study completes the first investigations made on the EmsB microsatellite origins and confirms the reliability of this highly discriminant molecular marker. PMID:25847697

  2. A matter of life or death: how microsatellites emerge in and vanish from the human genome.

    PubMed

    Kelkar, Yogeshwar D; Eckert, Kristin A; Chiaromonte, Francesca; Makova, Kateryna D

    2011-12-01

    Microsatellites--tandem repeats of short DNA motifs--are abundant in the human genome and have high mutation rates. While microsatellite instability is implicated in numerous genetic diseases, the molecular processes involved in their emergence and disappearance are still not well understood. Microsatellites are hypothesized to follow a life cycle, wherein they are born and expand into adulthood, until their degradation and death. Here we identified microsatellite births/deaths in human, chimpanzee, and orangutan genomes, using macaque and marmoset as outgroups. We inferred mutations causing births/deaths based on parsimony, and investigated local genomic environments affecting them. We also studied birth/death patterns within transposable elements (Alus and L1s), coding regions, and disease-associated loci. We observed that substitutions were the predominant cause for births of short microsatellites, while insertions and deletions were important for births of longer microsatellites. Substitutions were the cause for deaths of microsatellites of virtually all lengths. AT-rich L1 sequences exhibited elevated frequency of births/deaths over their entire length, while GC-rich Alus only in their 3' poly(A) tails and middle A-stretches, with differences depending on transposable element integration timing. Births/deaths were strongly selected against in coding regions. Births/deaths occurred in genomic regions with high substitution rates, protomicrosatellite content, and L1 density, but low GC content and Alu density. The majority of the 17 disease-associated microsatellites examined are evolutionarily ancient (were acquired by the common ancestor of simians). Our genome-wide investigation of microsatellite life cycle has fundamental applications for predicting the susceptibility of birth/death of microsatellites, including many disease-causing loci. PMID:21994250

  3. Genome-wide survey and analysis of microsatellites in the Pacific oyster genome: abundance, distribution, and potential for marker development

    NASA Astrophysics Data System (ADS)

    Wang, Jiafeng; Qi, Haigang; Li, Li; Zhang, Guofan

    2014-01-01

    Microsatellites are a ubiquitous component of the eukaryote genome and constitute one of the most popular sources of molecular markers for genetic studies. However, no data are currently available regarding microsatellites across the entire genome in oysters, despite their importance to the aquaculture industry. We present the first genome-wide investigation of microsatellites in the Pacific oyster Crassostrea gigas by analysis of the complete genome, resequencing, and expression data. The Pacific oyster genome is rich in microsatellites. A total of 604 653 repeats were identified, in average of one locus per 815 base pairs (bp). A total of 12 836 genes had coding repeats, and 7 332 were expressed normally, including genes with a wide range of molecular functions. Compared with 20 different species of animals, microsatellites in the oyster genome typically exhibited 1) an intermediate overall frequency; 2) relatively uniform contents of (A)n and (C)n repeats and abundant long (C)n repeats (≥24 bp); 3) large average length of (AG)n repeats; and 4) scarcity of trinucleotide repeats. The microsatellite-flanking regions exhibited a high degree of polymorphism with a heterozygosity rate of around 2.0%, but there was no correlation between heterozygosity and microsatellite abundance. A total of 19 462 polymorphic microsatellites were discovered, and dinucleotide repeats were the most active, with over 26% of loci found to harbor allelic variations. In all, 7 451 loci with high potential for marker development were identified. Better knowledge of the microsatellites in the oyster genome will provide information for the future design of a wide range of molecular markers and contribute to further advancements in the field of oyster genetics, particularly for molecular-based selection and breeding.

  4. Microsatellite spreading in the human genome: evolutionary mechanisms and structural implications.

    PubMed Central

    Nadir, E; Margalit, H; Gallily, T; Ben-Sasson, S A

    1996-01-01

    Microsatellites are tandem repeat sequences abundant in the genomes of higher eukaryotes and hitherto considered as "junk DNA." Analysis of a human genome representative data base (2.84 Mb) reveals a distinct juxtaposition of A-rich microsatellites and retroposons and suggests their coevolution. The analysis implies that most microsatellites were generated by a 3'-extension of retrotranscripts, similar to mRNA polyadenylylation, and that they serve in turn as "retroposition navigators," directing the retroposons via homology-driven integration into defined sites. Thus, they became instrumental in the preservation and extension of primordial genomic patterns. A role is assigned to these reiterating A-rich loci in the higher-order organization of the chromatin. The disease-associated triplet repeats are mostly found in coding regions and do not show an association with retroposons, constituting a unique set within the family of microsatellite sequences. Images Fig. 1 PMID:8692839

  5. Development of a Genomic Microsatellite Library in Perennial Ryegrass (Lolium perenne) and its Use in Trait Mapping

    PubMed Central

    King, J.; Thorogood, D.; Edwards, K. J.; Armstead, I. P.; Roberts, L.; Skøt, K.; Hanley, Z.; King, I. P.

    2008-01-01

    Background and Aims Perennial ryegrass (Lolium perenne) is one of the key forage and amenity grasses throughout the world. In the UK it accounts for 70 % of all agricultural land use with an estimated farm gate value of £6 billion per annum. However, in terms of the genetic resources available, L. perenne has lagged behind other major crops in Poaceae. The aim of this project was therefore the construction of a microsatellite-enriched genomic library for L. perenne to increase the number of genetic markers available for both marker-assisted selection in breeding programmes and gene isolation. Methods Primers for 229 non-redundant microsatellite markers were designed and used to screen two L. perenne genotypes, one amenity and one forage. Of the 229 microsatellites, 95 were found to show polymorphism between amenity and forage genotypes. A selection of microsatellite primers was selected from these 95 and used to screen two mapping populations derived from intercrossing and backcrossing the two forage and amenity grass genotypes. Key Results and Conclusions The utility of the resulting genetic maps for analysis of the genetic control of target traits was demonstrated by the mapping of genes associated with heading date to linkage groups 4 and 7. PMID:18281692

  6. Identification of common, unique and polymorphic microsatellites among 73 cyanobacterial genomes.

    PubMed

    Kabra, Ritika; Kapil, Aditi; Attarwala, Kherunnisa; Rai, Piyush Kant; Shanker, Asheesh

    2016-04-01

    Microsatellites also known as Simple Sequence Repeats are short tandem repeats of 1-6 nucleotides. These repeats are found in coding as well as non-coding regions of both prokaryotic and eukaryotic genomes and play a significant role in the study of gene regulation, genetic mapping, DNA fingerprinting and evolutionary studies. The availability of 73 complete genome sequences of cyanobacteria enabled us to mine and statistically analyze microsatellites in these genomes. The cyanobacterial microsatellites identified through bioinformatics analysis were stored in a user-friendly database named CyanoSat, which is an efficient data representation and query system designed using ASP.net. The information in CyanoSat comprises of perfect, imperfect and compound microsatellites found in coding, non-coding and coding-non-coding regions. Moreover, it contains PCR primers with 200 nucleotides long flanking region. The mined cyanobacterial microsatellites can be freely accessed at www.compubio.in/CyanoSat/home.aspx. In addition to this 82 polymorphic, 13,866 unique and 2390 common microsatellites were also detected. These microsatellites will be useful in strain identification and genetic diversity studies of cyanobacteria. PMID:27030027

  7. Characterization of genome-wide microsatellites of Saccharina japonica based on a preliminary assembly of Illumina sequencing reads

    NASA Astrophysics Data System (ADS)

    Zhang, Linan; Peng, Jie; Li, Xiaojie; Cui, Cuiju; Sun, Juan; Yang, Guanpin

    2016-06-01

    Microsatellites or simple sequence repeats (SSR) function widely and locate dependently in genome. However, their characteristics are often ignored due to the lack of genomic sequences of most species. Kelp ( Saccharina japonica), a brown macroalga, is extensively cultured in China. In this study, the genome of S. japonica was surveyed using an Illumina sequencing platform, and its microsatellites were characterized. The preliminarily assembled genome was 469.4 Mb in size, with a scaffold N50 of 20529 bp. Among the 128370 identified microsatellites, 90671, 25726 and 11973 were found in intergenic regions, introns and exons, averaging 339.3, 178.8 and 205.4 microsatellites per Mb, respectively. These microsatellites distributed unevenly in S. japonica genome. Mononucleotide motifs were the most abundant in the genome, while trinucleotide ones were the most prevalent in exons. The microsatellite abundance decreased significantly with the increase of motif repeat numbers, and the microsatellites with a small number of repeats accounted for a higher proportion of the exons than those of the intergenic regions and introns. C/G-rich motifs were more common in exons than in intergenic regions and introns. These characteristics of microsatellites in S. japonica genome may associate with their functions, and ultimately their adaptation and evolution. Among the 120140 pairs of designed microsatellite primers, approximately 75% were predicted to be able to amplify S. japonica DNA. These microsatellite markers will be extremely useful for the genetic breeding and population evolution studies of kelp.

  8. Genome-wide characterization of microsatellites in Triticeae species: abundance, distribution and evolution.

    PubMed

    Deng, Pingchuan; Wang, Meng; Feng, Kewei; Cui, Licao; Tong, Wei; Song, Weining; Nie, Xiaojun

    2016-01-01

    Microsatellites are an important constituent of plant genome and distributed across entire genome. In this study, genome-wide analysis of microsatellites in 8 Triticeae species and 9 model plants revealed that microsatellite characteristics were similar among the Triticeae species. Furthermore, genome-wide microsatellite markers were designed in wheat and then used to analyze the evolutionary relationship of wheat and other Triticeae species. Results displayed that Aegilops tauschii was found to be the closest species to Triticum aestivum, followed by Triticum urartu, Triticum turgidum and Aegilops speltoides, while Triticum monococcum, Aegilops sharonensis and Hordeum vulgare showed a relatively lower PCR amplification effectivity. Additionally, a significantly higher PCR amplification effectivity was found in chromosomes at the same subgenome than its homoeologous when these markers were subjected to search against different chromosomes in wheat. After a rigorous screening process, a total of 20,666 markers showed high amplification and polymorphic potential in wheat and its relatives, which were integrated with the public available wheat markers and then anchored to the genome of wheat (CS). This study not only provided the useful resource for SSR markers development in Triticeae species, but also shed light on the evolution of polyploid wheat from the perspective of microsatellites. PMID:27561724

  9. Genome-wide characterization of microsatellites in Triticeae species: abundance, distribution and evolution

    PubMed Central

    Deng, Pingchuan; Wang, Meng; Feng, Kewei; Cui, Licao; Tong, Wei; Song, Weining; Nie, Xiaojun

    2016-01-01

    Microsatellites are an important constituent of plant genome and distributed across entire genome. In this study, genome-wide analysis of microsatellites in 8 Triticeae species and 9 model plants revealed that microsatellite characteristics were similar among the Triticeae species. Furthermore, genome-wide microsatellite markers were designed in wheat and then used to analyze the evolutionary relationship of wheat and other Triticeae species. Results displayed that Aegilops tauschii was found to be the closest species to Triticum aestivum, followed by Triticum urartu, Triticum turgidum and Aegilops speltoides, while Triticum monococcum, Aegilops sharonensis and Hordeum vulgare showed a relatively lower PCR amplification effectivity. Additionally, a significantly higher PCR amplification effectivity was found in chromosomes at the same subgenome than its homoeologous when these markers were subjected to search against different chromosomes in wheat. After a rigorous screening process, a total of 20,666 markers showed high amplification and polymorphic potential in wheat and its relatives, which were integrated with the public available wheat markers and then anchored to the genome of wheat (CS). This study not only provided the useful resource for SSR markers development in Triticeae species, but also shed light on the evolution of polyploid wheat from the perspective of microsatellites. PMID:27561724

  10. Identification and Characterization of Microsatellite Markers Derived from the Whole Genome Analysis of Taenia solium

    PubMed Central

    Pajuelo, Mónica J.; Eguiluz, María; Dahlstrom, Eric; Requena, David; Guzmán, Frank; Ramirez, Manuel; Sheen, Patricia; Frace, Michael; Sammons, Scott; Cama, Vitaliano; Anzick, Sarah; Bruno, Dan; Mahanty, Siddhartha; Wilkins, Patricia; Nash, Theodore; Gonzalez, Armando; García, Héctor H.; Gilman, Robert H.; Porcella, Steve; Zimic, Mirko

    2015-01-01

    Background Infections with Taenia solium are the most common cause of adult acquired seizures worldwide, and are the leading cause of epilepsy in developing countries. A better understanding of the genetic diversity of T. solium will improve parasite diagnostics and transmission pathways in endemic areas thereby facilitating the design of future control measures and interventions. Microsatellite markers are useful genome features, which enable strain typing and identification in complex pathogen genomes. Here we describe microsatellite identification and characterization in T. solium, providing information that will assist in global efforts to control this important pathogen. Methods For genome sequencing, T. solium cysts and proglottids were collected from Huancayo and Puno in Peru, respectively. Using next generation sequencing (NGS) and de novo assembly, we assembled two draft genomes and one hybrid genome. Microsatellite sequences were identified and 36 of them were selected for further analysis. Twenty T. solium isolates were collected from Tumbes in the northern region, and twenty from Puno in the southern region of Peru. The size-polymorphism of the selected microsatellites was determined with multi-capillary electrophoresis. We analyzed the association between microsatellite polymorphism and the geographic origin of the samples. Results The predicted size of the hybrid (proglottid genome combined with cyst genome) T. solium genome was 111 MB with a GC content of 42.54%. A total of 7,979 contigs (>1,000 nt) were obtained. We identified 9,129 microsatellites in the Puno-proglottid genome and 9,936 in the Huancayo-cyst genome, with 5 or more repeats, ranging from mono- to hexa-nucleotide. Seven microsatellites were polymorphic and 29 were monomorphic within the analyzed isolates. T. solium tapeworms were classified into two genetic groups that correlated with the North/South geographic origin of the parasites. Conclusions/Significance The availability of draft

  11. Chromosomal distribution of microsatellite repeats in Amazon cichlids genome (Pisces, Cichlidae)

    PubMed Central

    Schneider, Carlos Henrique; Gross, Maria Claudia; Terencio, Maria Leandra; de Tavares, Édika Sabrina Girão Mitozo; Martins, Cesar; Feldberg, Eliana

    2015-01-01

    Abstract Fish of the family Cichlidae are recognized as an excellent model for evolutionary studies because of their morphological and behavioral adaptations to a wide diversity of explored ecological niches. In addition, the family has a dynamic genome with variable structure, composition and karyotype organization. Microsatellites represent the most dynamic genomic component and a better understanding of their organization may help clarify the role of repetitive DNA elements in the mechanisms of chromosomal evolution. Thus, in this study, microsatellite sequences were mapped in the chromosomes of Cichla monoculus Agassiz, 1831, Pterophyllum scalare Schultze, 1823, and Symphysodon discus Heckel, 1840. Four microsatellites demonstrated positive results in the genome of Cichla monoculus and Symphysodon discus, and five demonstrated positive results in the genome of Pterophyllum scalare. In most cases, the microsatellite was dispersed in the chromosome with conspicuous markings in the centromeric or telomeric regions, which suggests that sequences contribute to chromosome structure and may have played a role in the evolution of this fish family. The comparative genome mapping data presented here provide novel information on the structure and organization of the repetitive DNA region of the cichlid genome and contribute to a better understanding of this fish family’s genome. PMID:26753076

  12. FANCJ is essential to maintain microsatellite structure genome-wide during replication stress.

    PubMed

    Barthelemy, Joanna; Hanenberg, Helmut; Leffak, Michael

    2016-08-19

    Microsatellite DNAs that form non-B structures are implicated in replication fork stalling, DNA double strand breaks (DSBs) and human disease. Fanconi anemia (FA) is an inherited disorder in which mutations in at least nineteen genes are responsible for the phenotypes of genome instability and cancer predisposition. FA pathway proteins are active in the resolution of non-B DNA structures including interstrand crosslinks, G quadruplexes and DNA triplexes. In FANCJ helicase depleted cells, we show that hydroxyurea or aphidicolin treatment leads to loss of microsatellite polymerase chain reaction signals and to chromosome recombination at an ectopic hairpin forming CTG/CAG repeat in the HeLa genome. Moreover, diverse endogenous microsatellite signals were also lost upon replication stress after FANCJ depletion, and in FANCJ null patient cells. The phenotype of microsatellite signal instability is specific for FANCJ apart from the intact FA pathway, and is consistent with DSBs at microsatellites genome-wide in FANCJ depleted cells following replication stress. PMID:27179029

  13. Next generation sequencing and FISH reveal uneven and nonrandom microsatellite distribution in two grasshopper genomes.

    PubMed

    Ruiz-Ruano, Francisco J; Cuadrado, Ángeles; Montiel, Eugenia E; Camacho, Juan Pedro M; López-León, María Dolores

    2015-06-01

    Simple sequence repeats (SSRs), also known as microsatellites, are one of the prominent DNA sequences shaping the repeated fraction of eukaryotic genomes. In spite of their profuse use as molecular markers for a variety of genetic and evolutionary studies, their genomic location, distribution, and function are not yet well understood. Here we report the first thorough joint analysis of microsatellite motifs at both genomic and chromosomal levels in animal species, by a combination of 454 sequencing and fluorescent in situ hybridization (FISH) techniques performed on two grasshopper species. The in silico analysis of the 454 reads suggested that microsatellite expansion is not driving size increase of these genomes, as SSR abundance was higher in the species showing the smallest genome. However, the two species showed the same uneven and nonrandom location of SSRs, with clear predominance of dinucleotide motifs and association with several types of repetitive elements, mostly histone gene spacers, ribosomal DNA intergenic spacers (IGS), and transposable elements (TEs). The FISH analysis showed a dispersed chromosome distribution of microsatellite motifs in euchromatic regions, in coincidence with chromosome location patterns previously observed for many mobile elements in these species. However, some SSR motifs were clustered, especially those located in the histone gene cluster. PMID:25387401

  14. Microsatellite Interruptions Stabilize Primate Genomes and Exist as Population-Specific Single Nucleotide Polymorphisms within Individual Human Genomes

    PubMed Central

    Ananda, Guruprasad; Hile, Suzanne E.; Breski, Amanda; Wang, Yanli; Kelkar, Yogeshwar; Makova, Kateryna D.; Eckert, Kristin A.

    2014-01-01

    Interruptions of microsatellite sequences impact genome evolution and can alter disease manifestation. However, human polymorphism levels at interrupted microsatellites (iMSs) are not known at a genome-wide scale, and the pathways for gaining interruptions are poorly understood. Using the 1000 Genomes Phase-1 variant call set, we interrogated mono-, di-, tri-, and tetranucleotide repeats up to 10 units in length. We detected ∼26,000–40,000 iMSs within each of four human population groups (African, European, East Asian, and American). We identified population-specific iMSs within exonic regions, and discovered that known disease-associated iMSs contain alleles present at differing frequencies among the populations. By analyzing longer microsatellites in primate genomes, we demonstrate that single interruptions result in a genome-wide average two- to six-fold reduction in microsatellite mutability, as compared with perfect microsatellites. Centrally located interruptions lowered mutability dramatically, by two to three orders of magnitude. Using a biochemical approach, we tested directly whether the mutability of a specific iMS is lower because of decreased DNA polymerase strand slippage errors. Modeling the adenomatous polyposis coli tumor suppressor gene sequence, we observed that a single base substitution interruption reduced strand slippage error rates five- to 50-fold, relative to a perfect repeat, during synthesis by DNA polymerases α, β, or η. Computationally, we demonstrate that iMSs arise primarily by base substitution mutations within individual human genomes. Our biochemical survey of human DNA polymerase α, β, δ, κ, and η error rates within certain microsatellites suggests that interruptions are created most frequently by low fidelity polymerases. Our combined computational and biochemical results demonstrate that iMSs are abundant in human genomes and are sources of population-specific genetic variation that may affect genome stability. The

  15. The Landscape of Microsatellite Instability in Colorectal and Endometrial Cancer Genomes

    PubMed Central

    Kim, Tae-Min; Laird, Peter W.; Park, Peter J.

    2013-01-01

    Summary Microsatellites - simple tandem repeats present at millions of sites in the human genome - can shorten or lengthen due to a defect in DNA mismatch repair. We present here the first comprehensive genome-wide analysis of the prevalence, mutational spectrum and functional consequences of microsatellite instability (MSI) in cancer genomes. We analyzed MSI in 277 colorectal and endometrial cancer genomes (including 57 microsatellite-unstable ones) using exome and whole-genome sequencing data. Recurrent MSI events in coding sequences showed tumor type-specificity, elevated frameshift-to-inframe ratios, and lower transcript levels than wildtype alleles. Moreover, genome-wide analysis revealed differences in the distribution of MSI versus point mutations, including overrepresentation of MSI in euchromatic and intronic regions compared to heterochromatic and intergenic regions, respectively, and depletion of MSI at nucleosome-occupied sequences. Our results provide a panoramic view of MSI in cancer genomes, highlighting their tumor type-specificity, impact on gene expression, and the role of chromatin organization. PMID:24209623

  16. Assessing Genetic Diversity in Gossypium Arboreum L. Cultivars Using Genomic and EST-Derived Microsatellites.

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The cultivated diploid, Gossypium arboreum L., (A genome) is an invaluable genetic resource for improving modern tetraploid cotton (G. hirsutum L. and G. barbadense L.) cultivars. The objective of this research is to select a set of informative and robust microsatellites for studying genetic relatio...

  17. Polymorphic microsatellites in the human bloodfluke, Schistosoma japonicum, identified using a genomic resource

    PubMed Central

    2011-01-01

    Re-emergence of schistosomiasis in regions of China where control programs have ceased requires development of molecular-genetic tools to track gene flow and assess genetic diversity of Schistosoma populations. We identified many microsatellite loci in the draft genome of Schistosoma japonicum using defined search criteria and selected a subset for further analysis. From an initial panel of 50 loci, 20 new microsatellites were selected for eventual optimization and application to a panel of worms from endemic areas. All but one of the selected microsatellites contain simple tri-nucleotide repeats. Moderate to high levels of polymorphism were detected. Numbers of alleles ranged from 6 to 14 and observed heterozygosity was always >0.6. The loci reported here will facilitate high resolution population-genetic studies on schistosomes in re-emergent foci. PMID:21299863

  18. DNA Slippage Occurs at Microsatellite Loci without Minimal Threshold Length in Humans: A Comparative Genomic Approach

    PubMed Central

    Leclercq, Sébastien; Rivals, Eric; Jarne, Philippe

    2010-01-01

    The dynamics of microsatellite, or short tandem repeats (STRs), is well documented for long, polymorphic loci, but much less is known for shorter ones. For example, the issue of a minimum threshold length for DNA slippage remains contentious. Model-fitting methods have generally concluded that slippage only occurs over a threshold length of about eight nucleotides, in contradiction with some direct observations of tandem duplications at shorter repeated sites. Using a comparative analysis of the human and chimpanzee genomes, we examined the mutation patterns at microsatellite loci with lengths as short as one period plus one nucleotide. We found that the rates of tandem insertions and deletions at microsatellite loci strongly deviated from background rates in other parts of the human genome and followed an exponential increase with STR size. More importantly, we detected no lower threshold length for slippage. The rate of tandem duplications at unrepeated sites was higher than expected from random insertions, providing evidence for genome-wide action of indel slippage (an alternative mechanism generating tandem repeats). The rate of point mutations adjacent to STRs did not differ from that estimated elsewhere in the genome, except around dinucleotide loci. Our results suggest that the emergence of STR depends on DNA slippage, indel slippage, and point mutations. We also found that the dynamics of tandem insertions and deletions differed in both rates and size at which these mutations take place. We discuss these results in both evolutionary and mechanistic terms. PMID:20624737

  19. Development of genomic microsatellites in Gleditsia triacanthos (Fabaceae) using Illumina sequencing1

    PubMed Central

    Owusu, Sandra A.; Staton, Margaret; Jennings, Tara N.; Schlarbaum, Scott; Coggeshall, Mark V.; Romero-Severson, Jeanne; Carlson, John E.; Gailing, Oliver

    2013-01-01

    • Premise of the study: Fourteen genomic microsatellite markers were developed and characterized in honey locust, Gleditsia triacanthos, using Illumina sequencing. Due to their high variability, these markers can be applied in analyses of genetic diversity and structure, and in mating system and gene flow studies. • Methods and Results: Thirty-six individuals from across the species range were included in a genetic diversity analysis and yielded three to 20 alleles per locus. Observed heterozygosity and expected heterozygosity ranged from 0.214 to 0.944 and from 0.400 to 0.934, respectively, with minimal occurrence of null alleles. Regular segregation of maternal alleles was observed at seven loci and moderate segregation distortion at four of 11 loci that were heterozygous in the seed parent. • Conclusions: Honey locust is an important agroforestry tree capable of very fast growth and tolerance of poor site conditions. This is the first report of genomic microsatellites for this species. PMID:25202504

  20. Ancient whole genome enrichment using baits built from modern DNA.

    PubMed

    Enk, Jacob M; Devault, Alison M; Kuch, Melanie; Murgha, Yusuf E; Rouillard, Jean-Marie; Poinar, Hendrik N

    2014-05-01

    We report metrics from complete genome capture of nuclear DNA from extinct mammoths using biotinylated RNAs transcribed from an Asian elephant DNA extract. Enrichment of the nuclear genome ranged from 1.06- to 18.65-fold, to an apparent maximum threshold of ∼80% on-target. This projects an order of magnitude less costly complete genome sequencing from long-dead organisms, even when a reference genome is unavailable for bait design. PMID:24531081

  1. First whole genome based microsatellite DNA marker database of tomato for mapping and variety identification

    PubMed Central

    2013-01-01

    Background The cultivated tomato is second most consumed vegetable of the world and is an important part of a diverse and balanced diet as a rich source of vitamins, minerals, phenolic antioxidants and antioxidant lycopene having anti-cancer properties. To reap benefit of genomics of the domestic tomato (Solanum lycopersicum L.) unravelled by Tomato Genome Consortium (The Tomato Genome Consortium, 2012), the bulk mining of its markers in totality is imperative and critically required. The solgenomics has limited number of microsatellite DNA markers (2867) pertaining to solanaceae family. As these markers are of linkage map having relative distance, the choice of selected markers based on absolute distance as of physical map is missing. Only limited microsatellite markers with limitations are reported for variety identification thus there is a need for more markers supplementing DUS test and also for traceability of product in global market. Description We present here the first whole genome based microsatellite DNA marker database of tomato, TomSatDB (Tomato MicroSatellite Database) with more than 1.4 million markers mined in-silico, using MIcroSAtellite (MISA) tool. To cater the customized needs of wet lab, features with a novelty of an automated primer designing tool is added. TomSatDB (http://cabindb.iasri.res.in/tomsatdb), a user-friendly and freely accessible tool offers chromosome wise as well as location wise search of primers. It is an online relational database based on “three-tier architecture” that catalogues information of microsatellites in MySQL and user-friendly interface developed using PHP (Hypertext Pre Processor). Conclusion Besides abiotic stress, tomato is known to have biotic stress due to its susceptibility over 200 diseases caused by pathogenic fungi, bacteria, viruses and nematodes. These markers are expected to pave the way of germplasm management over abiotic and biotic stress as well as improvement through molecular breeding, leading

  2. Development of microsatellite markers for six Tetranychus species by transfer from Tetranychus urticae genome.

    PubMed

    Zhang, Jia; Sun, Jing-Tao; Jin, Peng-Yu; Hong, Xiao-Yue

    2016-09-01

    Microsatellite markers are frequently used to explore the population genetic structure of organisms. Spider mites (genus Tetranychus) are important agricultural pests. Several markers have been developed for T. urticae, but for other spider mites, few such markers are available, hampering studies of their population genetics. In this study, we developed and characterized microsatellite markers for six non-model spider mite species (T. truncatus, T. kanzawai, T. ludeni, T. piercei, T. phaselus and T. pueraricola) by cross-species amplification of markers in the T. urticae genome, in order to better understand the population structure of Tetranychus species. Among 228 screened loci, many were polymorphic, including 13 loci in T. urticae, 11 loci in T. truncatus, 15 loci in T. pueraricola, 23 loci in T. kanzawai, 19 loci in T. piercei, 11 loci in T. phaselus and 9 loci in T. ludeni. Sequence analysis determined that the fragment length variations of the transferred microsatellites were mainly due to the variations of the numbers of repeats. These new microsatellite markers should be useful for studying the population genetics of the seven Tetranychus species. PMID:27380501

  3. MICdb3.0: a comprehensive resource of microsatellite repeats from prokaryotic genomes.

    PubMed

    Mudunuri, Suresh B; Patnana, Sujan; Nagarajaram, Hampapathalu A

    2014-01-01

    The MICdb is a comprehensive relational database of perfect microsatellites extracted from completely sequenced and annotated genomes of bacteria and archaea. The current version MICdb3.0 is an updated and revised version of MICdb2.0. As compared with the previous version MICdb2.0, the current release is significantly improved in terms of much larger coverage of genomes, improved presentation of queried results, user-friendly administration module to manage Simple Sequence Repeat (SSR) data such as addition of new genomes, deletion of obsolete data, etc., and also removal of certain features deemed to be redundant. The new web-interface to the database called Microsatellite Analysis Server (MICAS) version 3.0 has been improved by the addition of powerful high-quality visualization tools to view the query results in the form of pie charts and bar graphs. All the query results and graphs can be exported in different formats so that the users can use them for further analysis. MICAS3.0 is also equipped with a unique genome comparison module using which users can do pair-wise comparison of genomes with regard to their microsatellite distribution. The advanced search module can be used to filter the repeats based on certain criteria such as filtering repeats of a particular motif/repeat size, extracting repeats of coding/non-coding regions, sort repeats, etc. The MICdb database has, therefore, been made portable to be administered by a person with the necessary administrative privileges. The MICdb3.0 database and analysis server can be accessed for free from www.cdfd.org.in/micas. Database URL: http://www.cdfd.org.in/micas. PMID:24536078

  4. Frequent genomic alterations in epithelium measured by microsatellite instability following allogeneic hematopoietic cell transplantation in humans.

    PubMed

    Faber, Philipp; Fisch, Paul; Waterhouse, Miguel; Schmitt-Gräff, Annette; Bertz, Hartmut; Finke, Jürgen; Spyridonidis, Alexandros

    2006-04-15

    Although typically found in cancers, frameshift mutations in microsatellites have also been detected in chronically inflamed tissues. Allogeneic hematopoietic cell transplantation (HCT) may potentially produce chronic tissue stress through graft-versus-host reactions. We examined non-neoplastic epithelial tissues (colon, buccal) obtained 1 to 5061 days after human allogeneic HCT for the presence of genomic alterations at 3 tetranucleotide and 3 mononucleotide microsatellite loci. Novel bands indicative of microsatellite instability (MSI) at tetranucleotide repeats were detected in laser-microdissected colonic crypts and in buccal smears of 75% and 42% of patients who received an allograft, respectively. In contrast, no MSI was found in similar tissues from control subjects and from patients after intensive chemotherapy or in buccal cells from patients after autologous HCT. The MSI found in colon, which was often affected by graft-versus-host disease, was not due to loss of expression or nitrosylation of DNA repair proteins. MSI in clinically intact oral mucosa was more frequently found at later time points after HCT. MSI was also found in 3 posttransplant squamous cell cancers examined. Our data show that genomic alterations in epithelium regularly occur after allogeneic HCT and may be implicated in the evolution of posttransplantation diseases, including secondary cancer. PMID:16368884

  5. Rapid identification of thousands of copperhead snake (Agkistrodon contortrix) microsatellite loci from modest amounts of 454 shotgun genome sequence.

    PubMed

    Castoe, Todd A; Poole, Alexander W; Gu, Wanjun; Jason de Koning, A P; Daza, Juan M; Smith, Eric N; Pollock, David D

    2010-03-01

    Optimal integration of next-generation sequencing into mainstream research requires re-evaluation of how problems can be reasonably overcome and what questions can be asked. One potential application is the rapid acquisition of genomic information to identify microsatellite loci for evolutionary, population genetic and chromosome linkage mapping research on non-model and not previously sequenced organisms. Here, we report on results using high-throughput sequencing to obtain a large number of microsatellite loci from the venomous snake Agkistrodon contortrix, the copperhead. We used the 454 Genome Sequencer FLX next-generation sequencing platform to sample randomly ∼27 Mbp (128 773 reads) of the copperhead genome, thus sampling about 2% of the genome of this species. We identified microsatellite loci in 11.3% of all reads obtained, with 14 612 microsatellite loci identified in total, 4564 of which had flanking sequences suitable for polymerase chain reaction primer design. The random sequencing-based approach to identify microsatellites was rapid, cost-effective and identified thousands of useful microsatellite loci in a previously unstudied species. PMID:21565030

  6. Enriched domain detector: a program for detection of wide genomic enrichment domains robust against local variations

    PubMed Central

    Lund, Eivind; Oldenburg, Anja R.; Collas, Philippe

    2014-01-01

    Nuclear lamins contact the genome at the nuclear periphery through large domains and are involved in chromatin organization. Among broad peak calling algorithms available to date, none are suited for mapping lamin–genome interactions genome wide. We disclose a novel algorithm, enriched domain detector (EDD), for analysis of broad enrichment domains from chromatin immunoprecipitation (ChIP)-seq data. EDD enables discovery of genomic domains interacting with broadly distributed proteins, such as A- and B-type lamins affinity isolated by ChIP. The advantages of EDD over existing broad peak callers are sensitivity to domain width rather than enrichment strength at a particular site, and robustness against local variations. PMID:24782521

  7. A genome-wide view of microsatellite instability: old stories of cancer mutations revisited with new sequencing technologies

    PubMed Central

    Kim, Tae-Min; Park, Peter J

    2014-01-01

    Microsatellites are simple tandem repeats that are present at millions of loci in the human genome. Microsatellite instability (MSI) refers to DNA slippage events on microsatellites that occur frequently in cancer genomes when there is a defect in the DNA mismatch repair system. These somatic mutations can result in inactivation of tumor suppressor genes or disrupt other non-coding regulatory sequences, thereby playing a role in carcinogenesis. Here, we will discuss the ways in which high-throughput sequencing data can facilitate a genome- or exome-wide discovery and more detailed investigation of MSI events in microsatellite-unstable cancer genomes. We will address the methodological aspects of this approach and highlight insights from recent analyses of colorectal and endometrial cancer genomes from The Cancer Genome Atlas project. These include identification of novel MSI targets within and across tumor types and the relationship between the likelihood of MSI events to chromatin structure. Given the increasing popularity of exome and genome sequencing of cancer genomes, a comprehensive characterization of MSI may serve as a valuable marker of cancer evolution and aid in a search for therapeutic targets. PMID:25371413

  8. High-throughput sequencing and graph-based cluster analysis facilitate microsatellite development from a highly complex genome.

    PubMed

    Shah, Abhijeet B; Schielzeth, Holger; Albersmeier, Andreas; Kalinowski, Joern; Hoffman, Joseph I

    2016-08-01

    Despite recent advances in high-throughput sequencing, difficulties are often encountered when developing microsatellites for species with large and complex genomes. This probably reflects the close association in many species of microsatellites with cryptic repetitive elements. We therefore developed a novel approach for isolating polymorphic microsatellites from the club-legged grasshopper (Gomphocerus sibiricus), an emerging quantitative genetic and behavioral model system. Whole genome shotgun Illumina MiSeq sequencing was used to generate over three million 300 bp paired-end reads, of which 67.75% were grouped into 40,548 clusters within RepeatExplorer. Annotations of the top 468 clusters, which represent 60.5% of the reads, revealed homology to satellite DNA and a variety of transposable elements. Evaluating 96 primer pairs in eight wild-caught individuals, we found that primers mined from singleton reads were six times more likely to amplify a single polymorphic microsatellite locus than primers mined from clusters. Our study provides experimental evidence in support of the notion that microsatellites associated with repetitive elements are less likely to successfully amplify. It also reveals how advances in high-throughput sequencing and graph-based repetitive DNA analysis can be leveraged to isolate polymorphic microsatellites from complex genomes. PMID:27547349

  9. Development and validation of microsatellite markers for Brachiaria ruziziensis obtained by partial genome assembly of Illumina single-end reads

    PubMed Central

    2013-01-01

    Background Brachiaria ruziziensis is one of the most important forage species planted in the tropics. The application of genomic tools to aid the selection of superior genotypes can provide support to B. ruziziensis breeding programs. However, there is a complete lack of information about the B. ruziziensis genome. Also, the availability of genomic tools, such as molecular markers, to support B. ruziziensis breeding programs is rather limited. Recently, next-generation sequencing technologies have been applied to generate sequence data for the identification of microsatellite regions and primer design. In this study, we present a first validated set of SSR markers for Brachiaria ruziziensis, selected from a de novo partial genome assembly of single-end Illumina reads. Results A total of 85,567 perfect microsatellite loci were detected in contigs with a minimum 10X coverage. We selected a set of 500 microsatellite loci identified in contigs with minimum 100X coverage for primer design and synthesis, and tested a subset of 269 primer pairs, 198 of which were polymorphic on 11 representative B. ruziziensis accessions. Descriptive statistics for these primer pairs are presented, as well as estimates of marker transferability to other relevant brachiaria species. Finally, a set of 11 multiplex panels containing the 30 most informative markers was validated and proposed for B. ruziziensis genetic analysis. Conclusions We show that the detection and development of microsatellite markers from genome assembled Illumina single-end DNA sequences is highly efficient. The developed markers are readily suitable for genetic analysis and marker assisted selection of Brachiaria ruziziensis. The use of this approach for microsatellite marker development is promising for species with limited genomic information, whose breeding programs would benefit from the use of genomic tools. To our knowledge, this is the first set of microsatellite markers developed for this important species

  10. Developing informative microsatellite makers for non-model species using reference mapping against a model species’ genome

    PubMed Central

    Hung, Chih-Ming; Yu, Ai-Yun; Lai, Yu-Ting; Shaner, Pei-Jen L.

    2016-01-01

    Microsatellites have a wide range of applications from behavioral biology, evolution, to agriculture-based breeding programs. The recent progress in the next-generation sequencing technologies and the rapidly increasing number of published genomes may greatly enhance the current applications of microsatellites by turning them from anonymous to informative markers. Here we developed an approach to anchor microsatellite markers of any target species in a genome of a related model species, through which the genomic locations of the markers, along with any functional genes potentially linked to them, can be revealed. We mapped the shotgun sequence reads of a non-model rodent species Apodemus semotus against the genome of a model species, Mus musculus, and presented 24 polymorphic microsatellite markers with detailed background information for A. semotus in this study. The developed markers can be used in other rodent species, especially those that are closely related to A. semotus or M. musculus. Compared to the traditional approaches based on DNA cloning, our approach is likely to yield more loci for the same cost. This study is a timely demonstration of how a research team can efficiently generate informative (neutral or function-associated) microsatellite markers for their study species and unique biological questions. PMID:26976328

  11. A novel genome-wide microsatellite resource for species of Eucalyptus with linkage-to-physical correspondence on the reference genome sequence.

    PubMed

    Grattapaglia, Dario; Mamani, Eva M C; Silva-Junior, Orzenil B; Faria, Danielle A

    2015-03-01

    Keystone species in their native ranges, eucalypts, are ecologically and genetically very diverse, growing naturally along extensive latitudinal and altitudinal ranges and variable environments. Besides their ecological importance, eucalypts are also the most widely planted trees for sustainable forestry in the world. We report the development of a novel collection of 535 microsatellites for species of Eucalyptus, 494 designed from ESTs and 41 from genomic libraries. A selected subset of 223 was evaluated for individual identification, parentage testing, and ancestral information content in the two most extensively studied species, Eucalyptus grandis and Eucalyptus globulus. Microsatellites showed high transferability and overlapping allele size range, suggesting they have arisen still in their common ancestor and confirming the extensive genome conservation between these two species. A consensus linkage map with 437 microsatellites, the most comprehensive microsatellite-only genetic map for Eucalyptus, was built by assembling segregation data from three mapping populations and anchored to the Eucalyptus genome. An overall colinearity between recombination-based and physical positioning of 84% of the mapped microsatellites was observed, with some ordering discrepancies and sporadic locus duplications, consistent with the recently described whole genome duplication events in Eucalyptus. The linkage map covered 95.2% of the 605.8-Mbp assembled genome sequence, placing one microsatellite every 1.55 Mbp on average, and an overall estimate of physical to recombination distance of 618 kbp/cM. The genetic parameters estimates together with linkage and physical position data for this large set of microsatellites should assist marker choice for genome-wide population genetics and comparative mapping in Eucalyptus. PMID:25146326

  12. Discovery of Genome-Wide Microsatellite Markers in Scombridae: A Pilot Study on Albacore Tuna

    PubMed Central

    Nikolic, Natacha; Duthoy, Stéphanie; Destombes, Antoine; Bodin, Nathalie; West, Wendy; Puech, Alexis; Bourjea, Jérôme

    2015-01-01

    Recent developments in sequencing technologies and bioinformatics analysis provide a greater amount of DNA sequencing reads at a low cost. Microsatellites are the markers of choice for a variety of population genetic studies, and high quality markers can be discovered in non-model organisms, such as tuna, with these recent developments. Here, we use a high-throughput method to isolate microsatellite markers in albacore tuna, Thunnus alalunga, based on coupling multiplex enrichment and next-generation sequencing on 454 GS-FLX Titanium pyrosequencing. The crucial minimum number of polymorphic markers to infer evolutionary and ecological processes for this species has been described for the first time. We provide 1670 microsatellite design primer pairs, and technical and molecular genetics selection resulting in 43 polymorphic microsatellite markers. On this panel, we characterized 34 random and selectively neutral markers («neutral») and 9 «non-neutral» markers. The variability of «neutral» markers was screened with 136 individuals of albacore tuna from southwest Indian Ocean (42), northwest Indian Ocean (31), South Africa (31), and southeast Atlantic Ocean (32). Power analysis demonstrated that the panel of genetic markers can be applied in diversity and population genetics studies. Global genetic diversity for albacore was high with a mean number of alleles at 16.94; observed heterozygosity 66% and expected heterozygosity 77%. The number of individuals was insufficient to provide accurate results on differentiation. Of the 9 «non-neutral» markers, 3 were linked to a sequence of known function. The one is located to a sequence having an immunity function (ThuAla-Tcell-01) and the other to a sequence having energy allocation function (ThuAla-Hki-01). These two markers were genotyped on the 136 individuals and presented different diversity levels. ThuAla-Tcell-01 has a high number of alleles (20), heterozygosity (87–90%), and assignment index. ThuAla-Hki-01

  13. Discovery of Genome-Wide Microsatellite Markers in Scombridae: A Pilot Study on Albacore Tuna.

    PubMed

    Nikolic, Natacha; Duthoy, Stéphanie; Destombes, Antoine; Bodin, Nathalie; West, Wendy; Puech, Alexis; Bourjea, Jérôme

    2015-01-01

    Recent developments in sequencing technologies and bioinformatics analysis provide a greater amount of DNA sequencing reads at a low cost. Microsatellites are the markers of choice for a variety of population genetic studies, and high quality markers can be discovered in non-model organisms, such as tuna, with these recent developments. Here, we use a high-throughput method to isolate microsatellite markers in albacore tuna, Thunnus alalunga, based on coupling multiplex enrichment and next-generation sequencing on 454 GS-FLX Titanium pyrosequencing. The crucial minimum number of polymorphic markers to infer evolutionary and ecological processes for this species has been described for the first time. We provide 1670 microsatellite design primer pairs, and technical and molecular genetics selection resulting in 43 polymorphic microsatellite markers. On this panel, we characterized 34 random and selectively neutral markers («neutral») and 9 «non-neutral» markers. The variability of «neutral» markers was screened with 136 individuals of albacore tuna from southwest Indian Ocean (42), northwest Indian Ocean (31), South Africa (31), and southeast Atlantic Ocean (32). Power analysis demonstrated that the panel of genetic markers can be applied in diversity and population genetics studies. Global genetic diversity for albacore was high with a mean number of alleles at 16.94; observed heterozygosity 66% and expected heterozygosity 77%. The number of individuals was insufficient to provide accurate results on differentiation. Of the 9 «non-neutral» markers, 3 were linked to a sequence of known function. The one is located to a sequence having an immunity function (ThuAla-Tcell-01) and the other to a sequence having energy allocation function (ThuAla-Hki-01). These two markers were genotyped on the 136 individuals and presented different diversity levels. ThuAla-Tcell-01 has a high number of alleles (20), heterozygosity (87-90%), and assignment index. ThuAla-Hki-01

  14. A genome-wide microsatellite polymorphism database for the indica and japonica rice.

    PubMed

    Zhang, Zhonghua; Deng, Yajun; Tan, Jun; Hu, Songnian; Yu, Jun; Xue, Qingzhong

    2007-02-28

    Microsatellite (MS) polymorphism is an important source of genetic diversity, providing support for map-based cloning and molecular breeding. We have developed a new database that contains 52 845 polymorphic MS loci between indica and japonica, composed of ample Class II MS markers, and integrated 18 828 MS loci from IRGSP and genetic markers from RGP. Based on genetic marker positions on the rice genome (http://rise.genomics.org.cn/rice2/index.jsp ), we determined the approximate genetic distances of these MS loci and validated 100 randomly selected markers experimentally with 90% success rate. In addition, we recorded polymorphic MS positions in indica cv. 9311 that is the most important paternal parent of the two-line hybrid rice in China. Our database will undoubtedly facilitate the application of MS markers in genetic researches and marker-assisted breeding. The data set is freely available from www.wigs.zju.edu.cn/achievment/polySSR. PMID:17452422

  15. Developing genome-wide microsatellite markers of bamboo and their applications on molecular marker assisted taxonomy for accessions in the genus Phyllostachys

    PubMed Central

    Zhao, Hansheng; Yang, Li; Peng, Zhenhua; Sun, Huayu; Yue, Xianghua; Lou, Yongfeng; Dong, Lili; Wang, Lili; Gao, Zhimin

    2015-01-01

    Morphology-based taxonomy via exiguously reproductive organ has severely limitation on bamboo taxonomy, mainly owing to infrequent and unpredictable flowering events of bamboo. Here, we present the first genome-wide analysis and application of microsatellites based on the genome of moso bamboo (Phyllostachys edulis) to assist bamboo taxonomy. Of identified 127,593 microsatellite repeat-motifs, the primers of 1,451 microsatellites were designed and 1,098 markers were physically mapped on the genome of moso bamboo. A total of 917 markers were successfully validated in 9 accessions with ~39.8% polymorphic potential. Retrieved from validated microsatellite markers, 23 markers were selected for polymorphic analysis among 78 accessions and 64 alleles were detected with an average of 2.78 alleles per primers. The cluster result indicated the majority of the accessions were consistent with their current taxonomic classification, confirming the suitability and effectiveness of the developed microsatellite markers. The variations of microsatellite marker in different species were confirmed by sequencing and in silico comparative genome mapping were investigated. Lastly, a bamboo microsatellites database (http://www.bamboogdb.org/ssr) was implemented to browse and search large information of bamboo microsatellites. Consequently, our results of microsatellite marker development are valuable for assisting bamboo taxonomy and investigating genomic studies in bamboo and related grass species. PMID:25620112

  16. Microsatellite markers for raspberry and blackberry

    Technology Transfer Automated Retrieval System (TEKTRAN)

    welve microsatellites were isolated from SSR-enriched genomic libraries of Rubus idaeus L.‘Meeker’ red raspberry (diploid) and R. loganobaccus L. H. Bailey ‘Marion’ blackberry-raspberry hybrid (hexaploid). These primer pairs, with the addition of one developed from a GenBank R. idaeus sequence, we...

  17. Microsatellite Markers for Raspberries and Blackberries

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Twelve microsatellites were isolated from SSR-enriched genomic libraries of Rubus idaeus L.‘Meeker’ red raspberry (diploid) and R. loganobaccus L. H. Bailey ‘Marion’ blackberry-raspberry hybrid (hexaploid). These primer pairs, with the addition of one developed from a GenBank R. idaeus sequence, w...

  18. Nonrandom distribution and frequencies of genomic and EST-derived microsatellite markers in rice, wheat, and barley

    PubMed Central

    La Rota, Mauricio; Kantety, Ramesh V; Yu, Ju-Kyung; Sorrells, Mark E

    2005-01-01

    Background Earlier comparative maps between the genomes of rice (Oryza sativa L.), barley (Hordeum vulgare L.) and wheat (Triticum aestivum L.) were linkage maps based on cDNA-RFLP markers. The low number of polymorphic RFLP markers has limited the development of dense genetic maps in wheat and the number of available anchor points in comparative maps. Higher density comparative maps using PCR-based anchor markers are necessary to better estimate the conservation of colinearity among cereal genomes. The purposes of this study were to characterize the proportion of transcribed DNA sequences containing simple sequence repeats (SSR or microsatellites) by length and motif for wheat, barley and rice and to determine in-silico rice genome locations for primer sets developed for wheat and barley Expressed Sequence Tags. Results The proportions of SSR types (di-, tri-, tetra-, and penta-nucleotide repeats) and motifs varied with the length of the SSRs within and among the three species, with trinucleotide SSRs being the most frequent. Distributions of genomic microsatellites (gSSRs), EST-derived microsatellites (EST-SSRs), and transcribed regions in the contiguous sequence of rice chromosome 1 were highly correlated. More than 13,000 primer pairs were developed for use by the cereal research community as potential markers in wheat, barley and rice. Conclusion Trinucleotide SSRs were the most common type in each of the species; however, the relative proportions of SSR types and motifs differed among rice, wheat, and barley. Genomic microsatellites were found to be primarily located in gene-rich regions of the rice genome. Microsatellite markers derived from the use of non-redundant EST-SSRs are an economic and efficient alternative to RFLP for comparative mapping in cereals. PMID:15720707

  19. Transferability, amplification quality, and genome specificity of microsatellites in Brassica carinata and related species.

    PubMed

    Marquez-Lema, A; Velasco, L; Perez-Vich, B

    2010-01-01

    No information is available on the transferability and amplification quality of microsatellite (SSR) markers of the public domain in Brassica carinata A. Braun. The objective of the presented research was to study the amplification of a set of 73 SSRs from B. nigra (L.) Koch and B. napus L. in B. carinata, and to compare the results with those obtained in the amplification of the same markers in other Brassica species of the U triangle. This set of SSRs from B. nigra (B genome) and B. napus (AC genome) allows the identification of the 3 basic genomes of the Brassica species tested. 94.3% of the SSR markers from B. nigra and 97.4% of those from B. napus amplified SSR-specific products in B. carinata. Very high-quality amplification with a strong signal and easy scoring in B. carinata was recorded for 52.8% of the specific loci from B. nigra SSRs and 59.3% of the specific loci from B. napus SSRs, compared to 66.7% in B. nigra and 62.8% in B. napus. Genome specificity and amplification quality of B. nigra and B. napus SSR markers in the 6 species under study is reported. High-quality transferable SSR markers provide an efficient and cost-effective platform to advance in molecular research in B. carinata. PMID:20453299

  20. Origin and genome evolution of polyploid green toads in Central Asia: evidence from microsatellite markers.

    PubMed

    Betto-Colliard, C; Sermier, R; Litvinchuk, S; Perrin, N; Stöck, M

    2015-03-01

    Polyploidization, which is expected to trigger major genomic reorganizations, occurs much less commonly in animals than in plants, possibly because of constraints imposed by sex-determination systems. We investigated the origins and consequences of allopolyploidization in Palearctic green toads (Bufo viridis subgroup) from Central Asia, with three ploidy levels and different modes of genome transmission (sexual versus clonal), to (i) establish a topology for the reticulate phylogeny in a species-rich radiation involving several closely related lineages and (ii) explore processes of genomic reorganization that may follow polyploidization. Sibship analyses based on 30 cross-amplifying microsatellite markers substantiated the maternal origins and revealed the paternal origins and relationships of subgenomes in allopolyploids. Analyses of the synteny of linkage groups identified three markers affected by translocation events, which occurred only within the paternally inherited subgenomes of allopolyploid toads and exclusively affected the linkage group that determines sex in several diploid species of the green toad radiation. Recombination rates did not differ between diploid and polyploid toad species, and were overall much reduced in males, independent of linkage group and ploidy levels. Clonally transmitted subgenomes in allotriploid toads provided support for strong genetic drift, presumably resulting from recombination arrest. The Palearctic green toad radiation seems to offer unique opportunities to investigate the consequences of polyploidization and clonal transmission on the dynamics of genomes in vertebrates. PMID:25370211

  1. Characterization of a minimal screening set of 172 microsatellite markers for genome-wide screens of the canine genome.

    PubMed

    Richman, M; Mellersh, C S; André, C; Galibert, F; Ostrander, E A

    2001-01-30

    We have characterized a subset of 172 microsatellite markers from the canine map, termed 'Minimal Screening Set 1' (Canine MSS-1), which we propose be used for initial genome-wide genetic linkage studies. Three hierarchical criteria were used to select markers from the current meiotic linkage and radiation hybrid maps for MSS-1. Markers were selected that (1) provided as complete coverage as possible of the canine genome, (2) were highly informative, and (3) have been ordered in linkage groups with a high degree of statistical support. This resulting screening set spans all reported meiotic linkage and RH groups, leaving only 10 known gaps > or = 20 cM. The average polymorphic information content (PIC) value of markers tested is 0.74. Coverage estimates suggest 42% of the genome is within 5 cM of at least one marker in the minimal screening set, 77% of the genome is within 10 cM. This minimal mapping set therefore provides an efficient and cost effective way to begin screening pedigrees of interest for genetic linkage. PMID:11179770

  2. Characterization of Microsatellite Loci in the Western Tarnished Plant Bug, Lygus hesperus Knight (Hemiptera: Miridae)

    Technology Transfer Automated Retrieval System (TEKTRAN)

    A microsatellite-enriched partial genomic DNA library of Lygus hesperus was generated and screened by sequencing. Ten polymorphic microsatellite marker loci were characterized by genotyping 92 insect samples. The observed number of alleles ranged from 3 to 7 with an average of 4.6 (S.E. ±0.45) while...

  3. Microsatellite markers for species of genus Dionda (Cyprinidae) from the American southwest

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Thirty-eight microsatellite markers were developed from an enriched genomic DNA library of the cyprinid fish (minnow) Dionda episcopa. The microsatellites include 31 perfect-repeat motifs (29 dinucleotide, 1 trinucleotide, and 1 tetranucleotide) and seven imperfect-repeat dinucleotide motifs. The ...

  4. The genomic Echinococcus microsatellite EmsB sequences: from a molecular marker to the epidemiological tool.

    PubMed

    Knapp, J; Bart, J M; Maillard, S; Gottstein, B; Piarroux, R

    2010-03-01

    In the field of molecular and epidemiological parasitology, characterization of fast evolving genetic markers appears as an important challenge to consider the diversity and genetic structure of parasites. The study of respective populations can help us to understand their adaptive strategies to survive and perpetuate the species within different host populations, all trying to resist infection. In the past, the relative monomorphic features of Echinococcus multilocularis, the causative agent of alveolar echinococcosis and a severe human parasitic disease, did not stimulate studies dealing with the genetic variability of Echinococcus species or respective populations. A recently developed, characterized and validated original multilocus microsatellite, named EmsB, tandemly repeated in the genome, offered an additional opportunity for this line of investigation. We have compiled in this review new insights brought by this molecular tracker on the transmission activity of Echinococcus among different hosts and at different geographical scales. PMID:20025824

  5. [Analysis of microsatellite loci of the chloroplast genome in the genus Capsicum (Pepper)].

    PubMed

    Ryzhova, N N; Kochieva, E Z

    2004-08-01

    Six plastome microsatellites were examined in 43 accessions of the genus Capsicum. In total, 33 allelic variants were detected. A specific haplotype of chloroplast DNA was identified for each Capsicum species. Species-specific allelic variants were found for most wild Capsicum species. The highest intraspecific variation was observed for the C. baccatum plastome. Low cpDNA polymorphism was characteristic of C. annuum: the cpSSRs were either monomorphic or dimorphic. The vast majority of C. annuum accessions each had alleles of one type. Another allele type was rare and occurred only in wild accessions. The results testified again to genetic conservation of C. annuum and especially its cultivated forms. The phylogenetic relationships established for the Capsicum species on the basis of plastome analysis were similar to those inferred from the morphological traits, isozyme patterns, and molecular analysis of the nuclear genome. PMID:15523848

  6. Characterization of novel polymorphic genomic microsatellite markers of Boehmeria tricuspis (Hance) Makino.

    PubMed

    Tang, Q; Chen, J H; Zang, G G; Luan, M B

    2016-01-01

    In the present study, 59 polymorphic microsatellite loci of Boehmeria tricuspis (Hance) Makino were developed from the specific length amplified fragment sequencing data library of genome. The number of alleles per locus ranged from two to five, and the observed and expected heterozygosities ranged from 0.0000 to 1.0000 and from 0.0769 to 0.6751, respectively. Among the 59 loci, 25 displayed significant deviations from Hardy-Weinberg expectations (P < 0.05). The developed simple sequence repeat markers should be useful for studying population genetics in B. tricuspis (Hance) Makino, for providing further knowledge on its population differentiation, breeding system, and dispersal ability, as well as quantitative trait locus mapping. These markers could also be valuable genetic resources for closely related species. PMID:27173265

  7. Genomic and genotyping characterization of haplotype-based polymorphic microsatellites in Prunus

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Efficient utilization of microsatellites in genetic studies remains impeded largely due to the unknown status of their primer reliability, chromosomal location, and allele polymorphism. Discovery and characterization of microsatellite polymorphisms in a taxon will disclose the unknowns and gain new ...

  8. Genotype-Environment Interactions in Microsatellite Stable/Microsatellite Instability-Low Colorectal Cancer: Results from a Genome-Wide Association Study

    PubMed Central

    Figueiredo, Jane C.; Lewinger, Juan Pablo; Song, Chi; Campbell, Peter T.; Conti, David V.; Edlund, Christopher K.; Duggan, Dave J.; Rangrej, Jagadish; Lemire, Mathieu; Hudson, Thomas; Zanke, Brent; Cotterchio, Michelle; Gallinger, Steven; Jenkins, Mark; Hopper, John; Haile, Robert; Newcomb, Polly; Potter, John; Baron, John A.; Marchand, Loic Le; Casey, Graham

    2011-01-01

    Background Genome-wide association studies (GWAS) have led to the identification of a number of common susceptibility loci for colorectal cancer (CRC); however, none of these GWAS have considered gene-environment (GxE) interactions. Therefore, it is unclear whether current hits are modified by environmental exposures or whether there are additional hits whose effects are dependent on environmental exposures. Methods We conducted a systematic search for GxE interactions using genome wide data from the Colon Cancer Family Registry that included 1,191 cases of microsatellite stable (MSS) or microsatellite instability (MSI)-low CRC and 999 controls genotyped using either the Illumina Human1M or Human1M-Duo BeadChip. We tested for interactions between genotypes and 14 environmental factors using three methods: a traditional case-control test, a case-only test, and the recently proposed two-step method by Murcray et al. All potentially significant findings were replicated in the ARCTIC Study. Results No GxE interactions were identified that reached genome-wide significance by any of the three methods. When analyzing previously reported susceptibility loci, seven significant GxE interactions were found at a 5% significance level. We investigated these seven interactions in an independent sample and none of the interactions were replicated. Conclusions Identifying GxE interactions will present challenges in a GWAS setting. Our power calculations illustrate the need for larger sample sizes; however, since CRC is a heterogeneous disease, a tradeoff between increasing sample size and heterogeneity needs to be considered. Impact The results from this first genome-wide analysis of GxE in CRC identify several challenges, which may be addressed by large consortium efforts. PMID:21357381

  9. Multiplexed microsatellite recovery using massively parallel sequencing

    USGS Publications Warehouse

    Jennings, T.N.; Knaus, B.J.; Mullins, T.D.; Haig, S.M.; Cronn, R.C.

    2011-01-01

    Conservation and management of natural populations requires accurate and inexpensive genotyping methods. Traditional microsatellite, or simple sequence repeat (SSR), marker analysis remains a popular genotyping method because of the comparatively low cost of marker development, ease of analysis and high power of genotype discrimination. With the availability of massively parallel sequencing (MPS), it is now possible to sequence microsatellite-enriched genomic libraries in multiplex pools. To test this approach, we prepared seven microsatellite-enriched, barcoded genomic libraries from diverse taxa (two conifer trees, five birds) and sequenced these on one lane of the Illumina Genome Analyzer using paired-end 80-bp reads. In this experiment, we screened 6.1 million sequences and identified 356958 unique microreads that contained di- or trinucleotide microsatellites. Examination of four species shows that our conversion rate from raw sequences to polymorphic markers compares favourably to Sanger- and 454-based methods. The advantage of multiplexed MPS is that the staggering capacity of modern microread sequencing is spread across many libraries; this reduces sample preparation and sequencing costs to less than $400 (USD) per species. This price is sufficiently low that microsatellite libraries could be prepared and sequenced for all 1373 organisms listed as 'threatened' and 'endangered' in the United States for under $0.5M (USD).

  10. A genome-wide scan of selective sweeps and association mapping of fruit traits using microsatellite markers in watermelon.

    PubMed

    Reddy, Umesh K; Abburi, Lavanya; Abburi, Venkata Lakshmi; Saminathan, Thangasamy; Cantrell, Robert; Vajja, Venkata Gopinath; Reddy, Rishi; Tomason, Yan R; Levi, Amnon; Wehner, Todd C; Nimmakayala, Padma

    2015-01-01

    Our genetic diversity study uses microsatellites of known map position to estimate genome level population structure and linkage disequilibrium, and to identify genomic regions that have undergone selection during watermelon domestication and improvement. Thirty regions that showed evidence of selective sweep were scanned for the presence of candidate genes using the watermelon genome browser (www.icugi.org). We localized selective sweeps in intergenic regions, close to the promoters, and within the exons and introns of various genes. This study provided an evidence of convergent evolution for the presence of diverse ecotypes with special reference to American and European ecotypes. Our search for location of linked markers in the whole-genome draft sequence revealed that BVWS00358, a GA repeat microsatellite, is the GAGA type transcription factor located in the 5' untranslated regions of a structure and insertion element that expresses a Cys2His2 Zinc finger motif, with presumed biological processes related to chitin response and transcriptional regulation. In addition, BVWS01708, an ATT repeat microsatellite, located in the promoter of a DTW domain-containing protein (Cla002761); and 2 other simple sequence repeats that association mapping link to fruit length and rind thickness. PMID:25425675

  11. A Genome-Wide Scan of Selective Sweeps and Association Mapping of Fruit Traits Using Microsatellite Markers in Watermelon

    PubMed Central

    Reddy, Umesh K.; Abburi, Lavanya; Abburi, Venkata Lakshmi; Saminathan, Thangasamy; Cantrell, Robert; Vajja, Venkata Gopinath; Reddy, Rishi; Tomason, Yan R.; Levi, Amnon; Wehner, Todd C.; Nimmakayala, Padma

    2015-01-01

    Our genetic diversity study uses microsatellites of known map position to estimate genome level population structure and linkage disequilibrium, and to identify genomic regions that have undergone selection during watermelon domestication and improvement. Thirty regions that showed evidence of selective sweep were scanned for the presence of candidate genes using the watermelon genome browser (www.icugi.org). We localized selective sweeps in intergenic regions, close to the promoters, and within the exons and introns of various genes. This study provided an evidence of convergent evolution for the presence of diverse ecotypes with special reference to American and European ecotypes. Our search for location of linked markers in the whole-genome draft sequence revealed that BVWS00358, a GA repeat microsatellite, is the GAGA type transcription factor located in the 5′ untranslated regions of a structure and insertion element that expresses a Cys2His2 Zinc finger motif, with presumed biological processes related to chitin response and transcriptional regulation. In addition, BVWS01708, an ATT repeat microsatellite, located in the promoter of a DTW domain-containing protein (Cla002761); and 2 other simple sequence repeats that association mapping link to fruit length and rind thickness. PMID:25425675

  12. Ultraconserved Elements Sequencing as a Low-Cost Source of Complete Mitochondrial Genomes and Microsatellite Markers in Non-Model Amniotes

    PubMed Central

    Raposo do Amaral, Fábio; Neves, Leandro G.; Resende, Márcio F. R.; Mobili, Flávia; Miyaki, Cristina Y.; Pellegrino, Katia C. M.; Biondo, Cibele

    2015-01-01

    Sequence capture of ultraconserved elements (UCEs) associated with massively parallel sequencing has become a common source of nuclear data for studies of animal systematics and phylogeography. However, mitochondrial and microsatellite variation are still commonly used in various kinds of molecular studies, and probably will complement genomic data in years to come. Here we show that besides providing abundant genomic data, UCE sequencing is an excellent source of both sequences for microsatellite loci design and complete mitochondrial genomes with high sequencing depth. Identification of dozens of microsatellite loci and assembly of complete mitogenomes is exemplified here using three species of Poospiza warbling finches from southern and southeastern Brazil. This strategy opens exciting opportunities to simultaneously analyze genome-wide nuclear datasets and traditionally used mtDNA and microsatellite markers in non-model amniotes at no additional cost. PMID:26379155

  13. Patterns of Evolutionary Conservation of Microsatellites (SSRs) Suggest a Faster Rate of Genome Evolution in Hymenoptera Than in Diptera

    PubMed Central

    Stolle, Eckart; Kidner, Jonathan H.; Moritz, Robin F.A.

    2013-01-01

    Microsatellites, or simple sequence repeats (SSRs), are common and widespread DNA elements in genomes of many organisms. However, their dynamics in genome evolution is unclear, whereby they are thought to evolve neutrally. More available genome sequences along with dated phylogenies allowed for studying the evolution of these repetitive DNA elements along evolutionary time scales. This could be used to compare rates of genome evolution. We show that SSRs in insects can be retained for several hundred million years. Different types of microsatellites seem to be retained longer than others. By comparing Dipteran with Hymenopteran species, we found very similar patterns of SSR loss during their evolution, but both taxa differ profoundly in the rate. Relative to divergence time, Diptera lost SSRs twice as fast as Hymenoptera. The loss of SSRs on the Drosophila melanogaster X-chromosome was higher than on the other chromosomes. However, accounting for generation time, the Diptera show an 8.5-fold slower rate of SSR loss than the Hymenoptera, which, in contrast to previous studies, suggests a faster genome evolution in the latter. This shows that generation time differences can have a profound effect. A faster genome evolution in these insects could be facilitated by several factors very different to Diptera, which is discussed in light of our results on the haplodiploid D. melanogaster X-chromosome. Furthermore, large numbers of SSRs can be found to be in synteny and thus could be exploited as a tool to investigate genome structure and evolution. PMID:23292136

  14. Genome-Wide Survey and Analysis of Microsatellite Sequences in Bovid Species

    PubMed Central

    Qi, Wen-Hua; Jiang, Xue-Mei; Du, Lian-Ming; Xiao, Guo-Sheng; Hu, Ting-Zhang; Yue, Bi-Song; Quan, Qiu-Mei

    2015-01-01

    Microsatellites or simple sequence repeats (SSRs) have become the most popular source of genetic markers, which are ubiquitously distributed in many eukaryotic and prokaryotic genomes. This is the first study examining and comparing SSRs in completely sequenced genomes of the Bovidae. We analyzed and compared the number of SSRs, relative abundance, relative density, guanine-cytosine (GC) content and proportion of SSRs in six taxonomically different bovid species: Bos taurus, Bubalus bubalis, Bos mutus, Ovis aries, Capra hircus, and Pantholops hodgsonii. Our analysis revealed that, based on our search criteria, the total number of perfect SSRs found ranged from 663,079 to 806,907 and covered from 0.44% to 0.48% of the bovid genomes. Relative abundance and density of SSRs in these Bovinae genomes were non-significantly correlated with genome size (Pearson, r < 0.420, p > 0.05). Perfect mononucleotide SSRs were the most abundant, followed by the pattern: perfect di- > tri- > penta- > tetra- > hexanucleotide SSRs. Generally, the number of SSRs, relative abundance, and relative density of SSRs decreased as the motif repeat length increased in each species of Bovidae. The most GC-content was in trinucleotide SSRs and the least was in the mononucleotide SSRs in the six bovid genomes. The GC-contents of tri- and pentanucleotide SSRs showed a great deal of similarity among different chromosomes of B. taurus, O. aries, and C. hircus. SSR number of all chromosomes in the B. taurus, O.aries, and C. hircus is closely positively correlated with chromosome sequence size (Pearson, r > 0.980, p < 0.01) and significantly negatively correlated with GC-content (Pearson, r < -0.638, p < 0.01). Relative abundance and density of SSRs in all chromosomes of the three species were significantly negatively correlated with GC-content (Pearson, r < -0.333, P < 0.05) but not significantly correlated with chromosome sequence size (Pearson, r < -0.185, P > 0.05). Relative abundances of the same

  15. D5S2500 is an ambiguously characterized STR: Identification and description of forensic microsatellites in the genomics age.

    PubMed

    Phillips, C; Parson, W; Amigo, J; King, J L; Coble, M D; Steffen, C R; Vallone, P M; Gettings, K B; Butler, J M; Budowle, B

    2016-07-01

    In the process of establishing short tandem repeat (STR) sequence variant nomenclature guidelines in anticipation of expanded forensic multiplexes for massively parallel sequencing (MPS), it was discovered that the STR D5S2500 has multiple positions and genomic characteristics reported. This ambiguity is because the marker named D5S2500 consists of two different microsatellites forming separate components in the capillary electrophoresis multiplexes of Qiagen's HDplex (Hilden, Germany) and AGCU ScienTech's non-CODIS STR 21plex (Wuxi, Jiangsu, China). This study outlines the genomic details used to identify each microsatellite and reveals the D5S2500 marker in HDplex has the correctly assigned STR name, while the D5S2500 marker in the AGCU 21plex, closely positioned a further 1643 nucleotides in the human reference sequence, is an unnamed microsatellite. The fact that the D5S2500 marker has existed as two distinct STR loci undetected for almost ten years, even with reported discordant genotypes for the standard control DNA, underlines the need for careful scrutiny of the genomic properties of forensic STRs, as they become adapted for sequence analysis with MPS systems. We make the recommendation that precise chromosome location data must be reported for any forensic marker under development but not in common use, so that the genomic characteristics of the locus are validated to the same level of accuracy as its allelic variation and forensic performance. To clearly differentiate each microsatellite, we propose the name D5S2800 be used to identify the Chromosome-5 STR in the AGCU 21plex. PMID:26974236

  16. Comparative genomic analysis reveals species-dependent complexities that explain difficulties with microsatellite marker development in molluscs.

    PubMed

    McInerney, C E; Allcock, A L; Johnson, M P; Bailie, D A; Prodöhl, P A

    2011-01-01

    Reliable population DNA molecular markers are difficult to develop for molluscs, the reasons for which are largely unknown. Identical protocols for microsatellite marker development were implemented in three gastropods. Success rates were lower for Gibbula cineraria compared to Littorina littorea and L. saxatilis. Comparative genomic analysis of 47.2 kb of microsatellite containing sequences (MCS) revealed a high incidence of cryptic repetitive DNA in their flanking regions. The majority of these were novel, and could be grouped into DNA families based upon sequence similarities. Significant inter-specific variation in abundance of cryptic repetitive DNA and DNA families was observed. Repbase scans show that a large proportion of cryptic repetitive DNA was identified as transposable elements (TEs). We argue that a large number of TEs and their transpositional activity may be linked to differential rates of DNA multiplication and recombination. This is likely to be an important factor explaining inter-specific variation in genome stability and hence microsatellite marker development success rates. Gastropods also differed significantly in the type of TEs classes (autonomous vs non-autonomous) observed. We propose that dissimilar transpositional mechanisms differentiate the TE classes in terms of their propensity for transposition, fixation and/or silencing. Consequently, the phylogenetic conservation of non-autonomous TEs, such as CvA, suggests that dispersal of these elements may have behaved as microsatellite-inducing elements. Results seem to indicate that, compared to autonomous, non-autonomous TEs maybe have a more active role in genome rearrangement processes. The implications of the findings for genomic rearrangement, stability and marker development are discussed. PMID:20424639

  17. Isolation and characterization of genomic microsatellite markers for small cardamom (Elettaria cardamomum Maton) for utility in genetic diversity analysis.

    PubMed

    Cyriac, Anu; Paul, Ritto; Anupama, K; Senthil Kumar, R; Sheeja, T E; Nirmal Babu, K; Parthasarathy, V A

    2016-04-01

    Microsatellite markers in small cardamom (Elettaria cardamomum Maton) were developed using the selective hybridization enrichment method. A total of 140 microsatellite repeats were identified from 270 clones. Primers were designed for 58 microsatellites and 44 primer pairs amplified products of expected size in cardamom. These markers were used for studying the diversity of 20 important small cardamom genotypes, and six markers were found to be polymorphic. The number of alleles ranged from 2 to 7 with an average of 3.6 per locus. Polymorphic information content values ranged from 0.14 to 0.38 based on dominant scoring. The two markers ECM 47a and ECMG 28 generated specific banding patterns for the genotypes MCC7 (Pink tiller) and APG434 (MA18) respectively. Dendrogram illustrated the genetic similarity between different genotypes of Kerala and Karnataka regions. It differentiated the closely related genotypes and released varieties into separate groups. Principal coordinate analysis revealed PV1 and ICRI 1 as the most divergent genotypes. The study demonstrated that these markers are informative and can be further utilized for generating reliable molecular data for assisting the crop improvement of small cardamom. Cross generic transferability (71.4 %) of the developed primers proved that they are useful for phylogenetic studies in the family Zingiberaceae. This is the first report of de novo isolation, characterisation and utilization of microsatellite markers for the genetic diversity analysis of small cardamom. PMID:27436913

  18. Characterization of Coffea chloroplast microsatellites and evidence for the recent divergence of C. arabica and C. eugenioides chloroplast genomes.

    PubMed

    Tesfaye, Kassahun; Borsch, Thomas; Govers, Kim; Bekele, Endashaw

    2007-12-01

    Comparative sequencing of >7 kb of highly variable chloroplast genome regions (atpB-rbcL, trnS-trnG, rpl22-rps19, and rps19-rpl2 spacers; introns in atpF, trnG, trnK, and rpl16) with microsatellites known from other angiosperms was carried out in Coffea. Samples comprised 8 diploid species of Coffea, 5 individuals of tetraploid C. arabica representing geographically distant wild populations from Ethiopia, 2 commercial cultivars of C. arabica, and Psilanthus leroyi and Ixora coccinea as outgroups. Phylogeny reconstruction using maximum parsimony and Bayesian inference resulted in congruent topologies with high support for C. arabica and C. eugenioides being sisters. Partitioned analyses showed that all regions except the atpB-rbcL spacer resolved this sister-group, although this was often unsupported. The large sequence data set further shows that chloroplast genomes of C. arabica and C. eugenioides each possess apomorphies, indicating that not C. eugenioides but an ancestor or close relative of C. eugenioides is the maternal parent of C. arabica. Seven variable chloroplast microsatellites were characterized in Coffea. Most microsatellites are poly(A/T) stretches, whereas one in the trnS-trnG spacer has an (AT)n motif. Most strikingly, all individuals of C. arabica possess identical sequences, suggesting a single chloroplast haplotype. This can be explained by a recent origin of C. arabica in a unique allopolyploidization event, or by severe bottleneck effects in the evolutionary history of the species. Reconstruction of the evolution of microstructural mutations shows much higher levels of homoplasy in microsatellite loci than in other parts of spacers and introns. Microsatellites are inferred to evolve by insertion and deletion of 1 to 3 motif copies in one step. PMID:18059539

  19. Localization and Characterization of 170 BAC-derived clones and mapping of Ninety-Four Microsatellites in the Hessian Fly

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Ninety-four microsatellites from enriched genomic libraries of Hessian fly (Mayetiola destructor (Say)) were localized to 170 cognate clones in a Hessian fly bacterial artificial chromosome (BAC) library. These microsatellite-positive BAC clones were physically mapped to polytene chromosomes by fl...

  20. Development of Multiple Polymorphic Microsatellite Markers for Ceratina calcarata (Hymenoptera: Apidae) Using Genome-Wide Analysis.

    PubMed

    Shell, Wyatt A; Rehan, Sandra M

    2016-01-01

    The small carpenter bee, Ceratina calcarata (Robertson), is a widespread native pollinator across eastern North America. The behavioral ecology and nesting biology of C. calcarata has been relatively well-studied and the species is emerging as a model organism for both native pollinator and social evolution research. C. calcarata is subsocial: reproductively mature females provide extended maternal care to their brood. As such, studies of C. calcarata may also reveal patterns of relatedness and demography unique to primitively social Hymenoptera. Here, we present 21 microsatellite loci, isolated from the recently completed C. calcarata genome. Screening in 39 individuals across their distribution revealed that no loci were in linkage disequilibrium, nor did any deviate significantly from Hardy-Weinberg following sequential Bonferroni correction. Allele count ranged from 2 to 14, and observed and expected heterozygosities ranged from 0.08 to 0.82 (mean 0.47) and 0.26 to 0.88 (mean 0.56), respectively. These markers will enable studies of population-wide genetic structuring across C. calcarata's distribution. Such tools will also allow for exploration of between and within-colony relatedness in this subsocial native pollinator. PMID:27324584

  1. Development of Multiple Polymorphic Microsatellite Markers for Ceratina calcarata (Hymenoptera: Apidae) Using Genome-Wide Analysis

    PubMed Central

    Shell, Wyatt A.; Rehan, Sandra M.

    2016-01-01

    The small carpenter bee, Ceratina calcarata (Robertson), is a widespread native pollinator across eastern North America. The behavioral ecology and nesting biology of C. calcarata has been relatively well-studied and the species is emerging as a model organism for both native pollinator and social evolution research. C. calcarata is subsocial: reproductively mature females provide extended maternal care to their brood. As such, studies of C. calcarata may also reveal patterns of relatedness and demography unique to primitively social Hymenoptera. Here, we present 21 microsatellite loci, isolated from the recently completed C. calcarata genome. Screening in 39 individuals across their distribution revealed that no loci were in linkage disequilibrium, nor did any deviate significantly from Hardy-Weinberg following sequential Bonferroni correction. Allele count ranged from 2 to 14, and observed and expected heterozygosities ranged from 0.08 to 0.82 (mean 0.47) and 0.26 to 0.88 (mean 0.56), respectively. These markers will enable studies of population-wide genetic structuring across C. calcarata’s distribution. Such tools will also allow for exploration of between and within-colony relatedness in this subsocial native pollinator. PMID:27324584

  2. Reverse random amplified microsatellite polymorphism reveals enhanced polymorphisms in the 3' end of simple sequence repeats in the pepper genome.

    PubMed

    Min, Woong-Ki; Han, Jung-Heon; Kang, Won-Hee; Lee, Heung-Ryul; Kim, Byung-Dong

    2008-09-30

    Microsatellites or simple sequence repeats (SSR) are widely distributed in eukaryotic genomes and are informative genetic markers. Despite many advantages of SSR markers such as a high degree of allelic polymorphisms, co-dominant inheritance, multi-allelism, and genome-wide coverage in various plant species, they also have shortcomings such as low polymorphic rates between genetically close lines, especially in Capsicum annuum. We developed an alternative technique to SSR by normalizing and alternating anchored primers in random amplified microsatellite polymorphisms (RAMP). This technique, designated reverse random amplified microsatellite polymorphism (rRAMP), allows the detection of nucleotide variation in the 3' region flanking an SSR using normalized anchored and random primer combinations. The reproducibility and frequency of polymorphic loci in rRAMP was vigorously enhanced by translocation of the 5' anchor of repeat sequences to the 3' end position and selective use of moderate arbitrary primers. In our study, the PCR banding pattern of rRAMP was highly dependent on the frequency of repeat motifs and primer combinations with random primers. Linkage analysis showed that rRAMP markers were well scattered on an intra-specific pepper map. Based on these results, we suggest that this technique is useful for studying genetic diversity, molecular fingerprinting, and rapidly constructing molecular maps for diverse plant species. PMID:18483466

  3. Genome-wide SNP and microsatellite variation illuminate population-level epidemiology in the Leishmania donovani species complex.

    PubMed

    Downing, Tim; Stark, Olivia; Vanaerschot, Manu; Imamura, Hideo; Sanders, Mandy; Decuypere, Saskia; de Doncker, Simonne; Maes, Ilse; Rijal, Suman; Sundar, Shyam; Dujardin, Jean-Claude; Berriman, Matthew; Schönian, Gabriele

    2012-01-01

    The species of the Leishmania donovani species complex cause visceral leishmaniasis, a debilitating infectious disease transmitted by sandflies. Understanding molecular changes associated with population structure in these parasites can help unravel their epidemiology and spread in humans. In this study, we used a panel of standard microsatellite loci and genome-wide SNPs to investigate population-level diversity in L. donovani strains recently isolated from a small geographic area spanning India, Bihar and Nepal, and compared their variation to that found in diverse strains of the L. donovani complex isolates from Europe, Africa and Asia. Microsatellites and SNPs could clearly resolve the phylogenetic relationships of the strains between continents, and microsatellite phylogenies indicated that certain older Indian strains were closely related to African strains. In the context of the anti-malaria spraying campaigns in the 1960s, this was consistent with a pattern of episodic population size contractions and clonal expansions in these parasites that was supported by population history simulations. In sharp contrast to the low resolution provided by microsatellites, SNPs retained a much more fine-scale resolution of population-level variability to the extent that they identified four different lineages from the same region one of which was more closely related to African and European strains than to Indian or Nepalese ones. Joining results of in vitro testing the antimonial drug sensitivity with the phylogenetic signals from the SNP data highlighted protein-level mutations revealing a distinct drug-resistant group of Nepalese and Indian L. donovani. This study demonstrates the power of genomic data for exploring parasite population structure. Furthermore, markers defining different genetic groups have been discovered that could potentially be applied to investigate drug resistance in clinical Leishmania strains. PMID:22119748

  4. Selective enrichment of damaged DNA molecules for ancient genome sequencing

    PubMed Central

    2014-01-01

    Contamination by present-day human and microbial DNA is one of the major hindrances for large-scale genomic studies using ancient biological material. We describe a new molecular method, U selection, which exploits one of the most distinctive features of ancient DNA—the presence of deoxyuracils—for selective enrichment of endogenous DNA against a complex background of contamination during DNA library preparation. By applying the method to Neanderthal DNA extracts that are heavily contaminated with present-day human DNA, we show that the fraction of useful sequence information increases ∼10-fold and that the resulting sequences are more efficiently depleted of human contamination than when using purely computational approaches. Furthermore, we show that U selection can lead to a four- to fivefold increase in the proportion of endogenous DNA sequences relative to those of microbial contaminants in some samples. U selection may thus help to lower the costs for ancient genome sequencing of nonhuman samples also. PMID:25081630

  5. Genomic sequencing and microsatellite marker development for Boswellia papyrifera, an economically important but threatened tree native to dry tropical forests.

    PubMed

    Addisalem, A B; Esselink, G Danny; Bongers, F; Smulders, M J M

    2015-01-01

    Microsatellite (or simple sequence repeat, SSR) markers are highly informative DNA markers often used in conservation genetic research. Next-generation sequencing enables efficient development of large numbers of SSR markers at lower costs. Boswellia papyrifera is an economically important tree species used for frankincense production, an aromatic resinous gum exudate from bark. It grows in dry tropical forests in Africa and is threatened by a lack of rejuvenation. To help guide conservation efforts for this endangered species, we conducted an analysis of its genomic DNA sequences using Illumina paired-end sequencing. The genome size was estimated at 705 Mb per haploid genome. The reads contained one microsatellite repeat per 5.7 kb. Based on a subset of these repeats, we developed 46 polymorphic SSR markers that amplified 2-12 alleles in 10 genotypes. This set included 30 trinucleotide repeat markers, four tetranucleotide repeat markers, six pentanucleotide markers and six hexanucleotide repeat markers. Several markers were cross-transferable to Boswellia pirrotae and B. popoviana. In addition, retrotransposons were identified, the reads were assembled and several contigs were identified with similarity to genes of the terpene and terpenoid backbone synthesis pathways, which form the major constituents of the bark resin. PMID:25573702

  6. Genomic sequencing and microsatellite marker development for Boswellia papyrifera, an economically important but threatened tree native to dry tropical forests

    PubMed Central

    Addisalem, A. B.; Esselink, G. Danny; Bongers, F.; Smulders, M. J. M.

    2015-01-01

    Microsatellite (or simple sequence repeat, SSR) markers are highly informative DNA markers often used in conservation genetic research. Next-generation sequencing enables efficient development of large numbers of SSR markers at lower costs. Boswellia papyrifera is an economically important tree species used for frankincense production, an aromatic resinous gum exudate from bark. It grows in dry tropical forests in Africa and is threatened by a lack of rejuvenation. To help guide conservation efforts for this endangered species, we conducted an analysis of its genomic DNA sequences using Illumina paired-end sequencing. The genome size was estimated at 705 Mb per haploid genome. The reads contained one microsatellite repeat per 5.7 kb. Based on a subset of these repeats, we developed 46 polymorphic SSR markers that amplified 2–12 alleles in 10 genotypes. This set included 30 trinucleotide repeat markers, four tetranucleotide repeat markers, six pentanucleotide markers and six hexanucleotide repeat markers. Several markers were cross-transferable to Boswellia pirrotae and B. popoviana. In addition, retrotransposons were identified, the reads were assembled and several contigs were identified with similarity to genes of the terpene and terpenoid backbone synthesis pathways, which form the major constituents of the bark resin. PMID:25573702

  7. Microsatellite primers resource developed from the mapped sequence scaffolds of Nisqually-1 genome. Submitted to New Phytologist

    SciTech Connect

    Yin, Tongming; ZHANG, Dr. XINYE; Gunter, Lee E; Li, Shuxian; Wullschleger, Stan D; Huang, Prof. Minren; Tuskan, Gerald A

    2009-01-01

    In this study, 148 428 simple sequence repeat (SSR) primer pairs were designed from the unambiguously mapped sequence scaffolds of the Nisqually-1 genome. The physical position of the priming sites were identified along each of the 19 Populus chromosomes, and it was specified whether the priming sequences belong to intronic, intergenic, exonic or UTR regions. A subset of 150 SSR loci were amplified and a high amplification success rate (72%) was obtained in P. tremuloides, which belongs to a divergent subgenus of Populus relative to Nisqually-1. PCR reactions showed that the amplification success rate of exonic primer pairs was much higher than that of the intronic/intergenic primer pairs. Applying ANOVA and regression analyses to the flanking sequences of microsatellites, the repeat lengths, the GC contents of the repeats, the repeat motif numbers, the repeat motif length and the base composition of the repeat motif, it was determined that only the base composition of the repeat motif and the repeat motif length significantly affect the microsatellite variability in P. tremuloides samples. The SSR primer resource developed in this study provides a database for selecting highly transferable SSR markers with known physical position in the Populus genome and provides a comprehensive genetic tool to extend the genome sequence of Nisqually-1 to genetic studies in different Populus species.

  8. Whole genome amplification and microsatellite genotyping of herbarium DNA revealed the identity of an ancient grapevine cultivar.

    PubMed

    Malenica, Nenad; Simon, Silvio; Besendorfer, Višnja; Maletić, Edi; Kontić, Jasminka Karoglan; Pejić, Ivan

    2011-09-01

    Reconstruction of the grapevine cultivation history has advanced tremendously during the last decade. Identification of grapevine cultivars by using microsatellite DNA markers has mostly become a routine. The parentage of several renowned grapevine cultivars, like Cabernet Sauvignon and Chardonnay, has been elucidated. However, the assembly of a complete grapevine genealogy is not yet possible because missing links might no longer be in cultivation or are even extinct. This problem could be overcome by analyzing ancient DNA from grapevine herbarium specimens and other historical remnants of once cultivated varieties. Here, we present the first successful genotyping of a grapevine herbarium specimen and the identification of the corresponding grapevine cultivar. Using a set of nine grapevine microsatellite markers, in combination with a whole genome amplification procedure, we found the 90-year-old Tribidrag herbarium specimen to display the same microsatellite profile as the popular American cultivar Zinfandel. This work, together with information from several historical documents, provides a new clue of Zinfandel cultivation in Croatia as early as the beginning of fifteenth century, under the native name Tribidrag. Moreover, it emphasizes substantial information potential of existing grapevine and other herbarium collections worldwide. PMID:21833713

  9. Whole genome amplification and microsatellite genotyping of herbarium DNA revealed the identity of an ancient grapevine cultivar

    NASA Astrophysics Data System (ADS)

    Malenica, Nenad; Šimon, Silvio; Besendorfer, Višnja; Maletić, Edi; Karoglan Kontić, Jasminka; Pejić, Ivan

    2011-09-01

    Reconstruction of the grapevine cultivation history has advanced tremendously during the last decade. Identification of grapevine cultivars by using microsatellite DNA markers has mostly become a routine. The parentage of several renowned grapevine cultivars, like Cabernet Sauvignon and Chardonnay, has been elucidated. However, the assembly of a complete grapevine genealogy is not yet possible because missing links might no longer be in cultivation or are even extinct. This problem could be overcome by analyzing ancient DNA from grapevine herbarium specimens and other historical remnants of once cultivated varieties. Here, we present the first successful genotyping of a grapevine herbarium specimen and the identification of the corresponding grapevine cultivar. Using a set of nine grapevine microsatellite markers, in combination with a whole genome amplification procedure, we found the 90-year-old Tribidrag herbarium specimen to display the same microsatellite profile as the popular American cultivar Zinfandel. This work, together with information from several historical documents, provides a new clue of Zinfandel cultivation in Croatia as early as the beginning of fifteenth century, under the native name Tribidrag. Moreover, it emphasizes substantial information potential of existing grapevine and other herbarium collections worldwide.

  10. Survey and analysis of simple sequence repeats in the Laccaria bicolor genome, with development of microsatellite markers

    SciTech Connect

    Labbe, Jessy L; Murat, Claude; Morin, Emmanuelle; Le Tacon, F; Martin, Francis

    2011-01-01

    It is becoming clear that simple sequence repeats (SSRs) play a significant role in fungal genome organization, and they are a large source of genetic markers for population genetics and meiotic maps. We identified SSRs in the Laccaria bicolor genome by in silico survey and analyzed their distribution in the different genomic regions. We also compared the abundance and distribution of SSRs in L. bicolor with those of the following fungal genomes: Phanerochaete chrysosporium, Coprinopsis cinerea, Ustilago maydis, Cryptococcus neoformans, Aspergillus nidulans, Magnaporthe grisea, Neurospora crassa and Saccharomyces cerevisiae. Using the MISA computer program, we detected 277,062 SSRs in the L. bicolor genome representing 8% of the assembled genomic sequence. Among the analyzed basidiomycetes, L. bicolor exhibited the highest SSR density although no correlation between relative abundance and the genome sizes was observed. In most genomes the short motifs (mono- to trinucleotides) were more abundant than the longer repeated SSRs. Generally, in each organism, the occurrence, relative abundance, and relative density of SSRs decreased as the repeat unit increased. Furthermore, each organism had its own common and longest SSRs. In the L. bicolor genome, most of the SSRs were located in intergenic regions (73.3%) and the highest SSR density was observed in transposable elements (TEs; 6,706 SSRs/Mb). However, 81% of the protein-coding genes contained SSRs in their exons, suggesting that SSR polymorphism may alter gene phenotypes. Within a L. bicolor offspring, sequence polymorphism of 78 SSRs was mainly detected in non-TE intergenic regions. Unlike previously developed microsatellite markers, these new ones are spread throughout the genome; these markers could have immediate applications in population genetics.

  11. Development and Integration of Genome-Wide Polymorphic Microsatellite Markers onto a Reference Linkage Map for Constructing a High-Density Genetic Map of Chickpea

    PubMed Central

    Gaur, Rashmi; Chattopadhyay, Debasis; Jain, Mukesh; Parida, Swarup K.; Bhatia, Sabhyata

    2015-01-01

    The identification of informative in silico polymorphic genomic and genic microsatellite markers by comparing the genome and transcriptome sequences of crop genotypes is a rapid, cost-effective and non-laborious approach for large-scale marker validation and genotyping applications, including construction of high-density genetic maps. We designed 1494 markers, including 1016 genomic and 478 transcript-derived microsatellite markers showing in-silico fragment length polymorphism between two parental genotypes (Cicer arietinum ICC4958 and C. reticulatum PI489777) of an inter-specific reference mapping population. High amplification efficiency (87%), experimental validation success rate (81%) and polymorphic potential (55%) of these microsatellite markers suggest their effective use in various applications of chickpea genetics and breeding. Intra-specific polymorphic potential (48%) detected by microsatellite markers in 22 desi and kabuli chickpea genotypes was lower than inter-specific polymorphic potential (59%). An advanced, high-density, integrated and inter-specific chickpea genetic map (ICC4958 x PI489777) having 1697 map positions spanning 1061.16 cM with an average inter-marker distance of 0.625 cM was constructed by assigning 634 novel informative transcript-derived and genomic microsatellite markers on eight linkage groups (LGs) of our prior documented, 1063 marker-based genetic map. The constructed genome map identified 88, including four major (7–23 cM) longest high-resolution genomic regions on LGs 3, 5 and 8, where the maximum number of novel genomic and genic microsatellite markers were specifically clustered within 1 cM genetic distance. It was for the first time in chickpea that in silico FLP analysis at genome-wide level was carried out and such a large number of microsatellite markers were identified, experimentally validated and further used in genetic mapping. To best of our knowledge, in the presently constructed genetic map, we mapped highest

  12. A microsatellite genetic linkage map of black rockfish ( Sebastes schlegeli)

    NASA Astrophysics Data System (ADS)

    Chu, Guannan; Jiang, Liming; He, Yan; Yu, Haiyang; Wang, Zhigang; Jiang, Haibin; Zhang, Quanqi

    2014-12-01

    Ovoviviparous black rockfish ( Sebastes schlegeli) is an important marine fish species for aquaculture and fisheries in China. Genetic information of this species is scarce because of the lack of microsatellite markers. In this study, a large number of microsatellite markers of black rockfish were isolated by constructing microsatellite-enriched libraries. Female- and male-specific genetic linkage maps were constructed using 435 microsatellite markers genotyped in a full-sib family of the fish species. The female linkage map contained 140 microsatellite markers, in which 23 linkage groups had a total genetic length of 1334.1 cM and average inter-marker space of 13.3 cM. The male linkage map contained 156 microsatellite markers, in which 25 linkage groups had a total genetic length of 1359.6 cM and average inter-marker distance of 12.4 cM. The genome coverage of the female and male linkage maps was 68.6% and 69.3%, respectively. The female-to-male ratio of the recombination rate was approximately 1.07:1 in adjacent microsatellite markers. This paper presents the first genetic linkage map of microsatellites in black rockfish. The collection of polymorphic markers and sex-specific linkage maps of black rockfish could be useful for further investigations on parental assignment, population genetics, quantitative trait loci mapping, and marker-assisted selection in related breeding programs.

  13. Ten polymorphic microsatellite loci identified from a small insert genomic library for Peronospora tabacina

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Eleven polymorphic microsatellite loci for the oomycete obligate biotrophic pathogen Peronospora tabacina of tobacco (Nicotiana tabacum) were developed. Loci were characterized using 44 isolates of P. tabacina collected from tobacco plants growing in Europe, Near East, and North and South America. ...

  14. Use of microsatellite markers for the assessment of bambara groundnut breeding system and varietal purity before genome sequencing.

    PubMed

    Ho, Wai Kuan; Muchugi, Alice; Muthemba, Samuel; Kariba, Robert; Mavenkeni, Busiso Olga; Hendre, Prasad; Song, Bo; Van Deynze, Allen; Massawe, Festo; Mayes, Sean

    2016-06-01

    Maximizing the research output from a limited investment is often the major challenge for minor and underutilized crops. However, such crops may be tolerant to biotic and abiotic stresses and are adapted to local, marginal, and low-input environments. Their development through breeding will provide an important resource for future agricultural system resilience and diversification in the context of changing climates and the need to achieve food security. The African Orphan Crops Consortium recognizes the values of genomic resources in facilitating the improvement of such crops. Prior to beginning genome sequencing there is a need for an assessment of line varietal purity and to estimate any residual heterozygosity. Here we present an example from bambara groundnut (Vigna subterranea (L.) Verdc.), an underutilized drought tolerant African legume. Two released varieties from Zimbabwe, identified as potential genotypes for whole genome sequencing (WGS), were genotyped with 20 species-specific SSR markers. The results indicate that the cultivars are actually a mix of related inbred genotypes, and the analysis allowed a strategy of single plant selection to be used to generate non-heterogeneous DNA for WGS. The markers also confirmed very low levels of heterozygosity within individual plants. The application of a pre-screen using co-dominant microsatellite markers is expected to substantially improve the genome assembly, compared to a cultivar bulking approach that could have been adopted. PMID:27244454

  15. New Holland honeyeater (Phylidonyris novaehollandiae) microsatellites: isolation and characterization of 15 novel markers using an enrichment method.

    PubMed

    Myers, Steven A; Gardner, Michael G; Donnellan, Stephen; Kleindorfer, Sonia

    2009-05-01

    The New Holland honeyeater (Phylidonyris novaehollandiae) plays a significant role in the pollination and sustainability of Australia's endemic flora, and hence fauna. Despite this key ecosystem function, knowledge of P. novaehollandiae life-history traits and population dynamics remain poorly understood. We describe the development of primers amplifying 22 P. novaehollandiae microsatellite loci. Fifteen of the loci were found to be polymorphic, with observed heterozygosity between 0.500 and 1.000, and from four to 17 alleles per locus in adult birds from the study site. PMID:21564837

  16. A microsatellite-based genetic linkage map and putative sex-determining genomic regions in Lake Victoria cichlids.

    PubMed

    Kudo, Yu; Nikaido, Masato; Kondo, Azusa; Suzuki, Hikoyu; Yoshida, Kohta; Kikuchi, Kiyoshi; Okada, Norihiro

    2015-04-15

    Cichlid fishes in East Africa have undergone extensive adaptive radiation, which has led to spectacular diversity in their morphology and ecology. To date, genetic linkage maps have been constructed for several tilapias (riverine), Astatotilapia burtoni (Lake Tanganyika), and hybrid lines of Lake Malawi cichlids to facilitate genome-wide comparative analyses. In the present study, we constructed a genetic linkage map of the hybrid line of Lake Victoria cichlids, so that maps of cichlids from all the major areas of East Africa will be available. The genetic linkage map shown here is derived from the F2 progeny of an interspecific cross between Haplochromis chilotes and Haplochromis sauvagei and is based on 184 microsatellite and two single-nucleotide polymorphism (SNP) markers. Most of the microsatellite markers used in the present study were originally designed for other genetic linkage maps, allowing us to directly compare each linkage group (LG) among different cichlid groups. We found 25 LGs, the total length of which was 1133.2cM with an average marker spacing of about 6.09cM. Our subsequent linkage mapping analysis identified two putative sex-determining loci in cichlids. Interestingly, one of these two loci is located on cichlid LG5, on which the female heterogametic ZW locus and several quantitative trait loci (QTLs) related to adaptive evolution have been reported in Lake Malawi cichlids. We also found that V1R1 and V1R2, candidate genes for the fish pheromone receptor, are located very close to the recently detected sex-determining locus on cichlid LG5. The genetic linkage map study presented here may provide a valuable foundation for studying the chromosomal evolution of East African cichlids and the possible role of sex chromosomes in generating their genomic diversity. PMID:25639358

  17. Distribution and localization of microsatellites in the Perigord black truffle genome and identification of new molecular markers.

    PubMed

    Murat, C; Riccioni, C; Belfiori, B; Cichocki, N; Labbé, J; Morin, E; Tisserant, E; Paolocci, F; Rubini, A; Martin, F

    2011-06-01

    The level of genetic diversity and genetic structure in the Perigord black truffle (Tuber melanosporum Vittad.) has been debated for several years, mainly due to the lack of appropriate genetic markers. Microsatellites or simple sequence repeats (SSRs) are important for the genome organisation, phenotypic diversity and are one of the most popular molecular markers. In this study, we surveyed the T. melanosporum genome (1) to characterise its SSR pattern; (2) to compare it with SSR patterns found in 48 other fungal and three oomycetes genomes and (3) to identify new polymorphic SSR markers for population genetics. The T. melanosporum genome is rich in SSRs with 22,425 SSRs with mono-nucleotides being the most frequent motifs. SSRs were found in all genomic regions although they are more frequent in non-coding regions (introns and intergenic regions). Sixty out of 135 PCR-amplified mono-, di-, tri-, tetra, penta, and hexa-nucleotides were polymorphic (44%) within black truffle populations and 27 were randomly selected and analysed on 139 T. melanosporum isolates from France, Italy and Spain. The number of alleles varied from 2 to 18 and the expected heterozygosity from 0.124 to 0.815. One hundred and thirty-two different multilocus genotypes out of the 139 T. melanosporum isolates were identified and the genotypic diversity was high (0.999). Polymorphic SSRs were found in UTR regulatory regions of fruiting bodies and ectomycorrhiza regulated genes, suggesting that they may play a role in phenotypic variation. In conclusion, SSRs developed in this study were highly polymorphic and our results showed that T. melanosporum is a species with an important genetic diversity, which is in agreement with its recently uncovered heterothallic mating system. PMID:20965267

  18. Novel genomic microsatellite markers for genetic population and diversity studies of tropical scalloped spiny lobster (Panulirus homarus) and their potential application in related Panulirus species.

    PubMed

    Delghandi, M; Goddard, S; Jerry, D R; Dao, H T; Al Hinai, M S N; Al-Amry, W; Al-Marzouqi, A

    2016-01-01

    Fourteen polymorphic microsatellites with perfect di-, tri-, and tetra-nucleotide repeats were identified for Panulirus homarus using Roche 454 whole-genome sequencing method. Microsatellites were efficiently co-amplified in four multiplexes and a singleplex, providing consistent and easily interpretable genotypes. The number of alleles per locus ranged from 2 to 11 with the observed and expected heterozygosity ranging between 0.000-0.532 and 0.031-0.836, respectively. A significant deviation from Hardy-Weinberg equilibrium was observed for majority of the loci, probably due to homozygote excess. Genetic linkage disequilibrium analysis between all the possible pairs of the loci showed significant departure from the null hypothesis in the loci pairs Pho-G11-Pho-G33 and Pho-G33-Pho-G57. High success in primer cross-species amplification of these microsatellite markers indicates their utility for genetic studies of different Panulirus species. PMID:27173289

  19. Genome-Wide Analysis of Microsatellite Markers Based on Sequenced Database in Chinese Spring Wheat (Triticum aestivum L.)

    PubMed Central

    Tang, Zhaohui; Ren, Yongkang; Li, Yali; Zhang, Dayong; Dong, Yanhui; Zhao, Xinghua

    2015-01-01

    Microsatellites or simple sequence repeats (SSRs) are distributed across both prokaryotic and eukaryotic genomes and have been widely used for genetic studies and molecular marker-assisted breeding in crops. Though an ordered draft sequence of hexaploid bread wheat have been announced, the researches about systemic analysis of SSRs for wheat still have not been reported so far. In the present study, we identified 364,347 SSRs from among 10,603,760 sequences of the Chinese spring wheat (CSW) genome, which were present at a density of 36.68 SSR/Mb. In total, we detected 488 types of motifs ranging from di- to hexanucleotides, among which dinucleotide repeats dominated, accounting for approximately 42.52% of the genome. The density of tri- to hexanucleotide repeats was 24.97%, 4.62%, 3.25% and 24.65%, respectively. AG/CT, AAG/CTT, AGAT/ATCT, AAAAG/CTTTT and AAAATT/AATTTT were the most frequent repeats among di- to hexanucleotide repeats. Among the 21 chromosomes of CSW, the density of repeats was highest on chromosome 2D and lowest on chromosome 3A. The proportions of di-, tri-, tetra-, penta- and hexanucleotide repeats on each chromosome, and even on the whole genome, were almost identical. In addition, 295,267 SSR markers were successfully developed from the 21 chromosomes of CSW, which cover the entire genome at a density of 29.73 per Mb. All of the SSR markers were validated by reverse electronic-Polymerase Chain Reaction (re-PCR); 70,564 (23.9%) were found to be monomorphic and 224,703 (76.1%) were found to be polymorphic. A total of 45 monomorphic markers were selected randomly for validation purposes; 24 (53.3%) amplified one locus, 8 (17.8%) amplified multiple identical loci, and 13 (28.9%) did not amplify any fragments from the genomic DNA of CSW. Then a dendrogram was generated based on the 24 monomorphic SSR markers among 20 wheat cultivars and three species of its diploid ancestors showing that monomorphic SSR markers represented a promising source to

  20. Genome-Wide Analysis of Microsatellite Markers Based on Sequenced Database in Chinese Spring Wheat (Triticum aestivum L.).

    PubMed

    Han, Bin; Wang, Changbiao; Tang, Zhaohui; Ren, Yongkang; Li, Yali; Zhang, Dayong; Dong, Yanhui; Zhao, Xinghua

    2015-01-01

    Microsatellites or simple sequence repeats (SSRs) are distributed across both prokaryotic and eukaryotic genomes and have been widely used for genetic studies and molecular marker-assisted breeding in crops. Though an ordered draft sequence of hexaploid bread wheat have been announced, the researches about systemic analysis of SSRs for wheat still have not been reported so far. In the present study, we identified 364,347 SSRs from among 10,603,760 sequences of the Chinese spring wheat (CSW) genome, which were present at a density of 36.68 SSR/Mb. In total, we detected 488 types of motifs ranging from di- to hexanucleotides, among which dinucleotide repeats dominated, accounting for approximately 42.52% of the genome. The density of tri- to hexanucleotide repeats was 24.97%, 4.62%, 3.25% and 24.65%, respectively. AG/CT, AAG/CTT, AGAT/ATCT, AAAAG/CTTTT and AAAATT/AATTTT were the most frequent repeats among di- to hexanucleotide repeats. Among the 21 chromosomes of CSW, the density of repeats was highest on chromosome 2D and lowest on chromosome 3A. The proportions of di-, tri-, tetra-, penta- and hexanucleotide repeats on each chromosome, and even on the whole genome, were almost identical. In addition, 295,267 SSR markers were successfully developed from the 21 chromosomes of CSW, which cover the entire genome at a density of 29.73 per Mb. All of the SSR markers were validated by reverse electronic-Polymerase Chain Reaction (re-PCR); 70,564 (23.9%) were found to be monomorphic and 224,703 (76.1%) were found to be polymorphic. A total of 45 monomorphic markers were selected randomly for validation purposes; 24 (53.3%) amplified one locus, 8 (17.8%) amplified multiple identical loci, and 13 (28.9%) did not amplify any fragments from the genomic DNA of CSW. Then a dendrogram was generated based on the 24 monomorphic SSR markers among 20 wheat cultivars and three species of its diploid ancestors showing that monomorphic SSR markers represented a promising source to

  1. Characterization of 19 microsatellite loci in the clonal monkshood Aconitum kusnezoffii (Ranunculaceae)1

    PubMed Central

    Ge, Xing-Yue; Tian, Hao; Liao, Wan-Jin

    2016-01-01

    Premise of the study: Microsatellite loci were isolated and characterized from Aconitum kusnezoffii (Ranunculaceae) to estimate male and female reproductive success and evaluate the effects of clonal growth on sexual reproduction. Methods and Results: A genomic enrichment approach was used to develop microsatellite markers. In three investigated A. kusnezoffii populations, a total of 19 microsatellite loci were successfully amplified, and 13 of these loci were polymorphic. Most of the primer pairs designed for the identified loci also amplified corresponding microsatellite loci in A. barbatum var. puberulum and A. alboviolaceum. Conclusions: The identified microsatellite loci will be useful for quantifying male and female fitness in A. kusnezoffii and evaluating the effects of clonal growth on sexual reproduction. PMID:27347450

  2. Development and characterization of 10 microsatellite markers in Sagina nodosa (Caryophyllaceae)1

    PubMed Central

    Singh, Tarjinder; Edwards, Joan; Maroja, Luana S.

    2014-01-01

    • Premise of the study: We developed 10 novel microsatellite loci for Sagina nodosa, a diploid perennial arctic-alpine herb. To our knowledge, these are the first microsatellite loci for a Sagina species. • Methods and Results: We performed a low-coverage 454 next-generation sequencing of enriched genomic fragments derived from one individual to generate a massive library of contigs containing potential polymorphic microsatellites. We present data for 10 novel polymorphic microsatellite loci containing di-, tri-, tetra-, and hexanucleotide repeats with two to nine alleles per locus assessed in 29 individuals. • Conclusions: These polymorphic microsatellite loci in S. nodosa will provide insights on the population structure and life history of S. nodosa in Isle Royale and other North American populations. PMID:25202593

  3. Comparison of microbial DNA enrichment tools for metagenomic whole genome sequencing.

    PubMed

    Thoendel, Matthew; Jeraldo, Patricio R; Greenwood-Quaintance, Kerryl E; Yao, Janet Z; Chia, Nicholas; Hanssen, Arlen D; Abdel, Matthew P; Patel, Robin

    2016-08-01

    Metagenomic whole genome sequencing for detection of pathogens in clinical samples is an exciting new area for discovery and clinical testing. A major barrier to this approach is the overwhelming ratio of human to pathogen DNA in samples with low pathogen abundance, which is typical of most clinical specimens. Microbial DNA enrichment methods offer the potential to relieve this limitation by improving this ratio. Two commercially available enrichment kits, the NEBNext Microbiome DNA Enrichment Kit and the Molzym MolYsis Basic kit, were tested for their ability to enrich for microbial DNA from resected arthroplasty component sonicate fluids from prosthetic joint infections or uninfected sonicate fluids spiked with Staphylococcus aureus. Using spiked uninfected sonicate fluid there was a 6-fold enrichment of bacterial DNA with the NEBNext kit and 76-fold enrichment with the MolYsis kit. Metagenomic whole genome sequencing of sonicate fluid revealed 13- to 85-fold enrichment of bacterial DNA using the NEBNext enrichment kit. The MolYsis approach achieved 481- to 9580-fold enrichment, resulting in 7 to 59% of sequencing reads being from the pathogens known to be present in the samples. These results demonstrate the usefulness of these tools when testing clinical samples with low microbial burden using next generation sequencing. PMID:27237775

  4. Mining microsatellites in the peach genome: development of new long-core SSR markers for genetic analyses in five Prunus species.

    PubMed

    Dettori, Maria Teresa; Micali, Sabrina; Giovinazzi, Jessica; Scalabrin, Simone; Verde, Ignazio; Cipriani, Guido

    2015-01-01

    A wide inventory of molecular markers is nowadays available for individual fingerprinting. Microsatellites, or simple sequence repeats (SSRs), play a relevant role due to their relatively ease of use, their abundance in the plant genomes, and their co-dominant nature, together with the availability of primer sequences in many important agricultural crops. Microsatellites with long-core motifs are more easily scored and were adopted long ago in human genetics but they were developed only in few crops, and Prunus species are not among them. In the present work the peach whole-genome sequence was used to select 216 SSRs containing long-core motifs with tri-, tetra- and penta-nucleotide repeats. Microsatellite primer pairs were designed and tested for polymorphism in the five diploid Prunus species of economic relevance (almond, apricot, Japanese plum, peach and sweet cherry). A set of 26 microsatellite markers covering all the eight chromosomes, was also selected and used in the molecular characterization, population genetics and structure analyses of a representative sample of the five diploid Prunus species, assessing their transportability and effectiveness. The combined probability of identity between two random individuals for the whole set of 26 SSRs was quite low, ranging from 2.30 × 10(-7) in peach to 9.48 × 10(-10) in almond, confirming the usefulness of the proposed set for fingerprinting analyses in Prunus species. PMID:26185739

  5. Microsatellite markers for the invasive plant species white sweetclover (Melilotus alba) and yellow sweetclover (Melilotus officinalis)

    Technology Transfer Automated Retrieval System (TEKTRAN)

    We describe specific primers and conditions to amplify eight tetranucleotide, one trinucleotide, and one dinucleotide microsatellite DNA loci isolated from an enriched genomic library of Melilotus alba, an invasive plant species throughout North America. The number of alleles per locus ranged from 2...

  6. Characterization of ten polymorphic microsatellite markers in Macrolophus pygmaeus (Rambur) (Heteroptera: Miridae)

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Macrolophus pygmaeus (Rambur) (Heteroptera: Miridae) is an important predator of arthropod pests in vegetable crops. A partial genomic library enriched for microsatellite sequences was screened to identify marker loci and for the design of primers. Nine polymorphic loci were identified in 96 adults ...

  7. Eight microsatellite loci in Phaedranassa schizantha Baker (Amaryllidaceae) and cross-amplification in other Phaedranassa species

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Phaedranassa schizantha is a species endemic to Ecuador from which eight polymorphic microsatellite loci were isolated from an enriched genomic library. A total of 31 alleles with an average of four alleles per locus were detected across 29 individuals from a single natural population of P. schizan...

  8. Genome-wide mining, characterization, and development of microsatellite markers in Marsupenaeus japonicus by genome survey sequencing

    NASA Astrophysics Data System (ADS)

    Lu, Xia; Luan, Sheng; Kong, Jie; Hu, Longyang; Mao, Yong; Zhong, Shengping

    2015-12-01

    The kuruma prawn, Marsupenaeus japonicus, is one of the most cultivated and consumed species of shrimp. However, very few molecular genetic/genomic resources are publically available for it. Thus, the characterization and distribution of simple sequence repeats (SSRs) remains ambiguous and the use of SSR markers in genomic studies and marker-assisted selection is limited. The goal of this study is to characterize and develop genome-wide SSR markers in M. japonicus by genome survey sequencing for application in comparative genomics and breeding. A total of 326 945 perfect SSRs were identifi ed, among which dinucleotide repeats were the most frequent class (44.08%), followed by mononucleotides (29.67%), trinucleotides (18.96%), tetranucleotides (5.66%), hexanucleotides (1.07%), and pentanucleotides (0.56%). In total, 151 541 SSR loci primers were successfully designed. A subset of 30 SSR primer pairs were synthesized and tested in 42 individuals from a wild population, of which 27 loci (90.0%) were successfully amplifi ed with specifi c products and 24 (80.0%) were polymorphic. For the amplifi ed polymorphic loci, the alleles ranged from 5 to 17 (with an average of 9.63), and the average PIC value was 0.796. A total of 58 256 SSR-containing sequences had signifi cant Gene Ontology annotation; these are good functional molecular marker candidates for association studies and comparative genomic analysis. The newly identifi ed SSRs signifi cantly contribute to the M. japonicus genomic resources and will facilitate a number of genetic and genomic studies, including high density linkage mapping, genome-wide association analysis, marker-aided selection, comparative genomics analysis, population genetics, and evolution.

  9. LOLA: enrichment analysis for genomic region sets and regulatory elements in R and Bioconductor

    PubMed Central

    Sheffield, Nathan C.; Bock, Christoph

    2016-01-01

    Summary: Genomic datasets are often interpreted in the context of large-scale reference databases. One approach is to identify significantly overlapping gene sets, which works well for gene-centric data. However, many types of high-throughput data are based on genomic regions. Locus Overlap Analysis (LOLA) provides easy and automatable enrichment analysis for genomic region sets, thus facilitating the interpretation of functional genomics and epigenomics data. Availability and Implementation: R package available in Bioconductor and on the following website: http://lola.computational-epigenetics.org. Contact: nsheffield@cemm.oeaw.ac.at or cbock@cemm.oeaw.ac.at PMID:26508757

  10. Development of diagnostic microsatellite markers from whole-genome sequences of Ammodramus sparrows for assessing admixture in a hybrid zone

    PubMed Central

    Kovach, Adrienne I; Walsh, Jennifer; Ramsdell, Jordan; Kelley Thomas, W

    2015-01-01

    Studies of hybridization and introgression and, in particular, the identification of admixed individuals in natural populations benefit from the use of diagnostic genetic markers that reliably differentiate pure species from each other and their hybrid forms. Such diagnostic markers are often infrequent in the genomes of closely related species, and genomewide data facilitate their discovery. We used whole-genome data from Illumina HiSeqS2000 sequencing of two recently diverged (600,000 years) and hybridizing, avian, sister species, the Saltmarsh (Ammodramus caudacutus) and Nelson's (A. nelsoni) Sparrow, to develop a suite of diagnostic markers for high-resolution identification of pure and admixed individuals. We compared the microsatellite repeat regions identified in the genomes of the two species and selected a subset of 37 loci that differed between the species in repeat number. We screened these loci on 12 pure individuals of each species and report on the 34 that successfully amplified. From these, we developed a panel of the 12 most diagnostic loci, which we evaluated on 96 individuals, including individuals from both allopatric populations and sympatric individuals from the hybrid zone. Using simulations, we evaluated the power of the marker panel for accurate assignments of individuals to their appropriate pure species and hybrid genotypic classes (F1, F2, and backcrosses). The markers proved highly informative for species discrimination and had high accuracy for classifying admixed individuals into their genotypic classes. These markers will aid future investigations of introgressive hybridization in this system and aid conservation efforts aimed at monitoring and preserving pure species. Our approach is transferable to other study systems consisting of closely related and incipient species. PMID:26078861

  11. Development of 304 new microsatellite markers for carrot. Analysis of their potential for linkage mapping, assessment of genetic diversity and cross-taxa utilization

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Two different approaches were used to isolate carrot SSRs: 1) Construction and analysis of a genomic DNA library enriched for SSR loci (GSSRs) and 2) Bioinformatic mining for SSR motifs in a 1.7 Mb BAC-end sequence database (BSSR). The SSR-enriched library yielded microsatellites with more repeats b...

  12. Targeted enrichment of genomic DNA regions for next-generation sequencing

    PubMed Central

    ElSharawy, Abdou; Sauer, Sascha; van Helvoort, Joop M.L.M.; van der Zaag, P.J.; Franke, Andre; Nilsson, Mats; Lehrach, Hans; Brookes, Anthony J.

    2011-01-01

    In this review, we discuss the latest targeted enrichment methods and aspects of their utilization along with second-generation sequencing for complex genome analysis. In doing so, we provide an overview of issues involved in detecting genetic variation, for which targeted enrichment has become a powerful tool. We explain how targeted enrichment for next-generation sequencing has made great progress in terms of methodology, ease of use and applicability, but emphasize the remaining challenges such as the lack of even coverage across targeted regions. Costs are also considered versus the alternative of whole-genome sequencing which is becoming ever more affordable. We conclude that targeted enrichment is likely to be the most economical option for many years to come in a range of settings. PMID:22121152

  13. A robust genomic signature for the detection of colorectal cancer patients with microsatellite instability phenotype and high mutation frequency.

    PubMed

    Tian, Sun; Roepman, Paul; Popovici, Vlad; Michaut, Magali; Majewski, Ian; Salazar, Ramon; Santos, Cristina; Rosenberg, Robert; Nitsche, Ulrich; Mesker, Wilma E; Bruin, Sjoerd; Tejpar, Sabine; Delorenzi, Mauro; Bernards, Rene; Simon, Iris

    2012-12-01

    Microsatellite instability (MSI) occurs in 10-20% of colorectal tumours and is associated with good prognosis. Here we describe the development and validation of a genomic signature that identifies colorectal cancer patients with MSI caused by DNA mismatch repair deficiency with high accuracy. Microsatellite status for 276 stage II and III colorectal tumours has been determined. Full-genome expression data was used to identify genes that correlate with MSI status. A subset of these samples (n = 73) had sequencing data for 615 genes available. An MSI gene signature of 64 genes was developed and validated in two independent validation sets: the first consisting of frozen samples from 132 stage II patients; and the second consisting of FFPE samples from the PETACC-3 trial (n = 625). The 64-gene MSI signature identified MSI patients in the first validation set with a sensitivity of 90.3% and an overall accuracy of 84.8%, with an AUC of 0.942 (95% CI, 0.888-0.975). In the second validation, the signature also showed excellent performance, with a sensitivity 94.3% and an overall accuracy of 90.6%, with an AUC of 0.965 (95% CI, 0.943-0.988). Besides correct identification of MSI patients, the gene signature identified a group of MSI-like patients that were MSS by standard assessment but MSI by signature assessment. The MSI-signature could be linked to a deficient MMR phenotype, as both MSI and MSI-like patients showed a high mutation frequency (8.2% and 6.4% of 615 genes assayed, respectively) as compared to patients classified as MSS (1.6% mutation frequency). The MSI signature showed prognostic power in stage II patients (n = 215) with a hazard ratio of 0.252 (p = 0.0145). Patients with an MSI-like phenotype had also an improved survival when compared to MSS patients. The MSI signature was translated to a diagnostic microarray and technically and clinically validated in FFPE and frozen samples. PMID:22926706

  14. A robust genomic signature for the detection of colorectal cancer patients with microsatellite instability phenotype and high mutation frequency#

    PubMed Central

    Tian, Sun; Roepman, Paul; Popovici, Vlad; Michaut, Magali; Majewski, Ian; Salazar, Ramon; Santos, Cristina; Rosenberg, Robert; Nitsche, Ulrich; Mesker, Wilma E; Bruin, Sjoerd; Tejpar, Sabine; Delorenzi, Mauro; Bernards, Rene; Simon, Iris

    2012-01-01

    Abstract Microsatellite instability (MSI) occurs in 10–20% of colorectal tumours and is associated with good prognosis. Here we describe the development and validation of a genomic signature that identifies colorectal cancer patients with MSI caused by DNA mismatch repair deficiency with high accuracy. Microsatellite status for 276 stage II and III colorectal tumours has been determined. Full-genome expression data was used to identify genes that correlate with MSI status. A subset of these samples (n = 73) had sequencing data for 615 genes available. An MSI gene signature of 64 genes was developed and validated in two independent validation sets: the first consisting of frozen samples from 132 stage II patients; and the second consisting of FFPE samples from the PETACC-3 trial (n = 625). The 64-gene MSI signature identified MSI patients in the first validation set with a sensitivity of 90.3% and an overall accuracy of 84.8%, with an AUC of 0.942 (95% CI, 0.888–0.975). In the second validation, the signature also showed excellent performance, with a sensitivity 94.3% and an overall accuracy of 90.6%, with an AUC of 0.965 (95% CI, 0.943–0.988). Besides correct identification of MSI patients, the gene signature identified a group of MSI-like patients that were MSS by standard assessment but MSI by signature assessment. The MSI-signature could be linked to a deficient MMR phenotype, as both MSI and MSI-like patients showed a high mutation frequency (8.2% and 6.4% of 615 genes assayed, respectively) as compared to patients classified as MSS (1.6% mutation frequency). The MSI signature showed prognostic power in stage II patients (n = 215) with a hazard ratio of 0.252 (p = 0.0145). Patients with an MSI-like phenotype had also an improved survival when compared to MSS patients. The MSI signature was translated to a diagnostic microarray and technically and clinically validated in FFPE and frozen samples. Copyright © 2012 Pathological Society of Great Britain and

  15. Development of novel simple sequence repeat markers in bitter gourd (Momordica charantia L.) through enriched genomic libraries and their utilization in analysis of genetic diversity and cross-species transferability.

    PubMed

    Saxena, Swati; Singh, Archana; Archak, Sunil; Behera, Tushar K; John, Joseph K; Meshram, Sudhir U; Gaikwad, Ambika B

    2015-01-01

    Microsatellite or simple sequence repeat (SSR) markers are the preferred markers for genetic analyses of crop plants. The availability of a limited number of such markers in bitter gourd (Momordica charantia L.) necessitates the development and characterization of more SSR markers. These were developed from genomic libraries enriched for three dinucleotide, five trinucleotide, and two tetranucleotide core repeat motifs. Employing the strategy of polymerase chain reaction-based screening, the number of clones to be sequenced was reduced by 81 % and 93.7 % of the sequenced clones contained in microsatellite repeats. Unique primer-pairs were designed for 160 microsatellite loci, and amplicons of expected length were obtained for 151 loci (94.4 %). Evaluation of diversity in 54 bitter gourd accessions at 51 loci indicated that 20 % of the loci were polymorphic with the polymorphic information content values ranging from 0.13 to 0.77. Fifteen Indian varieties were clearly distinguished indicative of the usefulness of the developed markers. Markers at 40 loci (78.4 %) were transferable to six species, viz. Momordica cymbalaria, Momordica subangulata subsp. renigera, Momordica balsamina, Momordica dioca, Momordica cochinchinesis, and Momordica sahyadrica. The microsatellite markers reported will be useful in various genetic and molecular genetic studies in bitter gourd, a cucurbit of immense nutritive, medicinal, and economic importance. PMID:25240849

  16. In-Solution Hybridization for the Targeted Enrichment of the Whole Mitochondrial Genome.

    PubMed

    Bekaert, B; Ellerington, R; Van den Abbeele, L; Decorte, R

    2016-01-01

    A detailed protocol is presented for the targeted enrichment of whole mitochondrial genomes based on an in-solution hybridization strategy. Bait is produced in-house by sonication of two long-range PCR amplicons and ligation of biotinylated double-stranded adapters. Indexed target DNA is hybridized with the bait in a multiplex enrichment reaction and pulled down using magnetic streptavidin beads followed by subsequent post-enrichment PCR and sequencing on an Illumina MiSeq. This strategy removes the need for expensive commercial bait probes while allowing enrichment of multiple samples in a single hybridization reaction. The method is particularly suitable for degraded DNA as it is able to enrich short DNA fragments and is not susceptible to polymerase artifacts introduced during PCR-based assays. PMID:27259740

  17. A Glance at Microsatellite Motifs from 454 Sequencing Reads of Watermelon Genomic DNA

    Technology Transfer Automated Retrieval System (TEKTRAN)

    A single 454 (Life Sciences Sequencing Technology) run of Charleston Gray watermelon (Citrullus lanatus var. lanatus) genomic DNA was performed and sequence data were assembled. A large scale identification of simple sequence repeat (SSR) was performed and SSR sequence data were used for the develo...

  18. Cranberry microsatellite marker development from assembled next-generation genomic sequence

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The large-fruited cranberry (Vaccinium macrocarpon Ait.) is a native North American fruit that is a rich source of dietary phytochemicals with demonstrated and potential benefits for human health. Cranberry is a perennial, self-fertile 2n=2x=24 diploid, with a haploid genome size about 570 Mbp. Pres...

  19. Development of Genomic Microsatellite Markers in Carthamus tinctorius L. (Safflower) Using Next Generation Sequencing and Assessment of Their Cross-Species Transferability and Utility for Diversity Analysis

    PubMed Central

    Variath, Murali Tottekkad; Joshi, Gopal; Bali, Sapinder; Agarwal, Manu; Kumar, Amar; Jagannath, Arun; Goel, Shailendra

    2015-01-01

    Background Safflower (Carthamus tinctorius L.), an Asteraceae member, yields high quality edible oil rich in unsaturated fatty acids and is resilient to dry conditions. The crop holds tremendous potential for improvement through concerted molecular breeding programs due to the availability of significant genetic and phenotypic diversity. Genomic resources that could facilitate such breeding programs remain largely underdeveloped in the crop. The present study was initiated to develop a large set of novel microsatellite markers for safflower using next generation sequencing. Principal Findings Low throughput genome sequencing of safflower was performed using Illumina paired end technology providing ~3.5X coverage of the genome. Analysis of sequencing data allowed identification of 23,067 regions harboring perfect microsatellite loci. The safflower genome was found to be rich in dinucleotide repeats followed by tri-, tetra-, penta- and hexa-nucleotides. Primer pairs were designed for 5,716 novel microsatellite sequences with repeat length ≥ 20 bases and optimal flanking regions. A subset of 325 microsatellite loci was tested for amplification, of which 294 loci produced robust amplification. The validated primers were used for assessment of 23 safflower accessions belonging to diverse agro-climatic zones of the world leading to identification of 93 polymorphic primers (31.6%). The numbers of observed alleles at each locus ranged from two to four and mean polymorphism information content was found to be 0.3075. The polymorphic primers were tested for cross-species transferability on nine wild relatives of cultivated safflower. All primers except one showed amplification in at least two wild species while 25 primers amplified across all the nine species. The UPGMA dendrogram clustered C. tinctorius accessions and wild species separately into two major groups. The proposed progenitor species of safflower, C. oxyacantha and C. palaestinus were genetically closer to

  20. Significant variance in genetic diversity among populations of Schistosoma haematobium detected using microsatellite DNA loci from a genome-wide database

    PubMed Central

    2013-01-01

    Background Urogenital schistosomiasis caused by Schistosoma haematobium is widely distributed across Africa and is increasingly being targeted for control. Genome sequences and population genetic parameters can give insight into the potential for population- or species-level drug resistance. Microsatellite DNA loci are genetic markers in wide use by Schistosoma researchers, but there are few primers available for S. haematobium. Methods We sequenced 1,058,114 random DNA fragments from clonal cercariae collected from a snail infected with a single Schistosoma haematobium miracidium. We assembled and aligned the S. haematobium sequences to the genomes of S. mansoni and S. japonicum, identifying microsatellite DNA loci across all three species and designing primers to amplify the loci in S. haematobium. To validate our primers, we screened 32 randomly selected primer pairs with population samples of S. haematobium. Results We designed >13,790 primer pairs to amplify unique microsatellite loci in S. haematobium, (available at http://www.cebio.org/projetos/schistosoma-haematobium-genome). The three Schistosoma genomes contained similar overall frequencies of microsatellites, but the frequency and length distributions of specific motifs differed among species. We identified 15 primer pairs that amplified consistently and were easily scored. We genotyped these 15 loci in S. haematobium individuals from six locations: Zanzibar had the highest levels of diversity; Malawi, Mauritius, Nigeria, and Senegal were nearly as diverse; but the sample from South Africa was much less diverse. Conclusions About half of the primers in the database of Schistosoma haematobium microsatellite DNA loci should yield amplifiable and easily scored polymorphic markers, thus providing thousands of potential markers. Sequence conservation among S. haematobium, S. japonicum, and S. mansoni is relatively high, thus it should now be possible to identify markers that are universal among Schistosoma

  1. Genome distribution and validation of novel microsatellite markers of Fusarium verticillioides and their transferability to other Fusarium species.

    PubMed

    Leyva-Madrigal, Karla Y; Larralde-Corona, Claudia P; Calderón-Vázquez, Carlos L; Maldonado-Mendoza, Ignacio E

    2014-06-01

    Improved population studies in the fungus Fusarium verticillioides require the development of reliable microsatellite markers. Here we report a set of ten microsatellite loci that can be used for genetic diversity analyses in F. verticillioides, and are equally applicable to other fungi, especially those belonging to the Gibberella fujikuroi clade. PMID:24704573

  2. Characterization of novel microsatellites from Drosophila transversa.

    PubMed

    Räisänen, L; Roininen, E; Liimatainen, J O

    2009-03-01

    We investigated a partial genomic library of Drosophila transversa for microsatellites and developed 12 markers for genetic analyses. This is the first time that microsatellite primers from the quinaria species group have been described. Four loci were cross-amplified in D. phalerata. Nine out of the 12 microsatellite markers developed are likely to be on the X chromosome. PMID:21564716

  3. Development of microsatellite markers in Fragaria, their use in genetic diversity analysis, and their potential for genetic linkage mapping.

    PubMed

    Hadonou, A M; Sargent, D J; Wilson, F; James, C M; Simpson, D W

    2004-06-01

    We have developed 21 new microsatellites in the model diploid perennial species Fragaria vesca from an enriched genomic library developed using F. vesca 'Ruegen'. The transferability of the primer pairs to other Fragaria species was high; all 31 primer pairs produced amplicons in 3 accessions of the octoploid strawberry Fragaria x ananassa, whereas 24 (77%) amplified a product in 7 other diploid Fragaria species. We analysed the allelic variation among 15 F. vesca accessions using the 21 microsatellites reported here and 10 F. vesca microsatellites described previously. The level of polymorphism detected at these microsatellite loci was high; five loci were monomorphic. Only two microsatellites were required to unambiguously discriminate among the 15 F. vesca accessions. A preliminary survey of segregation in an F2 progeny indicates that 20 of the 26 polymorphic loci (77%) could be mapped. PMID:15190360

  4. Sonication-based isolation and enrichment of Chlorella protothecoides chloroplasts for illumina genome sequencing

    SciTech Connect

    Angelova, Angelina; Park, Sang-Hycuk; Kyndt, John; Fitzsimmons, Kevin; Brown, Judith K

    2013-09-01

    With the increasing world demand for biofuel, a number of oleaginous algal species are being considered as renewable sources of oil. Chlorella protothecoides Krüger synthesizes triacylglycerols (TAGs) as storage compounds that can be converted into renewable fuel utilizing an anabolic pathway that is poorly understood. The paucity of algal chloroplast genome sequences has been an important constraint to chloroplast transformation and for studying gene expression in TAGs pathways. In this study, the intact chloroplasts were released from algal cells using sonication followed by sucrose gradient centrifugation, resulting in a 2.36-fold enrichment of chloroplasts from C. protothecoides, based on qPCR analysis. The C. protothecoides chloroplast genome (cpDNA) was determined using the Illumina HiSeq 2000 sequencing platform and found to be 84,576 Kb in size (8.57 Kb) in size, with a GC content of 30.8 %. This is the first report of an optimized protocol that uses a sonication step, followed by sucrose gradient centrifugation, to release and enrich intact chloroplasts from a microalga (C. prototheocoides) of sufficient quality to permit chloroplast genome sequencing with high coverage, while minimizing nuclear genome contamination. The approach is expected to guide chloroplast isolation from other oleaginous algal species for a variety of uses that benefit from enrichment of chloroplasts, ranging from biochemical analysis to genomics studies.

  5. Interspecific Utility of Microsatellites in Fish: A Case Study of (CT)(n) and (GT)(n) Markers in the Shanny Lipophrys pholis (Pisces: Blenniidae) and Their Use in Other Blennioidei.

    PubMed

    Guillemaud; Almada; Serrão Santos R; Cancela

    2000-05-01

    We report the development of new microsatellite markers that can be used for population analyses in the shanny Lipophrys pholis. The procedure involved the construction of a microsatellite-enriched genomic bank. Five (GT)(n) and (CT)(n) microsatellites have been characterized, four of which are polymorphic. The analysis of one population allowed us to verify their usefulness as markers in population studies. Moreover, interspecific amplifications have been performed using primers defined in other species to amplify Lipophrys pholis, or using the primers defined in Lipophrys pholis to amplify other species. We use these results to discuss the hypothesis that microsatellites are highly conserved in fish. PMID:10852803

  6. SBMDb: first whole genome putative microsatellite DNA marker database of sugarbeet for bioenergy and industrial applications.

    PubMed

    Iquebal, Mir Asif; Jaiswal, Sarika; Angadi, U B; Sablok, Gaurav; Arora, Vasu; Kumar, Sunil; Rai, Anil; Kumar, Dinesh

    2015-01-01

    DNA marker plays important role as valuable tools to increase crop productivity by finding plausible answers to genetic variations and linking the Quantitative Trait Loci (QTL) of beneficial trait. Prior approaches in development of Short Tandem Repeats (STR) markers were time consuming and inefficient. Recent methods invoking the development of STR markers using whole genomic or transcriptomics data has gained wide importance with immense potential in developing breeding and cultivator improvement approaches. Availability of whole genome sequences and in silico approaches has revolutionized bulk marker discovery. We report world's first sugarbeet whole genome marker discovery having 145 K markers along with 5 K functional domain markers unified in common platform using MySQL, Apache and PHP in SBMDb. Embedded markers and corresponding location information can be selected for desired chromosome, location/interval and primers can be generated using Primer3 core, integrated at backend. Our analyses revealed abundance of 'mono' repeat (76.82%) over 'di' repeats (13.68%). Highest density (671.05 markers/Mb) was found in chromosome 1 and lowest density (341.27 markers/Mb) in chromosome 6. Current investigation of sugarbeet genome marker density has direct implications in increasing mapping marker density. This will enable present linkage map having marker distance of ∼2 cM, i.e. from 200 to 2.6 Kb, thus facilitating QTL/gene mapping. We also report e-PCR-based detection of 2027 polymorphic markers in panel of five genotypes. These markers can be used for DUS test of variety identification and MAS/GAS in variety improvement program. The present database presents wide source of potential markers for developing and implementing new approaches for molecular breeding required to accelerate industrious use of this crop, especially for sugar, health care products, medicines and color dye. Identified markers will also help in improvement of bioenergy trait of

  7. SBMDb: first whole genome putative microsatellite DNA marker database of sugarbeet for bioenergy and industrial applications

    PubMed Central

    Iquebal, Mir Asif; Jaiswal, Sarika; Angadi, U.B.; Sablok, Gaurav; Arora, Vasu; Kumar, Sunil; Rai, Anil; Kumar, Dinesh

    2015-01-01

    DNA marker plays important role as valuable tools to increase crop productivity by finding plausible answers to genetic variations and linking the Quantitative Trait Loci (QTL) of beneficial trait. Prior approaches in development of Short Tandem Repeats (STR) markers were time consuming and inefficient. Recent methods invoking the development of STR markers using whole genomic or transcriptomics data has gained wide importance with immense potential in developing breeding and cultivator improvement approaches. Availability of whole genome sequences and in silico approaches has revolutionized bulk marker discovery. We report world’s first sugarbeet whole genome marker discovery having 145 K markers along with 5 K functional domain markers unified in common platform using MySQL, Apache and PHP in SBMDb. Embedded markers and corresponding location information can be selected for desired chromosome, location/interval and primers can be generated using Primer3 core, integrated at backend. Our analyses revealed abundance of ‘mono’ repeat (76.82%) over ‘di’ repeats (13.68%). Highest density (671.05 markers/Mb) was found in chromosome 1 and lowest density (341.27 markers/Mb) in chromosome 6. Current investigation of sugarbeet genome marker density has direct implications in increasing mapping marker density. This will enable present linkage map having marker distance of ∼2 cM, i.e. from 200 to 2.6 Kb, thus facilitating QTL/gene mapping. We also report e-PCR-based detection of 2027 polymorphic markers in panel of five genotypes. These markers can be used for DUS test of variety identification and MAS/GAS in variety improvement program. The present database presents wide source of potential markers for developing and implementing new approaches for molecular breeding required to accelerate industrious use of this crop, especially for sugar, health care products, medicines and color dye. Identified markers will also help in improvement of bioenergy trait

  8. Comparison of surrogate reporter systems for enrichment of cells with mutations induced by genome editors.

    PubMed

    He, Zuyong; Shi, Xuan; Liu, Meirui; Sun, Guangjie; Proudfoot, Chris; Whitelaw, C Bruce A; Lillico, Simon G; Chen, Yaosheng

    2016-03-10

    Genome editors are powerful tools that allow modification of the nuclear DNA in eukaryotic cells both in vitro and in vivo. In vitro modified cells are often phenotypically indistinguishable from unmodified cells, hampering their isolation for analysis. Episomal reporters encoding fluorescent proteins can be used for enrichment of modified cells by flow cytometry. Here we compare two surrogate reporters, RGS and SSA, for the enrichment of porcine embryonic fibroblasts containing mutations induced by ZFNs or CRISPR/Cas9. Both systems were effective for enrichment of edited porcine cells with the RGS reporter proving more effective than the SSA reporter. We noted a higher-fold enrichment when editing events were induced by Cas9 compared to those induced by ZFNs, allowing selection at frequencies as high as 70%. PMID:26778541

  9. Hybridization Capture Using Short PCR Products Enriches Small Genomes by Capturing Flanking Sequences (CapFlank)

    PubMed Central

    Tsangaras, Kyriakos; Wales, Nathan; Sicheritz-Pontén, Thomas; Rasmussen, Simon; Michaux, Johan; Ishida, Yasuko; Morand, Serge; Kampmann, Marie-Louise; Gilbert, M. Thomas P.; Greenwood, Alex D.

    2014-01-01

    Solution hybridization capture methods utilize biotinylated oligonucleotides as baits to enrich homologous sequences from next generation sequencing (NGS) libraries. Coupled with NGS, the method generates kilo to gigabases of high confidence consensus targeted sequence. However, in many experiments, a non-negligible fraction of the resulting sequence reads are not homologous to the bait. We demonstrate that during capture, the bait-hybridized library molecules add additional flanking library sequences iteratively, such that baits limited to targeting relatively short regions (e.g. few hundred nucleotides) can result in enrichment across entire mitochondrial and bacterial genomes. Our findings suggest that some of the off-target sequences derived in capture experiments are non-randomly enriched, and that CapFlank will facilitate targeted enrichment of large contiguous sequences with minimal prior target sequence information. PMID:25275614

  10. Microsatellite polymorphism among Chrysanthemum sp. polyploids: the influence of whole genome duplication

    PubMed Central

    Wang, Haibin; Qi, Xiangyu; Gao, Ri; Wang, Jingjing; Dong, Bin; Jiang, Jiafu; Chen, Sumei; Guan, Zhiyong; Fang, Weimin; Liao, Yuan; Chen, Fadi

    2014-01-01

    Polyploidy is common among flowering plants, including the Asteraceae, a relatively recent angiosperm group. EST-SSRs were used to characterize polymorphism among 29 Chrysanthemum and Ajania spp. accessions of various ploidy levels. Most EST-SSR loci were readily transferable between the species, 29 accessions were separated into three groups in terms of the number of fragments. It inferred that the formation from tetraploid to hexaploid and from octoploid to decaploid may be a recent event, while from the diploid to the tetraploid may be an ancient one in the Chrysanthemum lineage. EST-SSR polymorphism was found and some transcripts containing an SSR were transcribed differently in the de novo autotetraploid C. nankingense and C. lavandulifolium than in their progenitor diploid. EST-SSR could provide a potential molecular basis of adaptation during evolution, while whole genome duplication has a major effect on the mutational dynamics of EST-SSR loci, which could also affect gene regulation. PMID:25339092

  11. An Expressed Sequence Tag (EST)-enriched genetic map of turbot (Scophthalmus maximus): a useful framework for comparative genomics across model and farmed teleosts

    PubMed Central

    2012-01-01

    Background The turbot (Scophthalmus maximus) is a relevant species in European aquaculture. The small turbot genome provides a source for genomics strategies to use in order to understand the genetic basis of productive traits, particularly those related to sex, growth and pathogen resistance. Genetic maps represent essential genomic screening tools allowing to localize quantitative trait loci (QTL) and to identify candidate genes through comparative mapping. This information is the backbone to develop marker-assisted selection (MAS) programs in aquaculture. Expressed sequenced tag (EST) resources have largely increased in turbot, thus supplying numerous type I markers suitable for extending the previous linkage map, which was mostly based on anonymous loci. The aim of this study was to construct a higher-resolution turbot genetic map using EST-linked markers, which will turn out to be useful for comparative mapping studies. Results A consensus gene-enriched genetic map of the turbot was constructed using 463 SNP and microsatellite markers in nine reference families. This map contains 438 markers, 180 EST-linked, clustered at 24 linkage groups. Linkage and comparative genomics evidences suggested additional linkage group fusions toward the consolidation of turbot map according to karyotype information. The linkage map showed a total length of 1402.7 cM with low average intermarker distance (3.7 cM; ~2 Mb). A global 1.6:1 female-to-male recombination frequency (RF) ratio was observed, although largely variable among linkage groups and chromosome regions. Comparative sequence analysis revealed large macrosyntenic patterns against model teleost genomes, significant hits decreasing from stickleback (54%) to zebrafish (20%). Comparative mapping supported particular chromosome rearrangements within Acanthopterygii and aided to assign unallocated markers to specific turbot linkage groups. Conclusions The new gene-enriched high-resolution turbot map represents a

  12. Robotic Enrichment Processing of Roche 454 Titanium Emlusion PCR at the DOE Joint Genome Institute

    SciTech Connect

    Hamilton, Matthew; Wilson, Steven; Bauer, Diane; Miller, Don; Duffy-Wei, Kecia; Hammon, Nancy; Lucas, Susan; Pollard, Martin; Cheng, Jan-Fang

    2010-05-28

    Enrichment of emulsion PCR product is the most laborious and pipette-intensive step in the 454 Titanium process, posing the biggest obstacle for production-oriented scale up. The Joint Genome Institute has developed a pair of custom-made robots based on the Microlab Star liquid handling deck manufactured by Hamilton to mediate the complexity and ergonomic demands of the 454 enrichment process. The robot includes a custom built centrifuge, magnetic deck positions, as well as heating and cooling elements. At present processing eight emulsion cup samples in a single 2.5 hour run, these robots are capable of processing up to 24 emulsion cup samples. Sample emulsions are broken using the standard 454 breaking process and transferred from a pair of 50ml conical tubes to a single 2ml tube and loaded on the robot. The robot performs the enrichment protocol and produces beads in 2ml tubes ready for counting. The robot follows the Roche 454 enrichment protocol with slight exceptions to the manner in which it resuspends beads via pipette mixing rather than vortexing and a set number of null bead removal washes. The robotic process is broken down in similar discrete steps: First Melt and Neutralization, Enrichment Primer Annealing, Enrichment Bead Incubation, Null Bead Removal, Second Melt and Neutralization and Sequencing Primer Annealing. Data indicating our improvements in enrichment efficiency and total number of bases per run will also be shown.

  13. Systematic comparison of three genomic enrichment methods for massively parallel DNA sequencing.

    PubMed

    Teer, Jamie K; Bonnycastle, Lori L; Chines, Peter S; Hansen, Nancy F; Aoyama, Natsuyo; Swift, Amy J; Abaan, Hatice Ozel; Albert, Thomas J; Margulies, Elliott H; Green, Eric D; Collins, Francis S; Mullikin, James C; Biesecker, Leslie G

    2010-10-01

    Massively parallel DNA sequencing technologies have greatly increased our ability to generate large amounts of sequencing data at a rapid pace. Several methods have been developed to enrich for genomic regions of interest for targeted sequencing. We have compared three of these methods: Molecular Inversion Probes (MIP), Solution Hybrid Selection (SHS), and Microarray-based Genomic Selection (MGS). Using HapMap DNA samples, we compared each of these methods with respect to their ability to capture an identical set of exons and evolutionarily conserved regions associated with 528 genes (2.61 Mb). For sequence analysis, we developed and used a novel Bayesian genotype-assigning algorithm, Most Probable Genotype (MPG). All three capture methods were effective, but sensitivities (percentage of targeted bases associated with high-quality genotypes) varied for an equivalent amount of pass-filtered sequence: for example, 70% (MIP), 84% (SHS), and 91% (MGS) for 400 Mb. In contrast, all methods yielded similar accuracies of >99.84% when compared to Infinium 1M SNP BeadChip-derived genotypes and >99.998% when compared to 30-fold coverage whole-genome shotgun sequencing data. We also observed a low false-positive rate with all three methods; of the heterozygous positions identified by each of the capture methods, >99.57% agreed with 1M SNP BeadChip, and >98.840% agreed with the whole-genome shotgun data. In addition, we successfully piloted the genomic enrichment of a set of 12 pooled samples via the MGS method using molecular bar codes. We find that these three genomic enrichment methods are highly accurate and practical, with sensitivities comparable to that of 30-fold coverage whole-genome shotgun data. PMID:20810667

  14. Development of new genomic microsatellite markers from robusta coffee (Coffea canephora Pierre ex A. Froehner) showing broad cross-species transferability and utility in genetic studies

    PubMed Central

    Hendre, Prasad Suresh; Phanindranath, Regur; Annapurna, V; Lalremruata, Albert; Aggarwal, Ramesh K

    2008-01-01

    Background Species-specific microsatellite markers are desirable for genetic studies and to harness the potential of MAS-based breeding for genetic improvement. Limited availability of such markers for coffee, one of the most important beverage tree crops, warrants newer efforts to develop additional microsatellite markers that can be effectively deployed in genetic analysis and coffee improvement programs. The present study aimed to develop new coffee-specific SSR markers and validate their utility in analysis of genetic diversity, individualization, linkage mapping, and transferability for use in other related taxa. Results A small-insert partial genomic library of Coffea canephora, was probed for various SSR motifs following conventional approach of Southern hybridisation. Characterization of repeat positive clones revealed a very high abundance of DNRs (1/15 Kb) over TNRs (1/406 kb). The relative frequencies of different DNRs were found as AT >> AG > AC, whereas among TNRs, AGC was the most abundant repeat. The SSR positive sequences were used to design 58 primer pairs of which 44 pairs could be validated as single locus markers using a panel of arabica and robusta genotypes. The analysis revealed an average of 3.3 and 3.78 alleles and 0.49 and 0.62 PIC per marker for the tested arabicas and robustas, respectively. It also revealed a high cumulative PI over all the markers using both sib-based (10-6 and 10-12 for arabicas and robustas respectively) and unbiased corrected estimates (10-20 and 10-43 for arabicas and robustas respectively). The markers were tested for Hardy-Weinberg equilibrium, linkage dis-equilibrium, and were successfully used to ascertain generic diversity/affinities in the tested germplasm (cultivated as well as species). Nine markers could be mapped on robusta linkage map. Importantly, the markers showed ~92% transferability across related species/genera of coffee. Conclusion The conventional approach of genomic library was successfully

  15. Leveraging Genomic Annotations and Pleiotropic Enrichment for Improved Replication Rates in Schizophrenia GWAS

    PubMed Central

    Wang, Yunpeng; Thompson, Wesley K.; Schork, Andrew J.; Holland, Dominic; Chen, Chi-Hua; Bettella, Francesco; Desikan, Rahul S.; Li, Wen; Witoelar, Aree; Zuber, Verena; Devor, Anna; Nöthen, Markus M.; Rietschel, Marcella; Chen, Qiang; Werge, Thomas; Cichon, Sven; Weinberger, Daniel R.; Djurovic, Srdjan; O’Donovan, Michael; Visscher, Peter M.; Andreassen, Ole A.; Dale, Anders M.

    2016-01-01

    Most of the genetic architecture of schizophrenia (SCZ) has not yet been identified. Here, we apply a novel statistical algorithm called Covariate-Modulated Mixture Modeling (CM3), which incorporates auxiliary information (heterozygosity, total linkage disequilibrium, genomic annotations, pleiotropy) for each single nucleotide polymorphism (SNP) to enable more accurate estimation of replication probabilities, conditional on the observed test statistic (“z-score”) of the SNP. We use a multiple logistic regression on z-scores to combine information from auxiliary information to derive a “relative enrichment score” for each SNP. For each stratum of these relative enrichment scores, we obtain nonparametric estimates of posterior expected test statistics and replication probabilities as a function of discovery z-scores, using a resampling-based approach that repeatedly and randomly partitions meta-analysis sub-studies into training and replication samples. We fit a scale mixture of two Gaussians model to each stratum, obtaining parameter estimates that minimize the sum of squared differences of the scale-mixture model with the stratified nonparametric estimates. We apply this approach to the recent genome-wide association study (GWAS) of SCZ (n = 82,315), obtaining a good fit between the model-based and observed effect sizes and replication probabilities. We observed that SNPs with low enrichment scores replicate with a lower probability than SNPs with high enrichment scores even when both they are genome-wide significant (p < 5x10-8). There were 693 and 219 independent loci with model-based replication rates ≥80% and ≥90%, respectively. Compared to analyses not incorporating relative enrichment scores, CM3 increased out-of-sample yield for SNPs that replicate at a given rate. This demonstrates that replication probabilities can be more accurately estimated using prior enrichment information with CM3. PMID:26808560

  16. Leveraging Genomic Annotations and Pleiotropic Enrichment for Improved Replication Rates in Schizophrenia GWAS.

    PubMed

    Wang, Yunpeng; Thompson, Wesley K; Schork, Andrew J; Holland, Dominic; Chen, Chi-Hua; Bettella, Francesco; Desikan, Rahul S; Li, Wen; Witoelar, Aree; Zuber, Verena; Devor, Anna; Nöthen, Markus M; Rietschel, Marcella; Chen, Qiang; Werge, Thomas; Cichon, Sven; Weinberger, Daniel R; Djurovic, Srdjan; O'Donovan, Michael; Visscher, Peter M; Andreassen, Ole A; Dale, Anders M

    2016-01-01

    Most of the genetic architecture of schizophrenia (SCZ) has not yet been identified. Here, we apply a novel statistical algorithm called Covariate-Modulated Mixture Modeling (CM3), which incorporates auxiliary information (heterozygosity, total linkage disequilibrium, genomic annotations, pleiotropy) for each single nucleotide polymorphism (SNP) to enable more accurate estimation of replication probabilities, conditional on the observed test statistic ("z-score") of the SNP. We use a multiple logistic regression on z-scores to combine information from auxiliary information to derive a "relative enrichment score" for each SNP. For each stratum of these relative enrichment scores, we obtain nonparametric estimates of posterior expected test statistics and replication probabilities as a function of discovery z-scores, using a resampling-based approach that repeatedly and randomly partitions meta-analysis sub-studies into training and replication samples. We fit a scale mixture of two Gaussians model to each stratum, obtaining parameter estimates that minimize the sum of squared differences of the scale-mixture model with the stratified nonparametric estimates. We apply this approach to the recent genome-wide association study (GWAS) of SCZ (n = 82,315), obtaining a good fit between the model-based and observed effect sizes and replication probabilities. We observed that SNPs with low enrichment scores replicate with a lower probability than SNPs with high enrichment scores even when both they are genome-wide significant (p < 5x10-8). There were 693 and 219 independent loci with model-based replication rates ≥80% and ≥90%, respectively. Compared to analyses not incorporating relative enrichment scores, CM3 increased out-of-sample yield for SNPs that replicate at a given rate. This demonstrates that replication probabilities can be more accurately estimated using prior enrichment information with CM3. PMID:26808560

  17. Characterization of 24 microsatellite markers in eleven species of fire ants in the genus Solenopsis (Hymenoptera: Formicidae)

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The inquiline social parasite ant Solenopsis daguerrei infests colonies of several mound-building fire ant species within the S. saevissima species-group. Twenty-four microsatellite markers were isolated from a repeat-enriched genomic library of S. daguerrei. Eleven loci were polymorphic in the inq...

  18. Genomes of two new ammonia-oxidizing archaea enriched from deep marine sediments.

    PubMed

    Park, Soo-Je; Ghai, Rohit; Martín-Cuadrado, Ana-Belén; Rodríguez-Valera, Francisco; Chung, Won-Hyong; Kwon, KaeKyoung; Lee, Jung-Hyun; Madsen, Eugene L; Rhee, Sung-Keun

    2014-01-01

    Ammonia-oxidizing archaea (AOA) are ubiquitous and abundant and contribute significantly to the carbon and nitrogen cycles in the ocean. In this study, we assembled AOA draft genomes from two deep marine sediments from Donghae, South Korea, and Svalbard, Arctic region, by sequencing the enriched metagenomes. Three major microorganism clusters belonging to Thaumarchaeota, Epsilonproteobacteria, and Gammaproteobacteria were deduced from their 16S rRNA genes, GC contents, and oligonucleotide frequencies. Three archaeal genomes were identified, two of which were distinct and were designated Ca. "Nitrosopumilus koreensis" AR1 and "Nitrosopumilus sediminis" AR2. AR1 and AR2 exhibited average nucleotide identities of 85.2% and 79.5% to N. maritimus, respectively. The AR1 and AR2 genomes contained genes pertaining to energy metabolism and carbon fixation as conserved in other AOA, but, conversely, had fewer heme-containing proteins and more copper-containing proteins than other AOA. Most of the distinctive AR1 and AR2 genes were located in genomic islands (GIs) that were not present in other AOA genomes or in a reference water-column metagenome from the Sargasso Sea. A putative gene cluster involved in urea utilization was found in the AR2 genome, but not the AR1 genome, suggesting niche specialization in marine AOA. Co-cultured bacterial genome analysis suggested that bacterial sulfur and nitrogen metabolism could be involved in interactions with AOA. Our results provide fundamental information concerning the metabolic potential of deep marine sedimentary AOA. PMID:24798206

  19. Enrichment of sequencing targets from the human genome by solution hybridization

    PubMed Central

    2009-01-01

    To exploit fully the potential of current sequencing technologies for population-based studies, one must enrich for loci from the human genome. Here we evaluate the hybridization-based approach by using oligonucleotide capture probes in solution to enrich for approximately 3.9 Mb of sequence target. We demonstrate that the tiling probe frequency is important for generating sequence data with high uniform coverage of targets. We obtained 93% sensitivity to detect SNPs, with a calling accuracy greater than 99%. PMID:19835619

  20. A microsatellite linkage map for the cultivated strawberry (Fragaria × ananassa) suggests extensive regions of homozygosity in the genome that may have resulted from breeding and selection.

    PubMed

    Sargent, D J; Passey, T; Surbanovski, N; Lopez Girona, E; Kuchta, P; Davik, J; Harrison, R; Passey, A; Whitehouse, A B; Simpson, D W

    2012-05-01

    The linkage maps of the cultivated strawberry, Fragaria × ananassa (2n = 8x = 56) that have been reported to date have been developed predominantly from AFLPs, along with supplementation with transferrable microsatellite (SSR) markers. For the investigation of the inheritance of morphological characters in the cultivated strawberry and for the development of tools for marker-assisted breeding and selection, it is desirable to populate maps of the genome with an abundance of transferrable molecular markers such as microsatellites (SSRs) and gene-specific markers. Exploiting the recent release of the genome sequence of the diploid F. vesca, and the publication of an extensive number of polymorphic SSR markers for the genus Fragaria, we have extended the linkage map of the 'Redgauntlet' × 'Hapil' (RG × H) mapping population to include a further 330 loci, generated from 160 primer pairs, to create a linkage map for F. × ananassa containing 549 loci, 490 of which are transferrable SSR or gene-specific markers. The map covers 2140.3 cM in the expected 28 linkage groups for an integrated map (where one group is composed of two separate male and female maps), which represents an estimated 91% of the cultivated strawberry genome. Despite the relative saturation of the linkage map on the majority of linkage groups, regions of apparent extensive homozygosity were identified in the genomes of 'Redgauntlet' and 'Hapil' which may be indicative of allele fixation during the breeding and selection of modern F. × ananassa cultivars. The genomes of the octoploid and diploid Fragaria are largely collinear, but through comparison of mapped markers on the RG × H linkage map to their positions on the genome sequence of F. vesca, a number of inversions were identified that may have occurred before the polyploidisation event that led to the evolution of the modern octoploid strawberry species. PMID:22218676

  1. Characterization of the complete mitochondrial genome and a set of polymorphic microsatellite markers through next-generation sequencing for the brown brocket deer Mazama gouazoubira.

    PubMed

    Caparroz, Renato; Mantellatto, Aline M B; Bertioli, David J; Figueiredo, Marina G; Duarte, José Maurício B

    2015-01-01

    The complete mitochondrial genome of the brown brocket deer Mazama gouazoubira and a set of polymorphic microsatellite markers were identified by 454-pyrosequencing. De novo genome assembly recovered 98% of the mitochondrial genome with a mean coverage of 9-fold. The mitogenome consisted of 16,356 base pairs that included 13 protein-coding genes, two ribosomal subunit genes, 22 transfer RNAs and the control region, as found in other deer. The genetic divergence between the mitogenome described here and a previously published report was ∼0.5%, with the control region and ND5 gene showing the highest intraspecific variation. Seven polymorphic loci were characterized using 15 unrelated individuals; there was moderate genetic variation across most loci (mean of 5.6 alleles/locus, mean expected heterozygosity = 0.70), with only one locus deviating significantly from Hardy-Weinberg equilibrium, probably because of null alleles. Marker independence was confirmed with tests for linkage disequilibrium. The genetic variation of the mitogenome and characterization of microsatellite markers will provide useful tools for assessing the phylogeography and population genetic patterns in M. gouazoubira, particularly in the context of habitat fragmentation in South America. PMID:26500438

  2. Characterization of the complete mitochondrial genome and a set of polymorphic microsatellite markers through next-generation sequencing for the brown brocket deer Mazama gouazoubira

    PubMed Central

    Caparroz, Renato; Mantellatto, Aline M.B.; Bertioli, David J.; Figueiredo, Marina G.; Duarte, José Maurício B.

    2015-01-01

    The complete mitochondrial genome of the brown brocket deer Mazama gouazoubira and a set of polymorphic microsatellite markers were identified by 454-pyrosequencing. De novo genome assembly recovered 98% of the mitochondrial genome with a mean coverage of 9-fold. The mitogenome consisted of 16,356 base pairs that included 13 protein-coding genes, two ribosomal subunit genes, 22 transfer RNAs and the control region, as found in other deer. The genetic divergence between the mitogenome described here and a previously published report was ∼0.5%, with the control region and ND5 gene showing the highest intraspecific variation. Seven polymorphic loci were characterized using 15 unrelated individuals; there was moderate genetic variation across most loci (mean of 5.6 alleles/locus, mean expected heterozygosity = 0.70), with only one locus deviating significantly from Hardy-Weinberg equilibrium, probably because of null alleles. Marker independence was confirmed with tests for linkage disequilibrium. The genetic variation of the mitogenome and characterization of microsatellite markers will provide useful tools for assessing the phylogeography and population genetic patterns in M. gouazoubira, particularly in the context of habitat fragmentation in South America. PMID:26500438

  3. The complete chloroplast genome of 17 individuals of pest species Jacobaea vulgaris: SNPs, microsatellites and barcoding markers for population and phylogenetic studies.

    PubMed

    Doorduin, Leonie; Gravendeel, Barbara; Lammers, Youri; Ariyurek, Yavuz; Chin-A-Woeng, Thomas; Vrieling, Klaas

    2011-04-01

    Invasive individuals from the pest species Jacobaea vulgaris show different allocation patterns in defence and growth compared with native individuals. To examine if these changes are caused by fast evolution, it is necessary to identify native source populations and compare these with invasive populations. For this purpose, we are in need of intraspecific polymorphic markers. We therefore sequenced the complete chloroplast genomes of 12 native and 5 invasive individuals of J. vulgaris with next generation sequencing and discovered single-nucleotide polymorphisms (SNPs) and microsatellites. This is the first study in which the chloroplast genome of that many individuals within a single species was sequenced. Thirty-two SNPs and 34 microsatellite regions were found. For none of the individuals, differences were found between the inverted repeats. Furthermore, being the first chloroplast genome sequenced in the Senecioneae clade, we compared it with four other members of the Asteraceae family to identify new regions for phylogentic inference within this clade and also within the Asteraceae family. Five markers (ndhC-trnV, ndhC-atpE, rps18-rpl20, clpP and psbM-trnD) contained parsimony-informative characters higher than 2%. Finally, we compared two procedures of preparing chloroplast DNA for next generation sequencing. PMID:21444340

  4. The Complete Chloroplast Genome of 17 Individuals of Pest Species Jacobaea vulgaris: SNPs, Microsatellites and Barcoding Markers for Population and Phylogenetic Studies

    PubMed Central

    Doorduin, Leonie; Gravendeel, Barbara; Lammers, Youri; Ariyurek, Yavuz; Chin-A-Woeng, Thomas; Vrieling, Klaas

    2011-01-01

    Invasive individuals from the pest species Jacobaea vulgaris show different allocation patterns in defence and growth compared with native individuals. To examine if these changes are caused by fast evolution, it is necessary to identify native source populations and compare these with invasive populations. For this purpose, we are in need of intraspecific polymorphic markers. We therefore sequenced the complete chloroplast genomes of 12 native and 5 invasive individuals of J. vulgaris with next generation sequencing and discovered single-nucleotide polymorphisms (SNPs) and microsatellites. This is the first study in which the chloroplast genome of that many individuals within a single species was sequenced. Thirty-two SNPs and 34 microsatellite regions were found. For none of the individuals, differences were found between the inverted repeats. Furthermore, being the first chloroplast genome sequenced in the Senecioneae clade, we compared it with four other members of the Asteraceae family to identify new regions for phylogentic inference within this clade and also within the Asteraceae family. Five markers (ndhC-trnV, ndhC-atpE, rps18-rpl20, clpP and psbM-trnD) contained parsimony-informative characters higher than 2%. Finally, we compared two procedures of preparing chloroplast DNA for next generation sequencing. PMID:21444340

  5. Target enrichment of ultraconserved elements from arthropods provides a genomic perspective on relationships among Hymenoptera

    PubMed Central

    Faircloth, Brant C; Branstetter, Michael G; White, Noor D; Brady, Seán G

    2015-01-01

    Gaining a genomic perspective on phylogeny requires the collection of data from many putatively independent loci across the genome. Among insects, an increasingly common approach to collecting this class of data involves transcriptome sequencing, because few insects have high-quality genome sequences available; assembling new genomes remains a limiting factor; the transcribed portion of the genome is a reasonable, reduced subset of the genome to target; and the data collected from transcribed portions of the genome are similar in composition to the types of data with which biologists have traditionally worked (e.g. exons). However, molecular techniques requiring RNA as a template, including transcriptome sequencing, are limited to using very high-quality source materials, which are often unavailable from a large proportion of biologically important insect samples. Recent research suggests that DNA-based target enrichment of conserved genomic elements offers another path to collecting phylogenomic data across insect taxa, provided that conserved elements are present in and can be collected from insect genomes. Here, we identify a large set (n = 1510) of ultraconserved elements (UCEs) shared among the insect order Hymenoptera. We used in silico analyses to show that these loci accurately reconstruct relationships among genome-enabled hymenoptera, and we designed a set of RNA baits (n = 2749) for enriching these loci that researchers can use with DNA templates extracted from a variety of sources. We used our UCE bait set to enrich an average of 721 UCE loci from 30 hymenopteran taxa, and we used these UCE loci to reconstruct phylogenetic relationships spanning very old (≥220 Ma) to very young (≤1 Ma) divergences among hymenopteran lineages. In contrast to a recent study addressing hymenopteran phylogeny using transcriptome data, we found ants to be sister to all remaining aculeate lineages with complete support, although this result could be explained by

  6. Comparative genomics of "Dehalococcoides ethenogenes" 195 and an enrichment culture containing unsequenced "Dehalococcoides" strains.

    PubMed

    West, Kimberlee A; Johnson, David R; Hu, Ping; DeSantis, Todd Z; Brodie, Eoin L; Lee, Patrick K H; Feil, Helene; Andersen, Gary L; Zinder, Stephen H; Alvarez-Cohen, Lisa

    2008-06-01

    Tetrachloroethene (PCE) and trichloroethene (TCE) are prevalent groundwater contaminants that can be completely reductively dehalogenated by some "Dehalococcoides" organisms. A Dehalococcoides-organism-containing microbial consortium (referred to as ANAS) with the ability to degrade TCE to ethene, an innocuous end product, was previously enriched from contaminated soil. A whole-genome photolithographic microarray was developed based on the genome of "Dehalococcoides ethenogenes" 195. This microarray contains probes designed to hybridize to >99% of the predicted protein-coding sequences in the strain 195 genome. DNA from ANAS was hybridized to the microarray to characterize the genomic content of the ANAS enrichment. The microarray results revealed that the genes associated with central metabolism, including an apparently incomplete carbon fixation pathway, cobalamin-salvaging system, nitrogen fixation pathway, and five hydrogenase complexes, are present in both strain 195 and ANAS. Although the gene encoding the TCE reductase, tceA, was detected, 13 of the 19 reductive dehalogenase genes present in strain 195 were not detected in ANAS. Additionally, 88% of the genes in predicted integrated genetic elements in strain 195 were not detected in ANAS, consistent with these elements being genetically mobile. Sections of the tryptophan operon and an operon encoding an ABC transporter in strain 195 were also not detected in ANAS. These insights into the diversity of Dehalococcoides genomes will improve our understanding of the physiology and evolution of these bacteria, which is essential in developing effective strategies for the bioremediation of PCE and TCE in the environment. PMID:18359838

  7. Rapid enrichment of leucocytes and genomic DNA from blood based on bifunctional core shell magnetic nanoparticles

    NASA Astrophysics Data System (ADS)

    Xie, Xin; Nie, Xiaorong; Yu, Bingbin; Zhang, Xu

    2007-04-01

    A series of protocols are proposed to extract genomic DNA from whole blood at different scales using carboxyl-functionalized magnetic nanoparticles as solid-phase absorbents. The enrichment of leucocytes and the adsorption of genomic DNA can be achieved with the same carboxyl-functionalized magnetic nanoparticles. The DNA bound to the bead surfaces can be used directly as PCR templates. By coupling cell separation and DNA purification, the whole operation can be accomplished in a few minutes. Our simplified protocols proved to be rapid, low cost, and biologically and chemically non-hazardous, and are therefore promising for microfabrication of a DNA-preparation chip and routine laboratory use.

  8. Genomic features of uncultured methylotrophs in activated-sludge microbiomes grown under different enrichment procedures

    PubMed Central

    Fujinawa, Kazuki; Asai, Yusuke; Miyahara, Morio; Kouzuma, Atsushi; Abe, Takashi; Watanabe, Kazuya

    2016-01-01

    Methylotrophs are organisms that are able to grow on C1 compounds as carbon and energy sources. They play important roles in the global carbon cycle and contribute largely to industrial wastewater treatment. To identify and characterize methylotrophs that are involved in methanol degradation in wastewater-treatment plants, methanol-fed activated-sludge (MAS) microbiomes were subjected to phylogenetic and metagenomic analyses, and genomic features of dominant methylotrophs in MAS were compared with those preferentially grown in laboratory enrichment cultures (LECs). These analyses consistently indicate that Hyphomicrobium plays important roles in MAS, while Methylophilus occurred predominantly in LECs. Comparative analyses of bin genomes reconstructed for the Hyphomicrobium and Methylophilus methylotrophs suggest that they have different C1-assimilation pathways. In addition, function-module analyses suggest that their cell-surface structures are different. Comparison of the MAS bin genome with genomes of closely related Hyphomicrobium isolates suggests that genes unnecessary in MAS (for instance, genes for anaerobic respiration) have been lost from the genome of the dominant methylotroph. We suggest that genomic features and coded functions in the MAS bin genome provide us with insights into how this methylotroph adapts to activated-sludge ecosystems. PMID:27221669

  9. Genomic features of uncultured methylotrophs in activated-sludge microbiomes grown under different enrichment procedures.

    PubMed

    Fujinawa, Kazuki; Asai, Yusuke; Miyahara, Morio; Kouzuma, Atsushi; Abe, Takashi; Watanabe, Kazuya

    2016-01-01

    Methylotrophs are organisms that are able to grow on C1 compounds as carbon and energy sources. They play important roles in the global carbon cycle and contribute largely to industrial wastewater treatment. To identify and characterize methylotrophs that are involved in methanol degradation in wastewater-treatment plants, methanol-fed activated-sludge (MAS) microbiomes were subjected to phylogenetic and metagenomic analyses, and genomic features of dominant methylotrophs in MAS were compared with those preferentially grown in laboratory enrichment cultures (LECs). These analyses consistently indicate that Hyphomicrobium plays important roles in MAS, while Methylophilus occurred predominantly in LECs. Comparative analyses of bin genomes reconstructed for the Hyphomicrobium and Methylophilus methylotrophs suggest that they have different C1-assimilation pathways. In addition, function-module analyses suggest that their cell-surface structures are different. Comparison of the MAS bin genome with genomes of closely related Hyphomicrobium isolates suggests that genes unnecessary in MAS (for instance, genes for anaerobic respiration) have been lost from the genome of the dominant methylotroph. We suggest that genomic features and coded functions in the MAS bin genome provide us with insights into how this methylotroph adapts to activated-sludge ecosystems. PMID:27221669

  10. Survey of microsatellite clustering in eight fully sequenced species sheds light on the origin of compound microsatellites

    PubMed Central

    Kofler, Robert; Schlötterer, Christian; Luschützky, Evita; Lelley, Tamas

    2008-01-01

    Background Compound microsatellites are a special variation of microsatellites in which two or more individual microsatellites are found directly adjacent to each other. Until now, such composite microsatellites have not been investigated in a comprehensive manner. Results Our in silico survey of microsatellite clustering in genomes of Homo sapiens, Maccaca mulatta, Mus musculus, Rattus norvegicus, Ornithorhynchus anatinus, Gallus gallus, Danio rerio and Drosophila melanogaster revealed an unexpected high abundance of compound microsatellites. About 4 – 25% of all microsatellites could be categorized as compound microsatellites. Compound microsatellites are approximately 15 times more frequent than expected under the assumption of a random distribution of microsatellites. Interestingly, microsatellites do not only tend to cluster but the adjacent repeat types of compound microsatellites have very similar motifs: in most cases (>90%) these motifs differ only by a single mutation (base substitution or indel). We propose that the majority of the compound microsatellites originates by duplication of imperfections in a microsatellite tract. This process occurs mostly at the end of a microsatellite, leading to a new repeat type and a potential microsatellite repeat track. Conclusion Our findings suggest a more dynamic picture of microsatellite evolution than previously believed. Imperfections within microsatellites might not only cause the "death" of microsatellites they might also result in their "birth". PMID:19091106

  11. Reconstructing rare soil microbial genomes using in situ enrichments and metagenomics

    PubMed Central

    Delmont, Tom O.; Eren, A. Murat; Maccario, Lorrie; Prestat, Emmanuel; Esen, Özcan C.; Pelletier, Eric; Le Paslier, Denis; Simonet, Pascal; Vogel, Timothy M.

    2015-01-01

    Despite extensive direct sequencing efforts and advanced analytical tools, reconstructing microbial genomes from soil using metagenomics have been challenging due to the tremendous diversity and relatively uniform distribution of genomes found in this system. Here we used enrichment techniques in an attempt to decrease the complexity of a soil microbiome prior to sequencing by submitting it to a range of physical and chemical stresses in 23 separate microcosms for 4 months. The metagenomic analysis of these microcosms at the end of the treatment yielded 540 Mb of assembly using standard de novo assembly techniques (a total of 559,555 genes and 29,176 functions), from which we could recover novel bacterial genomes, plasmids and phages. The recovered genomes belonged to Leifsonia (n = 2), Rhodanobacter (n = 5), Acidobacteria (n = 2), Sporolactobacillus (n = 2, novel nitrogen fixing taxon), Ktedonobacter (n = 1, second representative of the family Ktedonobacteraceae), Streptomyces (n = 3, novel polyketide synthase modules), and Burkholderia (n = 2, includes mega-plasmids conferring mercury resistance). Assembled genomes averaged to 5.9 Mb, with relative abundances ranging from rare (<0.0001%) to relatively abundant (>0.01%) in the original soil microbiome. Furthermore, we detected them in samples collected from geographically distant locations, particularly more in temperate soils compared to samples originating from high-latitude soils and deserts. To the best of our knowledge, this study is the first successful attempt to assemble multiple bacterial genomes directly from a soil sample. Our findings demonstrate that developing pertinent enrichment conditions can stimulate environmental genomic discoveries that would have been impossible to achieve with canonical approaches that focus solely upon post-sequencing data treatment. PMID:25983722

  12. Deep Subsurface Life from North Pond: Enrichment, Isolation, Characterization and Genomes of Heterotrophic Bacteria

    PubMed Central

    Russell, Joseph A.; León-Zayas, Rosa; Wrighton, Kelly; Biddle, Jennifer F.

    2016-01-01

    Studies of subsurface microorganisms have yielded few environmentally relevant isolates for laboratory studies. In order to address this lack of cultivated microorganisms, we initiated several enrichments on sediment and underlying basalt samples from North Pond, a sediment basin ringed by basalt outcrops underlying an oligotrophic water-column west of the Mid-Atlantic Ridge at 22°N. In contrast to anoxic enrichments, growth was observed in aerobic, heterotrophic enrichments from sediment of IODP Hole U1382B at 4 and 68 m below seafloor (mbsf). These sediment depths, respectively, correspond to the fringes of oxygen penetration from overlying seawater in the top of the sediment column and upward migration of oxygen from oxic seawater from the basalt aquifer below the sediment. Here we report the enrichment, isolation, initial characterization and genomes of three isolated aerobic heterotrophs from North Pond sediments; an Arthrobacter species from 4 mbsf, and Paracoccus and Pseudomonas species from 68 mbsf. These cultivated bacteria are represented in the amplicon 16S rRNA gene libraries created from whole sediments, albeit at low (up to 2%) relative abundance. We provide genomic evidence from our isolates demonstrating that the Arthrobacter and Pseudomonas isolates have the potential to respire nitrate and oxygen, though dissimilatory nitrate reduction could not be confirmed in laboratory cultures. The cultures from this study represent members of abundant phyla, as determined by amplicon sequencing of environmental DNA extracts, and allow for further studies into geochemical factors impacting life in the deep subsurface. PMID:27242705

  13. Deep subsurface life from North Pond: Enrichment, isolation, characterization and genomes of heterotrophic bacteria

    DOE PAGESBeta

    Russell, Joseph A.; Leon-Zayas, Rosa; Wrighton, Kelly; Biddle, Jennifer F.

    2016-05-10

    Studies of subsurface microorganisms have yielded few environmentally relevant isolates for laboratory studies. In order to address this lack of cultivated microorganisms, we initiated several enrichments on sediment and underlying basalt samples from North Pond, a sediment basin ringed by basalt outcrops underlying an oligotrophic watercolumn west of the Mid-Atlantic Ridge at 22° N. In contrast to anoxic enrichments, growth was observed in aerobic, heterotrophic enrichments from sediment of IODP Hole U1382B at 4 and 68 m below seafloor (mbsf). These sediment depths, respectively, correspond to the fringes of oxygen penetration from overlying seawater in the top of the sedimentmore » column and upward migration of oxygen from oxic seawater from the basalt aquifer below the sediment. Here we report the enrichment, isolation, initial characterization and genomes of three isolated aerobic heterotrophs from North Pond sediments; an Arthrobacter species from 4 mbsf, and Paracoccus and Pseudomonas species from 68 mbsf. These cultivated bacteria are represented in the amplicon 16S rRNA gene libraries created from whole sediments, albeit at low (up to 2%) relative abundance. We provide genomic evidence from our isolates demonstrating that the Arthrobacter and Pseudomonas isolates have the potential to respire nitrate and oxygen, though dissimilatory nitrate reduction could not be confirmed in laboratory cultures. Furthermore, the cultures from this study represent members of abundant phyla, as determined by amplicon sequencing of environmental DNA extracts, and allow for further studies into geochemical factors impacting life in the deep subsurface.« less

  14. Deep Subsurface Life from North Pond: Enrichment, Isolation, Characterization and Genomes of Heterotrophic Bacteria.

    PubMed

    Russell, Joseph A; León-Zayas, Rosa; Wrighton, Kelly; Biddle, Jennifer F

    2016-01-01

    Studies of subsurface microorganisms have yielded few environmentally relevant isolates for laboratory studies. In order to address this lack of cultivated microorganisms, we initiated several enrichments on sediment and underlying basalt samples from North Pond, a sediment basin ringed by basalt outcrops underlying an oligotrophic water-column west of the Mid-Atlantic Ridge at 22°N. In contrast to anoxic enrichments, growth was observed in aerobic, heterotrophic enrichments from sediment of IODP Hole U1382B at 4 and 68 m below seafloor (mbsf). These sediment depths, respectively, correspond to the fringes of oxygen penetration from overlying seawater in the top of the sediment column and upward migration of oxygen from oxic seawater from the basalt aquifer below the sediment. Here we report the enrichment, isolation, initial characterization and genomes of three isolated aerobic heterotrophs from North Pond sediments; an Arthrobacter species from 4 mbsf, and Paracoccus and Pseudomonas species from 68 mbsf. These cultivated bacteria are represented in the amplicon 16S rRNA gene libraries created from whole sediments, albeit at low (up to 2%) relative abundance. We provide genomic evidence from our isolates demonstrating that the Arthrobacter and Pseudomonas isolates have the potential to respire nitrate and oxygen, though dissimilatory nitrate reduction could not be confirmed in laboratory cultures. The cultures from this study represent members of abundant phyla, as determined by amplicon sequencing of environmental DNA extracts, and allow for further studies into geochemical factors impacting life in the deep subsurface. PMID:27242705

  15. Development and optimization of sequence-tagged microsatellite site markers to detect genetic diversity within Colletotrichum capsici, a causal agent of chilli pepper anthracnose disease.

    PubMed

    Ranathunge, N P; Ford, R; Taylor, P W J

    2009-07-01

    Genomic libraries enriched for microsatellites from Colletotrichum capsici, one of the major causal agents of anthracnose disease in chilli pepper (Capsicum spp.), were developed using a modified hybridization procedure. Twenty-seven robust primer pairs were designed from microsatellite flanking sequences and were characterized using 52 isolates from three countries India, Sri Lanka and Thailand. Highest gene diversity of 0.857 was observed at the CCSSR1 with up to 18 alleles among all the isolates whereas the differentiation ranged from 0.05 to 0.45. The sequence-tagged microsatellite site markers developed in this study will be useful for genetic analyses of C. capsici populations. PMID:21564867

  16. Cell Context Dependent p53 Genome-Wide Binding Patterns and Enrichment at Repeats

    DOE PAGESBeta

    Botcheva, Krassimira; McCorkle, Sean R.

    2014-11-21

    The p53 ability to elicit stress specific and cell type specific responses is well recognized, but how that specificity is established remains to be defined. Whether upon activation p53 binds to its genomic targets in a cell type and stress type dependent manner is still an open question. Here we show that the p53 binding to the human genome is selective and cell context-dependent. We mapped the genomic binding sites for the endogenous wild type p53 protein in the human cancer cell line HCT116 and compared them to those we previously determined in the normal cell line IMR90. We reportmore » distinct p53 genome-wide binding landscapes in two different cell lines, analyzed under the same treatment and experimental conditions, using the same ChIP-seq approach. This is evidence for cell context dependent p53 genomic binding. The observed differences affect the p53 binding sites distribution with respect to major genomic and epigenomic elements (promoter regions, CpG islands and repeats). We correlated the high-confidence p53 ChIP-seq peaks positions with the annotated human repeats (UCSC Human Genome Browser) and observed both common and cell line specific trends. In HCT116, the p53 binding was specifically enriched at LINE repeats, compared to IMR90 cells. The p53 genome-wide binding patterns in HCT116 and IMR90 likely reflect the different epigenetic landscapes in these two cell lines, resulting from cancer-associated changes (accumulated in HCT116) superimposed on tissue specific differences (HCT116 has epithelial, while IMR90 has mesenchymal origin). In conclusion, our data support the model for p53 binding to the human genome in a highly selective manner, mobilizing distinct sets of genes, contributing to distinct pathways.« less

  17. Cell Context Dependent p53 Genome-Wide Binding Patterns and Enrichment at Repeats

    PubMed Central

    Botcheva, Krassimira; McCorkle, Sean R.

    2014-01-01

    The p53 ability to elicit stress specific and cell type specific responses is well recognized, but how that specificity is established remains to be defined. Whether upon activation p53 binds to its genomic targets in a cell type and stress type dependent manner is still an open question. Here we show that the p53 binding to the human genome is selective and cell context-dependent. We mapped the genomic binding sites for the endogenous wild type p53 protein in the human cancer cell line HCT116 and compared them to those we previously determined in the normal cell line IMR90. We report distinct p53 genome-wide binding landscapes in two different cell lines, analyzed under the same treatment and experimental conditions, using the same ChIP-seq approach. This is evidence for cell context dependent p53 genomic binding. The observed differences affect the p53 binding sites distribution with respect to major genomic and epigenomic elements (promoter regions, CpG islands and repeats). We correlated the high-confidence p53 ChIP-seq peaks positions with the annotated human repeats (UCSC Human Genome Browser) and observed both common and cell line specific trends. In HCT116, the p53 binding was specifically enriched at LINE repeats, compared to IMR90 cells. The p53 genome-wide binding patterns in HCT116 and IMR90 likely reflect the different epigenetic landscapes in these two cell lines, resulting from cancer-associated changes (accumulated in HCT116) superimposed on tissue specific differences (HCT116 has epithelial, while IMR90 has mesenchymal origin). Our data support the model for p53 binding to the human genome in a highly selective manner, mobilizing distinct sets of genes, contributing to distinct pathways. PMID:25415302

  18. Cell Context Dependent p53 Genome-Wide Binding Patterns and Enrichment at Repeats

    SciTech Connect

    Botcheva, Krassimira; McCorkle, Sean R.

    2014-11-21

    The p53 ability to elicit stress specific and cell type specific responses is well recognized, but how that specificity is established remains to be defined. Whether upon activation p53 binds to its genomic targets in a cell type and stress type dependent manner is still an open question. Here we show that the p53 binding to the human genome is selective and cell context-dependent. We mapped the genomic binding sites for the endogenous wild type p53 protein in the human cancer cell line HCT116 and compared them to those we previously determined in the normal cell line IMR90. We report distinct p53 genome-wide binding landscapes in two different cell lines, analyzed under the same treatment and experimental conditions, using the same ChIP-seq approach. This is evidence for cell context dependent p53 genomic binding. The observed differences affect the p53 binding sites distribution with respect to major genomic and epigenomic elements (promoter regions, CpG islands and repeats). We correlated the high-confidence p53 ChIP-seq peaks positions with the annotated human repeats (UCSC Human Genome Browser) and observed both common and cell line specific trends. In HCT116, the p53 binding was specifically enriched at LINE repeats, compared to IMR90 cells. The p53 genome-wide binding patterns in HCT116 and IMR90 likely reflect the different epigenetic landscapes in these two cell lines, resulting from cancer-associated changes (accumulated in HCT116) superimposed on tissue specific differences (HCT116 has epithelial, while IMR90 has mesenchymal origin). In conclusion, our data support the model for p53 binding to the human genome in a highly selective manner, mobilizing distinct sets of genes, contributing to distinct pathways.

  19. Targeted genome enrichment for efficient purification of endosymbiont DNA from host DNA.

    PubMed

    Geniez, Sandrine; Foster, Jeremy M; Kumar, Sanjay; Moumen, Bouziane; Leproust, Emily; Hardy, Owen; Guadalupe, Moraima; Thomas, Stephen J; Boone, Braden; Hendrickson, Cynthia; Bouchon, Didier; Grève, Pierre; Slatko, Barton E

    2012-12-01

    Wolbachia endosymbionts are widespread in arthropods and are generally considered reproductive parasites, inducing various phenotypes including cytoplasmic incompatibility, parthenogenesis, feminization and male killing, which serve to promote their spread through populations. In contrast, Wolbachia infecting filarial nematodes that cause human diseases, including elephantiasis and river blindness, are obligate mutualists. DNA purification methods for efficient genomic sequencing of these unculturable bacteria have proven difficult using a variety of techniques. To efficiently capture endosymbiont DNA for studies that examine the biology of symbiosis, we devised a parallel strategy to an earlier array-based method by creating a set of SureSelect™ (Agilent) 120-mer target enrichment RNA oligonucleotides ("baits") for solution hybrid selection. These were designed from Wolbachia complete and partial genome sequences in GenBank and were tiled across each genomic sequence with 60 bp overlap. Baits were filtered for homology against host genomes containing Wolbachia using BLAT and sequences with significant host homology were removed from the bait pool. Filarial parasite Brugia malayi DNA was used as a test case, as the complete sequence of both Wolbachia and its host are known. DNA eluted from capture was size selected and sequencing samples were prepared using the NEBNext® Sample Preparation Kit. One-third of a 50 nt paired-end sequencing lane on the HiSeq™ 2000 (Illumina) yielded 53 million reads and the entirety of the Wolbachia genome was captured. We then used the baits to isolate more than 97.1 % of the genome of a distantly related Wolbachia strain from the crustacean Armadillidium vulgare, demonstrating that the method can be used to enrich target DNA from unculturable microbes over large evolutionary distances. PMID:23482460

  20. Whole genome sequencing of enriched chloroplast DNA using the Illumina GAII platform

    PubMed Central

    2010-01-01

    Background Complete chloroplast genome sequences provide a valuable source of molecular markers for studies in molecular ecology and evolution of plants. To obtain complete genome sequences, recent studies have made use of the polymerase chain reaction to amplify overlapping fragments from conserved gene loci. However, this approach is time consuming and can be more difficult to implement where gene organisation differs among plants. An alternative approach is to first isolate chloroplasts and then use the capacity of high-throughput sequencing to obtain complete genome sequences. We report our findings from studies of the latter approach, which used a simple chloroplast isolation procedure, multiply-primed rolling circle amplification of chloroplast DNA, Illumina Genome Analyzer II sequencing, and de novo assembly of paired-end sequence reads. Results A modified rapid chloroplast isolation protocol was used to obtain plant DNA that was enriched for chloroplast DNA, but nevertheless contained nuclear and mitochondrial DNA. Multiply-primed rolling circle amplification of this mixed template produced sufficient quantities of chloroplast DNA, even when the amount of starting material was small, and improved the template quality for Illumina Genome Analyzer II (hereafter Illumina GAII) sequencing. We demonstrate, using independent samples of karaka (Corynocarpus laevigatus), that there is high fidelity in the sequence obtained from this template. Although less than 20% of our sequenced reads could be mapped to chloroplast genome, it was relatively easy to assemble complete chloroplast genome sequences from the mixture of nuclear, mitochondrial and chloroplast reads. Conclusions We report successful whole genome sequencing of chloroplast DNA from karaka, obtained efficiently and with high fidelity. PMID:20920211

  1. Enrichment of Root Endophytic Bacteria from Populus deltoides and Single-Cell-Genomics Analysis

    PubMed Central

    Utturkar, Sagar M.; Cude, W. Nathan; Robeson, Michael S.; Yang, Zamin K.; Klingeman, Dawn M.; Land, Miriam L.; Allman, Steve L.; Lu, Tse-Yuan S.; Brown, Steven D.; Schadt, Christopher W.; Podar, Mircea; Doktycz, Mitchel J.

    2016-01-01

    ABSTRACT Bacterial endophytes that colonize Populus trees contribute to nutrient acquisition, prime immunity responses, and directly or indirectly increase both above- and below-ground biomasses. Endophytes are embedded within plant material, so physical separation and isolation are difficult tasks. Application of culture-independent methods, such as metagenome or bacterial transcriptome sequencing, has been limited due to the predominance of DNA from the plant biomass. Here, we describe a modified differential and density gradient centrifugation-based protocol for the separation of endophytic bacteria from Populus roots. This protocol achieved substantial reduction in contaminating plant DNA, allowed enrichment of endophytic bacteria away from the plant material, and enabled single-cell genomics analysis. Four single-cell genomes were selected for whole-genome amplification based on their rarity in the microbiome (potentially uncultured taxa) as well as their inferred abilities to form associations with plants. Bioinformatics analyses, including assembly, contamination removal, and completeness estimation, were performed to obtain single-amplified genomes (SAGs) of organisms from the phyla Armatimonadetes, Verrucomicrobia, and Planctomycetes, which were unrepresented in our previous cultivation efforts. Comparative genomic analysis revealed unique characteristics of each SAG that could facilitate future cultivation efforts for these bacteria. IMPORTANCE Plant roots harbor a diverse collection of microbes that live within host tissues. To gain a comprehensive understanding of microbial adaptations to this endophytic lifestyle from strains that cannot be cultivated, it is necessary to separate bacterial cells from the predominance of plant tissue. This study provides a valuable approach for the separation and isolation of endophytic bacteria from plant root tissue. Isolated live bacteria provide material for microbiome sequencing, single-cell genomics, and analyses

  2. Effect of microsatellite selection on individual and population genetic inferences: an empirical study using cross-specific and species-specific amplifications.

    PubMed

    Queirós, J; Godinho, R; Lopes, S; Gortazar, C; de la Fuente, J; Alves, P C

    2015-07-01

    Although whole-genome sequencing is becoming more accessible and feasible for nonmodel organisms, microsatellites have remained the markers of choice for various population and conservation genetic studies. However, the criteria for choosing microsatellites are still controversial due to ascertainment bias that may be introduced into the genetic inference. An empirical study of red deer (Cervus elaphus) populations, in which cross-specific and species-specific microsatellites developed through pyrosequencing of enriched libraries, was performed for this study. Two different strategies were used to select the species-specific panels: randomly vs. highly polymorphic markers. The results suggest that reliable and accurate estimations of genetic diversity can be obtained using random microsatellites distributed throughout the genome. In addition, the results reinforce previous evidence that selecting the most polymorphic markers leads to an ascertainment bias in estimates of genetic diversity, when compared with randomly selected microsatellites. Analyses of population differentiation and clustering seem less influenced by the approach of microsatellite selection, whereas assigning individuals to populations might be affected by a random selection of a small number of microsatellites. Individual multilocus heterozygosity measures produced various discordant results, which in turn had impacts on the heterozygosity-fitness correlation test. Finally, we argue that picking the appropriate microsatellite set should primarily take into account the ecological and evolutionary questions studied. Selecting the most polymorphic markers will generally overestimate genetic diversity parameters, leading to misinterpretations of the real genetic diversity, which is particularly important in managed and threatened populations. PMID:25403329

  3. Enrichment of Root Endophytic Bacteria from Populus deltoides and Single-Cell-Genomics Analysis

    DOE PAGESBeta

    Utturkar, Sagar M.; Cude, W. Nathan; Robeson, Jr., Michael S.; Yang, Zamin Koo; Klingeman, Dawn Marie; Land, Miriam L.; Allman, Steve L.; Lu, Tse-Yuan S.; Brown, Steven D.; Schadt, Christopher Warren; et al

    2016-07-15

    Bacterial endophytes that colonize Populus trees contribute to nutrient acquisition, prime immunity responses, and directly or indirectly increase both above- and below-ground biomasses. Endophytes are embedded within plant material, so physical separation and isolation are difficult tasks. Application of culture-independent methods, such as metagenome or bacterial transcriptome sequencing, has been limited due to the predominance of DNA from the plant biomass. In this paper, we present a modified differential and density gradient centrifugation-based protocol for the separation of endophytic bacteria from Populus roots. This protocol achieved substantial reduction in contaminating plant DNA, allowed enrichment of endophytic bacteria away from themore » plant material, and enabled single-cell genomics analysis. Four single-cell genomes were selected for whole-genome amplification based on their rarity in the microbiome (potentially uncultured taxa) as well as their inferred abilities to form associations with plants. Bioinformatics analyses, including assembly, contamination removal, and completeness estimation, were performed to obtain single-amplified genomes (SAGs) of organisms from the phyla Armatimonadetes, Verrucomicrobia, and Planctomycetes, which were unrepresented in our previous cultivation efforts. Finally, comparative genomic analysis revealed unique characteristics of each SAG that could facilitate future cultivation efforts for these bacteria.« less

  4. Rapid, economical single-nucleotide polymorphism and microsatellite discovery based on de novo assembly of a reduced representation genome in a non-model organism: a case study of Atlantic cod Gadus morhua.

    PubMed

    Carlsson, J; Gauthier, D T; Carlsson, J E L; Coughlan, J P; Dillane, E; Fitzgerald, R D; Keating, U; McGinnity, P; Mirimin, L; Cross, T F

    2013-03-01

    By combining next-generation sequencing technology (454) and reduced representation library (RRL) construction, the rapid and economical isolation of over 25 000 potential single-nucleotide polymorphisms (SNP) and >6000 putative microsatellite loci from c. 2% of the genome of the non-model teleost, Atlantic cod Gadus morhua from the Celtic Sea, south of Ireland, was demonstrated. A small-scale validation of markers indicated that 80% (11 of 14) of SNP loci and 40% (6 of 15) of the microsatellite loci could be amplified and showed variability. The results clearly show that small-scale next-generation sequencing of RRL genomes is an economical and rapid approach for simultaneous SNP and microsatellite discovery that is applicable to any species. The low cost and relatively small investment in time allows for positive exploitation of ascertainment bias to design markers applicable to specific populations and study questions. PMID:23464553

  5. Mutation biases and mutation rate variation around very short human microsatellites revealed by human-chimpanzee-orangutan genomic sequence alignments.

    PubMed

    Amos, William

    2010-09-01

    I have studied mutation patterns around very short microsatellites, focusing mainly on sequences carrying only two repeat units. By using human-chimpanzee-orangutan alignments, inferences can be made about both the relative rates of mutations and which bases have mutated. I find remarkable non-randomness, with mutation rate depending on a base's position relative to the microsatellite, the identity of the base itself and the motif in the microsatellite. Comparing the patterns around AC2 with those around other four-base combinations reveals that AC2 does not stand out as being special in the sense that non-repetitive tetramers also generate strong mutation biases. However, comparing AC2 and AC3 with AC4 reveals a step change in both the rate and nature of mutations occurring, suggesting a transition state, AC4 exhibiting an alternating high-low mutation rate pattern consistent with the sequence patterning seen around longer microsatellites. Surprisingly, most changes in repeat number occur through base substitutions rather than slippage, and the relative probability of gaining versus losing a repeat in this way varies greatly with repeat number. Slippage mutations reveal rather similar patterns of mutability compared with point mutations, being rare at two repeats where most cause the loss of a repeat, with both mutation rate and the proportion of expansion mutations increasing up to 6-8 repeats. Inferences about longer repeat tracts are hampered by uncertainties about the proportion of multi-species alignments that fail due to multi-repeat mutations and other rearrangements. PMID:20700734

  6. When genetic distance matters: Measuring genetic differentiation at microsatellite loci in whole-genome scans of recent and incipient mosquito species

    PubMed Central

    Wang, Rui; Zheng, Liangbiao; Touré, Yeya T.; Dandekar, Thomas; Kafatos, Fotis C.

    2001-01-01

    Genetic distance measurements are an important tool to differentiate field populations of disease vectors such as the mosquito vectors of malaria. Here, we have measured the genetic differentiation between Anopheles arabiensis and Anopheles gambiae, as well as between proposed emerging species of the latter taxon, in whole genome scans by using 23–25 microsatellite loci. In doing so, we have reviewed and evaluated the advantages and disadvantages of standard parameters of genetic distance, FST, RST, (δμ)2, and D. Further, we have introduced new parameters, D′ and DK, which have well defined statistical significance tests and complement the standard parameters to advantage. D′ is a modification of D, whereas DK is a measure of covariance based on Pearson's correlation coefficient. We find that A. gambiae and A. arabiensis are closely related at most autosomal loci but appear to be distantly related on the basis of X-linked chromosomal loci within the chromosomal Xag inversion. The M and S molecular forms of A. gambiae are practically indistinguishable but differ significantly at two microsatellite loci from the proximal region of the X, outside the Xag inversion. At one of these loci, both M and S molecular forms differ significantly from A. arabiensis, but remarkably, at the other locus, A. arabiensis is indistinguishable from the M molecular form of A. gambiae. These data support the recent proposal of genetically differentiated M and S molecular forms of A. gambiae. PMID:11553812

  7. Development and characterization of microsatellite markers for lippia (Phyla canescens: Verbenaceae).

    PubMed

    Fatemi, M; Gross, C L

    2008-11-01

    Lippia (Phyla canescens: Verbenaceae) is a serious weed of wetlands, riparian zones and floodplains, particularly in eastern Australia where many Ramsar wetlands are threatened by hydrological changes precipitated by soil-accreting lippia mats. Enriched genomic DNA libraries were used to develop nine informative microsatellite markers. These markers will be valuable tools to understand the genetic structure of the lippia populations in different regions throughout the world. PMID:21586039

  8. Development and characterization of polymorphic microsatellite markers in Linum usitatissimum.

    PubMed

    Deng, Xin; Long, Songhua; He, Dongfeng; Li, Xiang; Wang, Yufu; Liu, Jia; Chen, Xinbo

    2010-01-01

    Thirty-five microsatellite loci were isolated and characterized in Linum usitatissimum using enriched genomic libraries. These loci were screened in eight cultivars from different countries and regions and were found to be polymorphic, with the number of alleles per locus ranging from two to six, and observed and expected heterozygosities ranging from 0.125 to 0.375 (mean 0.013) and from 0.233 to 0.842 (mean 0.601), respectively. These polymorphic new microsatellite loci will be useful for genetic linkage map construction, germplasm classification and identification, gene identification and quantitative trait loci mapping, and marker-assisted selection in breeding in L. usitatissimum. PMID:19882206

  9. Development and characterization of microsatellites markers from the macaw.

    PubMed

    Nucci, S M; Azevedo-Filho, J A; Colombo, C A; Priolli, R H G; Coelho, R M; Mata, T L; Zucchi, M I

    2008-01-01

    Macaw (Acrocomia aculeata) is a native palm tree from tropical forests, highly abundant in Brazil and cited as one of the principal sources of plant oil, thus presenting a high potential for biodiesel production. We have optimized and utilized a set of eight polymorphic microsatellite markers for A. aculeata from an enriched genomic library. Automatic sequencing and fluorescence detection were employed to analyse 43 individuals from natural populations. In this study, we have obtained an average number of five alleles per locus. These loci will be employed in future studies of population genetics by providing subsidy information for the species conservation and genetic breeding. PMID:21585762

  10. AN ENHANCED MICROSATELLITE MAP OF DIPLOID FRAGARIA

    Technology Transfer Automated Retrieval System (TEKTRAN)

    A total of 45 microsatellites (SSRs) were developed for mapping in Fragaria. They included 31 novel codominant genomic microsatellites (SSRs) from Fragaria nubicola and a further 14 derived from an expressed sequence tagged library (EST-SSRs) of F. x ananassa. These, and an additional, 64 previous...

  11. Microsatellite primers for red drum (Sciaenops ocellatus)

    Technology Transfer Automated Retrieval System (TEKTRAN)

    In this note, we document polymerase-chain-reaction (PCR) primer pairs for 101, nuclear-encoded microsatellites designed and developed from a red drum (Sciaenops ocellatus) genomic library. The 101 microsatellites (Genbank Accession Numbers EU015882-EU015982) were amplified successfully and used to...

  12. Distribution and localization of microsatellites in the Perigord black truffle genome and identification of new molecular markers (2010) Fungal Genetics and Biology

    SciTech Connect

    Murat, Claude; Riccioni, C; Belfiori, B; Cichocki, N; Labbe, Jessy L; Morin, Emmanuelle; Tisserant, Emilie; Paolocci, F; Rubini, A; Martin, Francis

    2011-01-01

    The level of genetic diversity and genetic structure in the Perigord black truffle (Tuber melanosporum Vittad.) has been debated for several years, mainly due to the lack of appropriate genetic markers. Microsatellites or simple sequence repeats (SSRs) are important for the genome organisation, phenotypic diversity and are one of the most popular molecular markers. In this study, we surveyed the T. melanosporum genome (1) to characterise its SSR pattern; (2) to compare it with SSR patterns found in 48 other fungal and three oomycetes genomes and (3) to identify new polymorphic SSR markers for population genetics. The T. melanosporum genome is rich in SSRs with 22,425 SSRs with mono-nucleotides being the most frequent motifs. SSRs were found in all genomic regions although they are more frequent in non-coding regions (introns and intergenic regions). Sixty out of 135 PCR-amplified mono-, di-, tri-, tetra, penta, and hexanucleotides were polymorphic (44%) within black truffle populations and 27 were randomly selected and analysed on 139 T. melanosporum isolates from France, Italy and Spain. The number of alleles varied from 2 to 18 and the expected heterozygosity from 0.124 to 0.815. One hundred and thirty-two different multilocus genotypes out of the 139 T. melanosporum isolates were identified and the genotypic diversity was high (0.999). Polymorphic SSRs were found in UTR regulatory regions of fruiting bodies and ectomycorrhiza regulated genes, suggesting that they may play a role in phenotypic variation. In conclusion, SSRs developed in this study were highly polymorphic and our results showed that T. melanosporum is a species with an important genetic diversity, which is in agreement with its recently uncovered heterothallic mating system.

  13. A novel ammonia-oxidizing archaeon from wastewater treatment plant: Its enrichment, physiological and genomic characteristics.

    PubMed

    Li, Yuyang; Ding, Kun; Wen, Xianghua; Zhang, Bing; Shen, Bo; Yang, Yunfeng

    2016-01-01

    Ammonia-oxidizing archaea (AOA) are recently found to participate in the ammonia removal processes in wastewater treatment plants (WWTPs), similar to their bacterial counterparts. However, due to lack of cultivated AOA strains from WWTPs, their functions and contributions in these systems remain unclear. Here we report a novel AOA strain SAT1 enriched from activated sludge, with its physiological and genomic characteristics investigated. The maximal 16S rRNA gene similarity between SAT1 and other reported AOA strain is 96% (with "Ca. Nitrosotenuis chungbukensis"), and it is affiliated with Wastewater Cluster B (WWC-B) based on amoA gene phylogeny, a cluster within group I.1a and specific for activated sludge. Our strain is autotrophic, mesophilic (25 °C-33 °C) and neutrophilic (pH 5.0-7.0). Its genome size is 1.62 Mb, with a large fragment inversion (accounted for 68% genomic size) inside. The strain could not utilize urea due to truncation of the urea transporter gene. The lack of the pathways to synthesize usual compatible solutes makes it intolerant to high salinity (>0.03%), but could adapt to low salinity (0.005%) environments. This adaptation, together with possibly enhanced cell-biofilm attachment ability, makes it suitable for WWTPs environment. We propose the name "Candidatus Nitrosotenuis cloacae" for the strain SAT1. PMID:27030530

  14. A novel ammonia-oxidizing archaeon from wastewater treatment plant: Its enrichment, physiological and genomic characteristics

    NASA Astrophysics Data System (ADS)

    Li, Yuyang; Ding, Kun; Wen, Xianghua; Zhang, Bing; Shen, Bo; Yang, Yunfeng

    2016-03-01

    Ammonia-oxidizing archaea (AOA) are recently found to participate in the ammonia removal processes in wastewater treatment plants (WWTPs), similar to their bacterial counterparts. However, due to lack of cultivated AOA strains from WWTPs, their functions and contributions in these systems remain unclear. Here we report a novel AOA strain SAT1 enriched from activated sludge, with its physiological and genomic characteristics investigated. The maximal 16S rRNA gene similarity between SAT1 and other reported AOA strain is 96% (with “Ca. Nitrosotenuis chungbukensis”), and it is affiliated with Wastewater Cluster B (WWC-B) based on amoA gene phylogeny, a cluster within group I.1a and specific for activated sludge. Our strain is autotrophic, mesophilic (25 °C–33 °C) and neutrophilic (pH 5.0–7.0). Its genome size is 1.62 Mb, with a large fragment inversion (accounted for 68% genomic size) inside. The strain could not utilize urea due to truncation of the urea transporter gene. The lack of the pathways to synthesize usual compatible solutes makes it intolerant to high salinity (>0.03%), but could adapt to low salinity (0.005%) environments. This adaptation, together with possibly enhanced cell-biofilm attachment ability, makes it suitable for WWTPs environment. We propose the name “Candidatus Nitrosotenuis cloacae” for the strain SAT1.

  15. A novel ammonia-oxidizing archaeon from wastewater treatment plant: Its enrichment, physiological and genomic characteristics

    PubMed Central

    Li, Yuyang; Ding, Kun; Wen, Xianghua; Zhang, Bing; Shen, Bo; Yang, Yunfeng

    2016-01-01

    Ammonia-oxidizing archaea (AOA) are recently found to participate in the ammonia removal processes in wastewater treatment plants (WWTPs), similar to their bacterial counterparts. However, due to lack of cultivated AOA strains from WWTPs, their functions and contributions in these systems remain unclear. Here we report a novel AOA strain SAT1 enriched from activated sludge, with its physiological and genomic characteristics investigated. The maximal 16S rRNA gene similarity between SAT1 and other reported AOA strain is 96% (with “Ca. Nitrosotenuis chungbukensis”), and it is affiliated with Wastewater Cluster B (WWC-B) based on amoA gene phylogeny, a cluster within group I.1a and specific for activated sludge. Our strain is autotrophic, mesophilic (25 °C–33 °C) and neutrophilic (pH 5.0–7.0). Its genome size is 1.62 Mb, with a large fragment inversion (accounted for 68% genomic size) inside. The strain could not utilize urea due to truncation of the urea transporter gene. The lack of the pathways to synthesize usual compatible solutes makes it intolerant to high salinity (>0.03%), but could adapt to low salinity (0.005%) environments. This adaptation, together with possibly enhanced cell-biofilm attachment ability, makes it suitable for WWTPs environment. We propose the name “Candidatus Nitrosotenuis cloacae” for the strain SAT1. PMID:27030530

  16. Resequencing diverse Chinese indigenous breeds to enrich the map of genomic variations in swine.

    PubMed

    Kang, Huimin; Wang, Haifei; Fan, Ziyao; Zhao, Pengju; Khan, Amjad; Yin, Zongjun; Wang, Jiafu; Bao, Wenbin; Wang, Aiguo; Zhang, Qin; Liu, Jian-Feng

    2015-11-01

    To enrich the map of genomic variations in swine, we randomly sequenced 13 domestic and wild individuals from China and Europe. We detected approximately 28.1 million single nucleotide variants (SNVs) and 3.6 million short insertions and deletions (INDELs), of which 2,530,248 SNVs and 3,456,626 INDELs were firstly identified compared with dbSNP 143. Moreover, 208,687 SNVs and 24,161 INDELs were uniquely observed in Chinese pigs, potentially accounting for phenotypic differences between Chinese and European pigs. Furthermore, significantly high correlation between SNV and INDEL was witnessed, which indicated that these two distinct variants may share similar etiologies. We also predicted loss of function genes and found that they were under weaker evolutionary constraints. This study gives interesting insights into the genomic features of the Chinese pig breeds. These data would be useful in the establishment of high-density SNP map and would lay a foundation for facilitating pig functional genomics study. PMID:26296457

  17. High-throughput microsatellite marker development for the distylous herb Primula mistassinica (Primulaceae)1

    PubMed Central

    Matheny, Hannah; Edwards, Joan; Maroja, Luana S.

    2013-01-01

    • Premise of the study: Twelve microsatellite markers were developed for Primula mistassinica, a distylous, diploid arctic-alpine plant. The markers will be used to investigate the landscape genetics of a disjunct population on Isle Royale, Michigan, and the phylogeographic patterns of the species. • Methods and Results: We used Roche/454 high-throughput technology to sequence microsatellite-enriched regions in the P. mistassinica genome. We developed 12 polymorphic microsatellite primer sets. These loci contained di-, tri-, and tetranucleotide repeats with two to nine alleles per locus when assessed in 23 individuals. • Conclusions: Understanding the historical movements of P. mistassinica will provide insight to the survival prospects of current Arctic plant populations, which face the pressures of global, anthropogenic climate change. PMID:25202573

  18. Isolation and characterization of eight polymorphic microsatellites for the spotted spiny lobster, Panulirus guttatus.

    PubMed

    Truelove, Nathan; Behringer, Donald C; Butler Iv, Mark J; Preziosi, Richard F

    2016-01-01

    Microsatellite sequences were isolated from enriched genomic libraries of the spotted spiny lobster, Panulirus guttatus using 454 pyrosequencing. Twenty-nine previously developed polymerase chain reaction primer pairs of Panulirus argus microsatellite loci were also tested for cross-species amplification in Panulirus guttatus. In total, eight consistently amplifying, and polymorphic loci were characterized for 57 individuals collected in the Florida Keys and Bermuda. The number of alleles per locus ranged from 8 to 20 and observed heterozygosities ranged from 0.409 to 0.958. Significant deviations from Hardy-Weinberg equilibrium were found in one locus from Florida and three loci from Bermuda. Quality control testing indicated that all loci were easy to score, highly polymorphic and showed no evidence of linkage disequilibrium. Null alleles were detected in three loci with moderate frequencies ranging from (20% to 22%). These eight microsatellites provide novel molecular markers for future conservation genetics research of P. guttatus. PMID:26855853

  19. DNA microsatellite markers for Swartzia glazioviana (Fabaceae), a threatened species from the Brazilian Atlantic Forest1

    PubMed Central

    Spoladore, Janaína; Mansano, Vidal F.; Dias de Freitas, Luan C.; Sebbenn, Alexandre M.; Lemes, Maristerra R.

    2016-01-01

    Premise of the study: Development and characterization of a set of DNA microsatellite markers for Swartzia glazioviana (Fabaceae), a naturally rare and threatened tree species, were carried out to investigate its conservation genetics. Methods and Results: Through an enriched genomic library procedure, 10 DNA microsatellite loci were isolated and characterized for the species. The mean expected heterozygosity was 0.776 (0.424–0.894). Cross-species amplifications of these loci were successfully tested for six congener taxa (S. apetala var. apetala, S. flaemingii, S. langsdorffii, S. macrostachya, S. myrtifolia var. elegans, and S. simplex var. continentalis). Conclusions: The 10 polymorphic microsatellite markers developed are quite informative and will provide a valuable resource to study the population and conservation genetics of S. glazioviana and other Swartzia species. PMID:26949573

  20. Genetic variation at microsatellite loci in the tropical herb Aphelandra aurantiaca (Acanthaceae)1

    PubMed Central

    Suárez-Montes, Pilar; Tapia-López, Rosalinda; Núñez-Farfán, Juan

    2015-01-01

    Premise of the study: To assess the effect of forest fragmentation on genetic variation and population structure of Aphelandra aurantiaca (Acanthaceae), a tropical and ornamental herbaceous perennial plant, we developed the first microsatellite primers for the species. Methods and Results: Fourteen microsatellite markers were isolated and characterized from A. aurantiaca genomic libraries enriched for di-, tri-, and tetranucleotide repeat motifs. Polymorphism was evaluated in 107 individuals from four natural populations. Twelve out of 14 genetic markers were polymorphic. The number of alleles per locus ranged from two to 12, and the observed and expected heterozygosities ranged from 0.22 to 0.96 and from 0.20 to 0.87, respectively. Fixation indices ranged from −0.41 to 0.44. Conclusions: These newly developed microsatellite markers for A. aurantiaca will be useful for future population genetic studies, specifically to detect the possible loss of genetic diversity due to habitat fragmentation. PMID:26649265

  1. Development and characterization of microsatellite markers for the endangered Amazonian tree Aniba rosaeodora (Lauraceae)1

    PubMed Central

    Angrizani, Rafael C.; Contim, Luis A. S.; Lemes, Maristerra R.

    2013-01-01

    • Premise of the study: Microsatellite loci were isolated and characterized for Brazilian rosewood (Aniba rosaeodora), an endangered neotropical hardwood tree, to investigate population and conservation genetics of this highly valuable nontimber forest resource. • Methods and Results: We used an enriched genomic library method to isolate and characterize 11 nuclear microsatellite loci for A. rosaeodora, which exhibited an average of 9.6 and 8.7 alleles per locus in two populations from central Amazonia. Mean observed and expected heterozygosities over the 11 loci were 0.604 and 0.687, and 0.807 and 0.828, respectively, in the two populations. • Conclusions: The polymorphic microsatellite loci developed for A. rosaeodora showed highly informative content and can be used as a powerful tool in genetic diversity and population structure, gene flow, and mating system studies for conservation purposes. PMID:25202581

  2. Isolation and characterization of eight polymorphic microsatellites for the spotted spiny lobster, Panulirus guttatus

    PubMed Central

    Behringer, Donald C.; Butler IV, Mark J.; Preziosi, Richard F.

    2016-01-01

    Microsatellite sequences were isolated from enriched genomic libraries of the spotted spiny lobster, Panulirus guttatus using 454 pyrosequencing. Twenty-nine previously developed polymerase chain reaction primer pairs of Panulirus argus microsatellite loci were also tested for cross-species amplification in Panulirus guttatus. In total, eight consistently amplifying, and polymorphic loci were characterized for 57 individuals collected in the Florida Keys and Bermuda. The number of alleles per locus ranged from 8 to 20 and observed heterozygosities ranged from 0.409 to 0.958. Significant deviations from Hardy–Weinberg equilibrium were found in one locus from Florida and three loci from Bermuda. Quality control testing indicated that all loci were easy to score, highly polymorphic and showed no evidence of linkage disequilibrium. Null alleles were detected in three loci with moderate frequencies ranging from (20% to 22%). These eight microsatellites provide novel molecular markers for future conservation genetics research of P. guttatus. PMID:26855853

  3. Characterization of 32 novel microsatellite loci for population and mating system studies using Campostoma anomalum (central stoneroller).

    PubMed

    Landis, J B; Hudman, S P; Grose, M J; Skalski, G T; Wiley, E O

    2009-01-01

    The central stoneroller (Campostoma anomalum) is an abundant, widespread and sexually dimorphic stream minnow that is a useful model for mating system studies as well as a sentinel species for understanding population-level processes for fishes in headwater communities. We developed one genomic library enriched for dinucleotide repeats and isolated 48 putative, novel microsatellite loci. Of those, we present 32 polymorphic and independent microsatellite markers with 3 to 16 alleles per locus and heterozygosity ranging from 0.23 to 0.95. Hence, these markers will be useful for future behavioural, ecological and evolutionary studies using C. anomalum. PMID:21564618

  4. Genome-wide enrichment analysis between endometriosis and obesity-related traits reveals novel susceptibility loci

    PubMed Central

    Rahmioglu, Nilufer; Macgregor, Stuart; Drong, Alexander W.; Hedman, Åsa K.; Harris, Holly R.; Randall, Joshua C.; Prokopenko, Inga; Nyholt, Dale R.; Morris, Andrew P.; Montgomery, Grant W.; Missmer, Stacey A.; Lindgren, Cecilia M.; Zondervan, Krina T.

    2015-01-01

    Endometriosis is a chronic inflammatory condition in women that results in pelvic pain and subfertility, and has been associated with decreased body mass index (BMI). Genetic variants contributing to the heritable component have started to emerge from genome-wide association studies (GWAS), although the majority remain unknown. Unexpectedly, we observed an intergenic locus on 7p15.2 that was genome-wide significantly associated with both endometriosis and fat distribution (waist-to-hip ratio adjusted for BMI; WHRadjBMI) in an independent meta-GWAS of European ancestry individuals. This led us to investigate the potential overlap in genetic variants underlying the aetiology of endometriosis, WHRadjBMI and BMI using GWAS data. Our analyses demonstrated significant enrichment of common variants between fat distribution and endometriosis (P = 3.7 × 10−3), which was stronger when we restricted the investigation to more severe (Stage B) cases (P = 4.5 × 10−4). However, no genetic enrichment was observed between endometriosis and BMI (P = 0.79). In addition to 7p15.2, we identify four more variants with statistically significant evidence of involvement in both endometriosis and WHRadjBMI (in/near KIFAP3, CAB39L, WNT4, GRB14); two of these, KIFAP3 and CAB39L, are novel associations for both traits. KIFAP3, WNT4 and 7p15.2 are associated with the WNT signalling pathway; formal pathway analysis confirmed a statistically significant (P = 6.41 × 10−4) overrepresentation of shared associations in developmental processes/WNT signalling between the two traits. Our results demonstrate an example of potential biological pleiotropy that was hitherto unknown, and represent an opportunity for functional follow-up of loci and further cross-phenotype comparisons to assess how fat distribution and endometriosis pathogenesis research fields can inform each other. PMID:25296917

  5. Core and region-enriched networks of behaviorally regulated genes and the singing genome

    PubMed Central

    Whitney, Osceola; Pfenning, Andreas R.; Howard, Jason T.; Blatti, Charles A; Liu, Fang; Ward, James M.; Wang, Rui; Audet, Jean-Nicolas; Kellis, Manolis; Mukherjee, Sayan; Sinha, Saurabh; Hartemink, Alexander J.; West, Anne E.; Jarvis, Erich D.

    2015-01-01

    Songbirds represent an important model organism for elucidating molecular mechanisms that link genes with complex behaviors, in part because they have discrete vocal learning circuits that have parallels with those that mediate human speech. We found that ~10% of the genes in the avian genome were regulated by singing, and we found a striking regional diversity of both basal and singing-induced programs in the four key song nuclei of the zebra finch, a vocal learning songbird. The region-enriched patterns were a result of distinct combinations of region-enriched transcription factors (TFs), their binding motifs, and presinging acetylation of histone 3 at lysine 27 (H3K27ac) enhancer activity in the regulatory regions of the associated genes. RNA interference manipulations validated the role of the calcium-response transcription factor (CaRF) in regulating genes preferentially expressed in specific song nuclei in response to singing. Thus, differential combinatorial binding of a small group of activity-regulated TFs and predefined epigenetic enhancer activity influences the anatomical diversity of behaviorally regulated gene networks. PMID:25504732

  6. Genome-wide characterization of microsatellites in Cucumis hystrix and in silico identification of polymorphic SSR markers

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Cucumis hystrix (2n = 2x = 24, genome HH) is a wild relative of cucumber (C. sativus L., 2n = 2x = 14) that possesses multiple disease resistances and has a great potential for cucumber improvement. Despite its importance, there is no genomic resource currently available for C. hystrix. To expedite ...

  7. Utility of sequenced genomes for microsatellite marker development in non-model organisms: a case study of functionally important genes in nine-spined sticklebacks (Pungitius pungitius)

    PubMed Central

    2010-01-01

    Background Identification of genes involved in adaptation and speciation by targeting specific genes of interest has become a plausible strategy also for non-model organisms. We investigated the potential utility of available sequenced fish genomes to develop microsatellite (cf. simple sequence repeat, SSR) markers for functionally important genes in nine-spined sticklebacks (Pungitius pungitius), as well as cross-species transferability of SSR primers from three-spined (Gasterosteus aculeatus) to nine-spined sticklebacks. In addition, we examined the patterns and degree of SSR conservation between these species using their aligned sequences. Results Cross-species amplification success was lower for SSR markers located in or around functionally important genes (27 out of 158) than for those randomly derived from genomic (35 out of 101) and cDNA (35 out of 87) libraries. Polymorphism was observed at a large proportion (65%) of the cross-amplified loci independently of SSR type. To develop SSR markers for functionally important genes in nine-spined sticklebacks, SSR locations were surveyed in or around 67 target genes based on the three-spined stickleback genome and these regions were sequenced with primers designed from conserved sequences in sequenced fish genomes. Out of the 81 SSRs identified in the sequenced regions (44,084 bp), 57 exhibited the same motifs at the same locations as in the three-spined stickleback. Di- and trinucleotide SSRs appeared to be highly conserved whereas mononucleotide SSRs were less so. Species-specific primers were designed to amplify 58 SSRs using the sequences of nine-spined sticklebacks. Conclusions Our results demonstrated that a large proportion of SSRs are conserved in the species that have diverged more than 10 million years ago. Therefore, the three-spined stickleback genome can be used to predict SSR locations in the nine-spined stickleback genome. While cross-species utility of SSR primers is limited due to low amplification

  8. Microsatellites from Conyza canadensis (horseweed)

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Microsatellite loci were identified from Conyza canadensis (horseweed). Primer pairs for 64 loci were developed and of these eight were optimized and screened using genomic DNA from 22 accessions of horseweed from North America. Most loci were polymorphic and the number of alleles per locus ranged ...

  9. Development and characterization of microsatellite markers for Lychnophora pinaster: a study for the conservation of a native medicinal plant.

    PubMed

    Haber, L H; Cavallari, M M; Santos, F R C; Marques, M O M; Gimenes, M A; Zucchi, M I

    2009-05-01

    Lychnophora pinaster Mart. (Asteraceae) is a Brazilian medicinal plant, extensively employed in popular medicine as an anti-inflammatory, analgesic and healing agent. Thirteen polymorphic microsatellite markers were developed and optimized for L. pinaster from an enriched genomic library. The markers were used to analyse 37 plants from two native populations, generating an average number of 6.6 alleles per polymorphic locus. These loci are important tools for future studies of population genetics. PMID:21564752

  10. Novel microsatellite markers acquired from Rubus coreanus Miq. and cross-amplification in other Rubus species.

    PubMed

    Lee, Gi-An; Song, Jae Young; Choi, Heh-Ran; Chung, Jong-Wook; Jeon, Young-Ah; Lee, Jung-Ro; Ma, Kyung-Ho; Lee, Myung-Chul

    2015-01-01

    The Rubus genus consists of more than 600 species that are distributed globally. Only a few Rubus species, including raspberries and blueberries, have been domesticated. Genetic diversity within and between Rubus species is an important resource for breeding programs. We developed genomic microsatellite markers using an SSR-enriched R. coreanus library to study the diversity of the Rubus species. Microsatellite motifs were discovered in 546 of 646 unique clones, and a dinucleotide repeat was the most frequent (75.3%) type of repeat. From 97 microsatellite loci with reproducible amplicons, we acquired 29 polymorphic microsatellite markers in the Rubus coreanus collection. The transferability values ranged from 59.8% to 84% across six Rubus species, and Rubus parvifolius had the highest transferability value (84%). The average number of alleles and the polymorphism information content were 5.7 and 0.541, respectively, in the R. coreanus collection. The diversity index of R. coreanus was similar to the values reported for other Rubus species. A phylogenetic dendrogram based on SSR profiles revealed that seven Rubus species could be allocated to three groups, and that R. coreanus was genetically close to Rubus crataegifolius (mountain berry). These new microsatellite markers might prove useful in studies of the genetic diversity, population structure, and evolutionary relationships among Rubus species. PMID:25867828

  11. Chronic periodontitis genome-wide association studies: gene-centric and gene set enrichment analyses.

    PubMed

    Rhodin, K; Divaris, K; North, K E; Barros, S P; Moss, K; Beck, J D; Offenbacher, S

    2014-09-01

    Recent genome-wide association studies (GWAS) of chronic periodontitis (CP) offer rich data sources for the investigation of candidate genes, functional elements, and pathways. We used GWAS data of CP (n = 4,504) and periodontal pathogen colonization (n = 1,020) from a cohort of adult Americans of European descent participating in the Atherosclerosis Risk in Communities study and employed a MAGENTA approach (i.e., meta-analysis gene set enrichment of variant associations) to obtain gene-centric and gene set association results corrected for gene size, number of single-nucleotide polymorphisms, and local linkage disequilibrium characteristics based on the human genome build 18 (National Center for Biotechnology Information build 36). We used the Gene Ontology, Ingenuity, KEGG, Panther, Reactome, and Biocarta databases for gene set enrichment analyses. Six genes showed evidence of statistically significant association: 4 with severe CP (NIN, p = 1.6 × 10(-7); ABHD12B, p = 3.6 × 10(-7); WHAMM, p = 1.7 × 10(-6); AP3B2, p = 2.2 × 10(-6)) and 2 with high periodontal pathogen colonization (red complex-KCNK1, p = 3.4 × 10(-7); Porphyromonas gingivalis-DAB2IP, p = 1.0 × 10(-6)). Top-ranked genes for moderate CP were HGD (p = 1.4 × 10(-5)), ZNF675 (p = 1.5 × 10(-5)), TNFRSF10C (p = 2.0 × 10(-5)), and EMR1 (p = 2.0 × 10(-5)). Loci containing NIN, EMR1, KCNK1, and DAB2IP had showed suggestive evidence of association in the earlier single-nucleotide polymorphism-based analyses, whereas WHAMM and AP2B2 emerged as novel candidates. The top gene sets included severe CP ("endoplasmic reticulum membrane," "cytochrome P450," "microsome," and "oxidation reduction") and moderate CP ("regulation of gene expression," "zinc ion binding," "BMP signaling pathway," and "ruffle"). Gene-centric analyses offer a promising avenue for efficient interrogation of large-scale GWAS data. These results highlight genes in previously identified loci and new candidate genes and pathways

  12. Ontology and diversity of transcript-associated microsatellites mined from a globe artichoke EST database

    PubMed Central

    Scaglione, Davide; Acquadro, Alberto; Portis, Ezio; Taylor, Christopher A; Lanteri, Sergio; Knapp, Steven J

    2009-01-01

    Background The globe artichoke (Cynara cardunculus var. scolymus L.) is a significant crop in the Mediterranean basin. Despite its commercial importance and its both dietary and pharmaceutical value, knowledge of its genetics and genomics remains scant. Microsatellite markers have become a key tool in genetic and genomic analysis, and we have exploited recently acquired EST (expressed sequence tag) sequence data (Composite Genome Project - CGP) to develop an extensive set of microsatellite markers. Results A unigene assembly was created from over 36,000 globe artichoke EST sequences, containing 6,621 contigs and 12,434 singletons. Over 12,000 of these unigenes were functionally assigned on the basis of homology with Arabidopsis thaliana reference proteins. A total of 4,219 perfect repeats, located within 3,308 unigenes was identified and the gene ontology (GO) analysis highlighted some GO term's enrichments among different classes of microsatellites with respect to their position. Sufficient flanking sequence was available to enable the design of primers to amplify 2,311 of these microsatellites, and a set of 300 was tested against a DNA panel derived from 28 C. cardunculus genotypes. Consistent amplification and polymorphism was obtained from 236 of these assays. Their polymorphic information content (PIC) ranged from 0.04 to 0.90 (mean 0.66). Between 176 and 198 of the assays were informative in at least one of the three available mapping populations. Conclusion EST-based microsatellites have provided a large set of de novo genetic markers, which show significant amounts of polymorphism both between and within the three taxa of C. cardunculus. They are thus well suited as assays for phylogenetic analysis, the construction of genetic maps, marker-assisted breeding, transcript mapping and other genomic applications in the species. PMID:19785740

  13. Genome-wide linkage disequilibruim revealed by microsatellite markers and association study of fiber quality traits in cotton

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The application of association mapping based on existing genome-wide linkage disequilibrium (LD) between DNA polymorphisms and genes underlying traits is becoming powerful tool that overcome many limitations (high cost, poor resolution, requirement for bi-parentally crossed lines assessing only two ...

  14. BAC-End Microsatellites from Intra and Inter-Genic Regions of the Common Bean Genome and Their Correlation with Cytogenetic Features

    PubMed Central

    Blair, Matthew Wohlgemuth; Córdoba, Juana Marcela; Muñóz, Claritza; Yuyó, Deissy K.

    2014-01-01

    Highly polymorphic markers such as simple sequence repeats (SSRs) or microsatellites are very useful for genetic mapping. In this study novel SSRs were identified in BAC-end sequences (BES) from non-contigged, non-overlapping bacterial artificial clones (BACs) in common bean (Phaseolus vulgaris L.). These so called “singleton” BACs were from the G19833 Andean gene pool physical map and the new BES-SSR markers were used for the saturation of the inter-gene pool, DOR364×G19833 genetic map. A total of 899 SSR loci were found among the singleton BES, but only 346 loci corresponded to the single di- or tri-nucleotide motifs that were likely to be polymorphic (ATT or AG motifs, principally) and useful for primer design and individual marker mapping. When these novel SSR markers were evaluated in the DOR364×G19833 population parents, 136 markers revealed polymorphism and 106 were mapped. Genetic mapping resulted in a map length of 2291 cM with an average distance between markers of 5.2 cM. The new genetic map was compared to the most recent cytogenetic analysis of common bean chromosomes. We found that the new singleton BES-SSR were helpful in filling peri-centromeric spaces on the cytogenetic map. Short genetic distances between some new singleton-derived BES-SSR markers was common showing suppressed recombination in these regions compared to other parts of the genome. The correlation of singleton-derived SSR marker distribution with other cytogenetic features of the bean genome is discussed. PMID:25254501

  15. Conservation of Human Microsatellites across 450 Million Years of Evolution

    PubMed Central

    Buschiazzo, Emmanuel; Gemmell, Neil J.

    2010-01-01

    The sequencing and comparison of vertebrate genomes have enabled the identification of widely conserved genomic elements. Chief among these are genes and cis-regulatory regions, which are often under selective constraints that promote their retention in related organisms. The conservation of elements that either lack function or whose functions are yet to be ascribed has been relatively little investigated. In particular, microsatellites, a class of highly polymorphic repetitive sequences considered by most to be neutrally evolving junk DNA that is too labile to be maintained in distant species, have not been comprehensively studied in a comparative genomic framework. Here, we used the UCSC alignment of the human genome against those of 11 mammalian and five nonmammalian vertebrates to identify and examine the extent of conservation of human microsatellites in vertebrate genomes. Out of 696,016 microsatellites found in human sequences, 85.39% were conserved in at least one other species, whereas 28.65% and 5.98% were found in at least one and three nonprimate species, respectively. An exponential decline of microsatellite conservation with increasing evolutionary time, a comparable distribution of conserved versus nonconserved microsatellites in the human genome, and a positive correlation between microsatellite conservation and overall sequence conservation, all suggest that most microsatellites are only maintained in genomes by chance, although exceptionally conserved human microsatellites were also found in distant mammals and other vertebrates. Our findings provide the first comprehensive survey of microsatellite conservation across deep evolutionary timescales, in this case 450 Myr of vertebrate evolution, and provide new tools for the identification of functional conserved microsatellites, the development of cross-species microsatellite markers and the study of microsatellite evolution above the species level. PMID:20333231

  16. Polymorphic microsatellites for forensic identification of agarwood (Aquilaria crassna).

    PubMed

    Eurlings, Marcel C M; van Beek, Henry Heuveling; Gravendeel, Barbara

    2010-04-15

    Tropical agarwood (Aquilaria) is in danger of extinction in the wild due to illegal logging. Its resin (Gaharu) is used for the production of highly valued incense throughout Asia. We have isolated and characterized microsatellite loci of Aquilaria crassna to detect the geographic origin of agarwood for forensic applications using a modified enrichment procedure based on the capture of repetitive sequences from restricted genomic DNA. We assessed the polymorphisms of five microsatellites amplified from fresh leaves of 22 trees from seven plantations in Vietnam and Thailand and dried leaves of a herbarium specimen of one wild tree. Cross specificity of these markers was confirmed on two related Aquilaria species occurring in China and Vietnam and one microsatellite locus was successfully amplified from wood and incense samples. Four of the loci were polymorphic and the number of alleles ranged from 3 to 15. The loci characterized here can provide a starting point for forensic identification of traded material and certification of sustainably produced agarwood. PMID:20056366

  17. Microsatellite marker development in the protozoan parasite Perkinsus olseni.

    PubMed

    Pardo, Belén G; Cao, Asunción; Vilas, Roman; Abollo, Elvira; Villalba, Antonio; Martínez, Paulino

    2011-04-01

    The analysis of an enriched partial genomic library and of public expressed sequence tag (EST) resources allowed the characterization of the first microsatellite loci in the protozoan parasite Perkinsus olseni. Clonal cultures from laboratory isolates derived from infected clams Ruditapes decussatus (from Spain), R. philippinarum (from Spain and Japan), and Austrovenus stutchburyi (from New Zealand) were used for the characterization of 12 microsatellites. Low variation was detected at most loci, with the number of alleles at polymorphic loci ranging from 2 to 7 (average 3.20 +/- 0.51) and gene diversity from 0.11 to 0.79 (average 0.40 +/- 0.07). Preliminary results show that (1) isolates of P. olseni are diploid cells, and (2) multiple infections can occur within a single host. Eight of the loci analyzed successfully cross-amplified in the congeneric species P. mediterraneus. These microsatellite markers will be useful to analyze in detail the population genetic structure of P. olseni, crucial for the efficient management of this parasitic disease. PMID:21648245

  18. Microsatellite primers for Parkia biglobosa (Fabaceae: Mimosoideae) reveal that a single plant sires all seeds per pod1

    PubMed Central

    Lassen, Kristin Marie; Kjær, Erik Dahl; Ouédraogo, Moussa; Nielsen, Lene Rostgaard

    2014-01-01

    • Premise of the study: Microsatellite primers were developed for an indigenous fruit tree, Parkia biglobosa, as a tool to study reproductive biology and population structure. Here we use the primers to determine the number of fathers per pod. • Methods and Results: Microsatellite loci were enriched in a genomic sample and isolated using pyrosequencing. Eleven primer pairs were characterized in two populations of P. biglobosa in Burkina Faso (each with 40 trees). The number of alleles per locus ranged from eight to 15, and one locus had null alleles. We genotyped seeds from 24 open-pollinated pods. The genotypic profiles of seeds per pod suggest that all seeds are outcrossed and that only one pollen donor sires all ovules in a single fruit. • Conclusions: Ten microsatellite markers were highly polymorphic. All seeds per pod of P. biglobosa were full siblings. The markers will be useful for reproductive and population genetic studies. PMID:25202634

  19. Genome Sequence of Candidatus Nitrososphaera evergladensis from Group I.1b Enriched from Everglades Soil Reveals Novel Genomic Features of the Ammonia-Oxidizing Archaea

    PubMed Central

    Zhalnina, Kateryna V.; Dias, Raquel; Leonard, Michael T.; Dorr de Quadros, Patricia; Camargo, Flavio A. O.; Drew, Jennifer C.; Farmerie, William G.; Daroub, Samira H.; Triplett, Eric W.

    2014-01-01

    The activity of ammonia-oxidizing archaea (AOA) leads to the loss of nitrogen from soil, pollution of water sources and elevated emissions of greenhouse gas. To date, eight AOA genomes are available in the public databases, seven are from the group I.1a of the Thaumarchaeota and only one is from the group I.1b, isolated from hot springs. Many soils are dominated by AOA from the group I.1b, but the genomes of soil representatives of this group have not been sequenced and functionally characterized. The lack of knowledge of metabolic pathways of soil AOA presents a critical gap in understanding their role in biogeochemical cycles. Here, we describe the first complete genome of soil archaeon Candidatus Nitrososphaera evergladensis, which has been reconstructed from metagenomic sequencing of a highly enriched culture obtained from an agricultural soil. The AOA enrichment was sequenced with the high throughput next generation sequencing platforms from Pacific Biosciences and Ion Torrent. The de novo assembly of sequences resulted in one 2.95 Mb contig. Annotation of the reconstructed genome revealed many similarities of the basic metabolism with the rest of sequenced AOA. Ca. N. evergladensis belongs to the group I.1b and shares only 40% of whole-genome homology with the closest sequenced relative Ca. N. gargensis. Detailed analysis of the genome revealed coding sequences that were completely absent from the group I.1a. These unique sequences code for proteins involved in control of DNA integrity, transporters, two-component systems and versatile CRISPR defense system. Notably, genomes from the group I.1b have more gene duplications compared to the genomes from the group I.1a. We suggest that the presence of these unique genes and gene duplications may be associated with the environmental versatility of this group. PMID:24999826

  20. Genome sequence of Candidatus Nitrososphaera evergladensis from group I.1b enriched from Everglades soil reveals novel genomic features of the ammonia-oxidizing archaea.

    PubMed

    Zhalnina, Kateryna V; Dias, Raquel; Leonard, Michael T; Dorr de Quadros, Patricia; Camargo, Flavio A O; Drew, Jennifer C; Farmerie, William G; Daroub, Samira H; Triplett, Eric W

    2014-01-01

    The activity of ammonia-oxidizing archaea (AOA) leads to the loss of nitrogen from soil, pollution of water sources and elevated emissions of greenhouse gas. To date, eight AOA genomes are available in the public databases, seven are from the group I.1a of the Thaumarchaeota and only one is from the group I.1b, isolated from hot springs. Many soils are dominated by AOA from the group I.1b, but the genomes of soil representatives of this group have not been sequenced and functionally characterized. The lack of knowledge of metabolic pathways of soil AOA presents a critical gap in understanding their role in biogeochemical cycles. Here, we describe the first complete genome of soil archaeon Candidatus Nitrososphaera evergladensis, which has been reconstructed from metagenomic sequencing of a highly enriched culture obtained from an agricultural soil. The AOA enrichment was sequenced with the high throughput next generation sequencing platforms from Pacific Biosciences and Ion Torrent. The de novo assembly of sequences resulted in one 2.95 Mb contig. Annotation of the reconstructed genome revealed many similarities of the basic metabolism with the rest of sequenced AOA. Ca. N. evergladensis belongs to the group I.1b and shares only 40% of whole-genome homology with the closest sequenced relative Ca. N. gargensis. Detailed analysis of the genome revealed coding sequences that were completely absent from the group I.1a. These unique sequences code for proteins involved in control of DNA integrity, transporters, two-component systems and versatile CRISPR defense system. Notably, genomes from the group I.1b have more gene duplications compared to the genomes from the group I.1a. We suggest that the presence of these unique genes and gene duplications may be associated with the environmental versatility of this group. PMID:24999826

  1. SNP-based pathway enrichment analysis for genome-wide association studies

    PubMed Central

    2011-01-01

    Background Recently we have witnessed a surge of interest in using genome-wide association studies (GWAS) to discover the genetic basis of complex diseases. Many genetic variations, mostly in the form of single nucleotide polymorphisms (SNPs), have been identified in a wide spectrum of diseases, including diabetes, cancer, and psychiatric diseases. A common theme arising from these studies is that the genetic variations discovered by GWAS can only explain a small fraction of the genetic risks associated with the complex diseases. New strategies and statistical approaches are needed to address this lack of explanation. One such approach is the pathway analysis, which considers the genetic variations underlying a biological pathway, rather than separately as in the traditional GWAS studies. A critical challenge in the pathway analysis is how to combine evidences of association over multiple SNPs within a gene and multiple genes within a pathway. Most current methods choose the most significant SNP from each gene as a representative, ignoring the joint action of multiple SNPs within a gene. This approach leads to preferential identification of genes with a greater number of SNPs. Results We describe a SNP-based pathway enrichment method for GWAS studies. The method consists of the following two main steps: 1) for a given pathway, using an adaptive truncated product statistic to identify all representative (potentially more than one) SNPs of each gene, calculating the average number of representative SNPs for the genes, then re-selecting the representative SNPs of genes in the pathway based on this number; and 2) ranking all selected SNPs by the significance of their statistical association with a trait of interest, and testing if the set of SNPs from a particular pathway is significantly enriched with high ranks using a weighted Kolmogorov-Smirnov test. We applied our method to two large genetically distinct GWAS data sets of schizophrenia, one from European

  2. Complete genome sequence of Methylophilus sp. TWE2 isolated from methane oxidation enrichment culture of tap-water.

    PubMed

    Xia, Fei; Zou, Bin; Shen, Cong; Zhu, Ting; Gao, Xin-Hua; Quan, Zhe-Xue

    2015-10-10

    The non-methane-utilizing methylotroph, Methylophilus sp. TWE2, was isolated from tap-water during the enrichment of methanotrophs with methane. The complete genome sequence of strain TWE2 showed that this bacterium may convert methanol to formaldehyde via catalysis of methanol dehydrogenase (MDH), after which formaldehyde would be assimilated to biomass through the ribulose monophosphate (RuMP) pathway or dissimilated via the tetrahydromethanopterin (H4MPT) pathway. The deficiency of glycolysis and the TCA cycle indicate that strain TWE2 may be an obligate methylotroph. This is the first complete genome sequence of the genus Methylophilus. PMID:26253961

  3. ZINBA integrates local covariates with DNA-seq data to identify broad and narrow regions of enrichment, even within amplified genomic regions

    PubMed Central

    2011-01-01

    ZINBA (Zero-Inflated Negative Binomial Algorithm) identifies genomic regions enriched in a variety of ChIP-seq and related next-generation sequencing experiments (DNA-seq), calling both broad and narrow modes of enrichment across a range of signal-to-noise ratios. ZINBA models and accounts for factors that co-vary with background or experimental signal, such as G/C content, and identifies enrichment in genomes with complex local copy number variations. ZINBA provides a single unified framework for analyzing DNA-seq experiments in challenging genomic contexts. Software website: http://code.google.com/p/zinba/ PMID:21787385

  4. Isolation and characterization of microsatellite markers in the Serra Spanish mackerel, Scomberomorus brasiliensis

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Thirteen nuclear-encoded microsatellites from a genomic DNA library of Serra Spanish mackerel, Scomberomorus brasiliensis, were isolated and characterized. The microsatellites include 10 perfect repeats (8 tetranucleotide and 2 dinucleotide) and 3 imperfect repeats (2 tetranucleotide and 1 dinucleo...

  5. Survey and analysis of simple sequence repeats in the Ustilaginoidea virens genome and the development of microsatellite markers.

    PubMed

    Yu, Mina; Yu, Junjie; Li, Huanhuan; Wang, Yahui; Yin, Xiaole; Bo, Huiwen; Ding, Hui; Zhou, Yuxin; Liu, Yongfeng

    2016-07-01

    Ustilaginoidea virens is the causal agent of rice false smut, causing quantitative and qualitative losses in rice industry. However, the development and application of simple sequence repeat (SSR) markers for genetic diversity studies in U. virens were limited. This study is the first to perform large-scale development of SSR markers of this pathogen at the genome level, to (1) compare these SSR markers with those of other fungi, (2) analyze the pattern of the SSRs, and (3) obtain more informative genetic markers. U. virens is rich in SSRs, and 13,778 SSRs were identified with a relative abundance of 349.7SSRs/Mb. The most common motifs in the genome or in noncoding regions were mononucleotides, whereas trinucleotides in coding sequences. A total of 6 out of 127 primers were randomly selected to be used to analyze 115 isolates, and these 6 primers showed high polymorphism in U. virens. This study may serve as an important resource for molecular genetic studies in U. virens. PMID:26992636

  6. Rapid microsatellite development for tree peony and its implications

    PubMed Central

    2013-01-01

    Background Microsatellites are ubiquitous in genomes of various organisms. With the realization that they play roles in developmental and physiological processes, rather than exist as ‘junk’ DNA, microsatellites are receiving increasing attention. Next-generation sequencing allows acquisition of large-scale microsatellite information, and is especially useful for plants without reference genome sequences. Results In this study, enriched DNA libraries of tree peony, a well-known ornamental woody shrub, were used for high-throughput microsatellite development by 454 GS-FLX Titanium pyrosequencing. We obtained 675,221 reads with an average length of 356 bp. The total size of examined sequences was 240,672,018 bp, from which 237,134 SSRs were identified. Of these sequences, 164,043 contained SSRs, with 27% featuring more than one SSR. Interestingly, a high proportion of SSRs (43%) were present in compound formation. SSRs with repeat motifs of 1–4 bp (mono-, di-, tri-, and tetra-nucleotide repeats) accounted for 99.8% of SSRs. Di-nucleotide repeats were the most abundant. As in most plants, the predominant motif in tree peony was (A/T)n, with (G/C)n less common. The lengths of SSRs were classified into 11 groups. The shortest SSRs (10 bp) represented 1% of the total number, whereas SSRs 21–30 and 101–110 bp long accounted for 26% and 29%, respectively, of all SSRs. Many sequences (42,111) were mapped to CDS (coding domain sequence) regions using Arabidopsis as a reference. GO annotation analysis predicted that CDSs with SSRs performed various functions associated with cellular components, molecular functions, and biological processes. Of 100 validated primer pairs, 24 were selected for polymorphism analysis among 23 genotypes; cluster analysis of the resulting data grouped genotypes according to known relationships, confirming the usefulness of the developed SSR markers. Conclusions The results of our large-scale SSR marker development using tree peony

  7. Divergent microsatellite evolution in the human and chimpanzee lineages.

    PubMed

    Gáspári, Zoltán; Ortutay, Csaba; Tóth, Gábor

    2007-05-29

    Comparison of the complete human genome sequence to one of its closest relatives, the chimpanzee genome, provides a unique opportunity for exploring recent evolutionary events affecting the microsatellites in these species. A simple assumption on microsatellite distribution is that the total length of perfect repeats is constant compared to that of imperfect ones regardless of the repeat sequence. In this paper, we show that this is valid for most of the chimpanzee genome but not for a number of human chromosomes. Our results suggest accelerated evolution of microsatellites in the human genome relative to the chimpanzee lineage. PMID:17498704

  8. Mining online genomic resources in Anolis carolinensis facilitates rapid and inexpensive development of cross-species microsatellite markers for the Anolis lizard genus.

    PubMed

    Wordley, Claire; Slate, Jon; Stapley, Jessica

    2011-01-01

    Online sequence databases can provide valuable resources for the development of cross-species genetic markers. In particular, mining expressed tag sequences (EST) for microsatellites and developing conserved cross-species microsatellite markers can provide a rapid and relatively inexpensive method to develop new markers for a range of species. Here, we adopt this approach to develop cross-species microsatellite markers in Anolis lizards, which is a model genus in evolutionary biology and ecology. Using EST sequences from Anolis carolinensis, we identified 127 microsatellites that satisfied our criteria, and tested 49 of these in five species of Anolis (carolinensis, distichus, apletophallus, porcatus and sagrei). We identified between 8 and 25 new variable genetic markers for five Anolis species. These markers will be a valuable resource for studies of population genetics, comparative mapping, mating systems, behavioural ecology and adaptive radiations in this diverse lineage. PMID:21429109

  9. Batch Isolation of Microsatellites for Tropical Plant Species Pyrosequencing

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Microsatellites were developed for ten tropical species using a method recently developed in our laboratory that involves a combination of two adapters at the SSR-enrichment stage and allows for cost saving and simultaneous loading of samples. The species for which microsatellites were isolated are...

  10. Draft Genome Sequence of Paenibacillus sp. Strain DMB5, Acclimatized and Enriched for Catabolizing Anthropogenic Compounds

    PubMed Central

    Johnson, Jenny; Shah, Binal; Jain, Kunal; Parmar, Nidhi; Hinsu, Ankit; Patel, Namrata

    2016-01-01

    Here, we present the draft genome sequence of Paenibacillus sp. strain DMB5, isolated from polluted sediments of the Kharicut Canal, Vatva, India, having a genome size of 7.5 Mbp and 7,077 coding sequences. The genome of this dye-degrading bacterium provides valuable information on the microbe-mediated biodegradation of anthropogenic compounds. PMID:27034501

  11. High frequency of submicroscopic chromosomal imbalances in patients with syndromic craniosynostosis detected by a combined approach of microsatellite segregation analysis, multiplex ligation-dependent probe amplification and array-based comparative genome hybridisation.

    PubMed

    Jehee, F S; Krepischi-Santos, A C V; Rocha, K M; Cavalcanti, D P; Kim, C A; Bertola, D R; Alonso, L G; D'Angelo, C S; Mazzeu, J F; Froyen, G; Lugtenberg, D; Vianna-Morgante, A M; Rosenberg, C; Passos-Bueno, M R

    2008-07-01

    We present the first comprehensive study, to our knowledge, on genomic chromosomal analysis in syndromic craniosynostosis. In total, 45 patients with craniosynostotic disorders were screened with a variety of methods including conventional karyotype, microsatellite segregation analysis, subtelomeric multiplex ligation-dependent probe amplification) and whole-genome array-based comparative genome hybridisation. Causative abnormalities were present in 42.2% (19/45) of the samples, and 27.8% (10/36) of the patients with normal conventional karyotype carried submicroscopic imbalances. Our results include a wide variety of imbalances and point to novel chromosomal regions associated with craniosynostosis. The high incidence of pure duplications or trisomies suggests that these are important mechanisms in craniosynostosis, particularly in cases involving the metopic suture. PMID:18456720

  12. Development of microsatellite loci for the endangered species Pityopsis ruthii (Asteraceae)1

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Premise of the study: Microsatellite loci were developed for the endangered species Pityopsis ruthii and will permit genetic and conservation studies of the species. Methods and Results:A microsatellite enriched library was used to develop 12 polymorphic microsatellite loci for P. ruthii. The loci ...

  13. Isolation and characterization of microsatellite Loci for Cornus sanguniea (Cornaceae) 1

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Premise of the study: Microsatellite loci were developed for Cornus sanguinea and will permit genetic and conservation studies of the species. Methods and Results: A microsatellite-enriched library was used to develop 16 polymorphic microsatellite loci for C. sanguinea. The loci amplified 5-11 allel...

  14. Development and characterization of microsatellite primers in Pogostemon cablin (Lamiaceae).

    PubMed

    Sandes, S S; Pinheiro, J B; Zucchi, M I; Monteiro, M; Arrigoni-Blank, M F; Blank, A F

    2013-01-01

    Microsatellite primers were developed and optimized for patchouli (Pogostemon cablin) to characterize the patchouli Active Germplasm Bank of Universidade Federal de Sergipe. Creation of a genomic library for patchouli enabled the design of 12 microsatellite primers. Six of these microsatellites were polymorphic, revealing two well-defined groups of individuals that possess exclusive alleles. The data allowed us to characterize the patchouli active Germplasm Bank, identify its genetic diversity, and provide new information for researching this species. PMID:24065640

  15. Pulling out the 1%: Whole-Genome Capture for the Targeted Enrichment of Ancient DNA Sequencing Libraries

    PubMed Central

    Carpenter, Meredith L.; Buenrostro, Jason D.; Valdiosera, Cristina; Schroeder, Hannes; Allentoft, Morten E.; Sikora, Martin; Rasmussen, Morten; Gravel, Simon; Guillén, Sonia; Nekhrizov, Georgi; Leshtakov, Krasimir; Dimitrova, Diana; Theodossiev, Nikola; Pettener, Davide; Luiselli, Donata; Sandoval, Karla; Moreno-Estrada, Andrés; Li, Yingrui; Wang, Jun; Gilbert, M. Thomas P.; Willerslev, Eske; Greenleaf, William J.; Bustamante, Carlos D.

    2013-01-01

    Most ancient specimens contain very low levels of endogenous DNA, precluding the shotgun sequencing of many interesting samples because of cost. Ancient DNA (aDNA) libraries often contain <1% endogenous DNA, with the majority of sequencing capacity taken up by environmental DNA. Here we present a capture-based method for enriching the endogenous component of aDNA sequencing libraries. By using biotinylated RNA baits transcribed from genomic DNA libraries, we are able to capture DNA fragments from across the human genome. We demonstrate this method on libraries created from four Iron Age and Bronze Age human teeth from Bulgaria, as well as bone samples from seven Peruvian mummies and a Bronze Age hair sample from Denmark. Prior to capture, shotgun sequencing of these libraries yielded an average of 1.2% of reads mapping to the human genome (including duplicates). After capture, this fraction increased substantially, with up to 59% of reads mapped to human and enrichment ranging from 6- to 159-fold. Furthermore, we maintained coverage of the majority of regions sequenced in the precapture library. Intersection with the 1000 Genomes Project reference panel yielded an average of 50,723 SNPs (range 3,062–147,243) for the postcapture libraries sequenced with 1 million reads, compared with 13,280 SNPs (range 217–73,266) for the precapture libraries, increasing resolution in population genetic analyses. Our whole-genome capture approach makes it less costly to sequence aDNA from specimens containing very low levels of endogenous DNA, enabling the analysis of larger numbers of samples. PMID:24568772

  16. Isolation and characterization of microsatellite loci for Bixa orellana, an important source of natural dyes.

    PubMed

    Dequigiovanni, G; Ramos, S L F; Zucchi, M I; Bajay, M M; Pinheiro, J B; Fabri, E G; Bressan, E A; Veasey, E A

    2014-01-01

    Annatto (Bixa orellana) is a plant native from the American continental tropical zone. The seeds are used to produce a carotenoid-based yellow to orange food coloring. Microsatellite markers were developed for the Brazilian native species Bixa orellana to describe its genetic diversity and structure as well as to support conservation studies. Twenty-five microsatellite loci were isolated and characterized using an enriched genomic library. Ten loci were polymorphic in the 50 accessions sampled in this study, while 15 were considered monomorphic. The mean number of alleles per locus was 3.8, ranging from 2 to 6 alleles per locus. Mean values for the observed and expected heterozygosities were 0.541 (ranging from 0 to 0.658) and 0.639 (ranging from 0.422 to 0.787), respectively. All markers described in this study will be useful in further studies evaluating the genetic diversity, population dynamics, and conservation genetics of Bixa orellana. PMID:25366801

  17. Isolation and characterization of 48 polymorphic microsatellite markers for the blood clam Scapharca broughtonii (Arcidae).

    PubMed

    Tian, J-T; Liu, Z-H; Zhou, L-Q; Wu, B; Liu, P; Yang, A-G

    2012-01-01

    Blood clams (Scapharca broughtonii) are widely cultivated and consumed in noutheast Asia. Forty-eight polymorphic microsatellite loci were developed for this clam using magnetic-bead hybridization enrichment. The number of alleles per locus ranged from 2 to 14. Polymorphism of these loci was assessed in 30 individuals from a population collected from coastal areas of Qingdao, China. The values of observed heterozygosity, expected heterozygosity and polymorphism information content per locus ranged from 0.1034 to 0.9655, from 0.1831 to 0.9208, and from 0.1638 to 0.8964, respectively. Forty-three of 48 loci conformed to Hardy-Weinberg equilibrium. These microsatellite loci would be useful for molecular genetic breeding, population genetics, genome mapping, and other relevant research on S. broughtonii. PMID:23096914

  18. Development and characterization of microsatellite markers for Piptadenia gonoacantha (Fabaceae)1

    PubMed Central

    Grando, Carolina; Bajay, Miklos M.; Bajay, Stephanie K.; Schwarcz, Kaiser D.; Campos, Jaqueline B.; Brancalion, Pedro H. S.; Pinheiro, José B.; Rodrigues, Ricardo R.; Souza, Anete P.; Zucchi, Maria I.

    2015-01-01

    • Premise of the study: Microsatellite primers were designed for Piptadenia gonoacantha (Fabaceae) and characterized to estimate genetic diversity parameters. The species is a native tree from the Atlantic Forest biome commonly used in forest restoration; it has medicinal potential and the wood is economically useful. • Methods and Results: Twenty-eight microsatellite loci were identified from an enriched genomic library. Fifteen loci resulted in successful amplifications and were characterized in a natural population of 94 individuals. Twelve loci were polymorphic, with allele numbers ranging from three to 15 per locus, and expected and observed heterozygosities ranging from 0.2142 to 0.8325 and 0.190 to 0.769, respectively. • Conclusions: The developed markers will be used in further studies of population genetics of P. gonoacantha, aimed at conservation and management of the species in natural populations and in forest restoration projects. PMID:25699220

  19. Isolation and Characterization of Twelve Polymorphic Microsatellite Loci for the Cocoa Mirid Bug Sahlbergella Singularis

    PubMed Central

    Babin, Régis; Fenouillet, Catherine; Legavre, Thierry; Blondin, Laurence; Calatayud, Caroline; Risterucci, Ange-Marie; Chapuis, Marie-Pierre

    2012-01-01

    Mirids are the primary pests affecting cocoa production in Africa, but no genetic studies have been conducted on these insects. Here we report the isolation and characterization of 12 polymorphic microsatellite loci for Sahlbergella singularis. A microsatellite-enriched genomic DNA library was developed and screened to identify marker loci. Twelve polymorphic loci were identified by screening 28 individuals collected from one presumed population in cocoa plantations in Southern Cameroon. The number of alleles ranged from 5 to 25, whereas the observed and the expected heterozygosities ranged from 0.179 to 0.786 and from 0.671 to 0.946, respectively. Tests showed significant deviations from HW equilibrium for four loci, but no linkage disequilibrium was detected at any of the loci. No cross-species amplification was observed in two other mirid pests in Africa. PMID:22605986

  20. Characterization of 10 new nuclear microsatellite markers in Acca sellowiana (Myrtaceae)1

    PubMed Central

    Klabunde, Gustavo H. F.; Olkoski, Denise; Vilperte, Vinicius; Zucchi, Maria I.; Nodari, Rubens O.

    2014-01-01

    • Premise of the study: Microsatellite primers were identified and characterized in Acca sellowiana in order to expand the limited number of pre-existing polymorphic markers for use in population genetic studies for conservation, phylogeography, breeding, and domestication. • Methods and Results: A total of 10 polymorphic microsatellite primers were designed from clones obtained from a simple sequence repeat (SSR)–enriched genomic library. The primers amplified di- and trinucleotide repeats with four to 27 alleles per locus. In all tested populations, the observed heterozygosity ranged from 0.269 to 1.0. • Conclusions: These new polymorphic SSR markers will allow future genetic studies to be denser, either for genetic structure characterization of natural populations or for studies involving genetic breeding and domestication process in A. sellowiana. PMID:25202632

  1. Development of 23 polymorphic microsatellite loci in invasive silver wattle, Acacia dealbata (Fabaceae)1

    PubMed Central

    Guillemaud, Thomas; Broadhurst, Linda; Legoff, Isabelle; Henery, Martin; Blin, Aurélie; Ducatillion, Catherine; Ferrando, Nathalie; Malausa, Thibaut

    2015-01-01

    Premise of the study: Microsatellite markers were developed for silver wattle, Acacia dealbata (Fabaceae), which is both an ornamental and an invasive weed species. It is native to southeastern Australia and invasive in Europe, Africa, Asia, and the Americas. Methods and Results: The pyrosequencing of a microsatellite-enriched genomic DNA library of A. dealbata produced 33,290 sequences and allowed the isolation of 201 loci with a minimum of seven repeats of microsatellite motifs. Amplification tests led to the setup of two multiplex PCR mixes allowing the amplification of 21 loci. The polymorphism of these markers was evaluated on a sample of 32 individuals collected in southeastern Australia. The number of alleles and the expected heterozygosity varied between two and 11, and between 0.11 and 0.88, respectively. Conclusions: The level of polymorphism of this set of 23 microsatellites is large enough to provide valuable information on the genetic structure and the invasion history of A. dealbata. PMID:25995979

  2. Characterization of polymorphic microsatellite loci in the Antarctic krill Euphausia superba

    PubMed Central

    2014-01-01

    Background The Antarctic krill, Euphausia superba is a pelagic crustacean, abundant in high-density swarms (10 000 – 30 000 ind/m2) with a circumpolar distribution and a key role in the food web of the Southern Ocean. Only three EST derived microsatellite markers have been used in previous genetic studies, hence we developed additional highly polymorphic microsatellite markers to allow robust studies of the genetic variability and population differentiation within this species. Findings The microsatellite markers described here were obtained through an enriched genomic library, followed by 454 pyrosequencing. A total of 10 microsatellite markers were tested in 32 individuals from the Antarctic Peninsula. One of the tested loci was fixed for one allele while the other was variable. Of the remaining nine markers, seven showed no departure from Hardy-Weinberg equilibrium. The mean number of alleles was 14.9. Conclusions These markers open perspectives for population genetic studies of this species to unravel genetic structure, dispersal and population biology, vital information for future conservation. PMID:24490686

  3. Microsatellites in the Endangered Species Dyckia distachya (Bromeliaceae) and Cross-Amplification in Other Bromeliads

    PubMed Central

    Zanella, Camila M.; Janke, Aline; Paggi, Gecele M.; Goetze, Márcia; Reis, Mauricio S.; Bered, Fernanda

    2012-01-01

    Microsatellite markers were isolated in Dyckia distachya, an endangered bromeliad from southern Brazil, which will be useful to assess the population genetic structure and reproductive success in introduced and natural populations of this species. Twenty microsatellite loci were developed from an enriched genomic library, and nine of these were amplified. The loci were characterized in 43 individuals from introduced and wild D. distachya populations. All nine loci were polymorphic, with four to ten alleles per locus. In an introduced population the observed and expected heterozygosities ranged from 0.136–0.667 and 0.543–0.877, respectively, while in a wild population it ranged from 0.000 to 0.895 and from 0.050 to 0.811, respectively. The development of these microsatellite markers will contribute to investigations of the reproductive potential and viability of introduced populations of D. distachya as well as the single known wild population. Cross-amplification in other Bromeliaceae species was successful, with high rates in four loci, demonstrating the applicability of these microsatellite markers in other taxa. PMID:23443098

  4. Development of 10 microsatellite markers from Pantala flavescens and their applicability in studying genetics diversity.

    PubMed

    Cao, Lingzhen; Fu, Xiaowei; Wu, Kongming

    2015-08-01

    Pantala flavescens (Fabricius 1798) is one of the most common species among migration dragonflies. It is often encountered in large swarms during migration or directed dispersal flights. For a better understanding of its gene flow, genetic structure and migration patterns throughout the world, 10 polymorphic microsatellite markers were isolated in this study. We respectively collected 32 P. flavescens from three places (Hunan, Liaoning and Heilongjiang) and 20 P. flavescens from Beijing. Partial genomic libraries containing microsatellite sequences were constructed with magnetic-bead enrichment method. By screening, sequence analysis, PCR amplification and so on, ten 10 polymorphic microsatellite markers were isolated. In order to assess their applicability, genetic diversity of these novel markers was tested in 96 individuals from three populations in China (Hunan, Liaoning and Heilongjiang). These markers were highly polymorphic, with 3-12 alleles per markers. The observed (Ho) and expected (He) heterozygosities ranged 0.321-0.667 and from 0.531 to 0.948 respectively. The genetic difference between Hunan and Liaoning is 0.429, while the genetic difference between Liaoning and Heilongjiang is 0.0508. These microsatellite markers for P. flavescens were developed for the first time, and will be a powerful tool for studying population genetic diversity and dispersal behavior of P. flavescens in China and worldwide. PMID:25788247

  5. Microsatellites in the endangered species Dyckia distachya (Bromeliaceae) and cross-amplification in other bromeliads.

    PubMed

    Zanella, Camila M; Janke, Aline; Paggi, Gecele M; Goetze, Márcia; Reis, Mauricio S; Bered, Fernanda

    2012-01-01

    Microsatellite markers were isolated in Dyckia distachya, an endangered bromeliad from southern Brazil, which will be useful to assess the population genetic structure and reproductive success in introduced and natural populations of this species. Twenty microsatellite loci were developed from an enriched genomic library, and nine of these were amplified. The loci were characterized in 43 individuals from introduced and wild D. distachya populations. All nine loci were polymorphic, with four to ten alleles per locus. In an introduced population the observed and expected heterozygosities ranged from 0.136-0.667 and 0.543-0.877, respectively, while in a wild population it ranged from 0.000 to 0.895 and from 0.050 to 0.811, respectively. The development of these microsatellite markers will contribute to investigations of the reproductive potential and viability of introduced populations of D. distachya as well as the single known wild population. Cross-amplification in other Bromeliaceae species was successful, with high rates in four loci, demonstrating the applicability of these microsatellite markers in other taxa. PMID:23443098

  6. Complete Genome Sequence of Pseudoxanthomonas suwonensis Strain J1, a Cellulose-Degrading Bacterium Isolated from Leaf- and Wood-Enriched Soil.

    PubMed

    Hou, Liyuan; Jiang, Jingwei; Xu, Zhihui; Zhou, Yun; Leung, Frederick Chi-Ching

    2015-01-01

    We report here the complete genome sequence of the cellulose-degrading bacterium Pseudoxanthomonas suwonensis strain J1, isolated from soil enriched with rotten leaves and wood from the Zhong Mountain Scenic Area in Nanjing, China. This complete genome may contribute to further investigation of plant biomass degradation. PMID:26067962

  7. Draft Genome Sequence of “Candidatus Methanomethylophilus” sp. 1R26, Enriched from Bovine Rumen, a Methanogenic Archaeon Belonging to the Methanomassiliicoccales Order

    PubMed Central

    Højberg, Ole; Urich, Tim

    2016-01-01

    Here, we present the draft genome of “Candidatus Methanomethylophilus” sp. 1R26, a member of the newly described Methanomassiliicoccales order of Euryarcheaota. The enrichment culture was established from bovine rumen contents and produced methane from trimethylamine and methanol. The draft genome contains genes for methanogenesis from methylated compounds. PMID:26893425

  8. Draft Genome Sequence of "Candidatus Methanomethylophilus" sp. 1R26, Enriched from Bovine Rumen, a Methanogenic Archaeon Belonging to the Methanomassiliicoccales Order.

    PubMed

    Noel, Samantha Joan; Højberg, Ole; Urich, Tim; Poulsen, Morten

    2016-01-01

    Here, we present the draft genome of "Candidatus Methanomethylophilus" sp. 1R26, a member of the newly described Methanomassiliicoccales order of Euryarcheaota. The enrichment culture was established from bovine rumen contents and produced methane from trimethylamine and methanol. The draft genome contains genes for methanogenesis from methylated compounds. PMID:26893425

  9. Long, polymorphic microsatellites in simple organisms.

    PubMed

    Field, D; Wills, C

    1996-02-22

    We have examined the phylogenetic distribution of the longest, perfect microsatellites in GenBank. Despite the large contributions of model higher-eukaryotic organisms to GenBank, the selective cloning of long microsatellites from these organisms as genetic markers, and the relative lack of concentration on the microsatellites in lower eukaryotes and prokaryotes, we found that simple organisms, defined here as slime molds, fungi, protists, prokaryotes, viruses, organelles and plasmids, contributed 78 of the 375 examined sequences. These 78 simple-organism microsatellites are characterized predominantly by trinucleotide repeats, nearly half of which lie in exons, and in general show a bias towards A+T rich motifs. Simple-organism microsatellites represented more than once in GenBank displayed length polymorphisms when independent clones were compared. These facts collectively raise speculation as to the role of these 'junk' sequences in such highly economical genomes, especially when precise changes in long microsatellites are known to regulate critical virulence factors in several prokaryotes. Regardless of their biological significance, simple-organism microsatellites may provide a general source of molecular markers to track disease outbreaks and the evolution of microorganisms in unprecedented detail. PMID:8728984

  10. Global Microsatellite Content Distinguishes Humans, Primates, Animals, and Plants

    PubMed Central

    McIver, L.J.; McCormick, J.F.; Skinner, M.A.; Xie, Y.; Gelhausen, R.A.; Ng, K.; Kumar, N.M.; Garner, H.R.

    2009-01-01

    Microsatellites are highly mutable, repetitive sequences commonly used as genetic markers, but they have never been studied en masse. Using a custom microarray to measure hybridization intensities of every possible repetitive nucleotide motif from 1-mers to 6-mers, we examined 25 genomes. Here, we show that global microsatellite content varies predictably by species, as measured by array hybridization signal intensities, correlating with established taxonomic relationships, and particular motifs are characteristic of one species versus another. For instance, hominid-specific microsatellite motifs were identified despite alignment of the human reference, Celera, and Venter genomic sequences indicating substantial variation (30–50%) among individuals. Differential microsatellite motifs were mainly associated with genes involved in developmental processes, whereas those found in intergenic regions exhibited no discernible pattern. This is the first description of a method for evaluating microsatellite content to classify individual genomes. PMID:19717526

  11. Robust physical methods that enrich genomic regions identical by descent for linkage studies: confirmation of a locus for osteogenesis imperfecta

    PubMed Central

    Brooks, Peter; Marcaillou, Charles; Vanpeene, Maud; Saraiva, Jean-Paul; Stockholm, Daniel; Francke, Stephan; Favis, Reyna; Cohen, Nadine; Rousseau, Francis; Tores, Frédéric; Lindenbaum, Pierre; Hager, Jörg; Philippi, Anne

    2009-01-01

    Background The monogenic disease osteogenesis imperfecta (OI) is due to single mutations in either of the collagen genes ColA1 or ColA2, but within the same family a given mutation is accompanied by a wide range of disease severity. Although this phenotypic variability implies the existence of modifier gene variants, genome wide scanning of DNA from OI patients has not been reported. Promising genome wide marker-independent physical methods for identifying disease-related loci have lacked robustness for widespread applicability. Therefore we sought to improve these methods and demonstrate their performance to identify known and novel loci relevant to OI. Results We have improved methods for enriching regions of identity-by-descent (IBD) shared between related, afflicted individuals. The extent of enrichment exceeds 10- to 50-fold for some loci. The efficiency of the new process is shown by confirmation of the identification of the Col1A2 locus in osteogenesis imperfecta patients from Amish families. Moreover the analysis revealed additional candidate linkage loci that may harbour modifier genes for OI; a locus on chromosome 1q includes COX-2, a gene implicated in osteogenesis. Conclusion Technology for physical enrichment of IBD loci is now robust and applicable for finding genes for monogenic diseases and genes for complex diseases. The data support the further investigation of genetic loci other than collagen gene loci to identify genes affecting the clinical expression of osteogenesis imperfecta. The discrimination of IBD mapping will be enhanced when the IBD enrichment procedure is coupled with deep resequencing. PMID:19331686

  12. Genome engineering uncovers 54 evolutionarily conserved and testis-enriched genes that are not required for male fertility in mice.

    PubMed

    Miyata, Haruhiko; Castaneda, Julio M; Fujihara, Yoshitaka; Yu, Zhifeng; Archambeault, Denise R; Isotani, Ayako; Kiyozumi, Daiji; Kriseman, Maya L; Mashiko, Daisuke; Matsumura, Takafumi; Matzuk, Ryan M; Mori, Masashi; Noda, Taichi; Oji, Asami; Okabe, Masaru; Prunskaite-Hyyrylainen, Renata; Ramirez-Solis, Ramiro; Satouh, Yuhkoh; Zhang, Qian; Ikawa, Masahito; Matzuk, Martin M

    2016-07-12

    Gene-expression analysis studies from Schultz et al. estimate that more than 2,300 genes in the mouse genome are expressed predominantly in the male germ line. As of their 2003 publication [Schultz N, Hamra FK, Garbers DL (2003) Proc Natl Acad Sci USA 100(21):12201-12206], the functions of the majority of these testis-enriched genes during spermatogenesis and fertilization were largely unknown. Since the study by Schultz et al., functional analysis of hundreds of reproductive-tract-enriched genes have been performed, but there remain many testis-enriched genes for which their relevance to reproduction remain unexplored or unreported. Historically, a gene knockout is the "gold standard" to determine whether a gene's function is essential in vivo. Although knockout mice without apparent phenotypes are rarely published, these knockout mouse lines and their phenotypic information need to be shared to prevent redundant experiments. Herein, we used bioinformatic and experimental approaches to uncover mouse testis-enriched genes that are evolutionarily conserved in humans. We then used gene-disruption approaches, including Knockout Mouse Project resources (targeting vectors and mice) and CRISPR/Cas9, to mutate and quickly analyze the fertility of these mutant mice. We discovered that 54 mutant mouse lines were fertile. Thus, despite evolutionary conservation of these genes in vertebrates and in some cases in all eukaryotes, our results indicate that these genes are not individually essential for male mouse fertility. Our phenotypic data are highly relevant in this fiscally tight funding period and postgenomic age when large numbers of genomes are being analyzed for disease association, and will prevent unnecessary expenditures and duplications of effort by others. PMID:27357688

  13. Genome engineering uncovers 54 evolutionarily conserved and testis-enriched genes that are not required for male fertility in mice

    PubMed Central

    Miyata, Haruhiko; Castaneda, Julio M.; Fujihara, Yoshitaka; Yu, Zhifeng; Archambeault, Denise R.; Isotani, Ayako; Kiyozumi, Daiji; Kriseman, Maya L.; Mashiko, Daisuke; Matsumura, Takafumi; Matzuk, Ryan M.; Mori, Masashi; Noda, Taichi; Oji, Asami; Okabe, Masaru; Prunskaite-Hyyrylainen, Renata; Ramirez-Solis, Ramiro; Satouh, Yuhkoh; Zhang, Qian; Ikawa, Masahito; Matzuk, Martin M.

    2016-01-01

    Gene-expression analysis studies from Schultz et al. estimate that more than 2,300 genes in the mouse genome are expressed predominantly in the male germ line. As of their 2003 publication [Schultz N, Hamra FK, Garbers DL (2003) Proc Natl Acad Sci USA 100(21):12201–12206], the functions of the majority of these testis-enriched genes during spermatogenesis and fertilization were largely unknown. Since the study by Schultz et al., functional analysis of hundreds of reproductive-tract–enriched genes have been performed, but there remain many testis-enriched genes for which their relevance to reproduction remain unexplored or unreported. Historically, a gene knockout is the “gold standard” to determine whether a gene’s function is essential in vivo. Although knockout mice without apparent phenotypes are rarely published, these knockout mouse lines and their phenotypic information need to be shared to prevent redundant experiments. Herein, we used bioinformatic and experimental approaches to uncover mouse testis-enriched genes that are evolutionarily conserved in humans. We then used gene-disruption approaches, including Knockout Mouse Project resources (targeting vectors and mice) and CRISPR/Cas9, to mutate and quickly analyze the fertility of these mutant mice. We discovered that 54 mutant mouse lines were fertile. Thus, despite evolutionary conservation of these genes in vertebrates and in some cases in all eukaryotes, our results indicate that these genes are not individually essential for male mouse fertility. Our phenotypic data are highly relevant in this fiscally tight funding period and postgenomic age when large numbers of genomes are being analyzed for disease association, and will prevent unnecessary expenditures and duplications of effort by others. PMID:27357688

  14. Isolation and characterization of microsatellite loci in the intertidal sponge Halichondria panicea

    USGS Publications Warehouse

    Knowlton, A.L.; Pierson, B. J.; Talbot, S.L.; Highsmith, R.C.

    2003-01-01

    GA- and CA-enriched genomic libraries were constructed for the intertidal sponge Halichondria panicea. Unique repeat motifs identified varied from the expected simple dinucleotide repeats to more complex repeat units. All sequences tended to be highly repetitive but did not necessarily contain the targeted motifs. Seven microsatellite loci were evaluated on sponges from the clone source population. All seven were polymorphic with 5.43??0.92 mean number of alleles. Six of the seven loci that could be resolved had mean heterozygosities of 0.14-0.68. The loci identified here will be useful for population studies.

  15. USE OF COMPETITIVE GENOMIC HYBRIDIZATION TO ENRICH FOR GENOME-SPECIFIC DIFFERENCES BETWEEN TWO CLOSELY RELATED HUMAN FECAL INDICATOR BACTERIA

    EPA Science Inventory

    Enterococci are frequently used as indicators of fecal pollution in surface waters. To accelerate the identification of Enterococcus faecalis-specific DNA sequences, we employed a comparative genomic strategy utilizing a positive selection process to compare E. faec...

  16. Microsatellite markers for the yam bean Pachyrhizus (Fabaceae)1

    PubMed Central

    Delêtre, Marc; Soengas, Beatriz; Utge, José; Lambourdière, Josie; Sørensen, Marten

    2013-01-01

    • Premise of the study: Microsatellite loci were developed for the understudied root crop yam bean (Pachyrhizus spp.) to investigate intraspecific diversity and interspecific relationships within the genus Pachyrhizus. • Methods and Results: Seventeen nuclear simple sequence repeat (SSR) markers with perfect di- and trinucleotide repeats were developed from 454 pyrosequencing of SSR-enriched genomic libraries. Loci were characterized in P. ahipa and wild and cultivated populations of four closely related species. All loci successfully cross-amplified and showed high levels of polymorphism, with number of alleles ranging from three to 12 and expected heterozygosity ranging from 0.095 to 0.831 across the genus. • Conclusions: By enabling rapid assessment of genetic diversity in three native neotropical crops, P. ahipa, P. erosus, and P. tuberosus, and two wild relatives, P. ferrugineus and P. panamensis, these markers will allow exploration of the genetic diversity and evolutionary history of the genus Pachyrhizus. PMID:25202568

  17. PCR primer pairs for 100 microsatellites in red drum (Sciaenops ocellatus)

    Technology Transfer Automated Retrieval System (TEKTRAN)

    One hundred nuclear-encoded microsatellites from a genomic DNA library of red drum (Sciaenops ocellatus) were isolated and characterized. Eight of the microsatellites had tetra-nucleotide motifs, while 92 had di-nucleotide motifs. The average number of alleles at the 100 microsatellites among a sa...

  18. Isolation and characterizaton of dinucleotide microsatellites in greater amberjack, Seriola dumerili

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Thirteen nuclear-encoded dinucleotide microsatellites were characterized from a genomic DNA library of greater amberjack, Seriola dumerili. The microsatellites include 12 perfect-repeat motifs and one imperfect-repeat motif. The number of alleles at the 13 microsatellites among a sample of 29 fish...

  19. Gap Closing/Finishing by Targeted Genomic Region Enrichment and Sequencing

    SciTech Connect

    Singh, Kanwar; Froula, Jeff; Trice, Hope; Pennacchio, Len A.; Chen, Feng

    2010-05-27

    Gap Closing/Finishing of draft genome assemblies is a labor and cost intensive process where several rounds of repetitious amplification and sequencing are required. Here we demonstrate a high throughput procedure where custom primers flanking gaps in draft genomes are designed. Primer libraries containing up to 4,000 unique pairs in independent droplets are merged with a fragmented genomic template. From this millions of picoliter scale droplets are formed, each one being the functional equivalent of an individual PCR reaction. The PCR products are concatenated and sequenced by Illumina which is then assembled and used for gap closure. Here we present an overall experimental strategy, primer design algorithm and initial results.

  20. IDENTIFICATION OF AVIAN-SPECIFIC FECAL METAGENOMIC SEQUENCES USING GENOME FRAGMENT ENRICHMENTS

    EPA Science Inventory

    Sequence analysis of microbial genomes has provided biologists the opportunity to compare genetic differences between closely related microorganisms. While random sequencing has also been used to study natural microbial communities, metagenomic comparisons via sequencing analysis...

  1. A microsatellite-based genome-wide analysis of genetic diversity and linkage disequilibrium in Upland cotton (Gossypium hirsutum L.) cultivars from major cotton-growing countries

    Technology Transfer Automated Retrieval System (TEKTRAN)

    To better understand the genetic diversity of the cultivated Upland cotton (Gossypium hirsutum L.) and its structure at the molecular level, 193 Upland cotton cultivars collected from 26 countries were genotyped using 448 microsatellite markers. These markers were selected based on their mapping po...

  2. THE DEVELOPMENT OF MICROSATELLITE MARKERS FOR PERSEA AMERICANA (AVOCADO).

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Because of their relative abundance, distribution across the genome, hypervariability and co-dominance, microsatellites, or simple sequence repeats are considered to be cost effective and efficient molecular genetic markers for parentage analysis, linkage mapping, association studies, and genetic fi...

  3. Genome-Wide Analyses in Bacteria Show Small-RNA Enrichment for Long and Conserved Intergenic Regions

    PubMed Central

    Tsai, Chen-Hsun; Liao, Rick; Chou, Brendan; Palumbo, Michael

    2014-01-01

    Interest in finding small RNAs (sRNAs) in bacteria has significantly increased in recent years due to their regulatory functions. Development of high-throughput methods and more sophisticated computational algorithms has allowed rapid identification of sRNA candidates in different species. However, given their various sizes (50 to 500 nucleotides [nt]) and their potential genomic locations in the 5′ and 3′ untranslated regions as well as in intergenic regions, identification and validation of true sRNAs have been challenging. In addition, the evolution of bacterial sRNAs across different species continues to be puzzling, given that they can exert similar functions with various sequences and structures. In this study, we analyzed the enrichment patterns of sRNAs in 13 well-annotated bacterial species using existing transcriptome and experimental data. All intergenic regions were analyzed by WU-BLAST to examine conservation levels relative to species within or outside their genus. In total, more than 900 validated bacterial sRNAs and 23,000 intergenic regions were analyzed. The results indicate that sRNAs are enriched in intergenic regions, which are longer and more conserved than the average intergenic regions in the corresponding bacterial genome. We also found that sRNA-coding regions have different conservation levels relative to their flanking regions. This work provides a way to analyze how noncoding RNAs are distributed in bacterial genomes and also shows conserved features of intergenic regions that encode sRNAs. These results also provide insight into the functions of regions surrounding sRNAs and into optimization of RNA search algorithms. PMID:25313390

  4. Application of targeted enrichment to next-generation sequencing of retroviruses integrated into the host human genome

    PubMed Central

    Miyazato, Paola; Katsuya, Hiroo; Fukuda, Asami; Uchiyama, Yoshikazu; Matsuo, Misaki; Tokunaga, Michiyo; Hino, Shinjiro; Nakao, Mitsuyoshi; Satou, Yorifumi

    2016-01-01

    The recent development and advancement of next-generation sequencing (NGS) technologies have enabled the characterization of the human genome at extremely high resolution. In the retrovirology field, NGS technologies have been applied to integration-site analysis and deep sequencing of viral genomes in combination with PCR amplification using virus-specific primers. However, virus-specific primers are not available for some epigenetic analyses, like chromatin immunoprecipitation sequencing (ChIP-seq) assays. Viral sequences are poorly detected without specific PCR amplification because proviral DNA is very scarce compared to human genomic DNA. Here, we have developed and evaluated the use of biotinylated DNA probes for the capture of viral genetic fragments from a library prepared for NGS. Our results demonstrated that viral sequence detection was hundreds or thousands of times more sensitive after enrichment, enabling us to reduce the economic burden that arises when attempting to analyze the epigenetic landscape of proviruses by NGS. In addition, the method is versatile enough to analyze proviruses that have mismatches compared to the DNA probes. Taken together, we propose that this approach is a powerful tool to clarify the mechanisms of transcriptional and epigenetic regulation of retroviral proviruses that have, until now, remained elusive. PMID:27321866

  5. Application of targeted enrichment to next-generation sequencing of retroviruses integrated into the host human genome.

    PubMed

    Miyazato, Paola; Katsuya, Hiroo; Fukuda, Asami; Uchiyama, Yoshikazu; Matsuo, Misaki; Tokunaga, Michiyo; Hino, Shinjiro; Nakao, Mitsuyoshi; Satou, Yorifumi

    2016-01-01

    The recent development and advancement of next-generation sequencing (NGS) technologies have enabled the characterization of the human genome at extremely high resolution. In the retrovirology field, NGS technologies have been applied to integration-site analysis and deep sequencing of viral genomes in combination with PCR amplification using virus-specific primers. However, virus-specific primers are not available for some epigenetic analyses, like chromatin immunoprecipitation sequencing (ChIP-seq) assays. Viral sequences are poorly detected without specific PCR amplification because proviral DNA is very scarce compared to human genomic DNA. Here, we have developed and evaluated the use of biotinylated DNA probes for the capture of viral genetic fragments from a library prepared for NGS. Our results demonstrated that viral sequence detection was hundreds or thousands of times more sensitive after enrichment, enabling us to reduce the economic burden that arises when attempting to analyze the epigenetic landscape of proviruses by NGS. In addition, the method is versatile enough to analyze proviruses that have mismatches compared to the DNA probes. Taken together, we propose that this approach is a powerful tool to clarify the mechanisms of transcriptional and epigenetic regulation of retroviral proviruses that have, until now, remained elusive. PMID:27321866

  6. New softwares for automated microsatellite marker development.

    PubMed

    Martins, Wellington; de Sousa, Daniel; Proite, Karina; Guimarães, Patrícia; Moretzsohn, Marcio; Bertioli, David

    2006-01-01

    Microsatellites are repeated small sequence motifs that are highly polymorphic and abundant in the genomes of eukaryotes. Often they are the molecular markers of choice. To aid the development of microsatellite markers we have developed a module that integrates a program for the detection of microsatellites (TROLL), with the sequence assembly and analysis software, the Staden Package. The module has easily adjustable parameters for microsatellite lengths and base pair quality control. Starting with large datasets of unassembled sequence data in the form of chromatograms and/or text data, it enables the creation of a compact database consisting of the processed and assembled microsatellite containing sequences. For the final phase of primer design, we developed a program that accepts the multi-sequence 'experiment file' format as input and produces a list of primer pairs for amplification of microsatellite markers. The program can take into account the quality values of consensus bases, improving success rate of primer pairs in PCR. The software is freely available and simple to install in both Windows and Unix-based operating systems. Here we demonstrate the software by developing primer pairs for 427 new candidate markers for peanut. PMID:16493138

  7. Microsatellites and Their Appliation in Flowering Dogwood

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Microsatellites, also known as simple sequence repeats (SSRs), are repeat units that are 1 to 6 base pairs long and repeat six or more times and are present throughout the entire eukaryotic genome. SSRs are useful genetic markers for studying genetic diversity and for creating linkage maps of plant...

  8. Microsatellites from Kousa dogwood (Cornus Kousa)

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Microsatellite loci were identified from Cornus kousa ‘National’. Primer pairs for 86 loci were developed and of these eight were optimized and screened using genomic DNA from 22 kousa cultivars. All optimized loci were polymorphic and the number of alleles per locus ranged from 3 to 17. Observed h...

  9. Survey and Analysis of Microsatellites in the Silkworm, Bombyx mori

    PubMed Central

    Prasad, M. Dharma; Muthulakshmi, M.; Madhu, M.; Archak, Sunil; Mita, K.; Nagaraju, J.

    2005-01-01

    We studied microsatellite frequency and distribution in 21.76-Mb random genomic sequences, 0.67-Mb BAC sequences from the Z chromosome, and 6.3-Mb EST sequences of Bombyx mori. We mined microsatellites of ≥15 bases of mononucleotide repeats and ≥5 repeat units of other classes of repeats. We estimated that microsatellites account for 0.31% of the genome of B. mori. Microsatellite tracts of A, AT, and ATT were the most abundant whereas their number drastically decreased as the length of the repeat motif increased. In general, tri- and hexanucleotide repeats were overrepresented in the transcribed sequences except TAA, GTA, and TGA, which were in excess in genomic sequences. The Z chromosome sequences contained shorter repeat types than the rest of the chromosomes in addition to a higher abundance of AT-rich repeats. Our results showed that base composition of the flanking sequence has an influence on the origin and evolution of microsatellites. Transitions/transversions were high in microsatellites of ESTs, whereas the genomic sequence had an equal number of substitutions and indels. The average heterozygosity value for 23 polymorphic microsatellite loci surveyed in 13 diverse silkmoth strains having 2–14 alleles was 0.54. Only 36 (18.2%) of 198 microsatellite loci were polymorphic between the two divergent silkworm populations and 10 (5%) loci revealed null alleles. The microsatellite map generated using these polymorphic markers resulted in 8 linkage groups. B. mori microsatellite loci were the most conserved in its immediate ancestor, B. mandarina, followed by the wild saturniid silkmoth, Antheraea assama. PMID:15371363

  10. Genome-wide association study identifies a maternal copy-number deletion in PSG11 enriched among preeclampsia patients

    PubMed Central

    2012-01-01

    Background Specific genetic contributions for preeclampsia (PE) are currently unknown. This genome-wide association study (GWAS) aims to identify maternal single nucleotide polymorphisms (SNPs) and copy-number variants (CNVs) involved in the etiology of PE. Methods A genome-wide scan was performed on 177 PE cases (diagnosed according to National Heart, Lung and Blood Institute guidelines) and 116 normotensive controls. White female study subjects from Iowa were genotyped on Affymetrix SNP 6.0 microarrays. CNV calls made using a combination of four detection algorithms (Birdseye, Canary, PennCNV, and QuantiSNP) were merged using CNVision and screened with stringent prioritization criteria. Due to limited DNA quantities and the deleterious nature of copy-number deletions, it was decided a priori that only deletions would be selected for assay on the entire case-control dataset using quantitative real-time PCR. Results The top four SNP candidates had an allelic or genotypic p-value between 10-5 and 10-6, however, none surpassed the Bonferroni-corrected significance threshold. Three recurrent rare deletions meeting prioritization criteria detected in multiple cases were selected for targeted genotyping. A locus of particular interest was found showing an enrichment of case deletions in 19q13.31 (5/169 cases and 1/114 controls), which encompasses the PSG11 gene contiguous to a highly plastic genomic region. All algorithm calls for these regions were assay confirmed. Conclusions CNVs may confer risk for PE and represent interesting regions that warrant further investigation. Top SNP candidates identified from the GWAS, although not genome-wide significant, may be useful to inform future studies in PE genetics. PMID:22748001

  11. Enrichment analysis of Alu elements with different spatial chromatin proximity in the human genome.

    PubMed

    Gu, Zhuoya; Jin, Ke; Crabbe, M James C; Zhang, Yang; Liu, Xiaolin; Huang, Yanyan; Hua, Mengyi; Nan, Peng; Zhang, Zhaolei; Zhong, Yang

    2016-04-01

    Transposable elements (TEs) have no longer been totally considered as "junk DNA" for quite a time since the continual discoveries of their multifunctional roles in eukaryote genomes. As one of the most important and abundant TEs that still active in human genome, Alu, a SINE family, has demonstrated its indispensable regulatory functions at sequence level, but its spatial roles are still unclear. Technologies based on 3C (chromosome conformation capture) have revealed the mysterious three-dimensional structure of chromatin, and make it possible to study the distal chromatin interaction in the genome. To find the role TE playing in distal regulation in human genome, we compiled the new released Hi-C data, TE annotation, histone marker annotations, and the genome-wide methylation data to operate correlation analysis, and found that the density of Alu elements showed a strong positive correlation with the level of chromatin interactions (hESC: r = 0.9, P < 2.2 × 10(16); IMR90 fibroblasts: r = 0.94, P < 2.2 × 10(16)) and also have a significant positive correlation with some remote functional DNA elements like enhancers and promoters (Enhancer: hESC: r = 0.997, P = 2.3 × 10(-4); IMR90: r = 0.934, P = 2 × 10(-2); Promoter: hESC: r = 0.995, P = 3.8 × 10(-4); IMR90: r = 0.996, P = 3.2 × 10(-4)). Further investigation involving GC content and methylation status showed the GC content of Alu covered sequences shared a similar pattern with that of the overall sequence, suggesting that Alu elements also function as the GC nucleotide and CpG site provider. In all, our results suggest that the Alu elements may act as an alternative parameter to evaluate the Hi-C data, which is confirmed by the correlation analysis of Alu elements and histone markers. Moreover, the GC-rich Alu sequence can bring high GC content and methylation flexibility to the regions with more distal chromatin contact, regulating the transcription of tissue-specific genes. PMID:26861146

  12. Methylation quantitative trait loci in the developing brain and their enrichment in schizophrenia-associated genomic regions

    PubMed Central

    Hannon, Eilis; Spiers, Helen; Viana, Joana; Pidsley, Ruth; Burrage, Joe; Murphy, Therese M; Troakes, Claire; Turecki, Gustavo; O’Donovan, Michael C.; Schalkwyk, Leonard C.; Bray, Nicholas J.; Mill, Jonathan

    2015-01-01

    We characterized DNA methylation quantitative trait loci (mQTLs) in a large collection (n=166) of human fetal brain samples spanning 56–166 days post-conception, identifying >16,000 fetal brain mQTLs. Fetal brain mQTLs are primarily cis-acting, enriched in regulatory chromatin domains and transcription factor binding sites, and show significant overlap with genetic variants also associated with gene expression in the brain. Using tissue from three distinct regions of the adult brain (prefrontal cortex, striatum and cerebellum) we show that most fetal brain mQTLs are developmentally stable, although a subset is characterized by fetal-specific effects. We show that fetal brain mQTLs are enriched amongst risk loci identified in a recent large-scale genome-wide association study (GWAS) of schizophrenia, a severe psychiatric disorder with a hypothesized neurodevelopmental component. Finally, we demonstrate how mQTLs can be used to refine GWAS loci through the identification of discrete sites of variable fetal brain methylation associated with schizophrenia risk variants. PMID:26619357

  13. Association Signals Unveiled by a Comprehensive Gene Set Enrichment Analysis of Dental Caries Genome-Wide Association Studies

    PubMed Central

    Cuenco, Karen T.; Zeng, Zhen; Feingold, Eleanor; Marazita, Mary L.; Wang, Lily; Zhao, Zhongming

    2013-01-01

    Gene set-based analysis of genome-wide association study (GWAS) data has recently emerged as a useful approach to examine the joint effects of multiple risk loci in complex human diseases or phenotypes. Dental caries is a common, chronic, and complex disease leading to a decrease in quality of life worldwide. In this study, we applied the approaches of gene set enrichment analysis to a major dental caries GWAS dataset, which consists of 537 cases and 605 controls. Using four complementary gene set analysis methods, we analyzed 1331 Gene Ontology (GO) terms collected from the Molecular Signatures Database (MSigDB). Setting false discovery rate (FDR) threshold as 0.05, we identified 13 significantly associated GO terms. Additionally, 17 terms were further included as marginally associated because they were top ranked by each method, although their FDR is higher than 0.05. In total, we identified 30 promising GO terms, including ‘Sphingoid metabolic process,’ ‘Ubiquitin protein ligase activity,’ ‘Regulation of cytokine secretion,’ and ‘Ceramide metabolic process.’ These GO terms encompass broad functions that potentially interact and contribute to the oral immune response related to caries development, which have not been reported in the standard single marker based analysis. Collectively, our gene set enrichment analysis provided complementary insights into the molecular mechanisms and polygenic interactions in dental caries, revealing promising association signals that could not be detected through single marker analysis of GWAS data. PMID:23967329

  14. Comprehensive profiling of retroviral integration sites using target enrichment methods from historical koala samples without an assembled reference genome.

    PubMed

    Cui, Pin; Löber, Ulrike; Alquezar-Planas, David E; Ishida, Yasuko; Courtiol, Alexandre; Timms, Peter; Johnson, Rebecca N; Lenz, Dorina; Helgen, Kristofer M; Roca, Alfred L; Hartman, Stefanie; Greenwood, Alex D

    2016-01-01

    Background. Retroviral integration into the host germline results in permanent viral colonization of vertebrate genomes. The koala retrovirus (KoRV) is currently invading the germline of the koala (Phascolarctos cinereus) and provides a unique opportunity for studying retroviral endogenization. Previous analysis of KoRV integration patterns in modern koalas demonstrate that they share integration sites primarily if they are related, indicating that the process is currently driven by vertical transmission rather than infection. However, due to methodological challenges, KoRV integrations have not been comprehensively characterized. Results. To overcome these challenges, we applied and compared three target enrichment techniques coupled with next generation sequencing (NGS) and a newly customized sequence-clustering based computational pipeline to determine the integration sites for 10 museum Queensland and New South Wales (NSW) koala samples collected between the 1870s and late 1980s. A secondary aim of this study sought to identify common integration sites across modern and historical specimens by comparing our dataset to previously published studies. Several million sequences were processed, and the KoRV integration sites in each koala were characterized. Conclusions. Although the three enrichment methods each exhibited bias in integration site retrieval, a combination of two methods, Primer Extension Capture and hybridization capture is recommended for future studies on historical samples. Moreover, identification of integration sites shows that the proportion of integration sites shared between any two koalas is quite small. PMID:27069793

  15. Comprehensive profiling of retroviral integration sites using target enrichment methods from historical koala samples without an assembled reference genome

    PubMed Central

    Alquezar-Planas, David E.; Ishida, Yasuko; Courtiol, Alexandre; Timms, Peter; Johnson, Rebecca N.; Lenz, Dorina; Helgen, Kristofer M.; Roca, Alfred L.; Hartman, Stefanie

    2016-01-01

    Background. Retroviral integration into the host germline results in permanent viral colonization of vertebrate genomes. The koala retrovirus (KoRV) is currently invading the germline of the koala (Phascolarctos cinereus) and provides a unique opportunity for studying retroviral endogenization. Previous analysis of KoRV integration patterns in modern koalas demonstrate that they share integration sites primarily if they are related, indicating that the process is currently driven by vertical transmission rather than infection. However, due to methodological challenges, KoRV integrations have not been comprehensively characterized. Results. To overcome these challenges, we applied and compared three target enrichment techniques coupled with next generation sequencing (NGS) and a newly customized sequence-clustering based computational pipeline to determine the integration sites for 10 museum Queensland and New South Wales (NSW) koala samples collected between the 1870s and late 1980s. A secondary aim of this study sought to identify common integration sites across modern and historical specimens by comparing our dataset to previously published studies. Several million sequences were processed, and the KoRV integration sites in each koala were characterized. Conclusions. Although the three enrichment methods each exhibited bias in integration site retrieval, a combination of two methods, Primer Extension Capture and hybridization capture is recommended for future studies on historical samples. Moreover, identification of integration sites shows that the proportion of integration sites shared between any two koalas is quite small. PMID:27069793

  16. Development and characterization of microsatellite markers for analysis of population differentiation in the tree legume Acacia koa (Fabaceae: Mimosoideae) in the Hawaiian Islands.

    PubMed

    Fredua-Agyeman, Rudolph; Adamski, Daniel; Liao, Richard Junfu; Morden, Clifford; Borthakur, Dulal

    2008-12-01

    The aim of this research was to develop and use microsatellite markers to characterize the high-value timber tree Acacia koa (koa), which is endemic to the Hawaiian Islands. Genomic DNA fragments of 300-1000 bp were cloned and sequenced following enrichment for microsatellite motifs by PCR using 7 oligonucleotide repeat primers in separate reactions. Among 96 sequences analyzed, 63 contained unique microsatellite motifs flanked by variable sequences. A dual PCR method involving a primer walking step was used to develop 15 primer pairs. Another 16 primer pairs were developed directly from the variable sequences on both sides of the microsatellite motifs. These 31 primer pairs were tested on 172 koa plants representing 11 populations collected from 4 of the major Hawaiian Islands. Nine of the primers that identified polymorphic microsatellite loci and 3 that detected unique alleles exclusively in some populations were used for genetic diversity studies of koa. Cluster analysis and multidimensional scaling of the allelic phenotype data revealed that koa from Kauai formed a distinct group separate from koa of the neighboring islands of Oahu, Maui, and Hawaii. The oldest of the four islands, Kauai, also had the most diverse populations of koa. PMID:19088813

  17. Microsatellite markers from the 'South American fruit fly' Anastrepha fraterculus: a valuable tool for population genetic analysis and SIT applications

    PubMed Central

    2014-01-01

    Background Anastrepha fraterculus Wiedemann is a horticultural pest which causes significant economic losses in the fruit-producing areas of the American continent and limits the access of products to international markets. The use of environmentally friendly control strategies against this pest is constrained due to the limited knowledge of its population structure. Results We developed microsatellite markers for A. fraterculus from four genomic libraries, which were enriched in CA, CAA, GA and CAT microsatellite motifs. Fifty microsatellite regions were evaluated and 14 loci were selected for population genetics studies. Genotypes of 122 individuals sampled from four A. fraterculus populations were analyzed. The level of polymorphism ranged from three to 13 alleles per locus and the mean expected heterozygosity ranged from 0.60 to 0.64. Comparison between allelic and genotypic frequencies showed significant differences among all pairs of populations. Conclusions This novel set of microsatellite markers provides valuable information for the description of genetic variability and population structure of wild populations and laboratory strains of A. fraterculus. This information will be used to identify and characterize candidate strains suitable to implement effective pest control strategies and might represent a first step towards having a more comprehensive knowledge about the genetics of this pest. PMID:25471285

  18. Characterization of ten highly polymorphic microsatellite loci for the intertidal mussel Perna perna, and cross species amplification within the genus

    PubMed Central

    2012-01-01

    Background The brown mussel Perna perna (Linnaeus, 1758) is a dominant constituent of intertidal communities and a strong invader with multiple non-native populations distributed around the world. In a previous study, two polymorphic microsatellite loci were developed and used to determine population-level genetic diversity in invasive and native P. perna populations. However, higher number of microsatellite markers are required for reliable population genetic studies. In this context, in order to understand P. perna origins and history of invasion and to compare population genetic structure in native versus invaded areas, we developed 10 polymorphic microsatellite markers. Findings Described microsatellite markers were developed from an enriched genomic library. Analyses and characterization of loci using 20 individuals from a population in Western Sahara revealed on average 11 alleles per locus (range: 5–27) and mean gene diversity of 0.75 (range: 0.31 - 0.95). One primer pair revealed possible linkage disequilibrium while heterozygote deficiency was significant at four loci. Six of these markers cross-amplified in P. canaliculus (origin: New Zealand). Conclusions Developed markers will be useful in addressing a variety of questions concerning P. perna, including dispersal scales, genetic variation and population structure, in both native and invaded areas. PMID:23039168

  19. Genome-Wide Association Studies Suggest Limited Immune Gene Enrichment in Schizophrenia Compared to 5 Autoimmune Diseases.

    PubMed

    Pouget, Jennie G; Gonçalves, Vanessa F; Spain, Sarah L; Finucane, Hilary K; Raychaudhuri, Soumya; Kennedy, James L; Knight, Jo

    2016-09-01

    There has been intense debate over the immunological basis of schizophrenia, and the potential utility of adjunct immunotherapies. The major histocompatibility complex is consistently the most powerful region of association in genome-wide association studies (GWASs) of schizophrenia and has been interpreted as strong genetic evidence supporting the immune hypothesis. However, global pathway analyses provide inconsistent evidence of immune involvement in schizophrenia, and it remains unclear whether genetic data support an immune etiology per se. Here we empirically test the hypothesis that variation in immune genes contributes to schizophrenia. We show that there is no enrichment of immune loci outside of the MHC region in the largest genetic study of schizophrenia conducted to date, in contrast to 5 diseases of known immune origin. Among 108 regions of the genome previously associated with schizophrenia, we identify 6 immune candidates (DPP4, HSPD1, EGR1, CLU, ESAM, NFATC3) encoding proteins with alternative, nonimmune roles in the brain. While our findings do not refute evidence that has accumulated in support of the immune hypothesis, they suggest that genetically mediated alterations in immune function may not play a major role in schizophrenia susceptibility. Instead, there may be a role for pleiotropic effects of a small number of immune genes that also regulate brain development and plasticity. Whether immune alterations drive schizophrenia progression is an important question to be addressed by future research, especially in light of the growing interest in applying immunotherapies in schizophrenia. PMID:27242348

  20. Retrotransposon- and microsatellite sequence-associated genomic changes in early 2 generations of a newly synthesized allotetraploid cucumis × hytivus Chen & Kirkbride

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Allopolyploidization is considered an essential evolutionary process in plants that could trigger genomic shock in allopolyploid genome through activation of transcription of retrotransposons, which may be important in plant evolution. Two retrotransposon-based markers, inter-retrotransposon amplifi...

  1. Evolutionary Dynamics of Microsatellite Distribution in Plants: Insight from the Comparison of Sequenced Brassica, Arabidopsis and Other Angiosperm Species

    PubMed Central

    Shi, Jiaqin; Huang, Shunmou; Fu, Donghui; Yu, Jinyin; Wang, Xinfa; Hua, Wei; Liu, Shengyi; Liu, Guihua; Wang, Hanzhong

    2013-01-01

    Despite their ubiquity and functional importance, microsatellites have been largely ignored in comparative genomics, mostly due to the lack of genomic information. In the current study, microsatellite distribution was characterized and compared in the whole genomes and both the coding and non-coding DNA sequences of the sequenced Brassica, Arabidopsis and other angiosperm species to investigate their evolutionary dynamics in plants. The variation in the microsatellite frequencies of these angiosperm species was much smaller than those for their microsatellite numbers and genome sizes, suggesting that microsatellite frequency may be relatively stable in plants. The microsatellite frequencies of these angiosperm species were significantly negatively correlated with both their genome sizes and transposable elements contents. The pattern of microsatellite distribution may differ according to the different genomic regions (such as coding and non-coding sequences). The observed differences in many important microsatellite characteristics (especially the distribution with respect to motif length, type and repeat number) of these angiosperm species were generally accordant with their phylogenetic distance, which suggested that the evolutionary dynamics of microsatellite distribution may be generally consistent with plant divergence/evolution. Importantly, by comparing these microsatellite characteristics (especially the distribution with respect to motif type) the angiosperm species (aside from a few species) all clustered into two obviously different groups that were largely represented by monocots and dicots, suggesting a complex and generally dichotomous evolutionary pattern of microsatellite distribution in angiosperms. Polyploidy may lead to a slight increase in microsatellite frequency in the coding sequences and a significant decrease in microsatellite frequency in the whole genome/non-coding sequences, but have little effect on the microsatellite distribution with

  2. Polymorphic microsatellite loci for the sand pocket mouse Chaetodipus arenarius, an endemic from the Baja California Peninsula

    USGS Publications Warehouse

    Munguia-Vega, A.; Rodriguez-Estrella, R.; Nachman, M.; Culver, M.

    2009-01-01

    Fifteen polymorphic microsatellite loci were isolated from an enriched genomic library of the sand pocket mouse Chaetodipus arenarius. The mean number of alleles per locus was 11.53 (range five to 19) and the average observed heterozygosity was 0.764 (range 0.121 to 1.0). The markers will be used for detecting the impact of human-induced habitat fragmentation on patterns of gene flow, genetic structure, and extinction risk. In addition, these markers will be useful across the genus because most of the loci cross-amplified and were polymorphic in three other species of Chaetodipus. ?? 2008 The Authors.

  3. Genome Sequence of Halomonas sp. Strain KO116, an Ionic Liquid-Tolerant Marine Bacterium Isolated from a Lignin-Enriched Seawater Microcosm.

    PubMed

    O'Dell, Kaela B; Woo, Hannah L; Utturkar, Sagar; Klingeman, Dawn; Brown, Steven D; Hazen, Terry C

    2015-01-01

    Halomonas sp. strain KO116 was isolated from Nile Delta Mediterranean Sea surface water enriched with insoluble organosolv lignin. It was further screened for growth on alkali lignin minimal salts medium agar. The strain tolerates the ionic liquid 1-ethyl-3-methylimidazolium acetate. Its complete genome sequence is presented in this report. PMID:25953187

  4. Genome Sequence of Halomonas sp. Strain KO116, an Ionic Liquid-Tolerant Marine Bacterium Isolated from a Lignin-Enriched Seawater Microcosm

    PubMed Central

    O’Dell, Kaela B.; Woo, Hannah L.; Utturkar, Sagar; Klingeman, Dawn; Brown, Steven D.

    2015-01-01

    Halomonas sp. strain KO116 was isolated from Nile Delta Mediterranean Sea surface water enriched with insoluble organosolv lignin. It was further screened for growth on alkali lignin minimal salts medium agar. The strain tolerates the ionic liquid 1-ethyl-3-methylimidazolium acetate. Its complete genome sequence is presented in this report. PMID:25953187

  5. Genome Sequence of Halomonas sp. Strain KO116, an Ionic Liquid- Tolerant Marine Bacterium Isolated from a Lignin-Enriched Seawater Microcosm

    DOE PAGESBeta

    O'Dell, Kaela; Woo, Hannah L.; Utturkar, Sagar M.; Klingeman, Dawn Marie; Brown, Steven D.; Hazen, Terry C.

    2015-05-07

    Halomonas sp. strain KO116 was isolated from Nile Delta Mediterranean Sea surface water enriched with insoluble organosolv lignin. It was further screened for growth on alkali lignin minimal salts medium agar. The strain tolerates the ionic liquid 1-ethyl-3-methylimidazolium acetate. Its complete genome sequence is presented in this report.

  6. B Chromosomes of Aegilops speltoides Are Enriched in Organelle Genome-Derived Sequences

    PubMed Central

    Ruban, Alevtina; Fuchs, Jörg; Marques, André; Schubert, Veit; Soloviev, Alexander; Raskina, Olga; Badaeva, Ekaterina; Houben, Andreas

    2014-01-01

    B chromosomes (Bs) are dispensable components of the genome exhibiting non-Mendelian inheritance. Chromosome counts and flow cytometric analysis of the grass species Aegilops speltoides revealed a tissue-type specific distribution of the roughly 570 Mbp large B chromosomes. To address the question whether organelle-to-nucleus DNA transfer is a mechanism that drives the evolution of Bs, in situ hybridization was performed with labelled organellar DNA. The observed B-specific accumulation of chloroplast- and mitochondria-derived sequences suggests a reduced selection against the insertion of organellar DNA in supernumerary chromosomes. The distribution of B-localised organellar-derived sequences and other sequences differs between genotypes of different geographical origins. PMID:24587288

  7. Microsatellite markers for an endemic Atlantic Forest tree, Manilkara multifida (Sapotaceae).

    PubMed

    Moraes, Ramiris C S; Vivas, Caio V; Oliveira, Fernanda A; Menezes, Ivandilson P P; van den Berg, Cassio; Gaiotto, Fernanda A

    2013-01-01

    Manilkara multifida is a tropical tree that is endemic to the Atlantic forests of southern Bahia, Brazil. Currently, populations of this species are restricted to fragmented landscapes that are susceptible to anthropogenic disturbances. Considering this issue, and that there is no genetic information available for this endangered species, we developed microsatellite markers for M. multifida to provide resources for future conservation genetics studies. Using an enriched genomic library, we isolated eight polymorphic microsatellite loci and optimized the amplification conditions for M. multifida. For each locus, we estimated the number of alleles, H E and H O, paternity exclusion Q, individual identity I and fixation index F, and examined the presence of null alleles. The mean number of alleles was 11.9, and the heterozygosity was high at all loci (average H E = 0.809 and H O = 0.777). The combined values for both paternity exclusion and individual identity were Q = 0.9959 and I = 5.45 × 10(-11), respectively. No evidence of null alleles was detected. The results of our analysis indicated that all eight microsatellites are promising for assessing questions involving inbreeding, gene flow, co-ancestry and mating patterns in M. multifida. PMID:23487575

  8. Comparison between Wild and Hatchery Populations of Korean Pen Shell (Atrina pectinata) Using Microsatellite DNA Markers

    PubMed Central

    An, Hye Suck; Kim, Byeong Hak; Lee, Jang Wook; Dong, Chun Mae; Kim, Shin Kwon; Kim, Yi Cheong

    2011-01-01

    Pen shell (Atrina pectinata) is a popular food source with a high commercial value in a number of Asian Pacific areas. The natural A. pectinata population has been declining continuously over the past several decades. Microsatellite DNA markers are a useful DNA-based tool for monitoring the genetic variation of pen shell populations. In this study, 20 polymorphic microsatellite (MS) DNA markers were identified from a partial genomic pen shell DNA library enriched in CA repeats, and used to compare allelic variation between wild and hatchery pen shell populations in Korea. A total of 438 alleles were detected at the 20 MS loci in the two populations. All loci were easily amplified and demonstrated allelic variability, with the number of alleles ranging from 5 to 35 in the wild population and from 5 to 22 in the farmed population. The average observed and expected heterozygosities were 0.69 and 0.82, respectively, in the hatchery samples and 0.69 and 0.83, respectively, in the wild samples. Statistical analysis of fixation index (FST) and analysis of molecular variance (AMOVA) showed minor, but significant, genetic differences between the wild and hatchery populations (FST = 0.0106, CI95% = 0.003–0.017). These microsatellite loci may be valuable for future aquaculture and population genetic studies for developing conservation and management plans. Further studies with additional pen shell samples are needed to conclusively determine the genetic diversity between the wild and hatchery populations. PMID:22016642

  9. Development of Microsatellite (SSR) Markers from Kousa Dogwood

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Microsatellites or simple sequence repeats (SSRs) are stretches of DNA that consist of tandemly repeated mono-, di-, tri-, tetra- or penta-nucleotide units and occur in abundance in the genomes of most eukaryotes. SSR markers are preferred markers in plant breeding because of the uniform genome cove...

  10. The Effects of Microsatellite Selection on Linked Sequence Diversity

    PubMed Central

    Haasl, Ryan J.; Johnson, Ross C.; Payseur, Bret A.

    2014-01-01

    The genome-wide scan for selection is an important method for identifying loci involved in adaptive evolution. However, theory that underlies standard scans for selection assumes a simple mutation model. In particular, recurrent mutation of the selective target is not considered. Although this assumption is reasonable for single-nucleotide variants (SNVs), a microsatellite targeted by selection will reliably violate this assumption due to high mutation rate. Moreover, the mutation rate of microsatellites is generally high enough to ensure that recurrent mutation is pervasive rather than occasional. It is therefore unclear if positive selection targeting microsatellites can be detected using standard scanning statistics. Examples of functional variation at microsatellites underscore the significance of understanding the genomic effects of microsatellite selection. Here, we investigate the joint effects of selection and complex mutation on linked sequence diversity, comparing simulations of microsatellite selection and SNV-based selective sweeps. We find that selection on microsatellites is generally difficult to detect using popular summaries of the site frequency spectrum, and, under certain conditions, using popular methods such as the integrated haplotype statistic and SweepFinder. However, comparisons of the number of haplotypes (K) and segregating sites (S) often provide considerable power to detect selection on microsatellites. We apply this knowledge to a scan of autosomes in the human CEU population (CEPH population sampled from Utah). In addition to the most commonly reported targets of selection in European populations, we identify numerous novel genomic regions that bear highly anomalous haplotype configurations. Using one of these regions—intron 1 of MAGI2—as an example, we show that the anomalous configuration is coincident with a perfect CA repeat of length 22. We conclude that standard genome-wide scans will commonly fail to detect mutationally

  11. Wild and hatchery populations of Korean starry flounder (Platichthys stellatus) compared using microsatellite DNA markers.

    PubMed

    An, Hye Suck; Byun, Soon Gyu; Kim, Yi Cheong; Lee, Jang Wook; Myeong, Jeong-In

    2011-01-01

    Starry flounder (Platichthys stellatus) is an important sport and food fish found around the margins of the North Pacific. Aquaculture production of this species in Korea has increased because of its commercial value. Microsatellite DNA markers are a useful DNA-based tool for monitoring the genetic variation of starry flounder populations. In this study, 12 polymorphic microsatellite DNA markers were identified from a partial genomic starry flounder DNA library enriched in CA repeats, and used to compare allelic variation between wild and hatchery starry flounder populations in Korea. All loci were readily amplified and demonstrated high allelic diversity, with the number of alleles ranging from 6 to 18 in the wild population and from 2 to 12 in the farmed population. A total of 136 alleles were detected at the 12 microsatellite loci in the two populations. The mean observed and expected heterozygosities were 0.62 and 0.68, respectively, in the hatchery samples and 0.67 and 0.75, respectively, in the wild samples. These results indicate lower genetic variability in the hatchery population as compared to the wild population. Significant shifts in allelic frequencies were detected at eight loci, which resulted in a small but significant genetic differences between the wild and hatchery populations (F(ST) = 0.043, P < 0.05). Further studies with additional starry flounder sample collections are needed for comprehensive determinations of the genetic varieties between the wild and hatchery populations. These microsatellite loci may be valuable for future population genetic studies, monitoring the genetic variation for successful aquaculture management and the preservation of aquatic biodiversity. PMID:22272127

  12. Five Hundred Microsatellite Loci for Peromyscus

    PubMed Central

    WEBER, JESSE N.; PETERS, MAUREEN B; TSYUSKO, OLGA V.; LINNEN, CATHERINE R.; HAGEN, CRIS; SCHABLE, NANCY A.; TUBERVILLE, TRACEY D.; MCKEE, ANNA M.; LANCE, STACEY L.; JONES, KENNETH L.; FISHER, HEIDI S.; DEWEY, MICHAEL J.; HOEKSTRA, HOPI E.; GLENN, TRAVIS C.

    2009-01-01

    Mice of the genus Peromyscus, including several endangered subspecies, occur throughout North America and have been important models for conservation research. We describe 526 primer pairs that amplify microsatellite DNA loci for P. maniculatus bairdii, 467 of which also amplify in P. polionotus subgriseus. For 12 of these loci, we report diversity data from a natural population. These markers will be an important resource for future genomic studies of Peromyscus evolution and mammalian conservation. PMID:20563244

  13. All SNPs are not created equal: genome-wide association studies reveal a consistent pattern of enrichment among functionally annotated SNPs.

    PubMed

    Schork, Andrew J; Thompson, Wesley K; Pham, Phillip; Torkamani, Ali; Roddey, J Cooper; Sullivan, Patrick F; Kelsoe, John R; O'Donovan, Michael C; Furberg, Helena; Schork, Nicholas J; Andreassen, Ole A; Dale, Anders M

    2013-04-01

    Recent results indicate that genome-wide association studies (GWAS) have the potential to explain much of the heritability of common complex phenotypes, but methods are lacking to reliably identify the remaining associated single nucleotide polymorphisms (SNPs). We applied stratified False Discovery Rate (sFDR) methods to leverage genic enrichment in GWAS summary statistics data to uncover new loci likely to replicate in independent samples. Specifically, we use linkage disequilibrium-weighted annotations for each SNP in combination with nominal p-values to estimate the True Discovery Rate (TDR = 1-FDR) for strata determined by different genic categories. We show a consistent pattern of enrichment of polygenic effects in specific annotation categories across diverse phenotypes, with the greatest enrichment for SNPs tagging regulatory and coding genic elements, little enrichment in introns, and negative enrichment for intergenic SNPs. Stratified enrichment directly leads to increased TDR for a given p-value, mirrored by increased replication rates in independent samples. We show this in independent Crohn's disease GWAS, where we find a hundredfold variation in replication rate across genic categories. Applying a well-established sFDR methodology we demonstrate the utility of stratification for improving power of GWAS in complex phenotypes, with increased rejection rates from 20% in height to 300% in schizophrenia with traditional FDR and sFDR both fixed at 0.05. Our analyses demonstrate an inherent stratification among GWAS SNPs with important conceptual implications that can be leveraged by statistical methods to improve the discovery of loci. PMID:23637621

  14. Large-scale sequencing based on full-length-enriched cDNA libraries in pigs: contribution to annotation of the pig genome draft sequence

    PubMed Central

    2012-01-01

    Background Along with the draft sequencing of the pig genome, which has been completed by an international consortium, collection of the nucleotide sequences of genes expressed in various tissues and determination of entire cDNA sequences are necessary for investigations of gene function. The sequences of expressed genes are also useful for genome annotation, which is important for isolating the genes responsible for particular traits. Results We performed a large-scale expressed sequence tag (EST) analysis in pigs by using 32 full-length-enriched cDNA libraries derived from 28 kinds of tissues and cells, including seven tissues (brain, cerebellum, colon, hypothalamus, inguinal lymph node, ovary, and spleen) derived from pigs that were cloned from a sow subjected to genome sequencing. We obtained more than 330,000 EST reads from the 5′-ends of the cDNA clones. Comparison with human and bovine gene catalogs revealed that the ESTs corresponded to at least 15,000 genes. cDNA clones representing contigs and singlets generated by assembly of the EST reads were subjected to full-length determination of inserts. We have finished sequencing 31,079 cDNA clones corresponding to more than 12,000 genes. Mapping of the sequences of these cDNA clones on the draft sequence of the pig genome has indicated that the clones are derived from about 15,000 independent loci on the pig genome. Conclusions ESTs and cDNA sequences derived from full-length-enriched libraries are valuable for annotation of the draft sequence of the pig genome. This information will also contribute to the exploration of promoter sequences on the genome and to molecular biology-based analyses in pigs. PMID:23150988

  15. CDH13 and HCRTR2 May Be Associated with Hypersomnia Symptom of Bipolar Depression: A Genome-Wide Functional Enrichment Pathway Analysis.

    PubMed

    Cho, Chul-Hyun; Lee, Heon-Jeong; Woo, Hyun Goo; Choi, Ji-Hye; Greenwood, Tiffany A; Kelsoe, John R

    2015-07-01

    Although bipolar disorder is highly heritable, the identification of specific genetic variations is limited because of the complex traits underlying the disorder. We performed a genome-wide association study of bipolar disorder using a subphenotype that shows hypersomnia symptom during a major depressive episode. We investigated a total of 2,191 cases, 1,434 controls, and 703,012 single nucleotide polymorphisms (SNPs) in the merged samples obtained from the Translational Genomics Institute and the Genetic Association Information Network. The gene emerging as the most significant by statistical analysis was rs1553441 (odds ratio=0.4093; p=1.20×10(-5); Permuted p=6.0×10(-6)). However, the 5×0(-8) threshold for statistical significance required in a genome-wide association study was not achieved. The functional enrichment pathway analysis showed significant enrichments in the adhesion, development-related, synaptic transmission-related, and cell recognition-related pathways. For further evaluation, each gene of the enriched pathways was reviewed and matched with genes that were suggested to be associated with psychiatric disorders by previous genetic studies. We found that the cadherin 13 and hypocretin (orexin) receptor 2 genes may be involved in the hypersomnia symptom during a major depressive episode of bipolar disorder. PMID:26207136

  16. CDH13 and HCRTR2 May Be Associated with Hypersomnia Symptom of Bipolar Depression: A Genome-Wide Functional Enrichment Pathway Analysis

    PubMed Central

    Cho, Chul-Hyun; Woo, Hyun Goo; Choi, Ji-Hye; Greenwood, Tiffany A.; Kelsoe, John R.

    2015-01-01

    Although bipolar disorder is highly heritable, the identification of specific genetic variations is limited because of the complex traits underlying the disorder. We performed a genome-wide association study of bipolar disorder using a subphenotype that shows hypersomnia symptom during a major depressive episode. We investigated a total of 2,191 cases, 1,434 controls, and 703,012 single nucleotide polymorphisms (SNPs) in the merged samples obtained from the Translational Genomics Institute and the Genetic Association Information Network. The gene emerging as the most significant by statistical analysis was rs1553441 (odds ratio=0.4093; p=1.20×10-5; Permuted p=6.0×10-6). However, the 5×0-8 threshold for statistical significance required in a genome-wide association study was not achieved. The functional enrichment pathway analysis showed significant enrichments in the adhesion, development-related, synaptic transmission-related, and cell recognition-related pathways. For further evaluation, each gene of the enriched pathways was reviewed and matched with genes that were suggested to be associated with psychiatric disorders by previous genetic studies. We found that the cadherin 13 and hypocretin (orexin) receptor 2 genes may be involved in the hypersomnia symptom during a major depressive episode of bipolar disorder. PMID:26207136

  17. Isolation and characterization of microsatellite markers in the Serra Spanish mackerel, Scomberomorus brasiliensis.

    PubMed

    Renshaw, Mark A; Douglas, Kory C; Rexroad Iii, Caird E; Jobity, Ann Marie C; Gold, John R

    2009-05-01

    Thirteen nuclear-encoded microsatellites from a genomic DNA library of Serra Spanish mackerel, Scomberomorus brasiliensis, were isolated and characterized. The microsatellites include 10 perfect repeats (eight tetranucleotide and two dinucleotide) and three imperfect repeats (two tetranucleotide and one dinucleotide). An additional five microsatellites, isolated originally from two congeneric species (S. cavalla and S. niphonius), were characterized in S. brasiliensis. Serra Spanish mackerel support artisanal fisheries along the Caribbean and Atlantic coasts of Central and South America, from Belize to Brazil. PMID:21564761

  18. Development of a multiplex PCR assay for fine-scale population genetic analysis of the Komodo monitor Varanus komodoensis based on 18 polymorphic microsatellite loci.

    PubMed

    Ciofi, Claudio; Tzika, Athanasia C; Natali, Chiara; Watts, Phillip C; Sulandari, Sri; Zein, Moch S A; Milinkovitch, Michel C

    2011-05-01

    Multiplex PCR assays for the coamplification of microsatellite loci allow rapid and cost-effective genetic analyses and the production of efficient screening protocols for international breeding programs. We constructed a partial genomic library enriched for di-nucleotide repeats and characterized 14 new microsatellite loci for the Komodo monitor (or Komodo dragon, Varanus komodoensis). Using these novel microsatellites and four previously described loci, we developed multiplex PCR assays that may be loaded on a genetic analyser in three separate panels. We tested the novel set of microsatellites for polymorphism using 69 individuals from three island populations and evaluated the resolving power of the entire panel of 18 loci by conducting (i) a preliminary assignment test to determine population(s) of origin and (ii) a parentage analysis for 43 captive Komodo monitors. This panel of polymorphic loci proved useful for both purposes and thus can be exploited for fine-scale population genetic analyses and as part of international captive breeding programs directed at maintaining genetically viable ex situ populations and reintroductions. PMID:21481213

  19. Mature Microsatellites: Mechanisms Underlying Dinucleotide Microsatellite Mutational Biases in Human Cells

    PubMed Central

    Baptiste, Beverly A.; Ananda, Guruprasad; Strubczewski, Noelle; Lutzkanin, Andrew; Khoo, Su Jen; Srikanth, Abhinaya; Kim, Nari; Makova, Kateryna D.; Krasilnikova, Maria M.; Eckert, Kristin A.

    2013-01-01

    Dinucleotide microsatellites are dynamic DNA sequences that affect genome stability. Here, we focused on mature microsatellites, defined as pure repeats of lengths above the threshold and unlikely to mutate below it in a single mutational event. We investigated the prevalence and mutational behavior of these sequences by using human genome sequence data, human cells in culture, and purified DNA polymerases. Mature dinucleotides (≥10 units) are present within exonic sequences of >350 genes, resulting in vulnerability to cellular genetic integrity. Mature dinucleotide mutagenesis was examined experimentally using ex vivo and in vitro approaches. We observe an expansion bias for dinucleotide microsatellites up to 20 units in length in somatic human cells, in agreement with previous computational analyses of germ-line biases. Using purified DNA polymerases and human cell lines deficient for mismatch repair (MMR), we show that the expansion bias is caused by functional MMR and is not due to DNA polymerase error biases. Specifically, we observe that the MutSα and MutLα complexes protect against expansion mutations. Our data support a model wherein different MMR complexes shift the balance of mutations toward deletion or expansion. Finally, we show that replication fork progression is stalled within long dinucleotides, suggesting that mutational mechanisms within long repeats may be distinct from shorter lengths, depending on the biochemistry of fork resolution. Our work combines computational and experimental approaches to explain the complex mutational behavior of dinucleotide microsatellites in humans. PMID:23450065

  20. Allelic imbalance regions on chromosomes 8p, 17p and 19p related to metastasis of hepatocellular carcinoma: comparison between matched primary and metastatic lesions in 22 patients by genome-wide microsatellite analysis.

    PubMed

    Zhang, Lian-Hai; Qin, Lun-Xiu; Ma, Zeng-Chen; Ye, Sheng-Long; Liu, Yin-Kun; Ye, Qing-Hai; Wu, Xin; Huang, Wei; Tang, Zhao-You

    2003-05-01

    To understand the molecular mechanisms of metastasis in hepatocellular carcinoma (HCC), it is necessary to identify the accumulating genetic alterations during its progression as well as those responsible for the acquisition of metastatic potential in cancer cells. In our previous study, using comparative genomic hybridization (CGH), we found that loss on chromosome 8p is more frequent in metastatic lesions than in matched primary tumors of HCC. Thus, 8p deletion might contribute to HCC metastasis. To narrow the location of metastasis-related alteration regions, we analyzed 22 primary and matched metastatic lesions of HCC by genome-wide microsatellite analysis. Common regions with high levels of allelic imbalance (AI) were identified on 17p, 8p11-cen, 8p21-23, 4q32-qter, 4q13-23, 16q, and 1p33. Regions with increased AI in metastatic lesions were 8p23.3, 8p11.2, 17p11.2-13.3, 4q21-22, 4q32-qter, 8q24.1, 9p11, 9q31, 11q23.1, 13q14.1-31, 13q32-qter, 16p13.3, 16q13, 16q22, and 19p13.1, and these were considered to be related to the metastasis phenotype. Among them, loss on 8p was again proved to be related to progression and metastasis of HCC, and 8p23.3 and 8p11.2 were two likely regions harboring metastasis-related genes. It was also shown for the first time in HCC that AI of 19p13.1 might also be related to metastatic potential. These results provide some candidate regions for further study to identify putative genes suppressing metastasis of HCC. PMID:12734753

  1. Isolation and characterization of 45 Polymorphie microsatellite loci of turbot ( Scophthalmus maximus) and cross-species amplification

    NASA Astrophysics Data System (ADS)

    Hou, Shiying; Ma, Aijun; Wang, Xin'an; Huang, Zhihui; Xue, Baogui; Yang, Zhi; Qu, Jiangbo

    2011-03-01

    Turbot ( Scophthalmus maximus) is a flatfish species commercially important for aquaculture. In this study, we generated a microsatellite-enriched genomic DNA library for Scophthalmus maximus, and then isolated and characterized 45 microsatellite loci by genotyping 30 individuals. The observed number of alleles ranged from 2 to 19 with an average of 6.24, while the effective number of alleles ranged from 1.30 to 11.11 with an average of 3.66. The expected heterozygosities varied from 0.235 to 0.925 4 and Polymorphie information content ranged from 0.2044 to 0.903 3, with an average of 0.622. Twelve loci deviated significantly from Hardy-Weinberg equilibrium, and no significant linkage disequilibrium was observed between any pair of loci after Bonferroni correction. In cross-species amplification, five flatfish species ( Paralichthys lethostigma, Verasper moseri, platichthys stellatus, Hippoglossoides dubius and Cynoglossus semilaevis) showed at least one Polymorphie locus. These Polymorphie microsatellite loci should prove useful for Population analysis of turbot and other related species.

  2. Isolation and characterization of microsatellite loci for the isopod crustacean Armadillidium vulgare and transferability in terrestrial isopods.

    PubMed

    Giraud, Isabelle; Valette, Victorien; Bech, Nicolas; Grandjean, Frédéric; Cordaux, Richard

    2013-01-01

    Armadillidium vulgare is a terrestrial isopod (Crustacea, Oniscidea) which harbors Wolbachia bacterial endosymbionts. A. vulgare is the major model for the study of Wolbachia-mediated feminization of genetic males in crustaceans. As a consequence of their impact on host sex determination mechanisms, Wolbachia endosymbionts are thought to significantly influence A. vulgare evolution on various grounds, including population genetic structure, diversity and reproduction strategies. To provide molecular tools for examining these questions, we isolated microsatellite loci through 454 pyrosequencing of a repeat-enriched A. vulgare genomic library. We selected 14 markers and developed three polymorphic microsatellite multiplex kits. We tested the kits on two A. vulgare natural populations and found high genetic variation, thereby making it possible to investigate the impact of Wolbachia endosymbionts on A. vulgare nuclear variation at unprecedented resolution. In addition, we tested the transferability of these kits by cross-species amplification in five other terrestrial isopod species harboring Wolbachia endosymbionts. The microsatellite loci showed good transferability in particular in Armadillidium nasatum and Chaetophiloscia elongata, for which these markers represent promising tools for future genetic studies. PMID:24098543

  3. Isolation and Characterization of Microsatellite Loci for the Isopod Crustacean Armadillidium vulgare and Transferability in Terrestrial Isopods

    PubMed Central

    Bech, Nicolas; Grandjean, Frédéric; Cordaux, Richard

    2013-01-01

    Armadillidium vulgare is a terrestrial isopod (Crustacea, Oniscidea) which harbors Wolbachia bacterial endosymbionts. A. vulgare is the major model for the study of Wolbachia-mediated feminization of genetic males in crustaceans. As a consequence of their impact on host sex determination mechanisms, Wolbachia endosymbionts are thought to significantly influence A. vulgare evolution on various grounds, including population genetic structure, diversity and reproduction strategies. To provide molecular tools for examining these questions, we isolated microsatellite loci through 454 pyrosequencing of a repeat-enriched A. vulgare genomic library. We selected 14 markers and developed three polymorphic microsatellite multiplex kits. We tested the kits on two A. vulgare natural populations and found high genetic variation, thereby making it possible to investigate the impact of Wolbachia endosymbionts on A. vulgare nuclear variation at unprecedented resolution. In addition, we tested the transferability of these kits by cross-species amplification in five other terrestrial isopod species harboring Wolbachia endosymbionts. The microsatellite loci showed good transferability in particular in Armadillidium nasatum and Chaetophiloscia elongata, for which these markers represent promising tools for future genetic studies. PMID:24098543

  4. Isolation of microsatellite loci and reliable genotyping using noninvasive samples of a critically endangered primate, Trachypithecus leucocephalus.

    PubMed

    Wang, Weiran; Qiao, Yu; Zheng, Yitao; Yao, Meng

    2016-07-01

    Genetic information can be critical in identifying conservation priorities and developing conservation strategies. There is an urgent need for noninvasive genetic tools to study the wild populations of Asian colobine monkeys. The majority of these species are threatened with habitat destruction, population reduction and even extinction, but generally lack information on their genetic diversity and population structure. Genetic sampling and tissue collection have been scarce in these species owing to strict regulations on manipulation of endangered species, and the difficulties and risks associated with capturing these arboreal and fast-moving monkeys in the challenging environments that they inhabit. These difficulties have hindered the development of molecular genetic markers, which are usually derived from tissues or blood. In this study, we present a method for de novo microsatellite isolation and genotyping using DNA from noninvasive origins of a critically endangered Asian colobine, the white-headed langur (Trachypithecus leucocephalus). Genomic DNA isolated from hair was shown to be sufficient for microsatellite enrichment and isolation, with similar isolation efficiencies as from tissue DNA. We identified and characterized 20 polymorphic microsatellite loci, and evaluated their amplification success and genotyping reliability with 86 field-collected fecal samples. These results show that this panel of loci can produce reliable genotypes from fecal samples, and represent a useful tool for noninvasive investigation of genetic structure, individual identification and kinship assessment in this highly endangered species. Our approach can be applied to conservation genetic studies of other wild species that lack sequence information and tissue samples. PMID:26889667

  5. Novel microsatellite control system

    SciTech Connect

    Moore, K.R.; Frigo, J.R.; Tilden, M.W.

    1996-12-31

    The authors are developing extremely simple yet quite capable analog pulse-coded neural networks for smaller-faster-cheaper spacecraft attitude and control systems. They will demonstrate a prototype microsatellite that uses the novel control system to autonomously stabilize itself in the ambient magnetic field and point itself at the brightest available light source.

  6. Genome-wide semiquantitative microsatellite analysis of human hepatocellular carcinoma: discrete mapping of smallest region of overlap of recurrent chromosomal gains and losses.

    PubMed

    Nishimura, Takafumi; Nishida, Naoshi; Komeda, Toshiki; Fukuda, Yoshihiro; Ikai, Iwao; Yamaoka, Yoshio; Nakao, Kazuwa

    2006-05-01

    Recurrent chromosomal gains at 1q, 6p, 8q, and 17q, or losses at 1p, 4q, 6q, 8p, 9p, 13q, 16q, and 17p are common features of human hepatocellular carcinoma (HCC). For precise determination of the shortest region of overlap (SRO), 49 HCC obtained at the time of surgery or autopsy were subjected to comprehensive microsatellite analysis by using 400 markers distributed at almost equal distances throughout the 22 autosomes and X chromosomes. Each allele showing imbalance was subjected to comparative duplex polymerase chain reaction using a retained allele as an internal control to determine whether the imbalance was the result of chromosomal gain or loss. The following SRO of recurrent chromosomal gains and losses were determined: -1p36.22 approximately p36.33, D1S450-D1S2893, 5.0 mega-base pairs (Mbp); +1q23.3 approximately q25.3, D1S2878-D1S2619, 16.9 Mbp; -4q21.2 approximately q24, D4S2964-D4S1572, 23.0 Mbp; -6q23.3 approximately qter, D6S292-qter, 34.7 Mb; -8p22 approximately p23.1, D8S549-D8S550, 4.8 Mbp; +8q12.2 approximately q24.13, D8S260-D8S514, 61.8 Mbp; -13q13.3 approximately q22.1, D13S218-D13S156, 35.6 Mbp; -16q22.1 approximately qter, D16S503-qter, 26.7 Mbp; and -17p12 approximately pter, D17S921-pter, 14.2 Mbp. Contrary to our initial expectations, many HCC showed major deletions or additions of chromosome arms, so that a number of genes were included in the SRO. Although some putative oncogenes or tumor suppressor genes mapped in these SRO may be important, relative copy number changes of numerous other genes may affect pathogenesis of HCC. PMID:16682288

  7. Sequences characterization of microsatellite DNA sequences in Pacific abalone ( Haliotis discus hannai)

    NASA Astrophysics Data System (ADS)

    Li, Qi; Akihiro, Kijima

    2007-01-01

    The microsatellite-enriched library was constructed using magnetic bead hybridization selection method, and the microsatellite DNA sequences were analyzed in Pacific abalone Haliotis discus hannai. Three hundred and fifty white colonies were screened using PCR-based technique, and 84 clones were identified to potentially contain microsatellite repeat motif. The 84 clones were sequenced, and 42 microsatellites and 4 minisatellites with a minimum of five repeats were found (13.1% of white colonies screened). Besides the motif of CA contained in the oligoprobe, we also found other 16 types of microsatellite repeats including a dinucleotide repeat, two tetranucleotide repeats, twelve pentanucleotide repeats and a hexanucleotide repeat. According to Weber (1990), the microsatellite sequences obtained could be categorized structurally into perfect repeats (73.3%), imperfect repeats (13.3%), and compound repeats (13.4%). Among the microsatellite repeats, relatively short arrays (<20 repeats) were most abundant, accounting for 75.0%. The largest length of microsatellites was 48 repeats, and the average number of repeats was 13.4. The data on the composition and length distribution of microsatellites obtained in the present study can be useful for choosing the repeat motifs for microsatellite isolation in other abalone species.

  8. Chloroplast and nuclear microsatellite analysis of Aegilops cylindrica.

    PubMed

    Gandhi, Harish T; Vales, M Isabel; Watson, Christy J W; Mallory-Smith, Carol A; Mori, Naoki; Rehman, Maqsood; Zemetra, Robert S; Riera-Lizarazu, Oscar

    2005-08-01

    Aegilops cylindrica Host (2n = 4x = 28, genome CCDD) is an allotetraploid formed by hybridization between the diploid species Ae. tauschii Coss. (2n = 2x = 14, genome DD) and Ae. markgrafii (Greuter) Hammer (2n = 2x = 14, genome CC). Previous research has shown that Ae. tauschii contributed its cytoplasm to Ae. cylindrica. However, our analysis with chloroplast microsatellite markers showed that 1 of the 36 Ae. cylindrica accessions studied, TK 116 (PI 486249), had a plastome derived from Ae. markgrafii rather than Ae. tauschii. Thus, Ae. markgrafii has also contributed its cytoplasm to Ae. cylindrica. Our analysis of chloroplast and nuclear microsatellite markers also suggests that D-type plastome and the D genome in Ae. cylindrica were closely related to, and were probably derived from, the tauschii gene pool of Ae. tauschii. A determination of the likely source of the C genome and the C-type plastome in Ae. cylindrica was not possible. PMID:15986256

  9. Development and characterization of microsatellite markers of the eastern keelback mullet (Liza affinis).

    PubMed

    Liu, L; Gao, T X; Han, Z Q; Li, C H; Sun, D R; Song, N

    2016-01-01

    Twenty-four polymorphic microsatellite loci were isolated and characterized for Liza affinis using a (GT)13-enriched genomic library. The number of alleles per locus ranged from 3 to 9, with a mean number of 6.250. The observed and expected heterozygosities ranged from 0.417 to 1.000 and from 0.550 to 0.861, with an average of 0.859 and 0.779, respectively. Deviation from Hardy-Weinberg proportions was detected at three loci. Evidence of null alleles was found at two loci. These markers will be useful in further studies investigating the genetic variation and population structure of this species, and may provide insights into the maintenance and efficient management of eastern keelback mullet resources. PMID:27323198

  10. Development and characterization of microsatellite markers for the oomyceta Aphanomyces euteiches.

    PubMed

    Mieuzet, Lucie; Quillévéré, A; Pilet, M L; Le May, C

    2016-06-01

    Aphanomyces euteiches Drechsler is a serious pathogen of leguminous crops that causes devastating root rot of pea worldwide. Given that A. euteiches is a diploid organism, robust, codominant markers are needed for population genetics studies. We have developed and screened a microsatellite-enriched small-insert genomic library for identification of A. euteiches SSR containing sequences. Fourteen out of the 48 primer pairs designed to amplify SSR, produced unambiguous polymorphic products in our test population of 94 isolates. The number of alleles at each locus ranged from one to four. The identification of new markers would enhance the ability to evaluate the genetic structure of A. euteiches populations, and pathogen evolution. PMID:26964907

  11. Development of microsatellite markers for Lagerstroemia indica (Lythraceae) and related species1

    PubMed Central

    Liu, Yang; He, Dan; Cai, Ming; Tang, Wan; Li, Xiao-Yuan; Pan, Hui-Tang; Zhang, Qi-Xiang

    2013-01-01

    • Premise of the study: Microsatellite markers were developed and characterized to analyze genetic diversity within Lagerstroemia cultivars and related species. • Methods and Results: Using simple sequence repeat (SSR)–enriched libraries, 11 species-specific polymorphic genomic SSRs were developed from L. indica ‘Hong Die Fei Wu’. All primers were tested on 48 L. indica individuals from China, the United States, and France. The primers amplified four to 12 alleles per locus, including di-, tri-, and tetranucleotide repeats. Observed and expected heterozygosities ranged from 0.1875 to 0.7609 and 0.2836 to 0.8385, respectively. The primers were also highly cross-transferrable to L. subcostata, L. limii, L. fauriei, L. caudata, and L. speciosa. • Conclusions: The new primers will enlarge the bank of SSRs available to genetic research of Lagerstroemia. These SSR markers will facilitate population genetics and molecular marker–assisted selection of L. indica. PMID:25202512

  12. Microsatellite primers for Camissoniopsis cheiranthifolia (Onagraceae) and cross-amplification in related species1

    PubMed Central

    López-Villalobos, Adriana; Samis, Karen E.; Eckert, Christopher G.

    2014-01-01

    • Premise of the study: We developed 24 nuclear microsatellite primers from an enriched genomic library for the Pacific coastal dune endemic Camissoniopsis cheiranthifolia to study the consequences of mating system differentiation, the genetics of species’ range limits, and hybridization with its closest sister taxon, C. bistorta. • Methods and Results: Twenty-four primer pairs were developed and characterized in four populations of C. cheiranthifolia and one population of C. bistorta. We also tested eight additional taxa for cross-amplification. The average number of alleles per locus per species was 4.3 and 6.0, respectively. The number of loci that amplified and were variable within the eight related taxa ranged from six to 17. • Conclusions: These markers will be useful in studying mating system evolution, the genetic structure of species’ ranges, hybridization, and the provenance of material used for habitat restoration in C. cheiranthifolia, C. bistorta, and related species. PMID:25309839

  13. KENeV: A web-application for the automated reconstruction and visualization of the enriched metabolic and signaling super-pathways deriving from genomic experiments.

    PubMed

    Pilalis, Eleftherios; Koutsandreas, Theodoros; Valavanis, Ioannis; Athanasiadis, Emmanouil; Spyrou, George; Chatziioannou, Aristotelis

    2015-01-01

    Gene expression analysis, using high throughput genomic technologies,has become an indispensable step for the meaningful interpretation of the underlying molecular complexity, which shapes the phenotypic manifestation of the investigated biological mechanism. The modularity of the cellular response to different experimental conditions can be comprehended through the exploitation of molecular pathway databases, which offer a controlled, curated background for statistical enrichment analysis. Existing tools enable pathway analysis, visualization, or pathway merging but none integrates a fully automated workflow, combining all above-mentioned modules and destined to non-programmer users. We introduce an online web application, named KEGG Enriched Network Visualizer (KENeV), which enables a fully automated workflow starting from a list of differentially expressed genes and deriving the enriched KEGG metabolic and signaling pathways, merged into two respective, non-redundant super-networks. The final networks can be downloaded as SBML files, for further analysis, or instantly visualized through an interactive visualization module. In conclusion, KENeV (available online at http://www.grissom.gr/kenev) provides an integrative tool, suitable for users with no programming experience, for the functional interpretation, at both the metabolic and signaling level, of differentially expressed gene subsets deriving from genomic experiments. PMID:26925206

  14. KENeV: A web-application for the automated reconstruction and visualization of the enriched metabolic and signaling super-pathways deriving from genomic experiments

    PubMed Central

    Pilalis, Eleftherios; Koutsandreas, Theodoros; Valavanis, Ioannis; Athanasiadis, Emmanouil; Spyrou, George; Chatziioannou, Aristotelis

    2015-01-01

    Gene expression analysis, using high throughput genomic technologies,has become an indispensable step for the meaningful interpretation of the underlying molecular complexity, which shapes the phenotypic manifestation of the investigated biological mechanism. The modularity of the cellular response to different experimental conditions can be comprehended through the exploitation of molecular pathway databases, which offer a controlled, curated background for statistical enrichment analysis. Existing tools enable pathway analysis, visualization, or pathway merging but none integrates a fully automated workflow, combining all above-mentioned modules and destined to non-programmer users. We introduce an online web application, named KEGG Enriched Network Visualizer (KENeV), which enables a fully automated workflow starting from a list of differentially expressed genes and deriving the enriched KEGG metabolic and signaling pathways, merged into two respective, non-redundant super-networks. The final networks can be downloaded as SBML files, for further analysis, or instantly visualized through an interactive visualization module. In conclusion, KENeV (available online at http://www.grissom.gr/kenev) provides an integrative tool, suitable for users with no programming experience, for the functional interpretation, at both the metabolic and signaling level, of differentially expressed gene subsets deriving from genomic experiments. PMID:26925206

  15. Length and sequence dependent accumulation of simple sequence repeats in vertebrates: potential role in genome organization and regulation.

    PubMed

    Ramamoorthy, Senthilkumar; Garapati, Hita Sony; Mishra, Rakesh Kumar

    2014-11-10

    Simple sequence repeats (SSRs) or microsatellites are tandemly repeated short DNA sequence motifs found to be abundant in higher eukaryotes. Enrichment of SSRs with increasing genome complexity points to a positive selection and their functional relevance. We analyzed genomes of 24 organisms to find features that may help understand the functional relevance of SSRs. Of the 501 possible SSRs, only 73 show length specific enrichment. We also noticed that ~45 bp is the optimum length for a majority of them particularly in the human genome. Finally, we observed non-random distribution of ACG and CCG, enriched around transcriptional start sites (TSSs) in several species. Taken together, these results suggest that SSRs are functionally relevant with potential regulatory role. We propose that such repeats are evolving under positive selection pressure like any other functional element in the genome. PMID:25172211

  16. Segregation studies and linkage analysis of Atlantic salmon microsatellites using haploid genetics.

    PubMed

    Slettan, A; Olsaker, I; Lie, O

    1997-06-01

    A genetic marker map of Atlantic salmon would facilitate the identification of loci influencing economically important traits. In the present paper we describe five new Atlantic salmon microsatellites. Segregation studies and linkage analysis of these and previously published microsatellites were carried out in pedigrees consisting of diploid dams and haploid gynogenetic offspring. We confirm earlier reports that salmon microsatellites tend to have a higher number of repeat units than those of mammals. Linkage analysis revealed that three microsatellites belong to a linkage group spanning approximately 50 cM of the genome, whereas the remaining 10 markers seem to be unlinked. PMID:9203354

  17. Comparative mapping of expressed sequence tags containing microsatellites in rainbow trout (Oncorhynchus mykiss)

    PubMed Central

    Rexroad, Caird E; Rodriguez, Maria F; Coulibaly, Issa; Gharbi, Karim; Danzmann, Roy G; DeKoning, Jenefer; Phillips, Ruth; Palti, Yniv

    2005-01-01

    Background Comparative genomics, through the integration of genetic maps from species of interest with whole genome sequences of other species, will facilitate the identification of genes affecting phenotypes of interest. The development of microsatellite markers from expressed sequence tags will serve to increase marker densities on current salmonid genetic maps and initiate in silico comparative maps with species whose genomes have been fully sequenced. Results Eighty-nine polymorphic microsatellite markers were generated for rainbow trout of which at least 74 amplify in other salmonids. Fifty-five have been associated with functional annotation and 30 were mapped on existing genetic maps. Homologous sequences were identified for 20 of the EST containing microsatellites to identify comparative assignments within the tetraodon, mouse, and/or human genomes. Conclusion The addition of microsatellite markers constructed from expressed sequence tag data will facilitate the development of high-density genetic maps for rainbow trout and comparative maps with other salmonids and better studied species. PMID:15836796

  18. Sequencing and comparative genomic analysis of 1227 Felis catus cDNA sequences enriched for developmental, clinical and nutritional phenotypes

    PubMed Central

    2012-01-01

    Background The feline genome is valuable to the veterinary and model organism genomics communities because the cat is an obligate carnivore and a model for endangered felids. The initial public release of the Felis catus genome assembly provided a framework for investigating the genomic basis of feline biology. However, the entire set of protein coding genes has not been elucidated. Results We identified and characterized 1227 protein coding feline sequences, of which 913 map to public sequences and 314 are novel. These sequences have been deposited into NCBI's genbank database and complement public genomic resources by providing additional protein coding sequences that fill in some of the gaps in the feline genome assembly. Through functional and comparative genomic analyses, we gained an understanding of the role of these sequences in feline development, nutrition and health. Specifically, we identified 104 orthologs of human genes associated with Mendelian disorders. We detected negative selection within sequences with gene ontology annotations associated with intracellular trafficking, cytoskeleton and muscle functions. We detected relatively less negative selection on protein sequences encoding extracellular networks, apoptotic pathways and mitochondrial gene ontology annotations. Additionally, we characterized feline cDNA sequences that have mouse orthologs associated with clinical, nutritional and developmental phenotypes. Together, this analysis provides an overview of the value of our cDNA sequences and enhances our understanding of how the feline genome is similar to, and different from other mammalian genomes. Conclusions The cDNA sequences reported here expand existing feline genomic resources by providing high-quality sequences annotated with comparative genomic information providing functional, clinical, nutritional and orthologous gene information. PMID:22257742

  19. Genome-Wide Computational Analysis of Musa Microsatellites: Classification, Cross-Taxon Transferability, Functional Annotation, Association with Transposons & miRNAs, and Genetic Marker Potential.

    PubMed

    Biswas, Manosh Kumar; Liu, Yuxuan; Li, Chunyu; Sheng, Ou; Mayer, Christoph; Yi, Ganjun

    2015-01-01

    The development of organized, informative, robust, user-friendly, and freely accessible molecular markers is imperative to the Musa marker assisted breeding program. Although several hundred SSR markers have already been developed, the number of informative, robust, and freely accessible Musa markers remains inadequate for some breeding applications. In view of this issue, we surveyed SSRs in four different data sets, developed large-scale non-redundant highly informative therapeutic SSR markers, and classified them according to their attributes, as well as analyzed their cross-taxon transferability and utility for the genetic study of Musa and its relatives. A high SSR frequency (177 per Mbp) was found in the Musa genome. AT-rich dinucleotide repeats are predominant, and trinucleotide repeats are the most abundant in transcribed regions. A significant number of Musa SSRs are associated with pre-miRNAs, and 83% of these SSRs are promising candidates for the development of therapeutic SSR markers. Overall, 74% of the SSR markers were polymorphic, and 94% were transferable to at least one Musa spp. Two hundred forty-three markers generated a total of 1047 alleles, with 2-8 alleles each and an average of 4.38 alleles per locus. The PIC values ranged from 0.31 to 0.89 and averaged 0.71. We report the largest set of non-redundant, polymorphic, new SSR markers to be developed in Musa. These additional markers could be a valuable resource for marker-assisted breeding, genetic diversity and genomic studies of Musa and related species. PMID:26121637

  20. Sixteen polymorphic microsatellite markers from Zizania latifolia Turcz. (Poaceae).

    PubMed

    Quan, Zhiwu; Pan, Lei; Ke, Weidong; Liu, Yiman; Ding, Yi

    2009-05-01

    Sixteen polymorphic microsatellite markers were isolated and identified in Zizania latifolia Turcz. (Poaceae), a perennial aquatic plant widespread in Eastern Asia. The microsatellite-enriched library was constructed using the fast isolation by AFLP of sequences containing repeats method. These markers revealed two to 14 alleles, with an average of 5.6 alleles per locus. The observed and expected heterozygosities varied from 0.071 to 0.690 and from 0.174 to 0.812, respectively. These markers will be useful for studying of gene flow and evaluating the genetic diversity of the Zizania latifolia population. PMID:21564779

  1. Microsatellite markers for Cariniana legalis (Lecythidaceae) and their transferability to C. estrellensis1

    PubMed Central

    Tambarussi, Evandro Vagner; Sebbenn, Alexandre Magno; Moreno, Maria Andréia; Ferraz, Elza Martins; Kageyama, Paulo Yoshio; Vencovsky, Roland

    2013-01-01

    • Premise of the study: Microsatellite primers were developed in the neotropical tree species Cariniana legalis (Lecythidaceae) to investigate its genetic diversity, mating system, and gene flow. • Methods and Results: We identified 96 clones containing 82 repeat motifs from a genomic library enriched for (CT)8 and (GT)8 motifs. Primer pairs were developed for 13 microsatellite loci and validated in 51 C. legalis specimens and 26 C. estrellensis specimens. Eleven loci were polymorphic, revealing a maximum of two to 15 alleles per locus in C. legalis and three to 12 in C. estrellensis. For C. legalis, the observed (Ho) and expected (He) heterozygosities ranged from 0 to 0.99 and from 0.07 to 0.90, respectively. For C. estrellensis, Ho and He ranged from 0 to 0.96 and from 0.14 to 0.91, respectively. • Conclusions: The primers identified polymorphic loci that are suitable to study genetic diversity and structure, mating system, and gene flow in C. legalis and the related species C. estrellensis. PMID:25202554

  2. Microsatellite markers for Cryptolestes ferrugineus (Coleoptera: Laemophloeidae) and other Cryptolestes species.

    PubMed

    Wu, Y; Li, F; Li, Z; Stejskal, V; Kučerová, Z; Opit, G; Aulicky, R; Zhang, T; He, P; Cao, Y

    2016-04-01

    Cryptolestes ferrugineus (Stephens, 1831) is an important insect pest of stored products. Due to its broad host range, short life cycle, and high reproductive capacity, this species has rapidly colonized temperate and tropical regions around the world. In this study, we isolated 18 novel polymorphic microsatellite loci from an enriched genomic library based on a biotin/streptavidin capture protocol. These loci will be useful tool to better understand the genetic structure and migration patterns of C. ferrugineus throughout the world. The genetic parameters were estimated based on 80 individual C. ferrugineus from two natural populations. The results revealed that 18 loci were different polymorphic levels. The numbers of alleles ranged from 3 to 12, and eleven loci demonstrated polymorphic information contents greater than 0.5. The observed (H O) and expected (H E) heterozygosities ranged from 0.051 to 0.883 and 0.173 to 0.815, respectively. Five locus/population combinations significantly deviated from Hardy-Weinberg equilibrium. We also demonstrated the potential utility of the C. ferrugineus microsatellites as population and species markers for four additional Cryptolestes species. PMID:26584625

  3. Transferability of Rubus Microsatellite Markers to Black Raspberry

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Microsatellite or simple sequence repeat (SSR) markers have been developed from genomic and expressed sequence tag (EST) libraries in red raspberry (Rubus idaeus L., subgenus Idaeobatus) and also in blackberry (Rubus L. subgenus Rubus). Recently, there has also been increased interest in the use of...

  4. The art of attrition: development of robust oat microsatellites

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Microsatellite or simple sequence repeat (SSR) markers are important tools for genetic analyses, especially those targeting diversity, based on the fact that multiple alleles can occur at a given locus. Currently, only 160 genomic-based SSR markers are publicly available for oat, most of which have...

  5. Indentification of 700 new microsatellite loci from cotton (G. hirsutum)

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Microsatellite markers, also known as SSRs, comprise a keystone technology for genetic linkage analysis, QTL mapping, marker-assisted breeding, and genome analysis. In order to contribute to a growing body of molecular marker resources for cotton research and improvement, we developed primers to am...

  6. Characterization of microsatellites in Fusicladium effusum, cause of pecan scab

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Pecan scab, caused by the plant pathogenic fungus Fusicladium effusum, is the most destructive disease of pecan. Little is known of the population genetic diversity of this pathogen. In this study, microsatellites were mined from the F. effusum genome, and flanking primers were subsequently designed...

  7. Microsatellites from the charcoal rot fungus (Macrophomina phaseolina)

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Microsatellite loci were identified from the charcoal rot fungus Macrophomina phaseolina. Primer pairs for 46 loci were developed and of these 13 were optimized and screened using genomic DNA from 44 fungal isolates collected predominantly from two soybean fields in MS. All optimized loci were poly...

  8. Phylogenetic marker development for target enrichment from transcriptome and genome skim data: the pipeline and its application in southern African Oxalis (Oxalidaceae).

    PubMed

    Schmickl, Roswitha; Liston, Aaron; Zeisek, Vojtěch; Oberlander, Kenneth; Weitemier, Kevin; Straub, Shannon C K; Cronn, Richard C; Dreyer, Léanne L; Suda, Jan

    2016-09-01

    Phylogenetics benefits from using a large number of putatively independent nuclear loci and their combination with other sources of information, such as the plastid and mitochondrial genomes. To facilitate the selection of orthologous low-copy nuclear (LCN) loci for phylogenetics in nonmodel organisms, we created an automated and interactive script to select hundreds of LCN loci by a comparison between transcriptome and genome skim data. We used our script to obtain LCN genes for southern African Oxalis (Oxalidaceae), a speciose plant lineage in the Greater Cape Floristic Region. This resulted in 1164 LCN genes greater than 600 bp. Using target enrichment combined with genome skimming (Hyb-Seq), we obtained on average 1141 LCN loci, nearly the whole plastid genome and the nrDNA cistron from 23 southern African Oxalis species. Despite a wide range of gene trees, the phylogeny based on the LCN genes was very robust, as retrieved through various gene and species tree reconstruction methods as well as concatenation. Cytonuclear discordance was strong. This indicates that organellar phylogenies alone are unlikely to represent the species tree and stresses the utility of Hyb-Seq in phylogenetics. PMID:26577756

  9. Microsatellite marker development for the rubber tree (Hevea brasiliensis): characterization and cross-amplification in wild Hevea species

    PubMed Central

    2012-01-01

    Background The rubber tree (Hevea brasiliensis) is native to the Amazon region and it is the major source of natural rubber in the world. Rubber tree breeding is time-consuming and expensive. However, molecular markers such as microsatellites can reduce the time required for these programs. This study reports new genomic microsatellite markers developed and characterized in H. brasiliensis and the evaluation of their transferability to other Hevea species. Findings We constructed di- and trinucleotide-enriched libraries. From these two libraries, 153 primer pairs were designed and initially evaluated using 9 genotypes of H. brasiliensis. A total of 119 primer pairs had a good amplification product, 90 of which were polymorphic. We chose 46 of the polymorphic markers and characterized them in 36 genotypes of H. brasiliensis. The expected and observed heterozygosities ranged from 0.1387 to 0.8629 and 0.0909 to 0.9167, respectively. The polymorphism information content (PIC) values ranged from 0.097 to 0.8339, and the mean number of alleles was 6.4 (2–17). These 46 microsatellites were also tested in 6 other Hevea species. The percentage of transferability ranged from 82% to 87%. Locus duplication was found in H. brasiliensis and also in 5 of other species in which transferability was tested. Conclusions This study reports new microsatellite markers for H. brasiliensis that can be used for genetic linkage mapping, quantitative trait loci identification and marker- assisted selection. The high percentage of transferability may be useful in the evaluations of genetic variability and to monitor introgression of genetic variability from different Hevea species into breeding programs. PMID:22731927

  10. Microsatellites Are Molecular Clocks That Support Accurate Inferences about History

    PubMed Central

    Mullikin, James C.; Patterson, Nick; Reich, David E.

    2009-01-01

    Microsatellite length mutations are often modeled using the generalized stepwise mutation process, which is a type of random walk. If this model is sufficiently accurate, one can estimate the coalescence time between alleles of a locus after a mathematical transformation of the allele lengths. When large-scale microsatellite genotyping first became possible, there was substantial interest in using this approach to make inferences about time and demography, but that interest has waned because it has not been possible to empirically validate the clock by comparing it with data in which the mutation process is well understood. We analyzed data from 783 microsatellite loci in human populations and 292 loci in chimpanzee populations, and compared them with up to one gigabase of aligned sequence data, where the molecular clock based upon nucleotide substitutions is believed to be reliable. We empirically demonstrate a remarkable linearity (r2 > 0.95) between the microsatellite average square distance statistic and sequence divergence. We demonstrate that microsatellites are accurate molecular clocks for coalescent times of at least 2 million years (My). We apply this insight to confirm that the African populations San, Biaka Pygmy, and Mbuti Pygmy have the deepest coalescent times among populations in the Human Genome Diversity Project. Furthermore, we show that microsatellites support unbiased estimates of population differentiation (FST) that are less subject to ascertainment bias than single nucleotide polymorphism (SNP) FST. These results raise the prospect of using microsatellite data sets to determine parameters of population history. When genotyped along with SNPs, microsatellite data can also be used to correct for SNP ascertainment bias. PMID:19221007

  11. A Microsatellite Genetic Linkage Map for Xiphophorus

    PubMed Central

    Walter, R. B.; Rains, J. D.; Russell, J. E.; Guerra, T. M.; Daniels, C.; Johnston, Dennis A.; Kumar, Jay; Wheeler, A.; Kelnar, K.; Khanolkar, V. A.; Williams, E. L.; Hornecker, J. L.; Hollek, L.; Mamerow, M. M.; Pedroza, A.; Kazianis, S.

    2004-01-01

    Interspecies hybrids between distinct species of the genus Xiphophorus are often used in varied research investigations to identify genomic regions associated with the inheritance of complex traits. There are 24 described Xiphophorus species and a greater number of pedigreed strains; thus, the number of potential interspecies hybrid cross combinations is quite large. Previously, select Xiphophorus experimental crosses have been shown to exhibit differing characteristics between parental species and among the hybrid fishes derived from crossing them, such as widely differing susceptibilities to chemical or physical agents. For instance, genomic regions harboring tumor suppressor and oncogenes have been identified via linkage association of these loci with a small set of established genetic markers. The power of this experimental strategy is related to the number of genetic markers available in the Xiphophorus interspecies cross of interest. Thus, we have undertaken the task of expanding the suite of easily scored markers by characterization of Xiphophorus microsatellite sequences. Using a cross between Xiphophorus maculatus and X. andersi, we report a linkage map predominantly composed of microsatellite markers. All 24 acrocentric chromosome sets of Xiphophorus are represented in the assembled linkage map with an average intergenomic distance of 7.5 cM. Since both male and female F1 hybrids were used to produce backcross progeny, these recombination rates were compared between “male” and “female” maps. Although several genomic regions exhibit differences in map length, male- and female-derived maps are similar. Thus Xiphophorus, in contrast to zebrafish, Danio rerio, and several other vertebrate species, does not show sex-specific differences in recombination. The microsatellite markers we report can be easily adapted to any Xiphophorus interspecies and some intraspecies crosses, and thus provide a means to directly compare results derived from independent

  12. Twelve polymorphic microsatellite loci from the Asian Citrus Psyllid, Diaphorina citri Kuwayama, the vector for citrus greening disease Huanglongbing

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Twelve polymorphic microsatellite markers were developed from microsatellite-enriched DNA libraries and mined from an EST library of Diaphorina citri, the vector of the devastating citrus greening disease (Huanglongbing). Analysis of 288 individuals from Florida, Texas, and Brazil showed allelic di...

  13. Characterization of polymorphic microsatellite loci for Blumeria graminis f. sp. tritici, cause of powdery mildew of wheat

    Technology Transfer Automated Retrieval System (TEKTRAN)

    In many wheat–growing regions of the world, powdery mildew, caused by Blumeria graminis f. sp. tritici is a major disease that results in significant yield losses. Using a microsatellite enrichment protocol, we developed primers for 10 microsatellite DNA loci to aid in studies of B. g. tritici popu...

  14. Microsatellite markers for characterization of native and introduced populations of Plasmopara viticola, the causal agent of grapevine downy mildew.

    PubMed

    Rouxel, Mélanie; Papura, Daciana; Nogueira, Marilise; Machefer, Virginie; Dezette, Damien; Richard-Cervera, Sylvie; Carrere, Sébastien; Mestre, Pere; Delmotte, François

    2012-09-01

    We reported 31 microsatellite markers that have been developed from microsatellite-enriched and direct shotgun pyrosequencing libraries of Plasmopara viticola, the causal agent of grapevine downy mildew. These markers were optimized for population genetics applications and used to characterize 96 P. viticola isolates from three European and three North American populations. PMID:22706046

  15. Microsatellite primer resource for Populus developed from

    SciTech Connect

    Yin, Tongming; Yang, Xiaohan; Gunter, Lee E; Tuskan, Gerald A; Wullschleger, Stan D; Huang, Prof. Minren; Li, Shuxian; Zhang, Xinye

    2008-01-01

    In this study, 148 428 simple sequence repeat (SSR) primer pairs were designed from the unambiguously mapped sequence scaffolds of the Nisqually-1 genome. The physical position of the priming sites were identified along each of the 19 Populus chromosomes, and it was specified whether the priming sequences belong to intronic, intergenic, exonic or UTR regions. A subset of 150 SSR loci were amplified and a high amplification success rate (72%) was obtained in P. tremuloides, which belongs to a divergent subgenus of Populus relative to Nisqually-1. PCR reactions showed that the amplification success rate of exonic primer pairs was much higher than that of the intronic/intergenic primer pairs. Applying ANOVA and regression analyses to the flanking sequences of microsatellites, the repeat lengths, the GC contents of the repeats, the repeat motif numbers, the repeat motif length and the base composition of the repeat motif, it was determined that only the base composition of the repeat motif and the repeat motif length significantly affect the microsatellite variability in P. tremuloides samples. The SSR primer resource developed in this study provides a database for selecting highly transferable SSR markers with known physical position in the Populus genome and provides a comprehensive genetic tool to extend the genome sequence of Nisqually-1 to genetic studies in different Populus species.

  16. Draft Genome Sequence of Ruminoclostridium sp. Ne3, Clostridia from an Enrichment Culture Obtained from Australian Subterranean Termite, Nasutitermes exitiosus

    PubMed Central

    Lin, Hai; Tran-Dinh, Nai; Li, Dongmei; Greenfield, Paul; Midgley, David J.

    2015-01-01

    The draft genome sequence of Ruminoclostridium sp. Ne3 was reconstructed from the metagenome of a hydrogenogenic microbial consortium growing on xylan. The organism is likely the primary hemicellulose degrader within the consortium. PMID:25908130

  17. Draft Genome Sequence of Ruminoclostridium sp. Ne3, Clostridia from an Enrichment Culture Obtained from Australian Subterranean Termite, Nasutitermes exitiosus.

    PubMed

    Wang, Han; Lin, Hai; Tran-Dinh, Nai; Li, Dongmei; Greenfield, Paul; Midgley, David J

    2015-01-01

    The draft genome sequence of Ruminoclostridium sp. Ne3 was reconstructed from the metagenome of a hydrogenogenic microbial consortium growing on xylan. The organism is likely the primary hemicellulose degrader within the consortium. PMID:25908130

  18. Exploring genetic variability within lentil (Lens culinaris Medik.) and across related legumes using a newly developed set of microsatellite markers.

    PubMed

    Verma, Priyanka; Sharma, Tilak R; Srivastava, Prem S; Abdin, M Z; Bhatia, Sabhyata

    2014-09-01

    Lentil (Lens culinaris Medik.) is an economically important grain legume, yet the genetic and genomic resources remain largely uncharacterized and unexploited in this crop. Microsatellites have become markers of choice for crop improvement applications. Hence, simple sequence repeat (SSR) markers were developed for lentil through the construction of genomic library enriched for GA/CT motifs. As a result 122 functional SSR primer pairs were developed from 151 microsatellite loci and validated in L. culinaris cv. Precoz. Thirty three SSR markers were utilized for the analysis of genetic relationships between cultivated and wild species of Lens and related legumes. A total of 123 alleles were amplified at 33 loci ranging from 2-5 alleles with an average of 3.73 alleles per locus. Polymorphic information content (PIC) for all the loci ranged from 0.13 to 0.99 with an average of 0.66 per locus. Varied levels of cross genera transferability were obtained ranging from 69.70 % across Pisum sativum to 12.12 % across Vigna radiata. The UPGMA based dendrogram was able to establish the uniqueness of each genotype and grouped them into two major clusters clearly resolving the genetic relationships within lentil and related species. The new set of SSR markers reported here were efficient and highly polymorphic and would add to the existing repertoire of lentil SSR markers to be utilized in molecular breeding. Moreover, the improved knowledge about intra- and inter-specific genetic relationships would facilitate germplasm utilization for lentil improvement. PMID:24893599

  19. Distribution, function and evolution characterization of microsatellite in Sargassum thunbergii (Fucales, Phaeophyta) transcriptome and their application in marker development

    PubMed Central

    Liu, Fuli; Hu, Zimin; Liu, Wenhui; Li, Jingjing; Wang, Wenjun; Liang, Zhourui; Wang, Feijiu; Sun, Xiutao

    2016-01-01

    Using transcriptome data to mine microsatellite and develop markers has growingly become prevalent. However, characterizing the possible function of microsatellite is relatively rare. In this study, we explored microsatellites in the transcriptome of the brown alga Sargassum thunbergii and characterized the frequencies, distribution, function and evolution, and developed primers to validate these microsatellites. Our results showed that Tri-nucleotide is the most abundant, followed by di- and mono-nucleotide. The length of microsatellite was significantly affected by the repeat motif size. The density of microsatellite in the CDS region is significantly lower than that in the UTR region. The annotation of the transcripts containing microsatellite showed that 573 transcripts have GO terms and can be categorized into 42 groups. Pathways enrichment showed that microsatellites were significantly overrepresented in the genes involved in pathways such as Ubiquitin mediated proteolysis, RNA degradation, Spliceosome, etc. Primers flanking 961 microsatellite loci were designed, and among the 30 pairs of primer selected randomly for availability test, 23 were proved to be efficient. These findings provided new insight into the function and evolution of microsatellite in transcriptome, and the identified microsatellite loci within the annotated gene will be useful for developing functional markers in S. thunbergii. PMID:26732855

  20. Distribution, function and evolution characterization of microsatellite in Sargassum thunbergii (Fucales, Phaeophyta) transcriptome and their application in marker development.

    PubMed

    Liu, Fuli; Hu, Zimin; Liu, Wenhui; Li, Jingjing; Wang, Wenjun; Liang, Zhourui; Wang, Feijiu; Sun, Xiutao

    2016-01-01

    Using transcriptome data to mine microsatellite and develop markers has growingly become prevalent. However, characterizing the possible function of microsatellite is relatively rare. In this study, we explored microsatellites in the transcriptome of the brown alga Sargassum thunbergii and characterized the frequencies, distribution, function and evolution, and developed primers to validate these microsatellites. Our results showed that Tri-nucleotide is the most abundant, followed by di- and mono-nucleotide. The length of microsatellite was significantly affected by the repeat motif size. The density of microsatellite in the CDS region is significantly lower than that in the UTR region. The annotation of the transcripts containing microsatellite showed that 573 transcripts have GO terms and can be categorized into 42 groups. Pathways enrichment showed that microsatellites were significantly overrepresented in the genes involved in pathways such as Ubiquitin mediated proteolysis, RNA degradation, Spliceosome, etc. Primers flanking 961 microsatellite loci were designed, and among the 30 pairs of primer selected randomly for availability test, 23 were proved to be efficient. These findings provided new insight into the function and evolution of microsatellite in transcriptome, and the identified microsatellite loci within the annotated gene will be useful for developing functional markers in S. thunbergii. PMID:26732855

  1. Microsatellite markers for Senna spectabilis var. excelsa (Caesalpinioideae, Fabaceae)1

    PubMed Central

    López-Roberts, M. Cristina; Barbosa, Ariane R.; Paganucci de Queiroz, Luciano; van den Berg, Cássio

    2016-01-01

    Premise of the study: Senna spectabilis var. excelsa (Fabaceae) is a South and Central American tree of great ecological importance and one of the most common species in several sites of seasonally dry forests. Our goal was to develop microsatellite markers to assess the genetic diversity and structure of this species. Methods and Results: We designed and assessed 53 loci obtained from a microsatellite-enriched library and an intersimple sequence repeat library. Fourteen loci were polymorphic, and they presented a total of 39 alleles in a sample of 61 individuals from six populations. The mean values of observed and expected heterozygosities were 0.355 and 0.479, respectively. Polymorphism information content was 0.390 and the Shannon index was 0.778. Conclusions: Polymorphism information content and Shannon index indicate that at least nine of the 14 microsatellite loci developed are moderate to highly informative, and potentially useful for population genetic studies in this species. PMID:26819856

  2. Genome-wide analysis of primary CD4+ and CD8+ T cell transcriptomes shows evidence for a network of enriched pathways associated with HIV disease

    PubMed Central

    2011-01-01

    Background HIV preferentially infects CD4+ T cells, and the functional impairment and numerical decline of CD4+ and CD8+ T cells characterize HIV disease. The numerical decline of CD4+ and CD8+ T cells affects the optimal ratio between the two cell types necessary for immune regulation. Therefore, this work aimed to define the genomic basis of HIV interactions with the cellular transcriptome of both CD4+ and CD8+ T cells. Results Genome-wide transcriptomes of primary CD4+ and CD8+ T cells from HIV+ patients were analyzed at different stages of HIV disease using Illumina microarray. For each cell subset, pairwise comparisons were performed and differentially expressed (DE) genes were identified (fold change >2 and B-statistic >0) followed by quantitative PCR validation. Gene ontology (GO) analysis of DE genes revealed enriched categories of complement activation, actin filament, proteasome core and proton-transporting ATPase complex. By gene set enrichment analysis (GSEA), a network of enriched pathways functionally connected by mitochondria was identified in both T cell subsets as a transcriptional signature of HIV disease progression. These pathways ranged from metabolism and energy production (TCA cycle and OXPHOS) to mitochondria meditated cell apoptosis and cell cycle dysregulation. The most unique and significant feature of our work was that the non-progressing status in HIV+ long-term non-progressors was associated with MAPK, WNT, and AKT pathways contributing to cell survival and anti-viral responses. Conclusions These data offer new comparative insights into HIV disease progression from the aspect of HIV-host interactions at the transcriptomic level, which will facilitate the understanding of the genetic basis of transcriptomic interaction of HIV in vivo and how HIV subverts the human gene machinery at the individual cell type level. PMID:21410942

  3. Mining new crystal protein genes from Bacillus thuringiensis on the basis of mixed plasmid-enriched genome sequencing and a computational pipeline.

    PubMed

    Ye, Weixing; Zhu, Lei; Liu, Yingying; Crickmore, Neil; Peng, Donghai; Ruan, Lifang; Sun, Ming

    2012-07-01

    We have designed a high-throughput system for the identification of novel crystal protein genes (cry) from Bacillus thuringiensis strains. The system was developed with two goals: (i) to acquire the mixed plasmid-enriched genomic sequence of B. thuringiensis using next-generation sequencing biotechnology, and (ii) to identify cry genes with a computational pipeline (using BtToxin_scanner). In our pipeline method, we employed three different kinds of well-developed prediction methods, BLAST, hidden Markov model (HMM), and support vector machine (SVM), to predict the presence of Cry toxin genes. The pipeline proved to be fast (average speed, 1.02 Mb/min for proteins and open reading frames [ORFs] and 1.80 Mb/min for nucleotide sequences), sensitive (it detected 40% more protein toxin genes than a keyword extraction method using genomic sequences downloaded from GenBank), and highly specific. Twenty-one strains from our laboratory's collection were selected based on their plasmid pattern and/or crystal morphology. The plasmid-enriched genomic DNA was extracted from these strains and mixed for Illumina sequencing. The sequencing data were de novo assembled, and a total of 113 candidate cry sequences were identified using the computational pipeline. Twenty-seven candidate sequences were selected on the basis of their low level of sequence identity to known cry genes, and eight full-length genes were obtained with PCR. Finally, three new cry-type genes (primary ranks) and five cry holotypes, which were designated cry8Ac1, cry7Ha1, cry21Ca1, cry32Fa1, and cry21Da1 by the B. thuringiensis Toxin Nomenclature Committee, were identified. The system described here is both efficient and cost-effective and can greatly accelerate the discovery of novel cry genes. PMID:22544259

  4. A novel methyl-binding domain protein enrichment method for identifying genome-wide tissue-specific DNA methylation from nanogram DNA samples

    PubMed Central

    2013-01-01

    Background Growing evidence suggests that DNA methylation plays a role in tissue-specific differentiation. Current approaches to methylome analysis using enrichment with the methyl-binding domain protein (MBD) are restricted to large (≥1 μg) DNA samples, limiting the analysis of small tissue samples. Here we present a technique that enables characterization of genome-wide tissue-specific methylation patterns from nanogram quantities of DNA. Results We have developed a methodology utilizing MBD2b/MBD3L1 enrichment for methylated DNA, kinase pre-treated ligation-mediated PCR amplification (MeKL) and hybridization to the comprehensive high-throughput array for relative methylation (CHARM) customized tiling arrays, which we termed MeKL-chip. Kinase modification in combination with the addition of PEG has increased ligation-mediated PCR amplification over 20-fold, enabling >400-fold amplification of starting DNA. We have shown that MeKL-chip can be applied to as little as 20 ng of DNA, enabling comprehensive analysis of small DNA samples. Applying MeKL-chip to the mouse retina (a limited tissue source) and brain, 2,498 tissue-specific differentially methylated regions (T-DMRs) were characterized. The top five T-DMRs (Rgs20, Hes2, Nfic, Cckbr and Six3os1) were validated by pyrosequencing. Conclusions MeKL-chip enables genome-wide methylation analysis of nanogram quantities of DNA with a wide range of observed-to-expected CpG ratios due to the binding properties of the MBD2b/MBD3L1 protein complex. This methodology enabled the first analysis of genome-wide methylation in the mouse retina, characterizing novel T-DMRs. PMID:23759032

  5. Microsatellite marker diversity in common bean (Phaseolus vulgaris L.).

    PubMed

    Blair, M W; Giraldo, M C; Buendía, H F; Tovar, E; Duque, M C; Beebe, S E

    2006-06-01

    A diversity survey was used to estimate allelic diversity and heterozygosity of 129 microsatellite markers in a panel of 44 common bean (Phaseolus vulgaris L.) genotypes that have been used as parents of mapping populations. Two types of microsatellites were evaluated, based respectively on gene coding and genomic sequences. Genetic diversity was evaluated by estimating the polymorphism information content (PIC), as well as the distribution and range of alleles sizes. Gene-based microsatellites proved to be less polymorphic than genomic microsatellites in terms of both number of alleles (6.0 vs. 9.2) and PIC values (0.446 vs. 0.594) while greater size differences between the largest and the smallest allele were observed for the genomic microsatellites than for the gene-based microsatellites (31.4 vs. 19.1 bp). Markers that showed a high number of alleles were identified with a maximum of 28 alleles for the marker BMd1. The microsatellites were useful for distinguishing Andean and Mesoamerican genotypes, for uncovering the races within each genepool and for separating wild accessions from cultivars. Greater polymorphism and race structure was found within the Andean gene pool than within the Mesoamerican gene pool and polymorphism rate between genotypes was consistent with genepool and race identity. Comparisons between Andean genotypes had higher polymorphism (53.0%) on average than comparisons among Mesoamerican genotypes (33.4%). Within the Mesoamerican parental combinations, the intra-racial combinations between Mesoamerica and Durango or Jalisco race genotypes showed higher average rates of polymorphism (37.5%) than the within-race combinations between Mesoamerica race genotypes (31.7%). In multiple correspondance analysis we found two principal clusters of genotypes corresponding to the Mesoamerican and Andean gene pools and subgroups representing specific races especially for the Nueva Granada and Peru races of the Andean gene pool. Intra population diversity

  6. Student's Microsatellite Project

    NASA Astrophysics Data System (ADS)

    Zelentsov, Victor; Kopik, Anatoliy; Karpenko, Stanislav; Mayorova, Victoria

    2002-01-01

    Nowadays BMSTU Youth space center carries on development of the microsatellite project. The project is based on principles of students direct involvement on all stages of development and maintenance of the satellite. The group of students was organized within the university with purpose of coordination of work at the program. Project current condition The work on creation of an experimental model of the micro satellite is performed. The aim is to define the structure and parameters of on-board devices (mass-overall dimensions characteristics, energy consumption and so on). developed. According to the simplified model an active stabilization system (three orthogonal electro-magnetic coils) and orientation characterization system (sunlight detector and magnitometer) are included in OCS structure. most suitable battery storage, power-supply controlling system. Student micro-satellite program goals 1.Scientific Information gaining in the field of Earth study- using perspective research methods. Studying of new devices behavior in space conditions. 2. Educative a. Students derive real experience of projecting, building of a spacecraft from the point of view of an experimenter, a constructor and a researcher. b. Organization of student's cooperation with key men of aerospace industry and other branches. c. Brainpower and material base preparation for micro-satellite systems' development. d. Attraction of youth interest to the topic, by: - Students' and pupils' groups attraction and involvement in experiments conduction and results processing. - Seminars and lections devoted to Earth study from the space organization - Specific scientific data distribution over World Wide Web. 3. International With purpose of program expansion, the developers' group looks to start of an international project. Within the project new experiments conduction and scientific information exchange are expected. 4. Status Bauman Moscow State Technical University's status improvement in the field

  7. Development and characterization of microsatellite primers for Chamaecyparis obtusa (Cupressaceae)1

    PubMed Central

    Kim, Young Mi; Shin, Yu Seung; Jeong, Ji Hee

    2016-01-01

    Premise of the study: Although several microsatellite markers of Chamaecyparis obtusa (Cupressaceae) have been reported in previous studies, we newly developed and evaluated polymorphic microsatellite markers of C. obtusa, an economically important species in Korea as a major forestation tree species, for further genetic studies. Methods and Results: Microsatellite-enrichment libraries were constructed according to the selective hybridization method. From this output, we obtained 10 polymorphic and five monomorphic microsatellite markers for C. obtusa. Five of these developed markers were successfully amplified for C. pisifera, a related species. Conclusions: These microsatellite markers can be valuable tools for further genetic studies of C. obtusa, and gathered genetic information may be useful for breeding program management. PMID:27213124

  8. Whole Genome Duplication and Enrichment of Metal Cation Transporters Revealed by De Novo Genome Sequencing of Extremely Halotolerant Black Yeast Hortaea werneckii

    PubMed Central

    Jackman, Shaun; Turk, Martina; Sadowski, Ivan; Nislow, Corey; Jones, Steven; Birol, Inanc; Cimerman, Nina Gunde; Plemenitaš, Ana

    2013-01-01

    Hortaea werneckii, ascomycetous yeast from the order Capnodiales, shows an exceptional adaptability to osmotically stressful conditions. To investigate this unusual phenotype we obtained a draft genomic sequence of a H. werneckii strain isolated from hypersaline water of solar saltern. Two of its most striking characteristics that may be associated with a halotolerant lifestyle are the large genetic redundancy and the expansion of genes encoding metal cation transporters. Although no sexual state of H. werneckii has yet been described, a mating locus with characteristics of heterothallic fungi was found. The total assembly size of the genome is 51.6 Mb, larger than most phylogenetically related fungi, coding for almost twice the usual number of predicted genes (23333). The genome appears to have experienced a relatively recent whole genome duplication, and contains two highly identical gene copies of almost every protein. This is consistent with some previous studies that reported increases in genomic DNA content triggered by exposure to salt stress. In hypersaline conditions transmembrane ion transport is of utmost importance. The analysis of predicted metal cation transporters showed that most types of transporters experienced several gene duplications at various points during their evolution. Consequently they are present in much higher numbers than expected. The resulting diversity of transporters presents interesting biotechnological opportunities for improvement of halotolerance of salt-sensitive species. The involvement of plasma P-type H+ ATPases in adaptation to different concentrations of salt was indicated by their salt dependent transcription. This was not the case with vacuolar H+ ATPases, which were transcribed constitutively. The availability of this genomic sequence is expected to promote the research of H. werneckii. Studying its extreme halotolerance will not only contribute to our understanding of life in hypersaline environments, but should also

  9. Whole genome duplication and enrichment of metal cation transporters revealed by de novo genome sequencing of extremely halotolerant black yeast Hortaea werneckii.

    PubMed

    Lenassi, Metka; Gostinčar, Cene; Jackman, Shaun; Turk, Martina; Sadowski, Ivan; Nislow, Corey; Jones, Steven; Birol, Inanc; Cimerman, Nina Gunde; Plemenitaš, Ana

    2013-01-01

    Hortaea werneckii, ascomycetous yeast from the order Capnodiales, shows an exceptional adaptability to osmotically stressful conditions. To investigate this unusual phenotype we obtained a draft genomic sequence of a H. werneckii strain isolated from hypersaline water of solar saltern. Two of its most striking characteristics that may be associated with a halotolerant lifestyle are the large genetic redundancy and the expansion of genes encoding metal cation transporters. Although no sexual state of H. werneckii has yet been described, a mating locus with characteristics of heterothallic fungi was found. The total assembly size of the genome is 51.6 Mb, larger than most phylogenetically related fungi, coding for almost twice the usual number of predicted genes (23333). The genome appears to have experienced a relatively recent whole genome duplication, and contains two highly identical gene copies of almost every protein. This is consistent with some previous studies that reported increases in genomic DNA content triggered by exposure to salt stress. In hypersaline conditions transmembrane ion transport is of utmost importance. The analysis of predicted metal cation transporters showed that most types of transporters experienced several gene duplications at various points during their evolution. Consequently they are present in much higher numbers than expected. The resulting diversity of transporters presents interesting biotechnological opportunities for improvement of halotolerance of salt-sensitive species. The involvement of plasma P-type H⁺ ATPases in adaptation to different concentrations of salt was indicated by their salt dependent transcription. This was not the case with vacuolar H⁺ ATPases, which were transcribed constitutively. The availability of this genomic sequence is expected to promote the research of H. werneckii. Studying its extreme halotolerance will not only contribute to our understanding of life in hypersaline environments, but should

  10. Development of microsatellite markers in potato and their transferability in some members of Solanaceae.

    PubMed

    Grover, Atul; Ramesh, B; Sharma, P C

    2009-10-01

    We have developed thirty new microsatellite markers in potato by screening genomic libraries and ESTs. Genomic libraries of potato cultivar Kufri Bahar were screened for sequences containing microsatellite motifs GA, GT, ACA, ATC, GAA, TAA and GATA. Using flanking sequences, PCR primers were designed for microsatellites identified from genomic libraries and ESTs. Sixteen new primer pairs from genomic libraries and fourteen from ESTs along with seven previously published primer pairs amplified PCR products in the selected genotypes comprising of 65 Solanum tuberosum lines and 14 other species of the potato gene pool. Neighbor-joining tree based on genetic distance matrix developed using microsatellite markers successfully distinguished all these genotypes in the expected size range. Seventeen microsatellites could also be cross-amplified in at least one of the five members of solanaceae, namely tomato, eggplant, pepper, petunia and tobacco. The new microsatellite markers obtained in this study will be useful in various genetic and taxonomic studies in potato and related genomes. PMID:23572945

  11. Development, characterization, and transferability to other Solanaceae of microsatellite markers in pepper (Capsicum annuum L.).

    PubMed

    Nagy, István; Stágel, Anikó; Sasvári, Zsuzsanna; Röder, Marion; Ganal, Martin

    2007-07-01

    A novel set of informative microsatellite markers for pepper (Capsicum annuum L.) is provided. Screening of approximately 168 000 genomic clones and 23 174 public database entries resulted in a total of 411 microsatellite-containing sequences that could be used for primer design and functional testing. A set of 154 microsatellite markers originated from short-insert genomic libraries and 257 markers originated from database sequences. Of those markers, 147 (61 from genomic libraries and 86 from database sequences) showed specific and scoreable amplification products and detected polymorphisms between at least 2 of the 33 lines of a test panel consisting of cultivated and wild Capsicum genotypes. These informative markers were subsequently surveyed for allelic variation and information content. The usefulness of the new markers for diversity and taxonomic studies was demonstrated by the construction of consistent phylogenetic trees based on the microsatellite polymorphisms. Conservation of a subset of microsatellite loci in pepper, tomato, and potato was proven by cross-species amplification and sequence comparisons. For several informative pepper microsatellite markers, homologous expressed sequence tag (EST) counterparts could be identified in these related species that also carry microsatellite motifs. Such orthologs can potentially be used as reference markers and common anchoring points on the genetic maps of different solanaceous species. PMID:17893745

  12. Quick genome sequencing of “Candidatus Liberibacter” strains by use of Enrichment-Enlargement-Next generation sequencing (EEN)

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Members of “Candidatus Liberibacter” are associated with several important plant diseases such as citrus Huanglongbing (HLB) and potato zebra chip (ZC) disease. Inability to culture and low titers in infected hosts have been major obstacles for research on these bacteria. The use of whole genome seq...

  13. Draft Genome Sequence of Clostridium beijerinckii Ne1, Clostridia from an Enrichment Culture Obtained from Australian Subterranean Termite, Nasutitermes exitiosus.

    PubMed

    Wang, Han; Lin, Hai; Tran-Dinh, Nai; Li, Dongmei; Greenfield, Paul; Midgley, David J

    2015-01-01

    The draft genome of Clostridium beijerinckii strain Ne1 was reconstructed from the metagenomic sequence of a mixed-microbial consortium that produced commercially significant quantities of hydrogen from xylan as a sole feedstock. The organism possesses relatively limited hemicellulolytic capacity and likely requires the action of other organisms to completely degrade xylan. PMID:25908128

  14. Draft Genome Sequence of Clostridium sp. Ne2, Clostridia from an Enrichment Culture Obtained from Australian Subterranean Termite, Nasutitermes exitiosus.

    PubMed

    Wang, Han; Lin, Hai; Tran-Dinh, Nai; Li, Dongmei; Greenfield, Paul; Midgley, David J

    2015-01-01

    The draft genome sequence of Clostridium sp. Ne2 was reconstructed from a metagenome of a hydrogenogenic microbial consortium. The organism is most closely related to Clostridium magnum and is a strict anaerobe that is predicted to ferment a range of simple sugars. PMID:25908129

  15. Draft Genome Sequence of Clostridium sp. Ne2, Clostridia from an Enrichment Culture Obtained from Australian Subterranean Termite, Nasutitermes exitiosus

    PubMed Central

    Lin, Hai; Tran-Dinh, Nai; Li, Dongmei; Greenfield, Paul; Midgley, David J.

    2015-01-01

    The draft genome sequence of Clostridium sp. Ne2 was reconstructed from a metagenome of a hydrogenogenic microbial consortium. The organism is most closely related to Clostridium magnum and is a strict anaerobe that is predicted to ferment a range of simple sugars. PMID:25908129

  16. Draft Genome Sequence of Clostridium beijerinckii Ne1, Clostridia from an Enrichment Culture Obtained from Australian Subterranean Termite, Nasutitermes exitiosus

    PubMed Central

    Lin, Hai; Tran-Dinh, Nai; Li, Dongmei; Greenfield, Paul; Midgley, David J.

    2015-01-01

    The draft genome of Clostridium beijerinckii strain Ne1 was reconstructed from the metagenomic sequence of a mixed-microbial consortium that produced commercially significant quantities of hydrogen from xylan as a sole feedstock. The organism possesses relatively limited hemicellulolytic capacity and likely requires the action of other organisms to completely degrade xylan. PMID:25908128

  17. The Genome of the Generalist Plant Pathogen Fusarium avenaceum Is Enriched with Genes Involved in Redox, Signaling and Secondary Metabolism

    PubMed Central

    Lysøe, Erik; Harris, Linda J.; Walkowiak, Sean; Subramaniam, Rajagopal; Divon, Hege H.; Riiser, Even S.; Llorens, Carlos; Gabaldón, Toni; Kistler, H. Corby; Jonkers, Wilfried; Kolseth, Anna-Karin; Nielsen, Kristian F.; Thrane, Ulf; Frandsen, Rasmus J. N.

    2014-01-01

    Fusarium avenaceum is a fungus commonly isolated from soil and associated with a wide range of host plants. We present here three genome sequences of F. avenaceum, one isolated from barley in Finland and two from spring and winter wheat in Canada. The sizes of the three genomes range from 41.6–43.1 MB, with 13217–13445 predicted protein-coding genes. Whole-genome analysis showed that the three genomes are highly syntenic, and share>95% gene orthologs. Comparative analysis to other sequenced Fusaria shows that F. avenaceum has a very large potential for producing secondary metabolites, with between 75 and 80 key enzymes belonging to the polyketide, non-ribosomal peptide, terpene, alkaloid and indole-diterpene synthase classes. In addition to known metabolites from F. avenaceum, fuscofusarin and JM-47 were detected for the first time in this species. Many protein families are expanded in F. avenaceum, such as transcription factors, and proteins involved in redox reactions and signal transduction, suggesting evolutionary adaptation to a diverse and cosmopolitan ecology. We found that 20% of all predicted proteins were considered to be secreted, supporting a life in the extracellular space during interaction with plant hosts. PMID:25409087

  18. Characterization of microsatellite markers for Baccharis dracunculifolia (Asteraceae)1

    PubMed Central

    Belini, Camila M. B.; Marques, Marcia O. M.; Figueira, Glyn M.; Bajay, Miklos M.; Campos, Jaqueline B.; Viana, João P. G.; Pinheiro, José B.; Zucchi, Maria I.

    2016-01-01

    Premise of the study: Baccharis dracunculifolia (Asteraceae) is a native plant of the Atlantic Forest that is used for the production of essential oil. Microsatellite markers were developed for this species to investigate the genetic diversity of three natural populations. Methods and Results: Seventeen out of 27 microsatellite loci identified in a genomic library used for the characterization of 315 individuals derived from three natural populations of B. dracunculifolia resulted in successful amplifications. Eleven polymorphic loci, ranging from two to seven alleles per locus, were obtained with expected and observed heterozygosity values ranging between 0.068 and 0.775 and 0.046 and 0.667, respectively. Conclusions: The microsatellite loci described in this study are tools that can be used for further studies of population genetics of B. dracunculifolia with a focus on deforested areas and conservation of natural populations. PMID:27011894

  19. Development of microsatellite markers for Crepis mollis (Asteraceae)1

    PubMed Central

    Duwe, Virginia K.; Muller, Ludo A. H.; Borsch, Thomas; Ismail, Sascha A.

    2016-01-01

    Premise of the study: Polymorphic microsatellite markers were developed for the threatened species Crepis mollis (Asteraceae) to investigate population and conservation genetics. Methods and Results: Illumina sequencing was conducted on pooled genomic DNA from 10 individuals of two populations. Ten polymorphic and 10 monomorphic microsatellite loci with di-, tri-, tetra-, penta-, and hexanucleotide repeat motifs were developed and characterized in C. mollis. In the polymorphic markers, up to 17 alleles per locus were detected with an observed and expected heterozygosity ranging from 0.120 to 0.780 and 0.102 to 0.834, respectively. Furthermore, the polymorphic markers were tested for cross-amplification in three congeneric species (C. biennis, C. foetida, and C. sancta) and amplified in up to three loci. Conclusions: The markers developed in this study are the first microsatellites tested on C. mollis and will be useful for performing population and conservation genetic studies in this threatened species. PMID:27437177

  20. A microsatellite genetic linkage map of human chromosome 18

    SciTech Connect

    Straub, R.E.; Speer, M.C.; Luo, Ying; Ott, J.; Gilliam, T.C. ); Rojas, K.; Overhauser, J. )

    1993-01-01

    We isolated nine new microsatellite markers from chromosome 18 and further characterized and mapped eight microsatellites developed in other laboratories. We have constructed a framework linkage map of chromosome 18 that includes 14 microsatellite markers (12 dinucleotide and 2 tetranucleotide) and 2 RFLP markers. Cytogenetic localization for the microsatellites was performed by PCR amplification of IS somatic cell hybrids containing different deletions of chromosome 18. Twelve of the microsatellites and one of the RFLPs have heterozygosities greater than 70%. The average heterozygosity of the markers included in the map is 72%. In addition, we have made provisional placements of 3 more microsatellite markers and 2 more RFLP markers. The map lengths (in Kosambi centimorgans) are as follows: sex-averaged, 109.3 cM; male, 72.4 cM; female, 161.2 cM. The average distance between markers in the sex-averaged map is 7.3 cM, and the largest gap between markers is 16.7 cM. Analysis of the data for differences in the female:male map distance ratio revealed significant evidence for a constant difference in the ratio (X[sup 2]=32.25; df = 1; P < 0.001; ratio = 2.5:1). Furthermore, there was significant evidence in favor of a variable female:male map distance ratio across the chromosome compared to a constant distance ratio (X[sup 2] = 27.78; df = 14; P = 0.015). To facilitate their use in genomic screening for disease genes, all of the microsatellite markers used here can be amplified under standard PCR conditions, and most can be used in duplex PCR reactions. 36 refs., 3 figs., 4 tabs.

  1. The use of sequence-based SSR mining for the development of a vast collection of microsatellites in Aquilegia formosa

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Numerous microsatellite markers were developed for Aquilegia formosa from sequences deposited within the Expressed Sequence Tag (EST), Genomic Survey Sequence (GSS), and Nucleotide databases in NCBI. Microsatellites (SSRs) were identified and primers designed for 9 SSR containing sequences in the Nu...

  2. Lung cancer diagnosed in the young is associated with enrichment for targetable genomic alterations and poor prognosis

    PubMed Central

    Sacher, Adrian G.; Dahlberg, Suzanne E.; Heng, Jennifer; Mach, Stacy; Jänne, Pasi A.; Oxnard, Geoffrey R.

    2016-01-01

    Importance NSCLC in the young is a rare entity and the genomics and clinical characteristics of this disease are poorly understood. In contrast, young age at diagnosis has been demonstrated to define unique disease biology in other cancers. Here we report on the association of young age with targetable genomic alterations and prognosis in a large cohort of NSCLC patients. Objective To determine the relationship between young age at diagnosis and both the presence of a potentially targetable genomic alteration as well as prognosis and natural history. Design All patients with NSCLC genotyped at the Dana-Farber Cancer Institute between 2002–2014 were identified. Tumor genotype, patient characteristics and clinical outcomes were collected. Multivariate logistic regression was used to analyze the relationship between age and mutation status. Multivariate Cox proportional hazard models were fitted for survival analysis. Setting A National Cancer Institute (NCI) designated comprehensive cancer center. Participants All patients with NSCLC seen at the Dana-Farber Cancer Institute between 2002–2014 who underwent tumor genotyping. Main Outcome Measure The frequency of targetable genomic alterations by defined age categories as well as the association of these age groups with survival. Results 2237 patients with NSCLC were studied. EGFR (p=0.02) and ALK (P<0.01) were associated with younger age, and a similar trend existed for HER2 (p=0.15) and ROS1 (p=0.1) but not BRAF V600E (p=0.43). Amongst patients tested for all 5 targetable genomic alterations, younger age was associated with an increased frequency of a targetable genotype (p<0.01). Those diagnosed at age 50 or younger have a 59% increased likelihood of harboring a targetable genotype. While presence of a potentially targetable genomic alteration treated with a targeted agent was associated with improved survival, the youngest and oldest age groupings had similarly poor outcomes even when a targetable genotype was

  3. A Novel Approach for Characterizing Microsatellite Instability in Cancer Cells

    PubMed Central

    Lu, Yuheng; Soong, T. David; Elemento, Olivier

    2013-01-01

    Microsatellite instability (MSI) is characterized by the expansion or contraction of DNA repeat tracts as a consequence of DNA mismatch repair deficiency (MMRD). Accurate detection of MSI in cancer cells is important since MSI is associated with several cancer subtypes and can help inform therapeutic decisions. Although experimental assays have been developed to detect MSI, they typically depend on a small number of known microsatellite loci or mismatch repair genes and have limited reliability. Here, we report a novel genome-wide approach for MSI detection based on the global detection of insertions and deletions (indels) in microsatellites found in expressed genes. Our large-scale analyses of 20 cancer cell lines and 123 normal individuals revealed striking indel features associated with MSI: there is a significant increase of short microsatellite deletions in MSI samples compared to microsatellite stable (MSS) ones, suggesting a mechanistic bias of repair efficiency between insertions and deletions in normal human cells. By incorporating this observation into our MSI scoring metric, we show that our approach can correctly distinguish between MSI and MSS cancer cell lines. Moreover, when we applied this approach to primal tumor samples, our metric is also well consistent with diagnosed MSI status. Thus, our study offers new insight into DNA mismatch repair system, and also provides a novel MSI diagnosis method for clinical oncology with better reliability. PMID:23671654

  4. A polymorphic microsatellite from the Squalius alburnoides complex (Osteichthyes, Cyprinidae) cloned by serendipity can be useful in genetic analysis of polyploids

    PubMed Central

    Boto, Luis; Cunha, Carina; Doadrio, Ignacio

    2011-01-01

    A new microsatellite locus (SAS1) for Squalius alburnoides was obtained through cloning by serendipity. The possible usefulness of this new species-specific microsatellite in genetic studies of this hybrid-species complex, was explored. The polymorphism exhibited by SAS1 microsatellite is an important addition to the set of microsatellites previously used in genetic studies in S. alburnoides complex, that mostly relied in markers described for other species. Moreover, the SAS1 microsatellite could be used to identify the parental genomes of the complex, complementing other methods recently described for the same purpose.. PMID:21931529

  5. Combining genetic mapping with genome-wide expression in experimental autoimmune encephalomyelitis highlights a gene network enriched for T cell functions and candidate genes regulating autoimmunity

    PubMed Central

    Thessen Hedreul, Melanie; Möller, Steffen; Stridh, Pernilla; Gupta, Yask; Gillett, Alan; Daniel Beyeen, Amennai; Öckinger, Johan; Flytzani, Sevasti; Diez, Margarita; Olsson, Tomas; Jagodic, Maja

    2013-01-01

    The experimental autoimmune encephalomyelitis (EAE) is an autoimmune disease of the central nervous system commonly used to study multiple sclerosis (MS). We combined clinical EAE phenotypes with genome-wide expression profiling in spleens from 150 backcross rats between susceptible DA and resistant PVG rat strains during the chronic EAE phase. This enabled correlation of transcripts with genotypes, other transcripts and clinical EAE phenotypes and implicated potential genetic causes and pathways in EAE. We detected 2285 expression quantitative trait loci (eQTLs). Sixty out of 599 cis-eQTLs overlapped well-known EAE QTLs and constitute positional candidate genes, including Ifit1 (Eae7), Atg7 (Eae20-22), Klrc3 (eEae22) and Mfsd4 (Eae17). A trans-eQTL that overlaps Eae23a regulated a large number of small RNAs and implicates a master regulator of transcription. We defined several disease-correlated networks enriched for pathways involved in cell-mediated immunity. They include C-type lectins, G protein coupled receptors, mitogen-activated protein kinases, transmembrane proteins, suppressors of transcription (Jundp2 and Nr1d1) and STAT transcription factors (Stat4) involved in interferon signaling. The most significant network was enriched for T cell functions, similar to genetic findings in MS, and revealed both established and novel gene interactions. Transcripts in the network have been associated with T cell proliferation and differentiation, the TCR signaling and regulation of regulatory T cells. A number of network genes and their family members have been associated with MS and/or other autoimmune diseases. Combining disease and genome-wide expression phenotypes provides a link between disease risk genes and distinct molecular pathways that are dysregulated during chronic autoimmune inflammation. PMID:23900079

  6. Genomic Survey and Biochemical Analysis of Recombinant Candidate Cyanobacteriochromes Reveals Enrichment for Near UV/Violet Sensors in the Halotolerant and Alkaliphilic Cyanobacterium Microcoleus IPPAS B353.

    PubMed

    Cho, Sung Mi; Jeoung, Sae Chae; Song, Ji-Young; Kupriyanova, Elena V; Pronina, Natalia A; Lee, Bong-Woo; Jo, Seong-Whan; Park, Beom-Seok; Choi, Sang-Bong; Song, Ji-Joon; Park, Youn-Il

    2015-11-20

    Cyanobacteriochromes (CBCRs), which are exclusive to and widespread among cyanobacteria, are photoproteins that sense the entire range of near-UV and visible light. CBCRs are related to the red/far-red phytochromes that utilize linear tetrapyrrole (bilin) chromophores. Best characterized from the unicellular cyanobacterium Synechocystis sp. PCC 6803 and the multicellular heterocyst forming filamentous cyanobacteria Nostoc punctiforme ATCC 29133 and Anabaena sp. PCC 7120, CBCRs have been poorly investigated in mat-forming, nonheterocystous cyanobacteria. In this study, we sequenced the genome of one of such species, Microcoleus IPPAS B353 (Microcoleus B353), and identified two phytochromes and seven CBCRs with one or more bilin-binding cGMP-specific phosphodiesterase, adenylyl cyclase and FhlA (GAF) domains. Biochemical and spectroscopic measurements of 23 purified GAF proteins from phycocyanobilin (PCB) producing recombinant Escherichia coli indicated that 13 of these proteins formed near-UV and visible light-absorbing covalent adducts: 10 GAFs contained PCB chromophores, whereas three contained the PCB isomer, phycoviolobilin (PVB). Furthermore, the complement of Microcoleus B353 CBCRs is enriched in near-UV and violet sensors, but lacks red/green and green/red CBCRs that are widely distributed in other cyanobacteria. We hypothesize that enrichment in short wavelength-absorbing CBCRs is critical for acclimation to high-light environments where this organism is found. PMID:26405033

  7. Population analysis of microsatellite genotypes reveals a signature associated with ovarian cancer.

    PubMed

    Fonville, Natalie C; Vaksman, Zalman; McIver, Lauren J; Garner, Harold R

    2015-05-10

    Ovarian cancer (OV) ranks fifth in cancer deaths among women, yet there remain few informative biomarkers for this disease. Microsatellites are repetitive genomic regions which we hypothesize could be a source of novel biomarkers for OV and have traditionally been under-appreciated relative to Single Nucleotide Polymorphisms (SNPs). In this study, we explore microsatellite variation as a potential novel source of genomic variation associated with OV. Exomes from 305 OV patient germline samples and 54 tumors, sequenced as part of The Cancer Genome Atlas, were analyzed for microsatellite variation and compared to healthy females sequenced as part of the 1,000 Genomes Project. We identified a subset of 60 microsatellite loci with genotypes that varied significantly between the OV and healthy female populations. Using these loci as a signature set, we classified germline genomes as 'at risk' for OV with a sensitivity of 90.1% and a specificity of 87.6%. Cross-analysis with a similar set of breast cancer associated loci identified individuals 'at risk' for both diseases. This study revealed a genotype-based microsatellite signature present in the germlines of individuals diagnosed with OV, and provides the basis for a potential novel risk assessment diagnostic for OV and new personal genomics targets in tumors. PMID:25779658

  8. ve-SEQ: Robust, unbiased enrichment for streamlined detection and whole-genome sequencing of HCV and other highly diverse pathogens

    PubMed Central

    Trebes, Amy; Brown, Anthony; Klenerman, Paul; Buck, David; Piazza, Paolo; Barnes, Eleanor; Bowden, Rory

    2015-01-01

    The routine availability of high-depth virus sequence data would allow the sensitive detection of resistance-associated variants that can jeopardize HIV or hepatitis C virus (HCV) treatment. We introduce ve-SEQ, a high-throughput method for sequence-specific enrichment and characterization of whole-virus genomes at up to 20% divergence from a reference sequence and 1,000-fold greater sensitivity than direct sequencing. The extreme genetic diversity of HCV led us to implement an algorithm for the efficient design of panels of oligonucleotide probes to capture any sequence among a defined set of targets without detectable bias. ve-SEQ enables efficient detection and sequencing of any HCV genome, including mixtures and intra-host variants, in a single experiment, with greater tolerance of sequence diversity than standard amplification methods and greater sensitivity than metagenomic sequencing, features that are directly applicable to other pathogens or arbitrary groups of target organisms, allowing the combination of sensitive detection with sequencing in many settings. PMID:27092241

  9. Using Next Generation RAD Sequencing to Isolate Multispecies Microsatellites for Pilosocereus (Cactaceae).

    PubMed

    Bonatelli, Isabel A S; Carstens, Bryan C; Moraes, Evandro M

    2015-01-01

    Microsatellite markers (also known as SSRs, Simple Sequence Repeats) are widely used in plant science and are among the most informative molecular markers for population genetic investigations, but the development of such markers presents substantial challenges. In this report, we discuss how next generation sequencing can replace the cloning, Sanger sequencing, identification of polymorphic loci, and testing cross-amplification that were previously required to develop microsatellites. We report the development of a large set of microsatellite markers for five species of the Neotropical cactus genus Pilosocereus using a restriction-site-associated DNA sequencing (RAD-seq) on a Roche 454 platform. We identified an average of 165 microsatellites per individual, with the absolute numbers across individuals proportional to the sequence reads obtained per individual. Frequency distribution of the repeat units was similar in the five species, with shorter motifs such as di- and trinucleotide being the most abundant repeats. In addition, we provide 72 microsatellites that could be potentially amplified in the sampled species and 22 polymorphic microsatellites validated in two populations of the species Pilosocereus machrisii. Although low coverage sequencing among individuals was observed for most of the loci, which we suggest to be more related to the nature of the microsatellite markers and the possible bias inserted by the restriction enzymes than to the genome size, our work demonstrates that an NGS approach is an efficient method to isolate multispecies microsatellites even in non-model organisms. PMID:26561396

  10. Microsatellite analyses across three diverse vertebrate transcriptomes (Acipenser fulvescens, Ambystoma tigrinum, and Dipodomys spectabilis).

    PubMed

    Doyle, Jacqueline M; Siegmund, Gregor; Ruhl, Joseph D; Eo, Soo Hyung; Hale, Matthew C; Marra, Nicholas J; Waser, Peter M; Dewoody, J Andrew

    2013-07-01

    Historically, many population genetics studies have utilized microsatellite markers sampled at random from the genome and presumed to be selectively neutral. Recent studies, however, have shown that microsatellites can occur in transcribed regions, where they are more likely to be under selection. In this study, we mined microsatellites from transcriptomes generated by 454-pyrosequencing for three vertebrate species: lake sturgeon (Acipenser fulvescens), tiger salamander (Ambystoma tigrinum), and kangaroo rat (Dipodomys spectabilis). We evaluated (i) the occurrence of microsatellites across species; (ii) whether particular gene ontology terms were over-represented in genes that contained microsatellites; (iii) whether repeat motifs were located in untranslated regions or coding sequences of genes; and (iv) in silico polymorphism. Microsatellites were less common in tiger salamanders than in either lake sturgeon or kangaroo rats. Across libraries, trinucleotides were found more frequently than any other motif type, presumably because they do not cause frameshift mutations. By evaluating variation across reads assembled to a given contig, we were able to identify repeat motifs likely to be polymorphic. Our study represents one of the first comparative data sets on the distribution of vertebrate microsatellites within expressed genes. Our results reinforce the idea that microsatellites do not always occur in noncoding DNA, but commonly occur in expressed genes. PMID:24099393

  11. Using Next Generation RAD Sequencing to Isolate Multispecies Microsatellites for Pilosocereus (Cactaceae)

    PubMed Central

    Bonatelli, Isabel A. S.; Carstens, Bryan C.; Moraes, Evandro M.

    2015-01-01

    Microsatellite markers (also known as SSRs, Simple Sequence Repeats) are widely used in plant science and are among the most informative molecular markers for population genetic investigations, but the development of such markers presents substantial challenges. In this report, we discuss how next generation sequencing can replace the cloning, Sanger sequencing, identification of polymorphic loci, and testing cross-amplification that were previously required to develop microsatellites. We report the development of a large set of microsatellite markers for five species of the Neotropical cactus genus Pilosocereus using a restriction-site-associated DNA sequencing (RAD-seq) on a Roche 454 platform. We identified an average of 165 microsatellites per individual, with the absolute numbers across individuals proportional to the sequence reads obtained per individual. Frequency distribution of the repeat units was similar in the five species, with shorter motifs such as di- and trinucleotide being the most abundant repeats. In addition, we provide 72 microsatellites that could be potentially amplified in the sampled species and 22 polymorphic microsatellites validated in two populations of the species Pilosocereus machrisii. Although low coverage sequencing among individuals was observed for most of the loci, which we suggest to be more related to the nature of the microsatellite markers and the possible bias inserted by the restriction enzymes than to the genome size, our work demonstrates that an NGS approach is an efficient method to isolate multispecies microsatellites even in non-model organisms. PMID:26561396

  12. Development and characterization of microsatellite loci for the Moroccan endemic endangered species Argania spinosa (Sapotaceae)1

    PubMed Central

    El Bahloul, Yasmina; Dauchot, Nicolas; Machtoun, Ikrame; Gaboun, Fatima; Van Cutsem, Pierre

    2014-01-01

    • Premise of the study: Microsatellite loci were developed for the Moroccan endemic endangered species Argania spinosa with a combination of a typical library enrichment procedure and a 454 GS FLX Titanium–based high-throughput sequencing approach. • Methods and Results: A genomic DNA library was enriched and further screened using (GA)15, (GTA)8, and (TTC)8 biotin-labeled probes coupled with chemi-luminescence detection. To increase simple sequence repeat (SSR) loci number, an ultra-high-throughput sequencing-based approach was used. Evaluation of all primer pairs was performed with labeled dUTP on an ABI 3130xl sequencer. Eleven polymorphic SSR loci were selected out of 79 SSR regions and extensively characterized on 150 individuals from eight populations. Total alleles ranged from six to 19 alleles per locus while expected heterozygosity ranged from 0.618 to 0.869. • Conclusions: The SSRs developed here will be used to further characterize the genetic diversity of A. spinosa across its distribution range, mainly in the southern part of Morocco and southwestern Algeria. They may also be transferable to other Sapotaceae species. PMID:25202614

  13. Microsatellites in the Eukaryotic DNA Mismatch Repair Genes as Modulators of Evolutionary Mutation Rate

    NASA Technical Reports Server (NTRS)

    Chang, Dong Kyung; Metzgar, David; Wills, Christopher; Boland, C. Richard

    2003-01-01

    All "minor" components of the human DNA mismatch repair (MMR) system-MSH3, MSH6, PMS2, and the recently discovered MLH3-contain mononucleotide microsatellites in their coding sequences. This intriguing finding contrasts with the situation found in the major components of the DNA MMR system-MSH2 and MLH1-and, in fact, most human genes. Although eukaryotic genomes are rich in microsatellites, non-triplet microsatellites are rare in coding regions. The recurring presence of exonal mononucleotide repeat sequences within a single family of human genes would therefore be considered exceptional.

  14. Design and Implementation of Degenerate Microsatellite Primers for the Mammalian Clade

    PubMed Central

    Buschiazzo, Emmanuel; Beck, Josephine S.; Gemmell, Neil J.

    2011-01-01

    Microsatellites are popular genetic markers in molecular ecology, genetic mapping and forensics. Unfortunately, despite recent advances, the isolation of de novo polymorphic microsatellite loci often requires expensive and intensive groundwork. Primers developed for a focal species are commonly tested in a related, non-focal species of interest for the amplification of orthologous polymorphic loci; when successful, this approach significantly reduces cost and time of microsatellite development. However, transferability of polymorphic microsatellite loci decreases rapidly with increasing evolutionary distance, and this approach has shown its limits. Whole genome sequences represent an under-exploited resource to develop cross-species primers for microsatellites. Here we describe a three-step method that combines a novel in silico pipeline that we use to (1) identify conserved microsatellite loci from a multiple genome alignments, (2) design degenerate primer pairs, with (3) a simple PCR protocol used to implement these primers across species. Using this approach we developed a set of primers for the mammalian clade. We found 126,306 human microsatellites conserved in mammalian aligned sequences, and isolated 5,596 loci using criteria based on wide conservation. From a random subset of ∼1000 dinucleotide repeats, we designed degenerate primer pairs for 19 loci, of which five produced polymorphic fragments in up to 18 mammalian species, including the distinctly related marsupials and monotremes, groups that diverged from other mammals 120–160 million years ago. Using our method, many more cross-clade microsatellite loci can be harvested from the currently available genomic data, and this ability is set to improve exponentially as further genomes are sequenced. PMID:22216321

  15. Enhanced cross-species utility of conserved microsatellite markers in shorebirds

    PubMed Central

    Küpper, Clemens; Burke, Terry; Székely, Tamás; Dawson, Deborah A

    2008-01-01

    Background Microsatellite markers are popular genetic markers frequently used in forensic biology. Despite their popularity, the characterisation of polymorphic microsatellite loci and development of suitable markers takes considerable effort. Newly-available genomic databases make it feasible to identify conserved genetic markers. We examined the utility and characteristics of conserved microsatellite markers in Charadriiformes (plovers, sandpipers, gulls and auks). This order harbours many species with diverse breeding systems, life histories and extraordinary migration biology whose genetics warrant investigation. However, research has been largely restrained by the limited availability of genetic markers. To examine the utility of conserved microsatellite loci as genetic markers we collated a database of Charadriiformes microsatellites, searched for homologues in the chicken genome and tested conserved markers for amplification and polymorphism in a range of charadriiform species. Results Sixty-eight (42%) of 161 charadriiform microsatellite loci were assigned to a single location in the chicken genome based on their E-value. Fifty-five primers designed from conserved microsatellite loci with an E-value of E-10 or lower amplified across a wider range of charadriiform species than a control group of primers from ten anonymous microsatellite loci. Twenty-three of 24 examined conserved markers were polymorphic, each in on average 3 of 12 species tested. Conclusion Genomic sequence databases are useful tools to identify conserved genetic markers including those located in non-coding regions. By maximising primer sequence similarity between source species and database species, markers can be further improved and provide additional markers to study the molecular ecology of populations of non-model organisms. PMID:18950482

  16. Recurrent Rare Genomic Copy Number Variants and Bicuspid Aortic Valve Are Enriched in Early Onset Thoracic Aortic Aneurysms and Dissections

    PubMed Central

    Prakash, Siddharth; Kuang, Shao-Qing; Regalado, Ellen; Guo, Dongchuan; Milewicz, Dianna

    2016-01-01

    Thoracic Aortic Aneurysms and Dissections (TAAD) are a major cause of death in the United States. The spectrum of TAAD ranges from genetic disorders, such as Marfan syndrome, to sporadic isolated disease of unknown cause. We hypothesized that genomic copy number variants (CNVs) contribute causally to early onset TAAD (ETAAD). We conducted a genome-wide SNP array analysis of ETAAD patients of European descent who were enrolled in the National Registry of Genetically Triggered Thoracic Aortic Aneurysms and Cardiovascular Conditions (GenTAC). Genotyping was performed on the Illumina Omni-Express platform, using PennCNV, Nexus and CNVPartition for CNV detection. ETAAD patients (n = 108, 100% European American, 28% female, average age 20 years, 55% with bicuspid aortic valves) were compared to 7013 dbGAP controls without a history of vascular disease using downsampled Omni 2.5 data. For comparison, 805 sporadic TAAD patients with late onset aortic disease (STAAD cohort) and 192 affected probands from families with at least two affected relatives (FTAAD cohort) from our institution were screened for additional CNVs at these loci with SNP arrays. We identified 47 recurrent CNV regions in the ETAAD, FTAAD and STAAD groups that were absent or extremely rare in controls. Nine rare CNVs that were either very large (>1 Mb) or shared by ETAAD and STAAD or FTAAD patients were also identified. Four rare CNVs involved genes that cause arterial aneurysms when mutated. The largest and most prevalent of the recurrent CNVs were at Xq28 (two duplications and two deletions) and 17q25.1 (three duplications). The percentage of individuals harboring rare CNVs was significantly greater in the ETAAD cohort (32%) than in the FTAAD (23%) or STAAD (17%) cohorts. We identified multiple loci affected by rare CNVs in one-third of ETAAD patients, confirming the genetic heterogeneity of TAAD. Alterations of candidate genes at these loci may contribute to the pathogenesis of TAAD. PMID:27092555

  17. Estimating microsatellite based genetic diversity in Rhode Island Red chicken.

    PubMed

    Das, A K; Kumar, S; Rahim, A

    2015-01-01

    This study aimed to estimate microsatellite based genetic diversity in two lines (the selected RIR(S) and control line RIR(C)) of Rhode Island Red (RIR) chicken. Genomic DNA of 24 randomly selected birds maintained at Central Avian Research Institute (India) and 24 microsatellite markers were used. Microsatellite alleles were determined on 6% urea-PAGE, recorded using GelDoc system and the samples were genotyped. Nei's heterozygosity and Botstein's polymorphic information content (PIC) at each microsatellite locus were estimated. Wright's fixation indices and gene flow were estimated using POPGENE software. All the microsatellite loci were polymorphic and the estimated PIC ranged from 0.3648 (MCW0059) to 0.7819 (ADL0267) in RIR(S) and from 0.2392 (MCW0059) to 0.8620 (ADL0136) in RIR(C). Most of the loci were highly informative (PIC>0.50) in the both lines, except for five loci in RIR(S) and six loci in RIR(C) line. Nei's heterozygosity per locus ranged from 0.4800 (MCW0059) to 0.8056 (ADL0267) in RIR(S) and from 0.2778 (MCW0059) to 0.875 (ADL0136) in RIR(C). Out of 24 loci, 15 (62.5%) in RIR(S) and 14 loci (58.33%) in RIR(C) revealed moderate to high negative FIS index indicating heterozygote excess for these loci in corresponding lines, but the rest revealed positive FIS indicating heterozygosity deficiency. A mean FIS across the both lines indicated overall 10.77% heterozygosity deficit and a mean FIT indicated 17.19% inbreeding co-efficient favoring homozygosity over the two lines. The mean FST indicated that 10.18% of the microsatellite variation between the two lines was due to their genetic difference. PMID:27175188

  18. Assessment of population genetic structure in the arbovirus vector midge, Culicoides brevitarsis (Diptera: Ceratopogonidae), using multi-locus DNA microsatellites.

    PubMed

    Onyango, Maria G; Beebe, Nigel W; Gopurenko, David; Bellis, Glenn; Nicholas, Adrian; Ogugo, Moses; Djikeng, Appolinaire; Kemp, Steve; Walker, Peter J; Duchemin, Jean-Bernard

    2015-01-01

    Bluetongue virus (BTV) is a major pathogen of ruminants that is transmitted by biting midges (Culicoides spp.). Australian BTV serotypes have origins in Asia and are distributed across the continent into two distinct episystems, one in the north and another in the east. Culicoides brevitarsis is the major vector of BTV in Australia and is distributed across the entire geographic range of the virus. Here, we describe the isolation and use of DNA microsatellites and gauge their ability to determine population genetic connectivity of C. brevitarsis within Australia and with countries to the north. Eleven DNA microsatellite markers were isolated using a novel genomic enrichment method and identified as useful for genetic analyses of sampled populations in Australia, northern Papua New Guinea (PNG) and Timor-Leste. Significant (P < 0.05) population genetic subdivision was observed between all paired regions, though the highest levels of genetic sub-division involved pair-wise tests with PNG (PNG vs. Australia (FST = 0.120) and PNG vs. Timor-Leste (FST = 0.095)). Analysis of multi-locus allelic distributions using STRUCTURE identified a most probable two-cluster population model, which separated PNG specimens from a cluster containing specimens from Timor-Leste and Australia. The source of incursions of this species in Australia is more likely to be Timor-Leste than PNG. Future incursions of BTV positive C. brevitarsis into Australia may be genetically identified to their source populations using these microsatellite loci. The vector's panmictic genetic structure within Australia cannot explain the differential geographic distribution of BTV serotypes. PMID:26408175

  19. Microsatellites enabling multicaptor formation flying ; the Essaim demonstrator

    NASA Astrophysics Data System (ADS)

    Alary, D.; Carrin, G.

    2004-11-01

    In the last decade, the microsatellites capabilities have been strongly enhanced. On the same time, costs have been reduced to enable the conception of formation flying systems, sent to orbit with a single lauch. This kind of system is made of several identical satellites, each making an individual measurement ; all the individual measurements can be processed on ground to provide an enriched synthetic measurement, which would have required a big satellite for a less or equal level of performance. The techniques are well known since years, but micro or minisatellites can now turn them into real spaceborne applications. A few years ago, under a French MoD contract, EADS Astrium and THALES Airborne Systems started the development of the Essaim demonstrator. Essaim is designed to demonstrate the electro-magnetic signal interception feasibility from space, and the possibilities of a formation flying (swarm) system to prepare for coming fully operational systems. It is based onseveral microsatellites of 120kg each, flying in a "swarm" configuration, roughly controlled. All the microsatellites are launched simultaneously as piggyback payloads on ARIANE 5, by the end of this year. The microsatellites are built around the Myriade bus developed by CNES in cooperation with EADS Astrium. A three years experimentation phase is scheduled under the contract. This experiment opens the route to other experiments based on the same principle. Several months prior the launch, we already know that it shall be a very promising way.

  20. Genomic Signatures of North American Soybean Improvement Inform Diversity Enrichment Strategies and Clarify the Impact of Hybridization

    PubMed Central

    Vaughn, Justin N.; Li, Zenglu

    2016-01-01

    Crop improvement represents a long-running experiment in artificial selection on a complex trait, namely yield. How such selection relates to natural populations is unclear, but the analysis of domesticated populations could offer insights into the relative role of selection, drift, and recombination in all species facing major shifts in selective regimes. Because of the extreme autogamy exhibited by soybean (Glycine max), many “immortalized” genotypes of elite varieties spanning the last century have been preserved and characterized using ∼50,000 single nucleotide polymorphic (SNP) markers. Also due to autogamy, the history of North American soybean breeding can be roughly divided into pre- and posthybridization eras, allowing for direct interrogation of the role of recombination in improvement and selection. Here, we report on genome-wide characterization of the structure and history of North American soybean populations and the signature of selection in these populations. Supporting previous work, we find that maturity defines population structure. Though the diversity of North American ancestors is comparable to available landraces, prehybridization line selections resulted in a clonal structure that dominated early breeding and explains many of the reductions in diversity found in the initial generations of soybean hybridization. The rate of allele frequency change does not deviate sharply from neutral expectation, yet some regions bare hallmarks of strong selection, suggesting a highly variable range of selection strengths biased toward weak effects. We also discuss the importance of haplotypes as units of analysis when complex traits fall under novel selection regimes. PMID:27402364

  1. Genome-Centric Analysis of Microbial Populations Enriched by Hydraulic Fracture Fluid Additives in a Coal Bed Methane Production Well.

    PubMed

    Robbins, Steven J; Evans, Paul N; Parks, Donovan H; Golding, Suzanne D; Tyson, Gene W

    2016-01-01

    Coal bed methane (CBM) is generated primarily through the microbial degradation of coal. Despite a limited understanding of the microorganisms responsible for this process, there is significant interest in developing methods to stimulate additional methane production from CBM wells. Physical techniques including hydraulic fracture stimulation are commonly applied to CBM wells, however the effects of specific additives contained in hydraulic fracture fluids on native CBM microbial communities are poorly understood. Here, metagenomic sequencing was applied to the formation waters of a hydraulically fractured and several non-fractured CBM production wells to determine the effect of this stimulation technique on the in-situ microbial community. The hydraulically fractured well was dominated by two microbial populations belonging to the class Phycisphaerae (within phylum Planctomycetes) and candidate phylum Aminicenantes. Populations from these phyla were absent or present at extremely low abundance in non-fractured CBM wells. Detailed metabolic reconstruction of near-complete genomes from these populations showed that their high relative abundance in the hydraulically fractured CBM well could be explained by the introduction of additional carbon sources, electron acceptors, and biocides contained in the hydraulic fracture fluid. PMID:27375557

  2. Genome-Centric Analysis of Microbial Populations Enriched by Hydraulic Fracture Fluid Additives in a Coal Bed Methane Production Well

    PubMed Central

    Robbins, Steven J.; Evans, Paul N.; Parks, Donovan H.; Golding, Suzanne D.; Tyson, Gene W.

    2016-01-01

    Coal bed methane (CBM) is generated primarily through the microbial degradation of coal. Despite a limited understanding of the microorganisms responsible for this process, there is significant interest in developing methods to stimulate additional methane production from CBM wells. Physical techniques including hydraulic fracture stimulation are commonly applied to CBM wells, however the effects of specific additives contained in hydraulic fracture fluids on native CBM microbial communities are poorly understood. Here, metagenomic sequencing was applied to the formation waters of a hydraulically fractured and several non-fractured CBM production wells to determine the effect of this stimulation technique on the in-situ microbial community. The hydraulically fractured well was dominated by two microbial populations belonging to the class Phycisphaerae (within phylum Planctomycetes) and candidate phylum Aminicenantes. Populations from these phyla were absent or present at extremely low abundance in non-fractured CBM wells. Detailed metabolic reconstruction of near-complete genomes from these populations showed that their high relative abundance in the hydraulically fractured CBM well could be explained by the introduction of additional carbon sources, electron acceptors, and biocides contained in the hydraulic fracture fluid. PMID:27375557

  3. Genomic Signatures of North American Soybean Improvement Inform Diversity Enrichment Strategies and Clarify the Impact of Hybridization.

    PubMed

    Vaughn, Justin N; Li, Zenglu

    2016-01-01

    Crop improvement represents a long-running experiment in artificial selection on a complex trait, namely yield. How such selection relates to natural populations is unclear, but the analysis of domesticated populations could offer insights into the relative role of selection, drift, and recombination in all species facing major shifts in selective regimes. Because of the extreme autogamy exhibited by soybean (Glycine max), many "immortalized" genotypes of elite varieties spanning the last century have been preserved and characterized using ∼50,000 single nucleotide polymorphic (SNP) markers. Also due to autogamy, the history of North American soybean breeding can be roughly divided into pre- and posthybridization eras, allowing for direct interrogation of the role of recombination in improvement and selection. Here, we report on genome-wide characterization of the structure and history of North American soybean populations and the signature of selection in these populations. Supporting previous work, we find that maturity defines population structure. Though the diversity of North American ancestors is comparable to available landraces, prehybridization line selections resulted in a clonal structure that dominated early breeding and explains many of the reductions in diversity found in the initial generations of soybean hybridization. The rate of allele frequency change does not deviate sharply from neutral expectation, yet some regions bare hallmarks of strong selection, suggesting a highly variable range of selection strengths biased toward weak effects. We also discuss the importance of haplotypes as units of analysis when complex traits fall under novel selection regimes. PMID:27402364

  4. Genome-wide comparison of the transcriptomes of highly enriched normal and chronic myeloid leukemia stem and progenitor cell populations.

    PubMed

    Gerber, Jonathan M; Gucwa, Jessica L; Esopi, David; Gurel, Meltem; Haffner, Michael C; Vala, Milada; Nelson, William G; Jones, Richard J; Yegnasubramanian, Srinivasan

    2013-05-01

    The persistence leukemia stem cells (LSCs) in chronic myeloid leukemia (CML) despite tyrosine kinase inhibition (TKI) may explain relapse after TKI withdrawal. Here we performed genome-wide transcriptome analysis of highly refined CML and normal stem and progenitor cell populations to identify novel targets for the eradication of CML LSCs using exon microarrays. We identified 97 genes that were differentially expressed in CML versus normal stem and progenitor cells. These included cell surface genes significantly upregulated in CML LSCs: DPP4 (CD26), IL2RA (CD25), PTPRD, CACNA1D, IL1RAP, SLC4A4, and KCNK5. Further analyses of the LSCs revealed dysregulation of normal cellular processes, evidenced by alternative splicing of genes in key cancer signaling pathways such as p53 signaling (e.g. PERP, CDKN1A), kinase binding (e.g. DUSP12, MARCKS), and cell proliferation (MYCN, TIMELESS); downregulation of pro-differentiation and TGF-β/BMP signaling pathways; upregulation of oxidative metabolism and DNA repair pathways; and activation of inflammatory cytokines, including CCL2, and multiple oncogenes (e.g., CCND1). These data represent an important resource for understanding the molecular changes in CML LSCs, which may be exploited to develop novel therapies for eradication these cells and achieve cure. PMID:23651669

  5. Development of Genic and Genomic SSR Markers of Robusta Coffee (Coffea canephora Pierre Ex A. Froehner)

    PubMed Central

    Hendre, Prasad S.; Aggarwal, Ramesh K.

    2014-01-01

    Coffee breeding and improvement efforts can be greatly facilitated by availability of a large repository of simple sequence repeats (SSRs) based microsatellite markers, which provides efficiency and high-resolution in genetic analyses. This study was aimed to improve SSR availability in coffee by developing new genic−/genomic-SSR markers using in-silico bioinformatics and streptavidin-biotin based enrichment approach, respectively. The expressed sequence tag (EST) based genic microsatellite markers (EST-SSRs) were developed using the publicly available dataset of 13,175 unigene ESTs, which showed a distribution of 1 SSR/3.4 kb of coffee transcriptome. Genomic SSRs, on the other hand, were developed from an SSR-enriched small-insert partial genomic library of robusta coffee. In total, 69 new SSRs (44 EST-SSRs and 25 genomic SSRs) were developed and validated as suitable genetic markers. Diversity analysis of selected coffee genotypes revealed these to be highly informative in terms of allelic diversity and PIC values, and eighteen of these markers (∼27%) could be mapped on a robusta linkage map. Notably, the markers described here also revealed a very high cross-species transferability. In addition to the validated markers, we have also designed primer pairs for 270 putative EST-SSRs, which are expected to provide another ca. 200 useful genetic markers considering the high success rate (88%) of marker conversion of similar pairs tested/validated in this study. PMID:25461752

  6. A methylome-wide study of aging using massively parallel sequencing of the methyl-CpG-enriched genomic fraction from blood in over 700 subjects.

    PubMed

    McClay, Joseph L; Aberg, Karolina A; Clark, Shaunna L; Nerella, Srilaxmi; Kumar, Gaurav; Xie, Lin Y; Hudson, Alexandra D; Harada, Aki; Hultman, Christina M; Magnusson, Patrik K E; Sullivan, Patrick F; Van Den Oord, Edwin J C G

    2014-03-01

    The central importance of epigenetics to the aging process is increasingly being recognized. Here we perform a methylome-wide association study (MWAS) of aging in whole blood DNA from 718 individuals, aged 25-92 years (mean = 55). We sequenced the methyl-CpG-enriched genomic DNA fraction, averaging 67.3 million reads per subject, to obtain methylation measurements for the ∼27 million autosomal CpGs in the human genome. Following extensive quality control, we adaptively combined methylation measures for neighboring, highly-correlated CpGs into 4 344 016 CpG blocks with which we performed association testing. Eleven age-associated differentially methylated regions (DMRs) passed Bonferroni correction (P-value < 1.15 × 10(-8)). Top findings replicated in an independent sample set of 558 subjects using pyrosequencing of bisulfite-converted DNA (min P-value < 10(-30)). To examine biological themes, we selected 70 DMRs with false discovery rate of <0.1. Of these, 42 showed hypomethylation and 28 showed hypermethylation with age. Hypermethylated DMRs were more likely to overlap with CpG islands and shores. Hypomethylated DMRs were more likely to be in regions associated with polycomb/regulatory proteins (e.g. EZH2) or histone modifications H3K27ac, H3K4m1, H3K4m2, H3K4m3 and H3K9ac. Among genes implicated by the top DMRs were protocadherins, homeobox genes, MAPKs and ryanodine receptors. Several of our DMRs are at genes with potential relevance for age-related disease. This study successfully demonstrates the application of next-generation sequencing to MWAS, by interrogating a large proportion of the methylome and returning potentially novel age DMRs, in addition to replicating several loci implicated in previous studies using microarrays. PMID:24135035

  7. Polymorphic microsatellite loci for Haumania danckelmaniana and transferability to H. liebrechtsiana (Marantaceae)1

    PubMed Central

    Ley, Alexandra C.; Hardy, Olivier J.

    2016-01-01

    Premise of the study: Microsatellite markers were developed for the species Haumania danckelmaniana (Marantaceae) from central tropical Africa. Methods and Results: Microsatellite isolation was performed simultaneously on three different species of Marantaceae through a procedure that combines multiplex microsatellite enrichment and next-generation sequencing. From 80 primers selected for initial screening, 20 markers positively amplified in H. danckelmaniana, of which 10 presented unambiguous amplification products within the expected size range and eight were polymorphic with four to nine alleles per locus. Positive transferability with the related species H. liebrechtsiana was observed for the same 10 markers. Conclusions: The polymorphic microsatellite markers are suitable for studies in genetic diversity and structure, mating system, and gene flow in H. danckelmaniana and the closely related species H. liebrechtsiana. PMID:27011899

  8. A microsatellite-based multilocus screen for the identification of local selective sweeps.

    PubMed Central

    Schlötterer, Christian

    2002-01-01

    With the availability of completely sequenced genomes, multilocus scans of natural variability have become a feasible approach for the identification of genomic regions subjected to natural and artificial selection. Here, I introduce a new multilocus test statistic, ln RV, which is based on the ratio of observed variances in repeat number at a set of microsatellite loci in two groups of populations. The distribution of ln RV values captures demographic history of the populations as well as variation in microsatellite mutation among loci. Given that microsatellite loci associated with a recent selective sweep differ from the remainder of the genome, they are expected to fall outside of the distribution of neutral ln RV values. The ln RV test statistic is applied to a data set of 94 loci typed in eight non-African and two African human populations. PMID:11861576

  9. Construction of a microsatellites-based linkage map for the white grouper (Epinephelus aeneus).

    PubMed

    Dor, Lior; Shirak, Andrey; Gorshkov, Sergei; Band, Mark R; Korol, Abraham; Ronin, Yefim; Curzon, Arie; Hulata, Gideon; Seroussi, Eyal; Ron, Micha

    2014-08-01

    The white grouper (Epinephelus aeneus) is a promising candidate for domestication and aquaculture due to its fast growth, excellent taste, and high market price. A linkage map is an essential framework for mapping quantitative trait loci for economic traits and the study of genome evolution. DNA of a single individual was deep-sequenced, and microsatellite markers were identified in 177 of the largest scaffolds of the sequence assembly. The success rate of developing polymorphic homologous markers was 94.9% compared with 63.1% of heterologous markers from other grouper species. Of the 12 adult mature fish present in the broodstock tank, two males and two females were identified as parents of the assigned offspring by parenthood analysis using 34 heterologous markers. A single full-sib family of 48 individuals was established for the construction of first-generation linkage maps based on genotyping data of 222 microsatellites. The markers were assigned to 24 linkage groups in accordance to the 24 chromosomal pairs. The female and male maps consisting of 203 and 202 markers spanned 1053 and 886 cM, with an average intermarker distance of 5.8 and 5.0 cM, respectively. Mapping of markers to linkage groups ends was enriched by using markers originating from scaffolds harboring telomeric repeat-containing RNA. Comparative mapping showed high synteny relationships among the white grouper, kelp grouper (E. bruneus), orange-spotted grouper (E. coioides), and Nile tilapia (Oreochromis niloticus). Thus, it would be useful to integrate the markers that were developed for different groupers, depending on sharing of sequence data, into a comprehensive consensus map. PMID:24902605

  10. Preliminary study on applicability of microsatellite DNA primers from parasite protozoa Trypanosoma cruzi in free-living protozoa

    NASA Astrophysics Data System (ADS)

    Zhang, Wenjing; Yu, Yuhe; Shen, Yunfen; Miao, Wei; Feng, Weisong

    2004-04-01

    In this paper, we took the lead in studying on specificity of the microsatellite DNA loci and applicability of microsatellite DNA primers in protozoa. In order to study characters of microsatellites in free-living protozoa, eight microsatellite loci primers developed from Trypanosoma cruzi (MCLE01, SCLE10, MCLE08, SCLE11, MCLF10, MCLG10, MCL03, MCL05) were employed to amplify microsatellite in four free-living protozoa, including Bodo designis, Euglena gracilis FACHB848, Paramecium bruzise and Tetrahymena thermophila BF1. In the amplification systems of P. bruzise, four loci (SCLE10, SCLE11, MCLF10, MCL03) were amplified successfully, and four amplification fragments were in proper size. In genome of E. gracilis FACHB848, five of eight primers brought five clear amplification bands. In B. designis, three (No.4, 5 and 7) of eight loci produced clear and sharp products without stutter bands, whereas no bands appeared in T. thermophila BF1. Further, eight 300 500 bp amplification fragments were cloned and sequenced. Nevertheless, all sequenced products did not contain corresponding microsatellite sequence, although Bodo is in the same order and has the nearest phylogenetic relation with Trypanosoma among these four species. Thus, the microsatellite DNA primers can not be applied among order or more far taxa, and the specificity of microsatellite DNA is very high in protozoa. The results of this study will contribute to our understanding of microsatellite DNA in protozoa.

  11. An Integrated Chromosome Map of Microsatellite Markers and Inversion Breakpoints for an Asian Malaria Mosquito, Anopheles stephensi

    PubMed Central

    Kamali, Maryam; Sharakhova, Maria V.; Baricheva, Elina; Karagodin, Dmitrii; Tu, Zhijian

    2011-01-01

    Anopheles stephensi is one of the major vectors of malaria in the Middle East and Indo-Pakistan subcontinent. Understanding the population genetic structure of malaria mosquitoes is important for developing adequate and successful vector control strategies. Commonly used markers for inferring anopheline taxonomic and population status include microsatellites and chromosomal inversions. Knowledge about chromosomal locations of microsatellite markers with respect to polymorphic inversions could be useful for better understanding a genetic structure of natural populations. However, fragments with microsatellites used in population genetic studies are usually too short for successful labeling and hybridization with chromosomes. We designed new primers for amplification of microsatellite loci identified in the A. stephensi genome sequenced with next-generation technologies. Twelve microsatellites were mapped to polytene chromosomes from ovarian nurse cells of A. stephensi using fluorescent in situ hybridization. All microsatellites hybridized to unique locations on autosomes, and 7 of them localized to the largest arm 2R. Ten microsatellites were mapped inside the previously described polymorphic chromosomal inversions, including 4 loci located inside the widespread inversion 2Rb. We analyzed microsatellite-based population genetic data available for A. stephensi in light of our mapping results. This study demonstrates that the chromosomal position of microsatellites may affect estimates of population genetic parameters and highlights the importance of developing physical maps for nonmodel organisms. PMID:21810771

  12. Does the evolutionary conservation of microsatellite loci imply function?

    SciTech Connect

    Shriver, M.D.; Deka, R.; Ferrell, R.E.

    1994-09-01

    Microsatellites are highly polymorphic tandem arrays of short (1-6 bp) sequence motifs which have been found widely distributed in the genomes of all eukaryotes. We have analyzed allele frequency data on 16 microsatellite loci typed in the great apes (human, chimp, orangutan, and gorilla). The majority of these loci (13) were isolated from human genomic libraries; three were cloned from chimpanzee genomic DNA. Most of these loci are not only present in all apes species, but are polymorphic with comparable levels of heterozygosity and have alleles which overlap in size. The extent of divergence of allele frequencies among these four species were studies using the stepwise-weighted genetic distance (Dsw), which was previously shown to conform to linearity with evolutionary time since divergence for loci where mutations exist in a stepwise fashion. The phylogenetic tree of the great apes constructed from this distance matrix was consistent with the expected topology, with a high bootstrap confidence (82%) for the human/chimp clade. However, the allele frequency distributions of these species are 10 times more similar to each other than expected when they were calibrated with a conservative estimate of the time since separation of humans and the apes. These results are in agreement with sequence-based surveys of microsatellites which have demonstrated that they are highly (90%) conserved over short periods of evolutionary time (< 10 million years) and moderately (30%) conserved over long periods of evolutionary time (> 60-80 million years). This evolutionary conservation has prompted some authors to speculate that there are functional constraints on microsatellite loci. In contrast, the presence of directional bias of mutations with constraints and/or selection against aberrant sized alleles can explain these results.

  13. Development and mapping of Oryza glumaepatula-derived microsatellite markers in the interspecific cross Oryza glumaepatula x O. sativa.

    PubMed

    Brondani, C; Brondani, R P; Rangel, P H; Ferreira, M E

    2001-01-01

    Wild germplasm of domesticated crops is a source of genetic variation little utilized in breeding programs. Interspecific crosses can potentially uncover novel gene combinations that can be important for quantitative trait analysis. The combined use of wide crosses and genetic maps of chromosomal regions associated with quantitative traits can be used to broaden the genetic basis of rice breeding programs. Oryza glumaepatula is a diploid (AA genome) wild rice species native from South and Central America. A genetic map was constructed with 162 PCR-based markers (155 microsatellite and 7 STS markers) using a backcross population derived from the cross O. glumaepatula, accession RS-16 from the Brazilian Amazon Region x O. sativa BG-90-2, an elite rice inbred line. The map included 47 new SSR markers developed from an O. glumaepatula genomic library enriched for AG/TC sequences. All SSR markers were able to amplify the O. sativa genome, indicating a high degree of SSR flanking region conservation between O. glumaepatula and O. sativa species. The map covered 1500.4 cM, with an average of one marker every 10 cM. Despite some chromosomes being more densely mapped, the overall coverage was similar to other maps developed for rice. The advantage to construct a SSR-based map is to permit the combination of the speed of the PCR reaction, and the codominant nature of the SSR marker, facilitating the QTL analysis and marker assisted selection for rice breeding programs. PMID:11525066

  14. Microsatellite Length Scoring by Single Molecule Real Time Sequencing - Effects of Sequence Structure and PCR Regime.

    PubMed

    Liljegren, Mikkel Meyn; de Muinck, Eric Jacques; Trosvik, Pål

    2016-01-01

    Microsatellites are DNA sequences consisting of repeated, short (1-6 bp) sequence motifs that are highly mutable by enzymatic slippage during replication. Due to their high intrinsic variability, microsatellites have important applications in population genetics, forensics, genome mapping, as well as cancer diagnostics and prognosis. The current analytical standard for microsatellites is based on length scoring by high precision electrophoresis, but due to increasing efficiency next-generation sequencing techniques may provide a viable alternative. Here, we evaluated single molecule real time (SMRT) sequencing, implemented in the PacBio series of sequencing apparatuses, as a means of microsatellite length scoring. To this end we carried out multiplexed SMRT sequencing of plasmid-carried artificial microsatellites of varying structure under different pre-sequencing PCR regimes. For each repeat structure, reads corresponding to the target length dominated. We found that pre-sequencing amplification had large effects on scoring accuracy and error distribution relative to controls, but that the effects of the number of amplification cycles were generally weak. In line with expectations enzymatic slippage decreased proportionally with microsatellite repeat unit length and increased with repetition number. Finally, we determined directional mutation trends, showing that PCR and SMRT sequencing introduced consistent but opposing error patterns in contraction and expansion of the microsatellites on the repeat motif and single nucleotide level. PMID:27414800

  15. FullSSR: Microsatellite Finder and Primer Designer

    PubMed Central

    Metz, Sebastián; Cabrera, Juan Manuel; Rueda, Eva; Giri, Federico; Amavet, Patricia

    2016-01-01

    Microsatellites are genomic sequences comprised of tandem repeats of short nucleotide motifs widely used as molecular markers in population genetics. FullSSR is a new bioinformatic tool for microsatellite (SSR) loci detection and primer design using genomic data from NGS assay. The software was tested with 2000 sequences of Oryza sativa shotgun sequencing project from the National Center of Biotechnology Information Trace Archive and with partial genome sequencing with ROCHE 454® from Caiman latirostris, Salvator merianae, Aegla platensis, and Zilchiopsis collastinensis. FullSSR performance was compared against other similar SSR search programs. The results of the use of this kind of approach depend on the parameters set by the user. In addition, results can be affected by the analyzed sequences because of differences among the genomes. FullSSR simplifies the detection of SSRs and primer design on a big data set. The command line interface of FullSSR was intended to be used as part of genomic analysis tools pipeline; however, it can be used as a stand-alone program because the results are easily interpreted for a nonexpert user. PMID:27366148

  16. FullSSR: Microsatellite Finder and Primer Designer.

    PubMed

    Metz, Sebastián; Cabrera, Juan Manuel; Rueda, Eva; Giri, Federico; Amavet, Patricia

    2016-01-01

    Microsatellites are genomic sequences comprised of tandem repeats of short nucleotide motifs widely used as molecular markers in population genetics. FullSSR is a new bioinformatic tool for microsatellite (SSR) loci detection and primer design using genomic data from NGS assay. The software was tested with 2000 sequences of Oryza sativa shotgun sequencing project from the National Center of Biotechnology Information Trace Archive and with partial genome sequencing with ROCHE 454® from Caiman latirostris, Salvator merianae, Aegla platensis, and Zilchiopsis collastinensis. FullSSR performance was compared against other similar SSR search programs. The results of the use of this kind of approach depend on the parameters set by the user. In addition, results can be affected by the analyzed sequences because of differences among the genomes. FullSSR simplifies the detection of SSRs and primer design on a big data set. The command line interface of FullSSR was intended to be used as part of genomic analysis tools pipeline; however, it can be used as a stand-alone program because the results are easily interpreted for a nonexpert user. PMID:27366148

  17. Development and characterization of microsatellite markers in the African deciduous tree Terminalia superba (Combretaceae)1

    PubMed Central

    Demenou, Boris B.; Migliore, Jérémy; Tosso, Felicien; Kaymak, Esra; Hardy, Olivier J.

    2015-01-01

    Premise of the study: Microsatellites were designed and characterized in the African timber forest tree Terminalia superba (Combretaceae). Due to their high variability, these markers are suitable to investigate gene flow patterns and the structure of genetic diversity. Methods and Results: From a genomic library obtained by next-generation sequencing, seven monomorphic and 14 polymorphic microsatellite loci were developed. The polymorphic microsatellites displayed two to 27 alleles (mean 11.4; expected heterozygosity range 0.283–0.940, mean 0.736) in one population from southeastern Cameroon. Genotypes were typical of an outbreeding diploid species, although null alleles explain a significant heterozygote deficit in three loci. Cross-amplification in three congeneric species (T. ivorensis, T. avicennioides, and T. mantaly) failed, suggesting that T. superba is rather divergent. Conclusions: This set of newly developed microsatellite markers will be useful for assessing the genetic diversity, population structure, and demographic history of T. superba in tropical African forests. PMID:26697276

  18. Microsatellite markers for the New Zealand endemic Myosotis pygmaea species group (Boraginaceae) amplify across species1

    PubMed Central

    Prebble, Jessica M.; Tate, Jennifer A.; Meudt, Heidi M.; Symonds, V. Vaughan

    2015-01-01

    Premise of the study: Microsatellite loci were developed as polymorphic markers for the New Zealand endemic Myosotis pygmaea species group (Boraginaceae) for use in species delimitation and population and conservation genetic studies. Methods and Results: Illumina MiSeq sequencing was performed on genomic DNA from seedlings of M. drucei. From trimmed paired-end sequences >400 bp, 484 microsatellite loci were identified. Twelve of 48 microsatellite loci tested were found to be polymorphic and consistently scorable when screened on 53 individuals from four populations representing the geographic range of M. drucei. They also amplify in all other species in the M. pygmaea species group, i.e., M. antarctica, M. brevis, M. glauca, and M. pygmaea, as well as 18 other Myosotis species. Conclusions: These 12 polymorphic microsatellite markers establish an important resource for research and conservation of the M. pygmaea species group and potentially other Southern Hemisphere Myosotis. PMID:26082880

  19. Development of 18 polymorphic microsatellite markers for Vinca minor (Apocynaceae) via 454 pyrosequencing1

    PubMed Central

    Moeller, Sina; Wöhrmann, Tina; Huettel, Bruno; Weising, Kurt

    2015-01-01

    Premise of the study: Polymorphic microsatellite markers were developed in Vinca minor (Apocynaceae) to evaluate the level of clonality, population structure, and genetic diversity of the species within its native and introduced range. Methods and Results: A total of 1371 microsatellites were found in 43,565 reads from 454 pyrosequencing of genomic V. minor DNA. Additional microsatellite loci were mined from publicly available cDNA sequences. After several rounds of screening, 18 primer pairs flanking di-, tri-, or tetranucleotide repeats were identified that revealed high levels of genetic diversity in two native Italian populations, with two to 11 alleles per locus. Clonal growth predominated in two populations from the introduced range in Germany. Five loci successfully cross-amplified in three additional Vinca species. Conclusions: The novel polymorphic microsatellite markers are promising tools for studying clonality and population genetics of V. minor and for assessing the historical origin of Central European populations. PMID:25995978

  20. Isolation of nuclear microsatellites in the African timber tree Lophira alata (Ochnaceae) and cross-amplification in L. lanceolata1

    PubMed Central

    Piñeiro, Rosalía; Staquet, Adrien; Hardy, Olivier J.

    2015-01-01

    Premise of the study: Microsatellite markers were isolated in the rainforest tree Lophira alata (Ochnaceae), an important timber tree from Central Africa, and cross-amplified on its savannah counterpart, L. lanceolata. Methods and Results: From a microsatellite-enriched library sequenced on a 454 GS FLX platform, 13 primer combinations were identified. Amplification was optimized in two multiplex reactions. The primers amplified di- and trinucelotide repeats, with two to seven alleles per locus. Eleven primers also amplified in L. lanceolata. Conclusions: Microsatellite primers developed for the genus Lophira displayed sufficient variation to investigate hybridization between congeneric species in the rainforest–savannah transition. PMID:26504680

  1. Draft Genome Sequence of Marinobacter sp. Strain P4B1, an Electrogenic Perchlorate-Reducing Strain Isolated from a Long-Term Mixed Enrichment Culture of Marine Bacteria

    PubMed Central

    Stepanov, Victor G.; Xiao, Yeyuan; Lopez, April J.

    2016-01-01

    The perchlorate-reducing strain Marinobacter sp. strain P4B1 was isolated from a long-term perchlorate-degrading enrichment culture seeded with marine sediment. The draft genome of Marinobacter sp. P4B1 is comprised of the bacterial chromosome (3.60 Mbp, G+C 58.51%, 3,269 predicted genes) and its associated plasmid pMARS01 (0.14 Mbp, G+C 52.95%, 165 predicted genes). PMID:26798109

  2. Draft Genome Sequence of Marinobacter sp. Strain P4B1, an Electrogenic Perchlorate-Reducing Strain Isolated from a Long-Term Mixed Enrichment Culture of Marine Bacteria.

    PubMed

    Stepanov, Victor G; Xiao, Yeyuan; Lopez, April J; Roberts, Deborah J; Fox, George E

    2016-01-01

    The perchlorate-reducing strain Marinobacter sp. strain P4B1 was isolated from a long-term perchlorate-degrading enrichment culture seeded with marine sediment. The draft genome of Marinobacter sp. P4B1 is comprised of the bacterial chromosome (3.60 Mbp, G+C 58.51%, 3,269 predicted genes) and its associated plasmid pMARS01 (0.14 Mbp, G+C 52.95%, 165 predicted genes). PMID:26798109

  3. Blueberry Microsatellite Markers Identify Cranberries

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Forty-six blueberry simple sequence repeat (SSR) markers or microsatellites were tested for the ability to amplify a polymorphic marker in eight American cranberry accessions. Sixteen SSRs resulted in informative and polymorphic SSR primer pairs and were used to fingerprint 16 economically important...

  4. Extensive Microsatellite Variation in Rice Induced by Introgression from Wild Rice (Zizania latifolia Griseb.)

    PubMed Central

    Dong, Zhenying; Wang, Hongyan; Dong, Yuzhu; Wang, Yongming; Liu, Wei; Miao, Gaojian; Lin, Xiuyun; Wang, Daqing; Liu, Bao

    2013-01-01

    Background It is widely accepted that interspecific hybridization may induce genomic instability in the resultant hybrids. However, few studies have been performed on the genomic analysis of homoploid hybrids and introgression lines. We have reported previously that by introgressive hybridization, a set of introgression lines between rice (Oryza sativa L.) and wild rice (Zizania latifolia Griseb.) was successfully generated, and which have led to the release of several cultivars. Methodology Using 96 microsatellite markers located in the nuclear and organelle genomes of rice, we investigated microsatellite stability in three typical introgression lines. Expression of a set of mismatch repair (MMR) genes and microsatellite-containing genes was also analyzed. Results/Conclusions Compared with the recipient rice cultivar (Matsumae), 55 of the 96 microsatellite loci revealed variation in one or more of the introgression lines, and 58.2% of the altered alleles were shared by at least two lines, indicating that most of the alterations had occurred in the early stages of introgression before their further differentiation. 73.9% of the non-shared variations were detected only in one introgression line, i.e. RZ2. Sequence alignment showed that the variations included substitutions and indels that occurred both within the repeat tracts and in the flanking regions. Interestingly, expression of a set of MMR genes altered dramatically in the introgression lines relative to their rice parent, suggesting participation of the MMR system in the generation of microsatellite variants. Some of the altered microsatellite loci are concordant with changed expression of the genes harboring them, suggesting their possible cis-regulatory roles in controlling gene expression. Because these genes bear meaningful homology to known-functional proteins, we conclude that the introgression-induced extensive variation of microsatellites may have contributed to the novel phenotypes in the

  5. Index, comprehensive microsatellite, and unified linkage maps of human chromosome 14 with cytogenetic tie points and a telomere microsatellite marker

    SciTech Connect

    Pandit, S.D.; Wang, Jen C.; Veile, R.A.

    1995-10-10

    Three sets of linkage maps (index, comprehensive microsatellite, and unified) have been constructed for human chromosome 14 based on genotypes from the CEPH reference pedigrees. The index maps consist of 18 microsatellite markers, with heterozygosities of at least 68% and intermarker spacing no greater than 11 cM. The sex-average comprehensive microsatellite map is 125 cM in length and includes 115 markers with 54 loci uniquely placed with odds for marker order of at least 1000:1. The sex-average index map length is 121 cM, and the female- and male-specific maps are l43 and 101 cM, respectively. A unified map was also constructed from 147 loci (162 marker systems), which includes 32 RFLP markers in addition to the 115 microsatellites. The sex-average length of the unified map is 128 cM with 69 loci uniquely placed. Our maps are anchored by a microsatellite telomere marker sCAW1 (D14S826), developed from a telomere YAC clone TYAC196, which extends the linkage map to the physical terminus of the long arm of chromosome 14. Furthermore, we have also physically mapped seven of the loci by fluorscence in situ hybridization of cosmid clones or Alu-PCR products amplified from YACs containing the marker sequences. Together with previously established cytogenetic map designations for other loci, our maps display links between genetic markers for 10 of 13 cytogenetic bands of chromosome 14 at the 550 genome band resolution. 54 refs., 4 figs., 4 tabs.

  6. Evolutionary constraints over microsatellite abundance in larger mammals as a potential mechanism against carcinogenic burden

    PubMed Central

    Park, Jung Youn; An, Yong-Rock; An, Chul-Min; Kang, Jung-Ha; Kim, Eun Mi; Kim, Heebal; Cho, Seoae; Kim, Jaemin

    2016-01-01

    Larger organisms tend to live longer, have more potentially carcinogenic cells, and undergo more cell divisions. While one might intuitively expect cancer incidence to scale with body size, this assertion does not hold over the range of different mammals. Explaining this lack of correlation, so-called ‘Peto’s paradox’ can likely increase our understanding of how cancer defense mechanisms are shaped by natural selection. Here, we study the occurrence of microsatellite in mammal genomes and observe that animals with expanded body size restrain the number of microsatellite. To take into account of higher mutation rate in the microsatellite region compared to that of genome, limiting the abundance of somatic mutations might explain how larger organisms could overcome the burden of cancer. These observations may serve as the basis to better understand how evolution has modeled protective mechanisms against cancer development. PMID:27125812

  7. Evolutionary constraints over microsatellite abundance in larger mammals as a potential mechanism against carcinogenic burden.

    PubMed

    Park, Jung Youn; An, Yong-Rock; An, Chul-Min; Kang, Jung-Ha; Kim, Eun Mi; Kim, Heebal; Cho, Seoae; Kim, Jaemin

    2016-01-01

    Larger organisms tend to live longer, have more potentially carcinogenic cells, and undergo more cell divisions. While one might intuitively expect cancer incidence to scale with body size, this assertion does not hold over the range of different mammals. Explaining this lack of correlation, so-called 'Peto's paradox' can likely increase our understanding of how cancer defense mechanisms are shaped by natural selection. Here, we study the occurrence of microsatellite in mammal genomes and observe that animals with expanded body size restrain the number of microsatellite. To take into account of higher mutation rate in the microsatellite region compared to that of genome, limiting the abundance of somatic mutations might explain how larger organisms could overcome the burden of cancer. These observations may serve as the basis to better understand how evolution has modeled protective mechanisms against cancer development. PMID:27125812

  8. Novel Microsatellite Markers of Meretrix petechialis and Cross-species Amplification in Related Taxa (Bivalvia: Veneroida)

    PubMed Central

    Kang, Jung-Ha; Kim, Byeng-Hak; Park, Jung-Youn; Lee, Jung-Mi; Jeong, Ji-Eun; Lee, Jun-Sang; Ko, Hyun-Sook; Lee, Yong-Seok

    2012-01-01

    The Asian hard clam, Meretrix petechialis, is an economically important bivalve, but its catch and population sizes are decreasing rapidly, owing to many factors, including large-scale reclamation of its natural habitat on the western coast of the Korean peninsula. Attempts to restore the resources and production of this species require genetic structure and diversity information. In this study, we developed 15 microsatellite markers from a partial genomic library enriched in GT repeats. Nine of these markers were polymorphic, with an average allele number of six, and six were monomorphic in 95 tested individuals. No linkage disequilibrium was found between any pair of loci (p > 0.05), and deviations from the Hardy–Weinberg equilibrium (HWE) test showing excess of heterozygotes was observed in only one of nine loci. In addition, no null alleles or genetic differentiation between two tested populations were detected. A cross-species amplification in 12 species of four families resulted in two M. petechialis-specific loci and three possible universal markers. This information will be useful in the future development of high-quality artificial seedlings and sustainable resource management. PMID:23443103

  9. Microsatellite instability in bladder cancer.

    PubMed

    Gonzalez-Zulueta, M; Ruppert, J M; Tokino, K; Tsai, Y C; Spruck, C H; Miyao, N; Nichols, P W; Hermann, G G; Horn, T; Steven, K

    1993-12-01

    Somatic instability at microsatellite repeats was detected in 6 of 200 transitional cell carcinomas of the bladder. Instabilities were apparent as changes in (GT)n repeat lengths on human chromosome 9 for four tumors and as alterations in a (CAG)n repeat in the androgen receptor gene on the X chromosome for three tumors. Single locus alterations were detected in three tumors, while three other tumors revealed changes in two or more loci. In one tumor we found microsatellite instability in all five loci analyzed on chromosome 9. The alterations detected were either minor 2-base pair changes or larger (> 2 base pairs) alterations in repeat length. All six tumors were low stage (Ta-T1), suggesting that these alterations can occur early in bladder tumorigenesis. PMID:8242615

  10. A novel microsatellite control system

    SciTech Connect

    Moore, K.R.; Frigo, J.R.; Tilden, M.W.

    1998-02-01

    The authors are researching extremely simple yet quite capable analog pulse-coded neural networks for ``smaller-faster-cheaper`` spacecraft attitude and control systems. The will demonstrate a prototype microsatellite that uses their novel control method to autonomously stabilize itself in the ambient magnetic field and point itself at the brightest available light source. Though still in design infancy, the ``Nervous Net`` controllers described could allow for space missions not currently possible given conventional satellite hardware. Result, prospects and details are presented.

  11. Applications of Microsatellites in Two Big Bracted Dogwood Species, Flowering and Kousa Dogwood

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Microsatellite or simple sequence repeats (SSRs) are tandem 1-6 bases repeated motifs, found in coding and noncoding regions of prokaryotic and eukaryotic genomes. Due to the high nucleotide substitution rate in noncoding regions, SSRs exhibit a high degree of molecular polymorphism. SSRs markers ar...

  12. Development of microsatellites from Fothergilla xintermedia (Hamamelidaceae) and cross transfer to four other genera within Hamamelidaceae

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Premise of the study: Develop microsatellites from Fothergilla ×intermedia to establish loci capable of distinguishing species and cultivars, and assess genetic diversity for use by ornamental breeders, and for transfer within Hamamelidaceae. Methods and Results: A small insert genomic library enric...

  13. CHARACTERIZATION AND MAPPING OF NINETEEN POLYMORPHIC MICROSATELLITE MARKERS FOR RAINBOW TROUT (ONCORHYNCHUS MYKISS)

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Nineteen new polymorphic microsatellite markers were developed for QTL mapping and population genetics studies in rainbow trout (Oncorhynchus mykiss). The amount of polymorphism, percent heterozygosity, ability of each marker to amplify genomic DNA from other salmonids and two point linkage data wer...

  14. TWO SEX-CHROMOSOME-LINKED MICROSATELLITE LOCI SHOW GEOGRAPHIC VARIANCE AMONG NORTH AMERICAN OSTRINIA NUBILALIS

    Technology Transfer Automated Retrieval System (TEKTRAN)

    A (GAAAAT)n repeat microsatellite was isolated from a partial Ostrinia nubilalis genomic library. Pedigree analysis indicated the marker was female specific, and referred to as Ostrinia nubilalis W-chromosome marker 1 (ONW1). Polymerase chain reaction (PCR) and DNA sequence analysis indicated that ...

  15. A preliminary investigation of microsatellite-based genotyping in Trichomonas vaginalis.

    PubMed

    Prokopi, Marianna; Chatzitheodorou, Theodoros; Ackers, John P; Clark, C Graham

    2011-08-01

    The genetic epidemiology of Trichomonas vaginalis is poorly understood at present. The recent release of the organism's genome sequence opens the way to investigation of polymorphic markers allowing strain identification. We here report a preliminary analysis of microsatellite loci in T. vaginalis and show that this approach holds promise for future studies of infection transmission and organism diversity. PMID:21700304

  16. MICROSATELLITE DIVERSITY AND CROSSOVER REGIONS WITHIN HOMOZYGOUS AND HETEROZYGOUS SLA HAPLOTYPES OF DIFFERENT PIG BREEDS

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Our aim was to investigate microsatellite (MS) diversity and find crossover regions at 42 polymorphic MS loci in the SLA genomic region of 72 pigs with different homozygous and heterozygous well-defined SLA haplotypes. We analyzed the genetic polymorphisms of the 42 MS markers in 23 SLA homozygous/h...

  17. New carrot microsatellites – linkage mapping, diversity analysis and transferability to other apiaceae

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Nearly 300 new microsatellite, or simple sequence repeat (SSR) markers were developed from genomic sequences of carrot. Efforts to map these markers and evaluate their usefulness in diversity studies are underway. In one F2 carrot population, a total of 51 polymorphic markers, including 37 codominan...

  18. Bulk development and stringent selection of microsatellite markers in the western flower thrips Frankliniella occidentalis.

    PubMed

    Cao, Li-Jun; Li, Ze-Min; Wang, Ze-Hua; Zhu, Liang; Gong, Ya-Jun; Chen, Min; Wei, Shu-Jun

    2016-01-01

    Recent improvements in next-generation sequencing technologies have enabled investigation of microsatellites on a genome-wide scale. Faced with a huge amount of candidates, the use of appropriate marker selection criteria is crucial. Here, we used the western flower thrips Frankliniella occidentalis for an empirical microsatellite survey and validation; 132,251 candidate microsatellites were identified, 92,102 of which were perfect. Dinucleotides were the most abundant category, while (AG)n was the most abundant motif. Sixty primer pairs were designed and validated in two natural populations, of which 30 loci were polymorphic, stable, and repeatable, but not all in Hardy-Weinberg equilibrium (HWE) and linkage equilibrium. Four marker panels were constructed to understand effect of marker selection on population genetic analyses: (i) only accept loci with single nucleotide insertions (SNI); (ii) only accept the most polymorphic loci (MP); (iii) only accept loci that did not deviate from HWE, did not show SNIs, and had unambiguous peaks (SS) and (iv) all developed markers (ALL). Although the MP panel resulted in microsatellites of highest genetic diversity followed by the SNI, the SS performed best in individual assignment. Our study proposes stringent criteria for selection of microsatellites from a large-scale number of genomic candidates for population genetic studies. PMID:27197749

  19. Bulk development and stringent selection of microsatellite markers in the western flower thrips Frankliniella occidentalis

    PubMed Central

    Cao, Li-Jun; Li, Ze-Min; Wang, Ze-Hua; Zhu, Liang; Gong, Ya-Jun; Chen, Min; Wei, Shu-Jun

    2016-01-01

    Recent improvements in next-generation sequencing technologies have enabled investigation of microsatellites on a genome-wide scale. Faced with a huge amount of candidates, the use of appropriate marker selection criteria is crucial. Here, we used the western flower thrips Frankliniella occidentalis for an empirical microsatellite survey and validation; 132,251 candidate microsatellites were identified, 92,102 of which were perfect. Dinucleotides were the most abundant category, while (AG)n was the most abundant motif. Sixty primer pairs were designed and validated in two natural populations, of which 30 loci were polymorphic, stable, and repeatable, but not all in Hardy–Weinberg equilibrium (HWE) and linkage equilibrium. Four marker panels were constructed to understand effect of marker selection on population genetic analyses: (i) only accept loci with single nucleotide insertions (SNI); (ii) only accept the most polymorphic loci (MP); (iii) only accept loci that did not deviate from HWE, did not show SNIs, and had unambiguous peaks (SS) and (iv) all developed markers (ALL). Although the MP panel resulted in microsatellites of highest genetic diversity followed by the SNI, the SS performed best in individual assignment. Our study proposes stringent criteria for selection of microsatellites from a large-scale number of genomic candidates for population genetic studies. PMID:27197749

  20. Microsatellite based analysis of genetic diversity of popular black pepper genotypes in South India.

    PubMed

    Joy, Nisha; Prasanth, V P; Soniya, E V

    2011-08-01

    The genotypes of black pepper are morphologically and genotypically highly diverse and carry all the cumulative variations inherited and maintained through generations. The present study describes the Simple Sequence Repeat (SSR) or microsatellite based assessment of genetic diversity among forty popular genotypes and four different species of black pepper in Southern region of India. For isolation of SSR primers, our earlier attempts with enrichment strategies like 'Triplex affinity capture' did not extract a single SSR primer due to close proximity of restriction sites to the SSR motif. Hence we developed a 'Sequential Reverse Genome Walking (SRGW)' strategy with better enrichment efficiency of 72% that generated seven new SSR primers. Genotyping precisely discriminated majority of genotypes which indicated that the SSR primers are very informative. A total of 62 alleles with an average of 15.5 alleles over 4 loci were identified. All the SSR primers showed an average Polymorphism Information Content (PIC) value of 0.85. The estimated average Shared Allele Frequency ranged between 1.57 and 20.12%. The PCA plot revealed four closely related individual groups and identified Karimunda, Wild pepper and a local landrace 'local b' as the most divergent genotypes. Cluster analysis exposed the genetic relatedness between hybrids and selections with other known cultivars. The introduction of black pepper from South India to Malaysia was emphasized from the observation of genetic similarity of Malaysian cultivar 'Kuching' with other indigenous popular cultivars. The study was first to portray the precise genetic relatedness among the major indigenous genotypes of black pepper. PMID:21874534

  1. Polymorphism, monomorphism, and sequences in conserved microsatellites in primate species.

    PubMed

    Blanquer-Maumont, A; Crouau-Roy, B

    1995-10-01

    Dimeric short tandem repeats are a source of highly polymorphic markers in the mammalian genome. Genetic variation at these hypervariable loci is extensively used for linkage analysis, for the identification of individuals, and may be useful for interpopulation and interspecies studies. In this paper, we analyze the variability and the sequences of a segment including three microsatellites, first described in man, in several species of primates (chimpanzee, orangutan, gibbon, and macaque) using the heterologous primers (man primers). This region is located on the human chromosome 6p, near the tumor necrosis factor genes, in the major histocompatibility complex. The fact that these primers work in all species studied indicates that they are conserved throughout the different lineages of the two superfamilies, the Hominoidea and the Cercopithecidea, represented by the macaques. However, the intervening sequence displays intraspecific and interspecific variability. The sites of base substitutions and the insertion/deletion events are not evenly distributed within this region. The data suggest that it is necessary to have a minimal number of repeats to increase the rate of mutation sufficiently to allow the development of polymorphism. In some species, the microsatellites present single base variations which reduce the number of contiguous repeats, thus apparently slowing the rate of additional slippage events. Species with such variations or a low number of repeats are monomorphic. These microsatellite sequences are informative in the comparison of closely related species and reflect the phylogeny of the Old World monkeys, apes, and man. PMID:7563137

  2. Resistance gene enrichment sequencing (RenSeq) enables reannotation of the NB-LRR gene family from sequenced plant genomes and rapid mapping of resistance loci in segregating populations.

    PubMed

    Jupe, Florian; Witek, Kamil; Verweij, Walter; Sliwka, Jadwiga; Pritchard, Leighton; Etherington, Graham J; Maclean, Dan; Cock, Peter J; Leggett, Richard M; Bryan, Glenn J; Cardle, Linda; Hein, Ingo; Jones, Jonathan D G

    2013-11-01

    RenSeq is a NB-LRR (nucleotide binding-site leucine-rich repeat) gene-targeted, Resistance gene enrichment and sequencing method that enables discovery and annotation of pathogen resistance gene family members in plant genome sequences. We successfully applied RenSeq to the sequenced potato Solanum tuberosum clone DM, and increased the number of identified NB-LRRs from 438 to 755. The majority of these identified R gene loci reside in poorly or previously unannotated regions of the genome. Sequence and positional details on the 12 chromosomes have been established for 704 NB-LRRs and can be accessed through a genome browser that we provide. We compared these NB-LRR genes and the corresponding oligonucleotide baits with the highest sequence similarity and demonstrated that ~80% sequence identity is sufficient for enrichment. Analysis of the sequenced tomato S. lycopersicum 'Heinz 1706' extended the NB-LRR complement to 394 loci. We further describe a methodology that applies RenSeq to rapidly identify molecular markers that co-segregate with a pathogen resistance trait of interest. In two independent segregating populations involving the wild Solanum species S. berthaultii (Rpi-ber2) and S. ruiz-ceballosii (Rpi-rzc1), we were able to apply RenSeq successfully to identify markers that co-segregate with resistance towards the late blight pathogen Phytophthora infestans. These SNP identification workflows were designed as easy-to-adapt Galaxy pipelines. PMID:23937694

  3. Isolation and characterization of 12 microsatellite loci in soapbark, Quillaja saponaria (Quillajaceae)1

    PubMed Central

    Letelier, Luis; Harvey, Nick; Valderrama, Aly; Stoll, Alexandra; González-Rodríguez, Antonio

    2015-01-01

    Premise of the study: Microsatellite primers were developed for the endemic Chilean tree Quillaja saponaria (Quillajaceae), a common member of the sclerophyllous Mediterranean forest, to investigate intraspecific patterns of genetic diversity and structure. Methods and Results: Using an enriched library, 12 polymorphic microsatellite loci were developed in Q. saponaria. All loci consisted of dinucleotide repeats. The average number of alleles per locus was 5.3 (2–13), with a total of 64 alleles recorded in 39 individuals from three populations. Conclusions: The microsatellite markers described here are the first characterized for Q. saponaria. The polymorphic loci will be useful in studies of genetic diversity and genetic population differentiation in natural populations of this species. PMID:25995980

  4. Fourteen polymorphic microsatellite markers for the threatened Arnica montana (Asteraceae)1

    PubMed Central

    Duwe, Virginia K.; Ismail, Sascha A.; Buser, Andres; Sossai, Esther; Borsch, Thomas; Muller, Ludo A. H.

    2015-01-01

    • Premise of the study: Microsatellite markers were developed to investigate population genetic structure in the threatened species Arnica montana. • Methods and Results: Fourteen microsatellite markers with di-, tetra-, and hexanucleotide repeat motifs were developed for A. montana using 454 pyrosequencing without and with library-enrichment methods, resulting in 56,545 sequence reads and 14,467 sequence reads, respectively. All loci showed a high level of polymorphism, with allele numbers ranging from four to 11 in five individuals from five populations (25 samples) and an expected heterozygosity ranging from 0.192 to 0.648 across the loci. • Conclusions: This set of microsatellite markers is the first one described for A. montana and will facilitate conservation genetic applications as well as the understanding of phylogeographic patterns in this species. PMID:25606354

  5. Systematic Pathway Enrichment Analysis of a Genome-Wide Association Study on Breast Cancer Survival Reveals an Influence of Genes Involved in Cell Adhesion and Calcium Signaling on the Patients’ Clinical Outcome

    PubMed Central

    Woltmann, Andrea; Chen, Bowang; Lascorz, Jesús; Johansson, Robert; Eyfjörd, Jorunn E.; Hamann, Ute; Manjer, Jonas; Enquist-Olsson, Kerstin; Henriksson, Roger; Herms, Stefan; Hoffmann, Per; Hemminki, Kari; Lenner, Per; Försti, Asta

    2014-01-01

    Genome-wide association studies (GWASs) may help to understand the effects of genetic polymorphisms on breast cancer (BC) progression and survival. However, they give only a focused view, which cannot capture the tremendous complexity of this disease. Therefore, we investigated data from a previously conducted GWAS on BC survival for enriched pathways by different enrichment analysis tools using the two main annotation databases Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG). The goal was to identify the functional categories (GO terms and KEGG pathways) that are consistently overrepresented in a statistically significant way in the list of genes generated from the single nucleotide polymorphism (SNP) data. The SNPs with allelic p-value cut-offs 0.005 and 0.01 were annotated to the genes by excluding or including a 20 kb up-and down-stream sequence of the genes and analyzed by six different tools. We identified eleven consistently enriched categories, the most significant ones relating to cell adhesion and calcium ion binding. Moreover, we investigated the similarity between our GWAS and the enrichment analyses of twelve published gene expression signatures for breast cancer prognosis. Five of them were commonly used and commercially available, five were based on different aspects of metastasis formation and two were developed from meta-analyses of published prognostic signatures. This comparison revealed similarities between our GWAS data and the general and the specific brain metastasis gene signatures as well as the Oncotype DX signature. As metastasis formation is a strong indicator of a patient’s prognosis, this result reflects the survival aspect of the conducted GWAS and supports cell adhesion and calcium signaling as important pathways in cancer progression. PMID:24886783

  6. Characterization of microsatellites in the coding regions

    SciTech Connect

    Tuskan, Gerald A; Li, Shuxian; Yin, Tongming; Wang, Prof. Mingxiu

    2009-01-01

    With the development of high-throughput sequencing techniques, transcriptome sequencing projects which provide valuable resources for designing simple sequence repeat (SSR) primers have been carried out for many plants. However, the utility of SSRs for molecular breeding depends on genomewide distribution and coverage, as well as moderately high allelic variability, in the available SSR library. In this study, we characterized the exonic SSRs developed from the publicly available Populus genome as a case study to determine their value for molecular breeding. As expected, our results confirmed that microsatellites occurred approximately three times less often in coding regions than in non-coding regions. Mutability test also showed that exonic SSRs contained less allelic variability than intronic SSRs. More importantly, exonic SSRs were unevenly distributed both among and within chromosomes. Large exonic SSRs deserts were observed on several chromosomes. Differential selection between paralogous chromosomes, at the gene level, appears to be responsible for these SSR deserts, though the mechanisms that cause chromosome-specific SSR deserts are not known. This work provides ample evidence that the candidate gene approach based on unigenes identified from transcribed sequences may not be the best strategy to identify highly polymorphic SSRs.

  7. Evolutionary conservation of ten microsatellite loci in four species of Felidae.

    PubMed

    Menotti-Raymond, M A; O'Brien, S J

    1995-01-01

    Short tandem repeat polymorphisms (STRP), or microsatellites, are widespread among vertebrate genomes and are useful in gene mapping and population studies due to a high level of length polymorphism. We describe here the isolation, characterization, and PCR amplification of 10 microsatellite loci from the domestic cat, Felis catus. The flanking primer sequences were conserved among other Felidae species, and amplification products demonstrated abundant polymorphism in puma, lion, cheetah, and domestic cat. The cheetah sample exhibited the lowest level of polymorphism for these loci among felid species. PMID:7658003

  8. Survey and analysis of simple sequence repeats (SSRs) in three genomes of Candida species.

    PubMed

    Jia, Dongmei

    2016-06-15

    Simple sequence repeats (SSRs) or microsatellites, which composed of tandem repeated short units of 1-6bp, have been paying attention continuously. Here, the distribution, composition and polymorphism of microsatellites and compound microsatellites were analyzed in three available genomes of Candida species (Candida dubliniensis, Candida glabrata and Candida orthopsilosis). The results show that there were 118,047, 66,259 and 61,119 microsatellites in genomes of C. dubliniensis, C. glabrata and C. orthopsilosis, respectively. The SSRs covered more than 1/3 length of genomes in the three species. The microsatellites, which just consist of bases A and (or) T, such as (A)n, (T)n, (AT)n, (TA)n, (AAT)n, (TAA)n, (TTA)n, (ATA)n, (ATT)n and (TAT)n, were predominant in the three genomes. The length of microsatellites was focused on 6bp and 9bp either in the three genomes or in its coding sequences. What's more, the relative abundance (19.89/kbp) and relative density (167.87bp/kbp) of SSRs in sequence of mitochondrion of C. glabrata were significantly great than that in any one of genomes or chromosomes of the three species. In addition, the distance between any two adjacent microsatellites was an important factor to influence the formation of compound microsatellites. The analysis may be helpful for further studying the roles of microsatellites in genomes' origination, organization and evolution of Candida species. PMID:26883055

  9. The genome of the of the generalist plant pathogenic fungus Fusarium avenaceum is enriched with genes involved in redox, signaling and secondary metabolism

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Fusarium avenaceum is a fungus commonly isolated from soil and with a wide range of host plants. We present here three genome sequences of F. avenaceum, one isolated from barley in Finland and two from spring and winter wheat in Canada. The physical sizes of the three genomes range from 41.6-43.2 MB...

  10. Optimization of microsatellite analysis for genetic mapping

    SciTech Connect

    Hughes, A.E. )

    1993-02-01

    A method for typing microsatellite polymorphisms is described. It involves amplification using the polymerase chain reaction with one primer 5[prime] end-labeled with [sup 32]P. Alleles are separated by denaturing gel electrophoresis and detected by autoradiography. Standardized conditions allow accurate typing of almost all microsatellite polymorphisms, and results are usually obtained within 24 h. 4 refs., 1 fig.

  11. G-quadruplex (G4) motifs in the maize (Zea mays L.) genome are enriched at specific locations in thousands of genes coupled to energy status, hypoxia, low sugar, and nutrient deprivation.

    PubMed

    Andorf, Carson M; Kopylov, Mykhailo; Dobbs, Drena; Koch, Karen E; Stroupe, M Elizabeth; Lawrence, Carolyn J; Bass, Hank W

    2014-12-20

    The G-quadruplex (G4) elements comprise a class of nucleic acid structures formed by stacking of guanine base quartets in a quadruple helix. This G4 DNA can form within or across single-stranded DNA molecules and is mutually exclusive with duplex B-form DNA. The reversibility and structural diversity of G4s make them highly versatile genetic structures, as demonstrated by their roles in various functions including telomere metabolism, genome maintenance, immunoglobulin gene diversification, transcription, and translation. Sequence motifs capable of forming G4 DNA are typically located in telomere repeat DNA and other non-telomeric genomic loci. To investigate their potential roles in a large-genome model plant species, we computationally identified 149,988 non-telomeric G4 motifs in maize (Zea mays L., B73 AGPv2), 29% of which were in non-repetitive genomic regions. G4 motif hotspots exhibited non-random enrichment in genes at two locations on the antisense strand, one in the 5' UTR and the other at the 5' end of the first intron. Several genic G4 motifs were shown to adopt sequence-specific and potassium-dependent G4 DNA structures in vitro. The G4 motifs were prevalent in key regulatory genes associated with hypoxia (group VII ERFs), oxidative stress (DJ-1/GATase1), and energy status (AMPK/SnRK) pathways. They also showed statistical enrichment for genes in metabolic pathways that function in glycolysis, sugar degradation, inositol metabolism, and base excision repair. Collectively, the maize G4 motifs may represent conditional regulatory elements that can aid in energy status gene responses. Such a network of elements could provide a mechanistic basis for linking energy status signals to gene regulation in maize, a model genetic system and major world crop species for feed, food, and fuel. PMID:25527104

  12. Characterization of microsatellites in Xanthosoma sagittifolium (Araceae) and cross-amplification in related species1

    PubMed Central

    Cathebras, Chloe; Traore, Renan; Malapa, Roger; Risterucci, Ange-Marie; Chaïr, Hana

    2014-01-01

    • Premise of the study: To investigate the genetic diversity of a root crop, Xanthosoma sagittifolium, and to facilitate germplasm conservation, microsatellite loci were developed and characterized by genotyping 39 accessions from different geographic origins. • Methods and Results: Using a microsatellite-enriched library approach, 17 polymorphic microsatellite markers were identified and characterized. The number of alleles for each locus ranged from two to six. Observed and expected heterozygosities ranged from 0.00 to 0.97 and from 0.09 to 0.78, respectively. Additionally, cross-amplification of these microsatellite markers was tested successfully in other species of Xanthosoma and Caladium, with rates varying from 23.5% to 100%. • Conclusions: These results indicate the effectiveness of microsatellite loci developed for the characterization of X. sagittifolium genetic diversity. They are crucial for the future investigation of population dynamics and clonal identification and, therefore, for prioritizing germplasm conservation. They should also enable research on other related species. PMID:25202635

  13. EWS/FLI-responsive GGAA-microsatellites exhibit polymorphic differences between European and African populations

    PubMed Central

    Beck, Robert; Monument, Michael J.; Watkins, W. Scott; Smith, Richard; Boucher, Kenneth M.; Schiffman, Joshua D.; Jorde, Lynn B.; Randall, R. Lor; Lessnick, Stephen L.

    2012-01-01

    The genetics of Ewing sarcoma development remain obscure. The incidence of Ewing sarcoma is ten-fold less in Africans as compared to Europeans, irrespective of geographic location, suggesting population-specific genetic influences. Since GGAA-containing microsatellites within key target genes are necessary for Ewing sarcoma-specific EWS/FLI DNA binding and gene activation, and gene expression is positively correlated with the number of repeat motifs in the promoter/enhancer region, we sought to determine if significant polymorphisms exist between African and European populations which might contribute to observed differences in Ewing sarcoma incidence and outcomes. GGAA-microsatellites upstream of two critical EWS/FLI-target genes, NR0B1 and CAV1, were sequenced from subjects of European and African descent. While the characteristics of the CAV1 promoter microsatellites were similar across both populations, the NR0B1 microsatellite in African subjects was significantly larger, harboring more repeat motifs, a greater number of repeat segments, and longer consecutive repeats, than in European subjects. These results are biologically intriguing as NR0B1 was the most highly enriched EWS/FLI bound gene in prior studies, and is absolutely necessary for oncogenic transformation in Ewing sarcoma. These data suggest that GGAA-microsatellite polymorphisms in the NR0B1 gene might influence disease susceptibility and prognosis in Ewing sarcoma in unanticipated ways. PMID:22749036

  14. Rapid Microsatellite Isolation from a Butterfly by De Novo Transcriptome Sequencing: Performance and a Comparison with AFLP-Derived Distances

    PubMed Central

    Mikheyev, Alexander S.; Vo, Tanya; Wee, Brian; Singer, Michael C.; Parmesan, Camille

    2010-01-01

    Background The isolation of microsatellite markers remains laborious and expensive. For some taxa, such as Lepidoptera, development of microsatellite markers has been particularly difficult, as many markers appear to be located in repetitive DNA and have nearly identical flanking regions. We attempted to circumvent this problem by bioinformatic mining of microsatellite sequences from a de novo-sequenced transcriptome of a butterfly (Euphydryas editha). Principal Findings By searching the assembled sequence data for perfect microsatellite repeats we found 10 polymorphic loci. Although, like many expressed sequence tag-derived microsatellites, our markers show strong deviations from Hardy-Weinberg equilibrium in many populations, and, in some cases, a high incidence of null alleles, we show that they nonetheless provide measures of population differentiation consistent with those obtained by amplified fragment length polymorphism analysis. Estimates of pairwise population differentiation between 23 populations were concordant between microsatellite-derived data and AFLP analysis of the same samples (r = 0.71, p<0.00001, 425 individuals from 23 populations). Significance De novo transcriptional sequencing appears to be a rapid and cost-effective tool for developing microsatellite markers for difficult genomes. PMID:20585453

  15. Microsatellite Length Scoring by Single Molecule Real Time Sequencing – Effects of Sequence Structure and PCR Regime

    PubMed Central

    Liljegren, Mikkel Meyn; de Muinck, Eric Jacques; Trosvik, Pål

    2016-01-01

    Microsatellites are DNA sequences consisting of repeated, short (1–6 bp) sequence motifs that are highly mutable by enzymatic slippage during replication. Due to their high intrinsic variability, microsatellites have important applications in population genetics, forensics, genome mapping, as well as cancer diagnostics and prognosis. The current analytical standard for microsatellites is based on length scoring by high precision electrophoresis, but due to increasing efficiency next-generation sequencing techniques may provide a viable alternative. Here, we evaluated single molecule real time (SMRT) sequencing, implemented in the PacBio series of sequencing apparatuses, as a means of microsatellite length scoring. To this end we carried out multiplexed SMRT sequencing of plasmid-carried artificial microsatellites of varying structure under different pre-sequencing PCR regimes. For each repeat structure, reads corresponding to the target length dominated. We found that pre-sequencing amplification had large effects on scoring accuracy and error distribution relative to controls, but that the effects of the number of amplification cycles were generally weak. In line with expectations enzymatic slippage decreased proportionally with microsatellite repeat unit length and increased with repetition number. Finally, we determined directional mutation trends, showing that PCR and SMRT sequencing introduced consistent but opposing error patterns in contraction and expansion of the microsatellites on the repeat motif and single nucleotide level. PMID:27414800

  16. The report of my death was an exaggeration: A review for researchers using microsatellites in the 21st century1

    PubMed Central

    Hodel, Richard G. J.; Segovia-Salcedo, M. Claudia; Landis, Jacob B.; Crowl, Andrew A.; Sun, Miao; Liu, Xiaoxian; Gitzendanner, Matthew A.; Douglas, Norman A.; Germain-Aubrey, Charlotte C.; Chen, Shichao; Soltis, Douglas E.; Soltis, Pamela S.

    2016-01-01

    Microsatellites, or simple sequence repeats (SSRs), have long played a major role in genetic studies due to their typically high polymorphism. They have diverse applications, including genome mapping, forensics, ascertaining parentage, population and conservation genetics, identification of the parentage of polyploids, and phylogeography. We compare SSRs and newer methods, such as genotyping by sequencing (GBS) and restriction site associated DNA sequencing (RAD-Seq), and offer recommendations for researchers considering which genetic markers to use. We also review the variety of techniques currently used for identifying microsatellite loci and developing primers, with a particular focus on those that make use of next-generation sequencing (NGS). Additionally, we review software for microsatellite development and report on an experiment to assess the utility of currently available software for SSR development. Finally, we discuss the future of microsatellites and make recommendations for researchers preparing to use microsatellites. We argue that microsatellites still have an important place in the genomic age as they remain effective and cost-efficient markers. PMID:27347456

  17. The report of my death was an exaggeration: A review for researchers using microsatellites in the 21st century.

    PubMed

    Hodel, Richard G J; Segovia-Salcedo, M Claudia; Landis, Jacob B; Crowl, Andrew A; Sun, Miao; Liu, Xiaoxian; Gitzendanner, Matthew A; Douglas, Norman A; Germain-Aubrey, Charlotte C; Chen, Shichao; Soltis, Douglas E; Soltis, Pamela S

    2016-06-01

    Microsatellites, or simple sequence repeats (SSRs), have long played a major role in genetic studies due to their typically high polymorphism. They have diverse applications, including genome mapping, forensics, ascertaining parentage, population and conservation genetics, identification of the parentage of polyploids, and phylogeography. We compare SSRs and newer methods, such as genotyping by sequencing (GBS) and restriction site associated DNA sequencing (RAD-Seq), and offer recommendations for researchers considering which genetic markers to use. We also review the variety of techniques currently used for identifying microsatellite loci and developing primers, with a particular focus on those that make use of next-generation sequencing (NGS). Additionally, we review software for microsatellite development and report on an experiment to assess the utility of currently available software for SSR development. Finally, we discuss the future of microsatellites and make recommendations for researchers preparing to use microsatellites. We argue that microsatellites still have an important place in the genomic age as they remain effective and cost-efficient markers. PMID:27347456

  18. Development and characterization of new microsatellites for Eugenia dysenterica DC (Myrtaceae).

    PubMed

    Telles, M P C; Silva, J B; Resende, L V; Vianello, R P; Chaves, L J; Soares, T N; Collevatti, R G

    2013-01-01

    Microsatellite markers were developed for population genetic analyses of the Neotropical tree Eugenia dysenterica DC (Myrtaceae), after construction of a shotgun genomic library for microsatellite discovery. Nine primers were designed, of which 5 yielded amplified product. These primers were polymorphic for 97 individuals collected in 3 distinct localities. The number of alleles per locus (primer) ranged from 3 to 11 and expected heterozygosities varied from 0.309 to 0.884. The probability of locus identity was ~1.88 x 10(-4) and the probability of paternity exclusion was ~0.9367. The 5 microsatellite primer pairs may be suitable for population genetic studies such as parentage and fine-scale genetic analyses of this species. PMID:23420405

  19. Development and characterization of polymorphic microRNA-based microsatellite markers in Nelumbo nucifera (Nelumbonaceae)1

    PubMed Central

    Wang, Xiaolei; Gui, Songtao; Pan, Lei; Hu, Jihong; Ding, Yi

    2016-01-01

    Premise of the study: Polymorphic microRNA (miRNA)–based microsatellite markers were developed to investigate the genetic diversity and population structure of Nelumbo nucifera (Nelumbonaceae). Methods and Results: A total of 485 miRNA-based microsatellites were found from the genomic DNA sequences of N. nucifera. After several rounds of screening, 21 primer pairs flanking di-, tri-, or pentanucleotide repeats were identified that revealed high levels of genetic diversity in four populations with two to five alleles per locus. The observed and expected heterozygosity per locus ranged from 0.000 to 1.000 and from 0.000 to 0.803, respectively. Conclusions: The polymorphic microsatellite markers will be useful for studying the genetic diversity and population structure of N. nucifera. PMID:26819861

  20. Development and characterization of 25 microsatellite primers for Ilex chinensis (Aquifoliaceae)1

    PubMed Central

    Chen, Wen-Wen; Xiao, Zhen-Zhu; Tong, Xin; Liu, Yu-Pei; Li, Yuan-Yuan

    2015-01-01

    Premise of the study: To evaluate genetic variation and structure of Ilex chinensis (Aquifoliaceae), a dioecious evergreen tree, we developed 25 microsatellite markers from its nuclear genome. Methods and Results: Based on the biotin-streptavidin capture method, 10 polymorphic and 15 monomorphic microsatellite markers were developed. Ten polymorphic loci were characterized by 87 individuals sampled from three populations located in Zhejiang Province and Shanghai, China. The number of alleles per locus varied from two to 12. The observed and expected heterozygosities were 0.0435–0.9032 and 0.3121–0.8343, respectively. Conclusions: These microsatellite markers can be useful for further genetic studies of I. chinensis populations, and so contribute to forest restoration and management. PMID:26504681

  1. Isolation and characterization of novel microsatellite loci for the endangered orchid Cypripedium japonicum (Orchidaceae)1

    PubMed Central

    Yamashita, Yumi; Izuno, Ayako; Isagi, Yuji; Kurosawa, Takahide; Kaneko, Shingo

    2016-01-01

    Premise of the study: Twenty-six microsatellite markers were developed for the endangered orchid Cypripedium japonicum (Orchidaceae) to estimate the clonal diversity and genetic structure of the remaining populations in Japan. Methods and Results: Microsatellite loci of C. japonicum were isolated using Ion Personal Genome Machine (PGM) sequencing. The primer sets were tested on 55 ramets sampled from two populations in Japan. Sixteen loci showed polymorphism in at least one population, with two to five alleles per locus. Observed and expected heterozygosities for the two populations ranged from 0.00 to 0.92 and 0.00 to 0.71, respectively. Conclusions: The microsatellite markers developed here provide a useful tool to analyze clonal structure and sexual regeneration status and will help to manage the remaining genetic variation within C. japonicum. PMID:26949576

  2. New polymorphic microsatellite markers in the human MHC class III region.

    PubMed

    Matsuzaka, Y; Makino, S; Nakajima, K; Tomizawa, M; Oka, A; Bahram, S; Kulski, J K; Tamiya, G; Inoko, H

    2001-05-01

    The human major histocompatibility complex (MHC) class III region spanning approximately 760 kb is characterized by a remarkably high gene density with 59 expressed genes (one gene every 12.9 kb). Recently, susceptibility loci to numerous diseases, such as Graves disease, Crohn disease, and SLE have been suggested to be localized to this region, as assessed by associations mainly with genetic polymorphisms of TNF and TNF-linked microsatellite loci. However, it has been difficult to precisely localize these susceptibility loci to a single gene due to a paucity to date of polymorphic markers in the HLA class III region. To facilitate disease mapping within this region, we have analyzed 2 approximately 5 bases short tandem repeats (microsatellites) in this region. A total of 297 microsatellites were identified from the genomic sequence, consisting of 69 di-, 62 tri-, 107 tetra-, and 59 penta-nucleotide repeats. It was noted that among them as many as 17 microsatellites were located within the coding sequence of expressed genes (NOTCH4, PBX2, RAGE, G16, LPAAT, PPT2, TNXB, P450-CYP21B, G9a, HSP70-2, HSP70-1, HSP-hom, MuTSH5 and BAT2). Eight microsatellite repeats were collected as polymorphic markers due to their high number of alleles (11.9 on average) as well as their high polymorphic content value (PIC) (0.63). By combining the 38 and the 22 polymorphic microsatellites we have previously collected in the HLA class I and class II regions, respectively, we have now established a total of 68 novel genetic markers which are uniformly interspersed with a high density of one every 63.3 kb throughout the HLA region. This collection of polymorphic microsatellites will enable us to search for the location of any disease susceptible loci within the HLA region by association analysis. PMID:11556964

  3. DNA polymerase kappa microsatellite synthesis: two distinct mechanisms of slippage-mediated errors.

    PubMed

    Baptiste, Beverly A; Eckert, Kristin A

    2012-12-01

    Microsatellite tandem repeats are frequent sites of strand slippage mutagenesis in the human genome. Microsatellite mutations often occur as insertion/deletion of a repeat motif (unit-based indels), and increase in frequency with increasing repeat length after a threshold is reached. We recently demonstrated that DNA polymerase κ (Pol κ) produces fewer unit-based indel errors within dinucleotide microsatellites than does polymerase δ. Here, we examined human Pol κ's error profile within microsatellite alleles of varying sequence composition and length, using an in vitro HSV-tk gap-filling assay. We observed that Pol κ displays relatively accurate synthesis for unit-based indels, using di- and tetranucleotide repeat templates longer than the threshold length. We observed an abrupt increase in the unit-based indel frequency when the total microsatellite length exceeds 28 nucleotides, suggesting that extended Pol κ protein-DNA interactions enhance fidelity of the enzyme when synthesizing these microsatellite alleles. In contrast, Pol κ is error-prone within the HSV-tk coding sequence, producing frequent single-base errors in a manner that is highly biased with regard to sequence context. Single-nucleotide errors are also created by Pol κ within di- and tetranucleotide repeats, independently of the microsatellite allele length and at a frequency per nucleotide similar to the frequency of single base errors within the coding sequence. These single-base errors represent the mutational signature of Pol κ, and we propose them a mechanism independent of homology-stabilized slippage. Pol κ's dual fidelity nature provides a unique research tool to explore the distinct mechanisms of slippage-mediated mutagenesis. PMID:22965905

  4. Microsatellite instability in human mammary epithelial cells transformed by heavy ions

    NASA Astrophysics Data System (ADS)

    Yanada, S.; Yang, T. C.; George, K.; Okayasu, R.; Ando, K.; Tsujii, H.

    1998-11-01

    We analyzed DNA and proteins obtained from normal and transformed human mammary epithelial cells for studying the neoplastic transformation by high-LET irradiation in vitro. We also examined microsatellite instability in human mammary cells transformed to various stages of carcinogenesis, such as normal, growth variant and tumorigenic, using microsatellite marker D5S177 on the chromosome 5 and CY17 on the Chromosome 10. Microsatellite instabilities were detected in the tumorigenic stage. These results suggest that microsatellite instability may play a role in the progression of tumorigenecity. The cause of the genomic instability has been suggested as abnormalities of DNA-repair systems which may be due to one of the three reasons: 1) alterations of cell cycle regulating genes. 2) mutations in any of the DNA mismatch repair genes, 3) mutation in any of the DNA strand breaks repair genes. No abnormality of these genes and encoded proteins, however was found in the present studies. These studies thus suggest that the microsatellite instability is induced by an alternative mechanism.

  5. Isolation and characterization of novel microsatellites for Abies koreana and A. nephrolepis (Pinaceae).

    PubMed

    Hong, J K; Lim, J; Lee, B Y; Kwak, M

    2016-01-01

    Abies koreana is an endemic and rare species from Korea and is classified as endangered by the International Union for Conservation of Nature. Although the genetic diversity assessment for current population of A. koreana needs to be performed urgently, no microsatellite markers have been developed for this species. In the present study, we developed 22 novel polymorphic microsatellite loci and the characteristics of these loci were determined in A. koreana as well as in Abies nephrolepis, the most closely related species, and these loci were compared with previously reported microsatellite markers developed for the Abies genus. Genomic sequence (161 Mbp; 325,776 reads) was obtained from one individual of A. koreana using Roche 454 GS-FLX Titanium sequencing and 19,258 repeat motifs were identified from it. A total of 288 primer pairs with high copy numbers of di-repeat motifs were evaluated for amplification in A. koreana and A. nephrolepis. A total of 71 primer pairs successfully amplified fragments, of which 22 showed polymorphisms in A. koreana and A. nephrolepis. The average expected diversity was 0.767 and 0.717 in A. koreana and A. nephrolepis, respectively; these heterozygosity levels were moderate compared to the previously reported microsatellite loci from Abies species. This is the first set of microsatellite markers developed for A. koreana as well as A. nephrolepis and further population genetic studies of both species and genetic delimitation can be carried out for the species conservation and management. PMID:27173282

  6. Genomes Behave as Social Entities: Alien Chromatin Minorities Evolve Through Specificities Reduction

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Hybridization and chromosome doubling entailed by allopolyploidization requires genetic and epigenetic modifications, resulting in the adjustment of different genomes to the same nuclear environment. Recently, the main role of retrotransposon/microsatellite-rich regions of the genome in DNA sequenc...

  7. CicArMiSatDB: the chickpea microsatellite database

    PubMed Central

    2014-01-01

    Background Chickpea (Cicer arietinum) is a widely grown legume crop in tropical, sub-tropical and temperate regions. Molecular breeding approaches seem to be essential for enhancing crop productivity in chickpea. Until recently, limited numbers of molecular markers were available in the case of chickpea for use in molecular breeding. However, the recent advances in genomics facilitated the development of large scale markers especially SSRs (simple sequence repeats), the markers of choice in any breeding program. Availability of genome sequence very recently opens new avenues for accelerating molecular breeding approaches for chickpea improvement. Description In order to assist genetic studies and breeding applications, we have developed a user friendly relational database named the Chickpea Microsatellite Database (CicArMiSatDB http://cicarmisatdb.icrisat.org). This database provides detailed information on SSRs along with their features in the genome. SSRs have been classified and made accessible through an easy-to-use web interface. Conclusions This database is expected to help chickpea community in particular and legume community in general, to select SSRs of particular type or from a specific region in the genome to advance both basic genomics research as well as applied aspects of crop improvement. PMID:24952649

  8. The academic Chibis-M microsatellite

    NASA Astrophysics Data System (ADS)

    Zelenyi, L. M.; Gurevich, A. V.; Klimov, S. I.; Angarov, V. N.; Batanov, O. V.; Bogomolov, A. V.; Bogomolov, V. V.; Bodnar, L.; Vavilov, D. I.; Vladimirova, G. A.; Garipov, G. K.; Gotlib, V. M.; Dobriyan, M. B.; Dolgonosov, M. S.; Ivlev, N. A.; Kalyuzhnyi, A. V.; Karedin, V. N.; Karpenko, S. O.; Kozlov, V. M.; Kozlov, I. V.; Korepanov, V. E.; Lizunov, A. A.; Ledkov, A. A.; Nazarov, V. N.; Panasyuk, M. I.; Papkov, A. P.; Rodin, V. G.; Segedi, P.; Svertilov, S. I.; Sukhanov, A. A.; Ferenz, Ch.; Eysmont, N. A.; Yashin, I. V.

    2014-03-01

    This paper describes the scientific goals and design developments of the Chibis microsatellite platform and the Groza scientific equipment, which are aimed at studying new physical mechanisms of high-altitude electrical discharges in the atmosphere. A description of the Groza scientific equipment is presented, which is a united flying instrument that determines the basic requirements for the Chibis-M microsatellite. The problems of ground training of the space experiment, methods of launching the microsatellite in the ISS infrastructure into orbit, and command and telemetry control in flight, as well as the first scientific results, are presented.

  9. Accurate human microsatellite genotypes from high-throughput resequencing data using informed error profiles.

    PubMed

    Highnam, Gareth; Franck, Christopher; Martin, Andy; Stephens, Calvin; Puthige, Ashwin; Mittelman, David

    2013-01-01

    Repetitive sequences are biologically and clinically important because they can influence traits and disease, but repeats are challenging to analyse using short-read sequencing technology. We present a tool for genotyping microsatellite repeats called RepeatSeq, which uses Bayesian model selection guided by an empirically derived error model that incorporates sequence and read properties. Next, we apply RepeatSeq to high-coverage genomes from the 1000 Genomes Project to evaluate performance and accuracy. The software uses common formats, such as VCF, for compatibility with existing genome analysis pipelines. Source code and binaries are available at http://github.com/adaptivegenome/repeatseq. PMID:23090981

  10. Job Enrichment

    ERIC Educational Resources Information Center

    Sanders, Rick

    1970-01-01

    Job enrichment means giving people more decision-making power, more responsibility, more grasp of the totality of the job, and a sense of their own importance in the company. This article presents evidence of the successful working of this approach (Donnelly Mirrors), and the lack of success with an opposing approach (General Motors). (NL)

  11. A microsatellite-based genetic linkage map for channel catfish, Ictalurus punctatus.

    PubMed Central

    Waldbieser, G C; Bosworth, B G; Nonneman, D J; Wolters, W R

    2001-01-01

    Microsatellite loci were identified in channel catfish gene sequences or random clones from a small insert genomic DNA library. Outbred populations of channel catfish contained an average of eight alleles per locus and an average heterozygosity of 0.70. A genetic linkage map of the channel catfish genome (N = 29) was constructed from two reference families. A total of 293 microsatellite loci were polymorphic in one or both families, with an average of 171 informative meioses per locus. Nineteen type I loci, 243 type II loci, and one EST were placed in 32 multipoint linkage groups covering 1958 cM. Nine more type II loci were contained in three two-point linkage groups covering 24.5 cM. Twenty-two type II loci remained unlinked. Multipoint linkage groups ranged in size from 11.9 to 110.5 cM with an average intermarker distance of 8.7 cM. Seven microsatellite loci were closely linked with the sex-determining locus. The microsatellite loci and genetic linkage map will increase the efficiency of selective breeding programs for channel catfish. PMID:11404336

  12. Microsatellite polymorphism in the sexually transmitted human pathogen Trichomonas vaginalis indicates a genetically diverse parasite.

    PubMed

    Conrad, Melissa; Zubacova, Zuzana; Dunn, Linda A; Upcroft, Jacqui; Sullivan, Steven A; Tachezy, Jan; Carlton, Jane M

    2011-01-01

    Given the growing appreciation of serious health sequelae from widespread Trichomonas vaginalis infection, new tools are needed to study the parasite's genetic diversity. To this end we have identified and characterized a panel of 21 microsatellites and six single-copy genes from the T. vaginalis genome, using seven laboratory strains of diverse origin. We have (1) adapted our microsatellite typing method to incorporate affordable fluorescent labeling, (2) determined that the microsatellite loci remain stable in parasites continuously cultured for up to 17 months, and (3) evaluated microsatellite marker coverage of the six chromosomes that comprise the T. vaginalis genome, using fluorescent in situ hybridization (FISH). We have used the markers to show that T. vaginalis is a genetically diverse parasite in a population of commonly used laboratory strains. In addition, we have used phylogenetic methods to infer evolutionary relationships from our markers in order to validate their utility in future population analyses. Our panel is the first series of robust polymorphic genetic markers for T. vaginalis that can be used to classify and monitor lab strains, as well as provide a means to measure the genetic diversity and population structure of extant and future T. vaginalis isolates. PMID:20813140

  13. Microsatellite instability in Marek’s Disease Virus infected primary chicken embryo fibroblasts

    PubMed Central

    2012-01-01

    Background Marek’s disease virus (MDV), an oncogenic α-herpes virus, causes a devastating disease in chickens characterized by development of lymphoblastoid tumors in multiple organs. Microsatellite instability (MSI), a symptom of defect in DNA mismatch repair function, is a form of genomic instability frequently detected in many types of tumors. However, the involvement of MSI in MDV-infected cells has not been investigated. In this study, we determined the presence and frequency of MSI in primary chicken embryo fibroblasts infected with or without MDV strain in vitro. Results 118 distinct microsatellite markers were analyzed by polymerase chain reaction (PCR) in 21 samples. MSI was found in 91 of 118 markers, and 12 out of 118 demonstrated frequency of MSI at ≥ 40%. 27 of 118 microsatellite loci did not show microsatellite instability. Conclusions These findings showed that MSI was a real event occurring in primary chicken embryo fibroblasts infected with MDV in vitro as evidenced by the high frequency of MSI, and may be specifically associated with genome alteration of host cells during MDV infected. PMID:22967357

  14. Isolation and characterization of polymorphic microsatellite markers from Coilia ectenes.

    PubMed

    Rong, X J; Xu, Y J; Wang, Q Y; Liao, M J; Liu, X Z; Pan, C Y; Zhang, Z; Wang, Y G

    2013-01-01

    Coilia ectenes (Jordan and Seale 1905) is an important anadromous species that is an important resource at risk of extinction because of over-fishing, pollution, and coastal construction. To evaluate the genetic diversity of C. ectenes for use in breeding programs, elite microsatellite-enriched libraries were constructed and novel microsatellite markers were developed, and applied to genetically detect wild populations. Out of 92 randomly selected and sequenced clones, 89 contained a CA or GA repeat motif. Twenty-two pairs of primers were designed to investigate the polymorphism and genetic structure of a wild population collected from the Yellow River estuary, China. It was found that 2 loci were monomorphic and 20 loci were polymorphic. The number of alleles per polymorphic loci ranged from 3 to 13, with an average of 7.9. The expected heterozygosity per locus ranged from 0.05 to 0.89, with an average of 0.68. The isolated polymorphic markers are expected to be of use in future genetic breeding programs for C. ectenes, and in the assessment of genetic variation within this species. PMID:24338395

  15. [Genetic diversity of microsatellite loci in captive Amur tigers].

    PubMed

    Zhang, Yu-Gaung; Li, Di-Qiang; Xiao, Qi-Ming; Rao, Li-Qun; Zhang, Xue-Wen

    2004-09-01

    microsatellie loci had high or medium polymorphism in these Amur tigers and had high genetic diversity. At the same time, we only found even bases variability which showed the even bases repeat sequence (CA/GT) maybe the basic unit for length variability of microsatellite in all loci. In this study, the samples were made up of 75 hair specimens, 23 blood specimens and 15 tissue specimens, we obtained the genome DNA from hairs using the non-invasive DNA technology and demonstrated that DNA derived from hair samples is as good as that obtained from blood samples for the analysis of microsatellite polymorphism. These results imply that microsatellite DNA markers and non-invasive DNA technology can help study the genetic diversity of Amur tiger. This method could be used in the captive management of other endangered species. PMID:15640074

  16. Draft Genome Sequence of Bacillus pumilus Fairview, an Isolate Recovered from a Microbial Methanogenic Enrichment of Coal Seam Gas Formation Water from Queensland, Australia

    PubMed Central

    Greenfield, Paul; Tran-Dinh, Nai; Midgley, David J.

    2014-01-01

    Despite its global abundance, Bacillus pumilus is poorly studied. The Fairview strain was obtained from a methanogenic anaerobic coal digester. The draft genome sequence was 3.8 Mbp long and contained 3,890 protein-coding genes. Like the SAFR-032 strain, it includes B. pumilus-specific proteins that likely confer enhanced resistance to environmental stresses. PMID:24744330

  17. Pilot Sequencing of Onion Genomic DNA Reveals Fragments of Transposable Elements, Low Gene Densities, and Significant Gene Enrichment After Methyl Filtration

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Onion (Allium cepa) is a diploid (2n=2x=16) monocot with one of the largest nuclear genomes among cultivated plants, over 6 and 16 times that of maize and rice, respectively. In this study, we sequenced onion BACs to estimate gene densities and investigate the nature and distribution of repetitive ...

  18. Microsatellite characterization of Cimarron Uruguayo dogs

    PubMed Central

    Gagliardi, Rosa; Llambí, Silvia; García, Cristina; Arruga, María Victoria

    2011-01-01

    Various genetic markers, including microsatellites, have been used to analyze the genetic polymorphism and heterozygosity in canine breeds. In this work, we used nine microsatellite markers to investigate the genetic variability in Cimarron Uruguayo dogs, the only officially recognized native canine breed in Uruguay. DNA from 30 Cimarron Uruguayo dogs from northeastern and southern Uruguay was analyzed. The allelic frequencies for each microsatellite, the genetic variability and the consanguinity were calculated, as were the polymorphic information content (PIC) and the probability of exclusion (PE). All of the microsatellites studied were polymorphic. FH 2361, FH 2305 and PEZ 03 were the most informative, with PIC values > 0.7, in agreement with results for other canine breeds. The PE values for the markers were within the ranges previously described and were generally greater for microsatellites with higher PIC values. The heterozygosity value (0.649) was considered high since only nine microsatellites were analyzed. Compared with data for other breeds, the results obtained here indicate that Cimarron Uruguayo dogs have high genetic diversity. PMID:21637561

  19. Genetic diversity in Capsicum germplasm based on microsatellite and random amplified microsatellite polymorphism markers.

    PubMed

    Rai, Ved Prakash; Kumar, Rajesh; Kumar, Sanjay; Rai, Ashutosh; Kumar, Sanjeet; Singh, Major; Singh, Sheo Pratap; Rai, Awadesh Bahadur; Paliwal, Rajneesh

    2013-10-01

    A sound knowledge of the genetic diversity among germplasm is vital for strategic germplasm collection, maintenance, conservation and utilisation. Genomic simple sequence repeats (SSRs) and random amplified microsatellite polymorphism (RAMPO) markers were used to analyse diversity and relationships among 48 pepper (Capsicum spp.) genotypes originating from nine countries. These genotypes covered 4 species including 13 germplasm accessions, 30 improved lines of 4 domesticated species and 5 landraces derived from natural interspecific crosses. Out of 106 SSR markers, 25 polymorphic SSR markers (24 %) detected a total of 76 alleles (average, 3.04; range, 2-5). The average polymorphic information content (PIC) was 0.69 (range, 0.29-0.92). Seventeen RAMPO markers produced 87 polymorphic fragments with average PIC of 0.63 (range, 0.44-0.81). Dendrograms based on SSRs and RAMPOs generated two clusters. All 38 Capsicum annuum genotypes and an interspecific landrace clustered together, whereas nine non-annuum (three Capsicum frutescens, one Capsicum chinense, one Capsicum baccatum and four interspecific landraces) genotypes clustered separately. Genetic variation within non-annuum genotypes was greater than the C. annuum genotypes. Distinctness of interspecific derivative landraces grown in northeast India was validated; natural crossing between sympatric Capsicum species has been proposed as the mechanism of their origin. PMID:24431527

  20. Application of Microsatellite Markers in Conservation Genetics and Fisheries Management: Recent Advances in Population Structure Analysis and Conservation Strategies

    PubMed Central

    Abdul-Muneer, P. M.

    2014-01-01

    Microsatellites are the most popular and versatile genetic marker with myriads of applications in population genetics, conservation biology, and evolutionary biology. These are the arrays of DNA sequences, consisting of tandemly repeating mono-, di-, tri-, and tetranucleotide units, which are distributed throughout the genomes of most eukaryotic species. Microsatellites are codominant in nature, highly polymorphic, easily typed, and Mendelian inherited, all properties which make them very suitable for the study of population structure and pedigree analysis and capable of detecting differences among closely related species. PCR for microsatellites can be automated for identifying simple sequence repeat polymorphism. Small amount of blood samples or alcohol preserved tissue is adequate for analyzing them. Most of the microsatellites are noncoding, and therefore variations are independent of natural selection. These properties make microsatellites ideal genetic markers for conservation genetics and fisheries management. This review addresses the applications of microsatellite markers in conservation genetics and recent advances in population structure analysis in the context of fisheries management. PMID:24808959

  1. Microsatellite Typing of Clinical and Environmental Cryptococcus neoformans var. grubii Isolates from Cuba Shows Multiple Genetic Lineages

    PubMed Central

    Illnait-Zaragozi, Maria-Teresa; Martínez-Machín, Gerardo F.; Fernández-Andreu, Carlos M.; Boekhout, Teun; Meis, Jacques F.; Klaassen, Corné H. W.

    2010-01-01

    Background Human cryptococcal infections have been associated with bird droppings as a likely source of infection. Studies toward the local and global epidemiology of Cryptococcus spp. have been hampered by the lack of rapid, discriminatory, and exchangeable molecular typing methods. Methodology/Principal Findings We selected nine microsatellite markers for high-resolution fingerprinting from the genome of C. neoformans var. grubii. This panel of markers was applied to a collection of clinical (n = 122) and environmental (n = 68; from pigeon guano) C. neoformans var. grubii isolates from Cuba. All markers proved to be polymorphic. The average number of alleles per marker was 9 (range 5–51). A total of 104 genotypes could be distinguished. The discriminatory power of this panel of markers was 0.993. Multiple clusters of related genotypes could be discriminated that differed in only one or two microsatellite markers. These clusters were assigned as microsatellite complexes. The majority of environmental isolates (>70%) fell into 1 microsatellite complex containing only few clinical isolates (49 environmental versus 2 clinical). Clinical isolates were segregated over multiple microsatellite complexes. Conclusions/Significance A large genotypic variation exists in C. neoformans var. grubii. The genotypic segregation between clinical and environmental isolates from pigeon guano suggests additional source(s) of human cryptococcal infections. The selected panel of microsatellite markers is an excellent tool to study the epidemiology of C. neoformans var. grubii. PMID:20161737

  2. Cross-amplification and characterization of microsatellite loci in Acropora austera from the south-western Indian Ocean.

    PubMed

    Montoya-Maya, P H; Macdonald, A H H; Schleyer, M H

    2014-01-01

    Here, we report the successful cross-species amplification of previously published acroporid microsatellite markers in the coral Acropora austera from the south-western Indian Ocean. This fast-growing species is a major reef-building coral on South African reefs; however, it is the most damaged coral by scuba diving activity, and is known to be very susceptible to coral bleaching. Neither genetic information nor symbiont-free host tissue was available to develop novel microsatellite markers for this species. Cross-species amplification of previously published microsatellite markers was considered as an alternative to overcome these problems. Of the 21 microsatellite markers tested, 6 were reliably amplified, scored, and found to contain polymorphic loci (3-15 alleles). Although microsatellite sequences are believed to be scarce in the Acropora genome because of its small size, the results of this study and previous research indicate that the microsatellite sequences are well conserved across Acropora species. A detailed screening process identified and quantified the sources of error and bias in the application of these markers (e.g., allele scoring error, failure rates, frequency of null alleles), and may be accounted for in the study of the contemporary gene flow of A. austera in the south-western Indian Ocean. PMID:24634181

  3. Genome Distribution of Replication-independent Histone H1 Variants Shows H1.0 Associated with Nucleolar Domains and H1X Associated with RNA Polymerase II-enriched Regions*

    PubMed Central

    Mayor, Regina; Izquierdo-Bouldstridge, Andrea; Millán-Ariño, Lluís; Bustillos, Alberto; Sampaio, Cristina; Luque, Neus; Jordan, Albert

    2015-01-01

    Unlike core histones, the linker histone H1 family is more evolutionarily diverse, and many organisms have multiple H1 variants or subtypes. In mammals, the H1 family includes seven somatic H1 variants; H1.1 to H1.5 are expressed in a replication-dependent manner, whereas H1.0 and H1X are replication-independent. Using ChIP-sequencing data and cell fractionation, we have compared the genomic distribution of H1.0 and H1X in human breast cancer cells, in which we previously observed differential distribution of H1.2 compared with the other subtypes. We have found H1.0 to be enriched at nucleolus-associated DNA repeats and chromatin domains, whereas H1X is associated with coding regions, RNA polymerase II-enriched regions, and hypomethylated CpG islands. Further, H1X accumulates within constitutive or included exons and retained introns and toward the 3′ end of expressed genes. Inducible H1X knockdown does not affect cell proliferation but dysregulates a subset of genes related to cell movement and transport. In H1X-depleted cells, the promoters of up-regulated genes are not occupied specifically by this variant, have a lower than average H1 content, and, unexpectedly, do not form an H1 valley upon induction. We conclude that H1 variants are not distributed evenly across the genome and may participate with some specificity in chromatin domain organization or gene regulation. PMID:25645921

  4. Isolation of mini- and microsatellite loci from chromosome 19 library

    SciTech Connect

    Prosnyak, M.I.; Belajeva, O.V.; Polukarova, L.G.

    1994-09-01

    Mini- and microsatellite sequences are abundant in the human genome and are very useful as genetic markers. We report the isolation of a panel of clones containing marker sequences from chromosome 19. We screened 10,000 clones from the chromosome 19 cosmid library for the presence of di-(CA)n, tri-(TCC)n, (CAC)n microsatellites and M13-like minisatellite sequences. For this we have used synthetic oligonucleotides and polynucleotides, including micro- (CA, TCC, CAC) and minisatellite (M13 core) sequences. Preliminary results indicated that the chromosome 19 cosmid library contained both human and hamster clones. In order to identify human sequences from this library we have developed the technique of colony and blot hybridization with Alu-PCR, L1-PCR and B1-PCR probes. Dozens of clones have been selected, some of which were analyzed by conventional Southern blot analysis and non-radioactive in situ hybridization of chromosomes. Highly informative markers derived from these clones will be used for physical and genetic mapping of chromosome 19.

  5. Microsatellite instability and loss of heterozygosity in gastric cancer

    SciTech Connect

    Schneider, B.G.; Pulitzer, D.R.; Moehlmann, R.D.

    1994-09-01

    In order to detect regions of DNA containing tumor suppressor genes involved in the development of gastric cancer, we evaluated loss of heterozygosity (LOH) in 78 gastric adenocarcinomas. A total of 46 microsatellite markers were employed, which detected at least one site per arm of each autosome in the human genome, including several markers linked to known tumor suppressor genes (TP53, APC, DCC, RB1, and BRCA1). We detected elevated rates of LOH at D3S1478 on chromosome 3p21 (44%, or 22 of 50 cases), at D12S78 at 12q14q24.33 (39%), and 37% at D9S157 on 9p, three sites not previously known to be affected in gastric cancer. Another locus on chromosome 12q, D12S97, showed LOH in 40% of informative cases. LOH was detected on chromosome 17p near TP53 in 66% of informative cases (23 of 35). Microsatellite instability (MI) was observed in 22% of the cancers. Tumors varied greatly in percentage of sites exhibiting MI, from 0% to 77% of sites tested. These findings expand the description of the genetic lesions occurring in gastric cancer.

  6. Microsatellites Cross-Species Amplification across Some African Cichlids.

    PubMed

    Bezault, Etienne; Rognon, Xavier; Gharbi, Karim; Baroiller, Jean-Francois; Chevassus, Bernard

    2012-01-01

    The transfer of the genomic resources developed in the Nile tilapia, Oreochromis niloticus, to other Tilapiines sensu lato and African cichlid would provide new possibilities to study this amazing group from genetics, ecology, evolution, aquaculture, and conservation point of view. We tested the cross-species amplification of 32 O. niloticus microsatellite markers in a panel of 15 species from 5 different African cichlid tribes: Oreochromines (Oreochromis, Sarotherodon), Boreotilapiines (Tilapia), Chromidotilapines, Hemichromines, and Haplochromines. Amplification was successfully observed for 29 markers (91%), with a frequency of polymorphic (P(95)) loci per species around 70%. The mean number of alleles per locus and species was 3.2 but varied from 3.7 within Oreochromis species to 1.6 within the nontilapia species. The high level of cross-species amplification and polymorphism of the microsatellite markers tested in this study provides powerful tools for a wide range of molecular genetic studies within tilapia species as well as for other African cichlids. PMID:22701809

  7. Microsatellite evolutionary rate and pattern in Schistocerca gregaria inferred from direct observation of germline mutations.

    PubMed

    Chapuis, M-P; Plantamp, C; Streiff, R; Blondin, L; Piou, C

    2015-12-01

    Unravelling variation among taxonomic orders regarding the rate of evolution in microsatellites is crucial for evolutionary biology and population genetics research. The mean mutation rate of microsatellites tends to be lower in arthropods than in vertebrates, but data are scarce and mostly concern accumulation of mutations in model species. Based on parent-offspring segregations and a hierarchical Bayesian model, the mean rate of mutation in the orthopteran insect Schistocerca gregaria was estimated at 2.1e(-4) per generation per untranscribed dinucleotide locus. This is close to vertebrate estimates and one order of magnitude higher than estimates from species of other arthropod orders, such as Drosophila melanogaster and Daphnia pulex. We also found evidence of a directional bias towards expansions even for long alleles and exceptionally large ranges of allele sizes. Finally, at transcribed microsatellites, the mean rate of mutation was half the rate found at untranscribed loci and the mutational model deviated from that usually considered, with most mutations involving multistep changes that avoid disrupting the reading frame. Our direct estimates of mutation rate were discussed in the light of peculiar biological and genomic features of S. gregaria, including specificities in mismatch repair and the dependence of its activity to allele length. Shedding new light on the mutational dynamics of grasshopper microsatellites is of critical importance for a number of research fields. As an illustration, we showed how our findings improve microsatellite application in population genetics, by obtaining a more precise estimation of S. gregaria effective population size from a published data set based on the same microsatellites. PMID:26562076

  8. Parentage Reconstruction in Eucalyptus nitens Using SNPs and Microsatellite Markers: A Comparative Analysis of Marker Data Power and Robustness

    PubMed Central

    Telfer, Emily J.; Stovold, Grahame T.; Li, Yongjun; Silva-Junior, Orzenil B.; Grattapaglia, Dario G.; Dungey, Heidi S.

    2015-01-01

    Pedigree reconstruction using molecular markers enables efficient management of inbreeding in open-pollinated breeding strategies, replacing expensive and time-consuming controlled pollination. This is particularly useful in preferentially outcrossed, insect pollinated Eucalypts known to suffer considerable inbreeding depression from related matings. A single nucleotide polymorphism (SNP) marker panel consisting of 106 markers was selected for pedigree reconstruction from the recently developed high-density Eucalyptus Infinium SNP chip (EuCHIP60K). The performance of this SNP panel for pedigree reconstruction in open-pollinated progenies of two Eucalyptus nitens seed orchards was compared with that of two microsatellite panels with 13 and 16 markers respectively. The SNP marker panel out-performed one of the microsatellite panels in the resolution power to reconstruct pedigrees and out-performed both panels with respect to data quality. Parentage of all but one offspring in each clonal seed orchard was correctly matched to the expected seed parent using the SNP marker panel, whereas parentage assignment to less than a third of the expected seed parents were supported using the 13-microsatellite panel. The 16-microsatellite panel supported all but one of the recorded seed parents, one better than the SNP panel, although there was still a considerable level of missing and inconsistent data. SNP marker data was considerably superior to microsatellite data in accuracy, reproducibility and robustness. Although microsatellites and SNPs data provide equivalent resolution for pedigree reconstruction, microsatellite analysis requires more time and experience to deal with the uncertainties of allele calling and faces challenges for data transferability across labs and over time. While microsatellite analysis will continue to be useful for some breeding tasks due to the high information content, existing infrastructure and low operating costs, the multi-species SNP resource

  9. Microsatellite isolation and characterization for Colletotrichum spp, causal agent of anthracnose in Andean blackberry.

    PubMed

    Marulanda, M L; López, A M; Isaza, L; López, P

    2014-01-01

    The genus Colletotrichum, comprised of pathogenic fungi that affect plants grown worldwide, causes the disease known as anthracnose in several fruit and vegetable species. Several studies conducted on plants have shown that the disease is characterized by the presence of one or several species of the fungus attacking the fruit or other organs of the same host. To develop and implement effective control strategies, it is vital to understand the genetic structure of the fungus in agricultural systems, identify associated Colletotrichum species, and define the subpopulations responsible for the disease. Molecular tools were accordingly developed to characterize genotypic populations of Colletotrichum spp, causal agent of anthracnose in commercial crops of Andean blackberry (Rubus glaucus Benth.). A microsatellite-enriched library for Colletotrichum gloeosporioides was developed to identify and characterize microsatellite loci among isolates collected in R. glaucus plantations. Thirty microsatellites were developed and tested in 36 isolates gathered from eight different blackberry-production areas of Colombia. Ten pairs of microsatellites were polymorphic. PMID:25299081

  10. Characterization of novel microsatellite markers for Hyphantria cunea and implications for other Lepidoptera.

    PubMed

    Cao, L J; Wen, J B; Wei, S J; Liu, J; Yang, F; Chen, M

    2015-06-01

    This is the first report of microsatellite markers (simple sequence repeats, SSR) for fall webworm, Hyphantria cunea (Drury) (Lepidoptera: Arctiidae), an important quarantine pest in some European and Asian countries. Here, we developed 48 microsatellite markers for H. cunea from SSR enrichment libraries. Sequences isolated from libraries were sorted into four categories and analyzed. Our results suggest that sequences classified as Grouped should not be used for microsatellite primer design. The genetic diversity of microsatellite loci was assessed in 72 individuals from three populations. The number of alleles per locus ranged from 2 to 5 with an average of 3. The observed and expected heterozygosities of loci ranged from 0 to 0.958 and 0 to 0.773, respectively. A total of 18 out of 153 locus/population combinations deviated significantly from Hardy-Weinberg equilibrium. Moreover, significant linkage disequilibrium was detected in one pair of loci (1275 pairs in total). In the neutral test, two loci were grouped into the candidate category for positive selection and the remainder into the neutral category. In addition, a complex mutation pattern was observed for these loci, and F ST performed better than did R ST for the estimation of population differentiation in different mutation patterns. The results of the present study can be used for population genetic studies of H. cunea. PMID:25772405

  11. Development and characterization of microsatellite loci for Ocotea species (Lauraceae) threatened with extinction.

    PubMed

    Martins, E M; Martinelli, G; Arbetman, M P; Lamont, R W; Simões-Araújo, J L; Powell, D; Ciampi-Guillardi, M; Baldauf, C; Quinet, A; Galisa, P; Shapcott, A

    2014-01-01

    The Atlantic rainforest species Ocotea catharinensis, Ocotea odorifera, and Ocotea porosa have been extensively harvested in the past for timber and oil extraction and are currently listed as threatened due to overexploitation. To investigate the genetic diversity and population structure of these species, we developed 8 polymorphic microsatellite markers for O. odorifera from an enriched microsatellite library by using 2 dinucleotide repeats. The microsatellite markers were tested for cross-amplification in O. catharinensis and O. porosa. The average number of alleles per locus was 10.2, considering all loci over 2 populations of O. odorifera. Observed and expected heterozygosities for O. odorifera ranged from 0.39 to 0.93 and 0.41 to 0.92 across populations, respectively. Cross-amplification of all loci was successfully observed in O. catharinensis and O. porosa except 1 locus that was found to lack polymorphism in O. porosa. Combined probabilities of identity in the studied Ocotea species were very low ranging from 1.0 x 10-24 to 7.7 x 10-24. The probability of exclusion over all loci estimated for O. odorifera indicated a 99.9% chance of correctly excluding a random nonparent individual. The microsatellite markers described in this study have high information content and will be useful for further investigations on genetic diversity within these species and for subsequent conservation purposes. PMID:25061738

  12. COLD-PCR amplification of bisulfite-converted DNA allows the enrichment and sequencing of rare un-methylated genomic regions.

    PubMed

    Castellanos-Rizaldos, Elena; Milbury, Coren A; Karatza, Elli; Chen, Clark C; Makrigiorgos, G Mike; Merewood, Anne

    2014-01-01

    Aberrant hypo-methylation of DNA is evident in a range of human diseases including cancer and diabetes. Development of sensitive assays capable of detecting traces of un-methylated DNA within methylated samples can be useful in several situations. Here we describe a new approach, fast-COLD-MS-PCR, which amplifies preferentially un-methylated DNA sequences. By employing an appropriate denaturation temperature during PCR of bi-sulfite converted DNA, fast-COLD-MS-PCR enriches un-methylated DNA and enables differential melting analysis or bisulfite sequencing. Using methylation on the MGMT gene promoter as a model, it is shown that serial dilutions of controlled methylation samples lead to the reliable sequencing of un-methylated sequences down to 0.05% un-methylated-to-methylated DNA. Screening of clinical glioma tumor and infant blood samples demonstrated that the degree of enrichment of un-methylated over methylated DNA can be modulated by the choice of denaturation temperature, providing a convenient method for analysis of partially methylated DNA or for revealing and sequencing traces of un-methylated DNA. Fast-COLD-MS-PCR can be useful for the detection of loss of methylation/imprinting in cancer, diabetes or diet-related methylation changes. PMID:24728321

  13. Microsatellite based genetic diversity study in indigenous chicken ecotypes of Karnataka

    PubMed Central

    Rudresh, B. H.; Murthy, H. N. N.; Jayashankar, M. R.; Nagaraj, C. S.; Kotresh, A. M.; Byregowda, S. M.

    2015-01-01

    Aim: The current study was the first of its kind taken upon indigenous ecotypes of the Karnataka in order to unravel the diversity details at 20 chicken microsatellite regions. Materials and Methods: 210 indigenous chicken belonging to six districts of Bangalore and Mysore division formed the target sample for the present study. The genomic deoxyribonucleic acid was isolated by phenol chloroform isoamyl alcohol method. A panel of 20 microsatellite regions, including 14 recommended by FAO and six identified from published scientific literature became the targeted chicken genomic region. 27-33 samples were successfully genotyped in each of the six ecotypes through simplex or multiplex polymerase chain reactions, polyacrylamide gel electrophoresis and silver staining for the selected microsatellite panel. Results: The chickens of Ramanagara and Chamrajnagara were most distant with a Nei’s genetic distance value of 0.22. The chickens of Bangalore rural and Mysore were least distant with a value of 0.056. The Ramanagara and Chamrajnagara pair had Nei’s genetic identity value of 0.802, which is least among all pairs of ecotypes. There were five main nodes from which the six ecotypes evolved on the basis 20 microsatellite markers used in this study. This study indicates that the four ecotypes Ramnagara, Bangalore Rural, Chickaballapura and Mysore are genetically identical due to their common ancestral evolution while, Mandya and Chamrajnagara ecotypes formed a relatively different cluster due to a separate common ancestral chicken population and less number of generations since drifting from bifurcation node. Conclusion: Twenty microsatellite markers based genetic diversity study on six indigenous ecotypes indicated lower genetic distances as well as lower FST values compared to the distinguished breeds reported. There were two main clusters, which differentiated into six ecotypes. They may differentiate into more distinct varieties if bred in isolation for a longer

  14. Genomics and museum specimens.

    PubMed

    Nachman, Michael W

    2013-12-01

    Nearly 25 years ago, Allan Wilson and colleagues isolated DNA sequences from museum specimens of kangaroo rats (Dipodomys panamintinus) and compared these sequences with those from freshly collected animals (Thomas et al. 1990). The museum specimens had been collected up to 78 years earlier, so the two samples provided a direct temporal comparison of patterns of genetic variation. This was not the first time DNA sequences had been isolated from preserved material, but it was the first time it had been carried out with a population sample. Population geneticists often try to make inferences about the influence of historical processes such as selection, drift, mutation and migration on patterns of genetic variation in the present. The work of Wilson and colleagues was important in part because it suggested a way in which population geneticists could actually study genetic change in natural populations through time, much the same way that experimentalists can do with artificial populations in the laboratory. Indeed, the work of Thomas et al. (1990) spawned dozens of studies in which museum specimens were used to compare historical and present-day genetic diversity (reviewed in Wandeler et al. 2007). All of these studies, however, were limited by the same fundamental problem: old DNA is degraded into short fragments. As a consequence, these studies mostly involved PCR amplification of short templates, usually short stretches of mitochondrial DNA or microsatellites. In this issue, Bi et al. (2013) report a breakthrough that should open the door to studies of genomic variation in museum specimens. They used target enrichment (exon capture) and next-generation (Illumina) sequencing to compare patterns of genetic variation in historic and present-day population samples of alpine chipmunks (Tamias alpinus) (Fig. 1). The historic samples came from specimens collected in 1915, so the temporal span of this comparison is nearly 100 years. PMID:24138088

  15. Genomic amplification of 9p24.1 targeting JAK2, PD-L1, and PD-L2 is enriched in high-risk triple negative breast cancer

    PubMed Central

    Barrett, Michael T.; Anderson, Karen S.; Lenkiewicz, Elizabeth; Andreozzi, Mariacarla; Cunliffe, Heather E.; Klassen, Christine L.; Dueck, Amylou C.; McCullough, Ann E.; Reddy, Srikanth K.; Ramanathan, Ramesh K.; Northfelt, Donald W.; Pockaj, Barbara A.

    2015-01-01

    We used DNA content flow cytometry followed by oligonucleotide array based comparative genomic hybridization to survey the genomes of 326 tumors, including 41 untreated surgically resected triple negative breast cancers (TNBC). A high level (log2ratio ≥1) 9p24 amplicon was found in TNBC (12/41), glioblastomas (2/44), and colon carcinomas (2/68). The shortest region of overlap for the amplicon targets 9p24.1 and includes the loci for PD-L1, PD-L2, and JAK2 (PDJ amplicon). In contrast this amplicon was absent in ER+ (0/8) and HER2+ (0/15) breast tumors, and in pancreatic ductal adenocarcinomas (0/150). The PDJ amplicon in TNBCs was correlated with clinical outcomes in group comparisons by two-sample t-tests for continuous variables and chi-squared tests for categorical variables. TNBC patients with the PDJ amplicon had a worse outcome with worse disease-free and overall survival. Quantitative RT-PCR confirmed that the PDJ amplicon in TNBC is associated with elevated expression of JAK2 and of the PD-1 ligands. These initial findings demonstrate that the PDJ amplicon is enriched in TNBC, targets signaling pathways that activate the PD-1 mediated immune checkpoint, and identifies patients with a poor prognosis. PMID:26317899

  16. Genomic amplification of 9p24.1 targeting JAK2, PD-L1, and PD-L2 is enriched in high-risk triple negative breast cancer.

    PubMed

    Barrett, Michael T; Anderson, Karen S; Lenkiewicz, Elizabeth; Andreozzi, Mariacarla; Cunliffe, Heather E; Klassen, Christine L; Dueck, Amylou C; McCullough, Ann E; Reddy, Srikanth K; Ramanathan, Ramesh K; Northfelt, Donald W; Pockaj, Barbara A

    2015-09-22

    We used DNA content flow cytometry followed by oligonucleotide array based comparative genomic hybridization to survey the genomes of 326 tumors, including 41 untreated surgically resected triple negative breast cancers (TNBC). A high level (log2ratio ≥ 1) 9p24 amplicon was found in TNBC (12/41), glioblastomas (2/44), and colon carcinomas (2/68). The shortest region of overlap for the amplicon targets 9p24.1 and includes the loci for PD-L1, PD-L2, and JAK2 (PDJ amplicon). In contrast this amplicon was absent in ER+ (0/8) and HER2+ (0/15) breast tumors, and in pancreatic ductal adenocarcinomas (0/150). The PDJ amplicon in TNBCs was correlated with clinical outcomes in group comparisons by two-sample t-tests for continuous variables and chi-squared tests for categorical variables. TNBC patients with the PDJ amplicon had a worse outcome with worse disease-free and overall survival. Quantitative RT-PCR confirmed that the PDJ amplicon in TNBC is associated with elevated expression of JAK2 and of the PD-1 ligands. These initial findings demonstrate that the PDJ amplicon is enriched in TNBC, targets signaling pathways that activate the PD-1 mediated immune checkpoint, and identifies patients with a poor prognosis. PMID:26317899

  17. Helitrons shaping the genomic architecture of Drosophila: enrichment of DINE-TR1 in α- and β-heterochromatin, satellite DNA emergence, and piRNA expression.

    PubMed

    Dias, Guilherme B; Heringer, Pedro; Svartman, Marta; Kuhn, Gustavo C S

    2015-09-01

    Drosophila INterspersed Elements (DINEs) constitute an abundant but poorly understood group of Helitrons present in several Drosophila species. The general structure of DINEs includes two conserved blocks that may or not contain a region with tandem repeats in between. These central tandem repeats (CTRs) are similar within species but highly divergent between species. It has been assumed that CTRs have independent origins. Herein, we identify a subset of DINEs, termed DINE-TR1, which contain homologous CTRs of approximately 150 bp. We found DINE-TR1 in the sequenced genomes of several Drosophila species and in Bactrocera tryoni (Acalyptratae, Diptera). However, interspecific high sequence identity (∼ 88 %) is limited to the first ∼ 30 bp of each tandem repeat, implying that evolutionary constraints operate differently over the monomer length. DINE-TR1 is unevenly distributed across the Drosophila phylogeny. Nevertheless, sequence analysis suggests vertical transmission. We found that CTRs within DINE-TR1 have independently expanded into satellite DNA-like arrays at least twice within Drosophila. By analyzing the genome of Drosophila virilis and Drosophila americana, we show that DINE-TR1 is highly abundant in pericentromeric heterochromatin boundaries, some telomeric regions and in the Y chromosome. It is also present in the centromeric region of one autosome from D. virilis and dispersed throughout several euchromatic sites in both species. We further found that DINE-TR1 is abundant at piRNA clusters, and small DINE-TR1-derived RNA transcripts (∼25 nt) are predominantly expressed in the testes and the ovaries, suggesting active targeting by the piRNA machinery. These features suggest potential piRNA-mediated regulatory roles for DINEs at local and genome-wide scales in Drosophila. PMID:26408292

  18. Microsatellite markers for the Cabreúva tree, Myroxylon peruiferum (Fabaceae), an endangered medicinal species from the Brazilian Atlantic Forest.

    PubMed

    Schwarcz, K D; Bajay, M M; Macrini, C M T; Salazar, V L P; Souza, A P; Pinheiro, J B; Brancalion, P H S; Rodrigues, R R; Zucchi, M I

    2014-01-01

    The Cabreúva tree, Myroxylon peruiferum, is an endangered tropical species from Brazil used in forest restoration projects. It is known for its medicinal properties. Eleven microsatellite markers were developed for this species, from a microsatellite-enriched library. Nine of these markers, characterized in 30 individuals from a semideciduous forest remnant population in southeast Brazil, were polymorphic, with allele numbers ranging from 2 to 8 per locus; expected and observed heterozygosities ranged from 0.103 to 0.757 and 0.107 to 0.704, respectively. One locus (Mpe-C04) showed significant deviation from Hardy-Weinberg equilibrium, probably due to null alleles. Two other loci (Mpe-E09 and Mpe-H07) were monomorphic in this population. These microsatellite loci should be useful for future population genetic studies of this species. PMID:24737514

  19. Development of 14 microsatellite markers in Odontites vernus s.l. (Orobanchaceae) and cross-amplification in related taxa1

    PubMed Central

    Pinto-Carrasco, Daniel; Košnar, Jiří; López-González, Noemí; Koutecký, Petr; Těšitel, Jakub; Rico, Enrique; Martínez-Ortega, M. Montserrat

    2016-01-01

    Premise of the study: Microsatellite primers were developed for the first time in the root hemiparasite herb Odontites vernus (Orobanchaceae). These markers will be useful to investigate the role of polyploidization in the evolution of this diploid-tetraploid complex, as well as the extent of gene flow between different ploidy levels. Methods and Results: Fourteen polymorphic and reproducible loci were identified and optimized from O. vernus using a microsatellite-enriched library and 454 Junior sequencing. The set of primers amplified di- to pentanucleotide repeats and showed two to 13 alleles per locus. Transferability was tested in 30 taxa (19 belonging to Odontites and 11 from eight other genera of Orobanchaceae tribe Rhinantheae). Conclusions: The results indicate the utility of the newly developed microsatellites in O. vernus and several other species, which will be useful for taxon delimitation and conservation genetics studies. PMID:27011897

  20. RNA-protein interactions in unstable microsatellite diseases

    PubMed Central

    Mohan, Apoorva; Goodwin, Marianne; Swanson, Maurice S.

    2014-01-01

    A novel RNA-mediated disease mechanism has emerged from studies on dominantly inherited neurological disorders caused by unstable microsatellite expansions in non-coding regions of the genome. These non-coding tandem repeat expansions trigger the production of unusual RNAs that gain a toxic function, which involves the formation of RNA repeat structures that interact with, and alter the activities of, various factors required for normal RNA processing as well as additional cellular functions. In this review, we explore the deleterious effects of toxic RNA expression and discuss the various model systems currently available for studying RNA gain-of-function in neurologic diseases. Common themes, including bidirectional transcription and repeat-associated non-ATG (RAN) translation, have recently emerged from expansion disease studies. These and other discoveries have highlighted the need for further investigations designed to provide the additional mechanistic insights essential for future therapeutic development. PMID:24709120

  1. Microsatellites for the genus Cucurbita and an SSR-based genetic linkage map of Cucurbita pepo L.

    PubMed Central

    Gong, L.; Stift, G.; Kofler, R.; Pachner, M.

    2008-01-01

    Until recently, only a few microsatellites have been available for Cucurbita, thus their development is highly desirable. The Austrian oil-pumpkin variety Gleisdorfer Ölkürbis (C. pepo subsp. pepo) and the C. moschata cultivar Soler (Puerto Rico) were used for SSR development. SSR-enriched partial genomic libraries were established and 2,400 clones were sequenced. Of these 1,058 (44%) contained an SSR at least four repeats long. Primers were designed for 532 SSRs; 500 primer pairs produced fragments of expected size. Of these, 405 (81%) amplified polymorphic fragments in a set of 12 genotypes: three C. moschata, one C. ecuadorensis, and eight C. pepo representing all eight cultivar groups. On an average, C. pepo and C. moschata produced 3.3 alleles per primer pair, showing high inter-species transferability. There were 187 SSR markers detecting polymorphism between the USA oil-pumpkin variety “Lady Godiva” (O5) and the Italian crookneck variety “Bianco Friulano” (CN), which are the parents of our previous F2 mapping population. It has been used to construct the first published C. pepo map, containing mainly RAPD and AFLP markers. Now the updated map comprises 178 SSRs, 244 AFLPs, 230 RAPDs, five SCARs, and two morphological traits (h and B). It contains 20 linkage groups with a map density of 2.9 cM. The observed genome coverage (Co) is 86.8%. Electronic supplementary material The online version of this article (doi:10.1007/s00122-008-0750-2) contains supplementary material, which is available to authorized users. PMID:18379753

  2. Chemotherapeutic implications in microsatellite unstable colorectal cancer1

    PubMed Central

    Jo, Won-Seok; Carethers, John M.

    2016-01-01

    Chemotherapy for colorectal cancer is currently offered to patients based on the stage of their cancer, and there is evidence to show an overall survival benefit with 5-fluorouracil-based (5-FU) therapy for patients with lymph node metastasis who receive it. The pathogenesis of colorectal cancer involves genomic instability, with about 15% of tumors demonstrating a form of genomic instability called high-frequency microsatellite instability (MSI-H) and due to loss of DNA mismatch repair function, and the remainder of colorectal tumors lacking MSI-H with retained DNA mismatch repair function and called microsatellite stable (MSS), with a large proportion of these tumors demonstrating another form of genomic instability called chromosomal instability. There is now evidence to show that the form of genomic instability that is present in a patient’s colorectal cancer may predict a survival benefit from 5-FU. In particular, patients whose colorectal tumors have MSI-H do not gain a survival benefit with 5-FU as compared to patients with MSS tumors. In vitro evidence supports these findings, as MSI-H colon cancer cell lines are more resistant to 5-FU compared to MSS cell lines. More specifically, components of the DNA mismatch repair system have been shown to recognize and bind to 5-FU that becomes incorporated into DNA and which could be a trigger to induce cell death. The binding and subsequent cell death events would be absent in colorectal tumors with MSI-H, which have lost intact DNA mismatch repair function. These findings suggest that: (a) tumor cytotoxicity of 5-FU is mediated by DNA mechanisms in addition to well-known RNA mechanisms, and (b) patients whose tumors demonstrate MSI-H may not benefit from 5-FU therapy. Future studies should include a better understanding of the cellular mechanisms of the DNA recognition of 5-FU, multi-centered prospective trials investigating the survival benefit of 5-FU based on genomic instability, and the investigation of

  3. Plastid microsatellite markers in Carya

    Technology Transfer Automated Retrieval System (TEKTRAN)

    PCR primers capable of amplifying polymorphic regions of the plastid genome in Carya have broad applications for characterizing the genus and for conservation and improvement of pecan. We evaluated 8 "universal" plastid primers and qualified 3 as polymorphic and informative. Pecans of known lineag...

  4. STaRRRT: a table of short tandem repeats in regulatory regions of the human genome

    PubMed Central

    2013-01-01

    Background Tandem repeats (TRs) are unstable regions commonly found within genomes that have consequences for evolution and disease. In humans, polymorphic TRs are known to cause neurodegenerative and neuromuscular disorders as well as being associated with complex diseases such as diabetes and cancer. If present in upstream regulatory regions, TRs can modify chromatin structure and affect transcription; resulting in altered gene expression and protein abundance. The most common TRs are short tandem repeats (STRs), or microsatellites. Promoter located STRs are considerably more polymorphic than coding region STRs. As such, they may be a common driver of phenotypic variation. To study STRs located in regulatory regions, we have performed genome-wide analysis to identify all STRs present in a region that is 2 kilobases upstream and 1 kilobase downstream of the transcription start sites of genes. Results The Short Tandem Repeats in Regulatory Regions Table, STaRRRT, contains the results of the genome-wide analysis, outlining the characteristics of 5,264 STRs present in the upstream regulatory region of 4,441 human genes. Gene set enrichment analysis has revealed significant enrichment for STRs in cellular, transcriptional and neurological system gene promoters and genes important in ion and calcium homeostasis. The set of enriched terms has broad similarity to that seen in coding regions, suggesting that regulatory region STRs are subject to similar evolutionary pressures as STRs in coding regions and may, like coding region STRs, have an important role in controlling gene expression. Conclusions STaRRRT is a readily-searchable resource for investigating potentially polymorphic STRs that could influence the expression of any gene of interest. The processes and genes enriched for regulatory region STRs provide potential novel targets for diagnosing and treating disease, and support a role for these STRs in the evolution of the human genome. PMID:24228761

  5. First haploid genetic map based on microsatellite markers in Senegalese sole (Solea senegalensis, Kaup 1858).

    PubMed

    Molina-Luzón, Ma Jesús; Hermida, Miguel; Navajas-Pérez, Rafael; Robles, Francisca; Navas, José Ignacio; Ruiz-Rejón, Carmelo; Bouza, Carmen; Martínez, Paulino; de la Herrán, Roberto

    2015-02-01

    The Senegalese sole (Solea senegalensis, Kaup 1858) is a flatfish species of great value for aquaculture. In this study, we develop the first linkage map in this species based on microsatellite markers characterized from genomic DNA libraries and EST databases of Senegalese sole and from other flatfish species. Three reference gynogenetic families were obtained by chromosome-manipulation techniques: two haploid gynogenetics, used to assign and order microsatellites to linkage groups and another diploid gynogenetic family, used for estimating marker-centromere distances. The consensus map consists of 129 microsatellites distributed in 27 linkage groups (LG), with an average density of 4.7 markers per LG and comprising 1,004 centimorgans (cM). Additionally, 15 markers remained unlinked. Through half-tetrad analysis, we were able to estimate the centromere distance for 81 markers belonging to 24 LG, representing an average of 3 markers per LG. Comparative mapping was performed between flatfish species LG and model fish species chromosomes (stickleback, Tetraodon, medaka, fugu and zebrafish). The usefulness of microsatellite markers and the genetic map as tools for comparative mapping and evolution studies is discussed. PMID:25107689

  6. Isolation and characterization of cross-amplification microsatellite panels for species of Procapra (Bovidae; Antilopinae).

    PubMed

    Chen, Jing; Li, Chunlin; Yang, Ji; Luo, Zhenhua; Tang, Songhua; Li, Feng; Li, Chunwang; Liu, Bingwan; Jiang, Zhigang

    2012-01-01

    The three Procapra species, Tibetan gazelle (P. picticaudata), Mongolian gazelle (P. gutturosa) and Przewalski's gazelle (P. przewalskii) are endemic to Asia. Several intraspecific genetic issues have been studied with species-specific microsatellite loci in these Asian gazelles. However, cross-species microsatellite panels are absent, which inhibits comparative conservation and evolutionary studies of the Procapra. In this study, we isolated 20 cross-species microsatellite loci for Procapra from both related species and the genomic library of P. przewalskii. Fifty-three samples of the three gazelles were used to characterize the markers. Allele numbers ranged from three to 20, with a mean of 7.93 per locus. Observed heterozygosity (H(O)) averaged 0.680 and expected heterozygosity (H(E)) 0.767. The mean polymorphic information content (PIC) was 0.757 for P. picticaudata, 0.803 for P. gutturosa and 0.590 for P. przewalskii. Nine loci were significantly deviated from Hardy-Weinberg (H-W) equilibrium in the three species. Significant linkage disequilibrium was detected in four pairs of loci in P. przewalskii, five pairs in P. gutturosa and 51 pairs in P. picticaudata. Considering the abundance of published loci and their high success rates of cross-amplification, testing and utilization of loci from related species is efficient for wild species of Bovidae. The cross-species microsatellite loci we developed will facilitate further interspecies genetic studies in Procapra. PMID:22942736

  7. An empirical review: Characteristics of plant microsatellite markers that confer higher levels of genetic variation1

    PubMed Central

    Merritt, Benjamin J.; Culley, Theresa M.; Avanesyan, Alina; Stokes, Richard; Brzyski, Jessica

    2015-01-01

    During microsatellite marker development, researchers must choose from a pool of possible primer pairs to further test in their species of interest. In many cases, the goal is maximizing detectable levels of genetic variation. To guide researchers and determine which markers are associated with higher levels of genetic variation, we conducted a literature review based on 6782 genomic microsatellite markers published from 1997–2012. We examined relationships between heterozygosity (He or Ho) or allele number (A) with the following marker characteristics: repeat type, motif length, motif region, repeat frequency, and microsatellite size. Variation across taxonomic groups was also analyzed. There were significant differences between imperfect and perfect repeat types in A and He. Dinucleotide motifs exhibited significantly higher A, He, and Ho than most other motifs. Repeat frequency and motif region were positively correlated with A, He, and Ho, but correlations with microsatellite size were minimal. Higher taxonomic groups were disproportionately represented in the literature and showed little consistency. In conclusion, researchers should carefully consider marker characteristics so they can be tailored to the desired application. If researchers aim to target high genetic variation, dinucleotide motif lengths with large repeat frequencies may be best. PMID:26312192

  8. TPMD: a database and resources of microsatellite marker genotyped in Taiwanese populations.

    PubMed

    Chang, Ya-Hui; Su, Wen-Hui; Lee, Tso-Ching; Sun, Hsiao-Fang Sunny; Chen, Chia-Hsiang; Pan, Wen-Harn; Tsai, Shih-Feng; Jou, Yuh-Shan

    2005-01-01

    Taiwan Polymorphic Marker Database (TPMD) (http://tpmd.nhri.org.tw/) is a marker database designed to provide experimental details and useful marker information allelotyped in Taiwanese populations accompanied by resources and technical supports. The current version deposited more than 372,000 allelotyping data from 1425 frequently used and fluorescent-labeled microsatellite markers with variation types of dinucleotide, trinucleotide and tetranucleotide. TPMD contains text and map displays with searchable and retrievable options for marker names, chromosomal location in various human genome maps and marker heterozygosity in populations of Taiwanese, Japanese and Caucasian. The integration of marker information in map display is useful for the selection of high heterozygosity and commonly used microsatellite markers to refine mapping of diseases locus followed by identification of disease gene by positional candidate cloning. In addition, our results indicated that the number of markers with heterozygosity over 0.7 in Asian populations is lower than that in Caucasian. To increase accuracy and facilitate genetic studies using microsatellite markers, we also list markers with genotyping difficulty due to ambiguity of allele calling and recommend an optimal set of microsatellite markers for genotyping in Taiwanese, and possible extension of genotyping in other Mongoloid populations. PMID:15608171

  9. Lineage analysis by microsatellite loci deep sequencing in mice.

    PubMed

    Luo, Tao; He, Xionglei; Xing, Ke

    2016-05-01

    Lineage analysis is the identification of all the progeny of a single progenitor cell, and has become particularly useful for studying developmental processes and cancer biology. Here, we propose a novel and effective method for lineage analysis that combines sequence capture and next-generation sequencing technology. Genome-wide mononucleotide and dinucleotide microsatellite loci in eight samples from two mice were identified and used to construct phylogenetic trees based on somatic indel mutations at these loci, which were unique enough to distinguish and parse samples from different mice into different groups along the lineage tree. For example, biopsies from the liver and stomach, which originate from the endoderm, were located in the same clade, while samples in kidney, which originate from the mesoderm, were located in another clade. Yet, tissue with a common developmental origin may still contain cells of a mixed ancestry. This genome-wide approach thus provides a non-invasive lineage analysis method based on mutations that accumulate in the genomes of opaque multicellular organism somatic cells. Mol. Reprod. Dev. 83: 387-391, 2016. © 2016 Wiley Periodicals, Inc. PMID:26932355

  10. Characterization of 38 microsatellite loci in the European blackbird, Turdus merula (Turdidae, AVES).

    PubMed

    Simeoni, Michelle; Dawson, Deborah A; Gentle, Louise K; Coiffait, Lisette; Wolff, Kirsten; Evans, Karl L; Gaston, Kevin J; Hatchwell, Ben J

    2009-11-01

    We characterized 38 microsatellite loci in the European blackbird, Turdus merula. Thirty-seven loci were identified by testing 242 loci that had been originally isolated in other avian species. One additional locus was isolated from a European blackbird genomic library. All loci were characterized in 20-29 blackbirds from a population in the Czech Republic and displayed between two and 16 alleles, with observed heterozygosity ranging from 0.04 to 1.00. Thirty-seven loci could be assigned a chromosome location in the zebra finch (Taeniopygia guttata) genome based on sequence homology. PMID:21564948

  11. Overrepresentation of glutamate signaling in Alzheimer's disease: network-based pathway enrichment using meta-analysis of genome-wide association studies.

    PubMed

    Pérez-Palma, Eduardo; Bustos, Bernabé I; Villamán, Camilo F; Alarcón, Marcelo A; Avila, Miguel E; Ugarte, Giorgia D; Reyes, Ariel E; Opazo, Carlos; De Ferrari, Giancarlo V

    2014-01-01

    Genome-wide association studies (GWAS) have successfully identified several risk loci for Alzheimer's disease (AD). Nonetheless, these loci do not explain the entire susceptibility of the disease, suggesting that other genetic contributions remain to be identified. Here, we performed a meta-analysis combining data of 4,569 individuals (2,540 cases and 2,029 healthy controls) derived from three publicly available GWAS in AD and replicated a broad genomic region (>248,000 bp) associated with the disease near the APOE/TOMM40 locus in chromosome 19. To detect minor effect size contributions that could help to explain the remaining genetic risk, we conducted network-based pathway analyses either by extracting gene-wise p-values (GW), defined as the single strongest association signal within a gene, or calculated a more stringent gene-based association p-value using the extended Simes (GATES) procedure. Comparison of these strategies revealed that ontological sub-networks (SNs) involved in glutamate signaling were significantly overrepresented in AD (p<2.7×10(-11), p<1.9×10(-11); GW and GATES, respectively). Notably, glutamate signaling SNs were also found to be significantly overrepresented (p<5.1×10(-8)) in the Alzheimer's disease Neuroimaging Initiative (ADNI) study, which was used as a targeted replication sample. Interestingly, components of the glutamate signaling SNs are coordinately expressed in disease-related tissues, which are tightly related to known pathological hallmarks of AD. Our findings suggest that genetic variation within glutamate signaling contributes to the remaining genetic risk of AD and support the notion that functional biological networks should be targeted in future therapies aimed to prevent or treat this devastating neurological disorder. PMID:24755620

  12. Isolation and characterization of microsatellite loci in Byrsonima cydoniifolia (Malpighiaceae) and cross-amplification in B. crassifolia1

    PubMed Central

    Bernardes, Vanessa; dos Anjos, Daniela Elaine; Gondim, Sara Giselle de Cássia Alexandre; Murakami, Devanir Mitsuyuki; Bizão, Nair; Telles, Mariana Pires de Campos

    2014-01-01

    • Premise of the study: Microsatellite markers were developed and characterized in Byrsonima cydoniifolia (Malpighiaceae) to allow further investigation of genetic variation in natural populations. Cross-amplification was tested in the related species B. crassifolia. • Methods and Results: Seventeen microsatellite markers were isolated by a microsatellite-enriched library protocol. Fourteen polymorphic and three monomorphic loci were identified in B. cydoniifolia. The mean number of alleles in the three populations were 6.5, 6.5, and 8.2, ranging from three to 17 for different loci and populations. Mean observed and expected heterozygosities were 0.706 and 0.727, respectively. The fixation index was close to zero for all but two loci. Nine microsatellite loci were successfully cross-amplified in B. crassifolia. • Conclusions: This new set of microsatellite markers will be a useful tool for genetic studies of B. cydoniifolia, supporting strategies for maintaining the genetic diversity of this species and possibly that of many related species. PMID:25202627

  13. Development and characterization of microsatellite loci in the mistletoe Psittacanthus schiedeanus (Loranthaceae)1

    PubMed Central

    González, Clementina; Harvey, Nick; Ornelas, Juan Francisco

    2015-01-01

    • Premise of the study: Microsatellite primers were developed for the parasitic Psittacanthus schiedeanus, a common mistletoe species on cloud forest–adapted tree hosts in Mesoamerica, to investigate intraspecific genetic patterns of diversity and genetic structure. • Methods and Results: Using an enriched library, 10 polymorphic microsatellite loci were developed in P. schiedeanus. All loci consisted of dinucleotide repeats. Average alleles per locus were 12 (4–17), and a total of 120 alleles were recorded across 39 individuals from four populations in Mexico. Primers were tested in 11 additional species, but only amplified successfully in P. calyculatus and P. angustifolius. • Conclusions: The polymorphic loci described will be useful in studies of genetic diversity and genetic population differentiation in natural populations of these parasitic plants, and will provide valuable information to understand the importance of host distribution. PMID:25606357

  14. Development and characterization of polymorphic microsatellite loci for Saxifraga egregia (Saxifragaceae)1

    PubMed Central

    Zhang, Faqi; Li, Yinhu; Gao, Qingbo; Lei, Shuyun; Khan, Gulzar; Yang, Huiling; Chen, Shilong

    2015-01-01

    Premise of the study: Saxifraga egregia (Saxifragaceae) is a perennial herb that is endemic to the Qinghai–Tibet Plateau. We developed 12 polymorphic microsatellite loci for S. egregia to investigate its population genetics. Methods and Results: Forty-eight pairs of microsatellite primers (including 36 monomorphic loci) were isolated and characterized by magnetic bead enrichment. Twelve of these markers showed polymorphism, and the number of alleles per locus ranged from four to 14 across 50 individuals from three populations of S. egregia. No linkage disequilibrium was detected in any pair of loci. Conclusions: These polymorphic markers are expected to be helpful in further studies on the systematics and phylogeography of S. egregia in the Qinghai–Tibet Plateau. PMID:26312195

  15. Isolation and characterization of polymorphic microsatellite markers for blue fox (Alopex lagopus).

    PubMed

    Li, Y M; Guo, P C; Lu, J Y; Bai, C Y; Zhao, Z H; Yan, S Q

    2016-01-01

    The blue fox, belonging to the family Canidae, is a coat color variant of the native arctic fox (Alopex lagopus). To date, microsatellite loci in blue fox are typically amplified using canine simple sequence repeat primers. In the present study, we constructed an (AC)n enrichment library, and isolated and identified 17 polymorphic microsatellite markers for blue fox. The number of alleles per locus is from two to seven based on 24 examined individuals. The expected and observed heterozygosities were in the range of 0.3112 to 0.8236 and 0.2917 to 0.8750, respectively. The polymorphic information content per locus ranged from 0.2583 to 0.8022. These polymorphic markers can be useful for future population genetic studies of both farmed blue foxes and wild arctic foxes. PMID:27323129

  16. Origins of Microsatellite Diversity in the Trichophyton rubrum- T. violaceum Clade (Dermatophytes)

    PubMed Central

    Ohst, T.; de Hoog, S.; Presber, W.; Stavrakieva, V.; Gräser, Y.

    2004-01-01

    We analyzed the population structure of the anthropophilic dermatophyte species Trichophyton violaceum, which mainly causes tinea capitis, and T. rubrum, the most frequently isolated agent of dermatophytosis worldwide. A microsatellite marker (T1) was developed by using the enrichment technique for microsatellites. The T1 marker containing a (GT)8-10 repeat was proven to specifically amplify both species, underlining their close kinship. Four polymorphic alleles were detected within a set of about 130 strains by using polyacrylamide gel electrophoresis with this marker. An association with geographic origin of the isolates was apparent. Given the close relatedness of both species, these data suggest an African origin of the entire T. rubrum complex, followed by the emergence of a new genotype (B) in Asia with subsequent spread of this genotype over Europe and the United States. PMID:15472291

  17. Characterization and multiplexing of 21 microsatellite markers for the herb Noccaea caerulescens (Brassicaceae)1

    PubMed Central

    Mousset, Mathilde; Flaven, Elodie; Justy, Fabienne; Pouzadoux, Juliette; Gode, Cécile; Pauwels, Maxime; Gonneau, Cédric

    2015-01-01

    Premise of the study: Multiplexed microsatellite markers were developed for population genetic studies in the pseudometallophyte Noccaea caerulescens (Brassicaceae), a model species to investigate metal tolerance and hyperaccumulation in higher plants. Methods and Results: Microsatellite loci were isolated through pyrosequencing of an enriched DNA library. Three multiplexes combining four previously published and 17 newly designed markers were developed. The new markers were screened in metallicolous and nonmetallicolous populations from southern France. The total number of alleles per locus ranged from five to 18. The observed heterozygosity per locus and per population ranged from 0 to 0.83, and expected heterozygosity ranged from 0 to 0.89. Conclusions: The investigated loci showed reasonable to high levels of polymorphism at the regional scale. The multiplex set should be helpful in investigating genetic diversity, population structure, and demographic history in N. caerulescens at various spatial scales. PMID:26697274

  18. A Genome Scan for Positive Selection in Thoroughbred Horses

    PubMed Central

    Gu, Jingjing; Orr, Nick; Park, Stephen D.; Katz, Lisa M.; Sulimova, Galina; MacHugh, David E.; Hill, Emmeline W.

    2009-01-01

    Thoroughbred horses have been selected for exceptional racing performance resulting in system-wide structural and functional adaptations contributing to elite athletic phenotypes. Because selection has been recent and intense in a closed population that stems from a small number of founder animals Thoroughbreds represent a unique population within which to identify genomic contributions to exercise-related traits. Employing a population genetics-based hitchhiking mapping approach we performed a genome scan using 394 autosomal and X chromosome microsatellite loci and identified positively selected loci in the extreme tail-ends of the empirical distributions for (1) deviations from expected heterozygosity (Ewens-Watterson test) in Thoroughbred (n = 112) and (2) global differentiation among four geographically diverse horse populations (FST). We found positively selected genomic regions in Thoroughbred enriched for phosphoinositide-mediated signalling (3.2-fold enrichment; P<0.01), insulin receptor signalling (5.0-fold enrichment; P<0.01) and lipid transport (2.2-fold enrichment; P<0.05) genes. We found a significant overrepresentation of sarcoglycan complex (11.1-fold enrichment; P<0.05) and focal adhesion pathway (1.9-fold enrichment; P<0.01) genes highlighting the role for muscle strength and integrity in the Thoroughbred athletic phenotype. We report for the first time candidate athletic-performance genes within regions targeted by selection in Thoroughbred horses that are principally responsible for fatty acid oxidation, increased insulin sensitivity and muscle strength: ACSS1 (acyl-CoA synthetase short-chain family member 1), ACTA1 (actin, alpha 1, skeletal muscle), ACTN2 (actinin, alpha 2), ADHFE1 (alcohol dehydrogenase, iron containing, 1), MTFR1 (mitochondrial fission regulator 1), PDK4 (pyruvate dehydrogenase kinase, isozyme 4) and TNC (tenascin C). Understanding the genetic basis for exercise adaptation will be crucial for the identification of genes

  19. MICROSATELLITE MARKERS FOR VERIFYING PARENTAGE OF PECANS

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Microsatellite or Simple Sequence Repeat (SSR) markers are being developed in ongoing research in the USDA ARS Pecan Breeding Program. These co-dominant markers provide a powerful tool for the verification of parentage. To confirm their utility, SSR profiles were used to confirm the parentage of 1...

  20. Microsatellite gamma-ray spectroscopy experiment

    NASA Astrophysics Data System (ADS)

    Asa, G.; Ruzin, Arie; Jakobson, Claudio G.; Shaviv, G.; Nemirovsky, Yael

    1999-10-01

    Preliminary results from Gamma ray experiment installed on a micro-satellite, Techsat 1, are reported. The experiment is based on CdZnTe detectors coupled to custom designed CMOS electronics, which includes low noise charge sensitive preamplifiers, pulse shaping amplifiers and sampling circuits. It was realized as a mile stone towards a micro- satellite mounted Gamma ray space telescope. The experiment is a stand-alone spectroscopy system that measures the radiation inside the micro-satellite and transmits the spectra to ground station via the main satellite computer. The radiation level inside micro-satellites is expected to be significantly lower compared to that inside large satellites. Additional goal of the experiment is to test the CdZnTe detectors and the front-end electronics, implemented in a standard CMOS process, under space radiation environment. In particular, the degradation in performance will be monitored. The Techsat 1 micro-satellite has been designed and constructed at Technion-Israel Institute of Technology. The satellite is approximately 50 X 50 X 50 cm-3 cube with a total weight of about 50 kilograms. It was successfully launched in July 1998 to a 820 km orbit.

  1. Ten microsatellite loci from Zamia integrifolia (Zamiaceae)

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Ten microsatellite loci isolated from Zamia integrifolia are described. All 10 are polymorphic, with three to ten alleles across 36 members of a single population from South Florida. Heterozygosity ranged from 0.067 to 1. Two loci depart significantly from Hardy Weinberg Equilibrium, and exhibit het...

  2. Loss of heterozygosity and microsatellite instability as predictive markers among Iranian esophageal cancer patients

    PubMed Central

    Forghanifard, Mohammad Mahdi; Vahid, Elham Emami; Dadkhah, Ezzat; Gholamin, Mehran; Noghabi, Samaneh Broumand; Ghahraman, Martha; Farzadnia, Mehdi; Abbaszadegan, Mohammad Reza

    2016-01-01

    Objective(s): Variation in microsatellite sequences that are dispersed in the genome has been linked to a deficiency in cellular mismatch repair system and defects in several genes of this system are involved in carcinogenesis. Our aim in this study was to illustrate microsatellite DNA alteration in esophageal cancer. Materials and Methods: DNA was extracted from formalin fixed paraffin embedded (FFPE) tissues from surgical and matched margin-normal samples. Microsatellite instability (MSI) and loss of heterozygosity (LOH) were studied in 50 cases of esophageal squamous cell carcinoma (ESCC) by amplifying six microsatellite markers: D13S260 (13q12.3), D13S267 (13q12.3), D9S171 (9p21), D2S123 (2p), D5S2501 (5q21) and TP53 (17p13.1) analyzed on 6% denaturing polyacrylamide gel electrophoresis. Results: Statistical analysis indicated a near significant reverse correlation between grade and LOH (P= 0.068, correlation coefficient= -0.272). Specifically, increased LOH in tumor DNA has a significant correlation with increased differentiation from poorly differentiated to well differentiated tumors (P= 0.002 and P= 0.016 respectively). In addition, higher number of chromosomal loci with LOH showed a reverse correlation with lymph node metastasis (P= 0.026, correlation coefficient= -0.485). Furthermore, there was a positive correlation between addiction and MSI (P= 0.026, correlation coefficient= 0.465). Conclusion: Microsatellite DNA alterations may be a prognostic tool for detection and the evolution of prognosis in patients with SCC of esophagus. It can be concluded that regional lymph node metastasis would be less likely with increased heterozygote loci and addiction with any of opium, cigarette, water pipe or alcohol can be a susceptibility factor(s) for MSI.

  3. Spectrum of nonrandom associations between microsatellite loci on human chromosome 11p15.

    PubMed Central

    Zapata, C; Rodríguez, S; Visedo, G; Sacristán, F

    2001-01-01

    Most evidence about nonrandom association of alleles at different loci, or gametic disequilibrium, across extensive anonymous regions of the human genome is based on the analysis of overall disequilibrium between pairs of microsatellites. However, analysis of interallelic associations is also necessary for a more complete description of disequilibrium. Here, we report a study characterizing the frequency and strength of both overall and interallelic disequilibrium between pairs of 12 microsatellite loci (CA repeats) spanning 19 cM (14 Mb) on human chromosome 11p15, in a large sample (810 haplotypes deduced from 405 individuals) drawn from a single population. Characterization of disequilibrium was carried out, taking into account the sign of the observed disequilibria. This strategy facilitates detection of associations and gives more accurate estimates of their intensities. Our results demonstrate that the incidence of disequilibrium over an extensive human chromosomal region is much greater than is commonly considered for populations that have expanded in size. In total, 44% of the pairs of microsatellite loci and 18% of the pairs of alleles showed significant nonrandom association. All the loci were involved in disequilibrium, although both the frequency and strength of interallelic disequilibrium were distributed nonuniformly along 11p15. These findings are especially relevant since significant associations were detected between loci separated by as much as 17-19 cM (7 cM on average). It was also found that the overall disequilibrium masks complicated patterns of association between pairs of alleles, dependent on their frequency and size. We suggest that the complex mutational dynamics at microsatellite loci could explain the allele-dependent disequilibrium patterns. These observations are also relevant to evaluation of the usefulness of microsatellite markers for fine-scale localization of disease genes. PMID:11454771

  4. Multilocus microsatellite genotyping array for investigation of genetic epidemiology of Pneumocystis jirovecii.

    PubMed

    Parobek, Christian M; Jiang, Linda Y; Patel, Jaymin C; Alvarez-Martínez, Miriam J; Miro, Jose M; Worodria, William; Andama, Alfred; Fong, Serena; Huang, Laurence; Meshnick, Steven R; Taylor, Steve M; Juliano, Jonathan J

    2014-05-01

    Pneumocystis jirovecii is a symbiotic respiratory fungus that causes pneumonia (PcP) in immunosuppressed patients. Because P. jirovecii cannot be reliably cultured in vitro, it has proven difficult to study and gaps in our understanding of the organism persist. The release of a draft genome for the organism opens the door for the development of new genotyping approaches for studying its molecular epidemiology and global population structure. We identified and validated 8 putatively neutral microsatellite markers and 1 microsatellite marker linked to the dihydropteroate synthase gene (dhps), the enzymatic target of sulfa drugs used for PcP prevention and treatment. Using these tools, we analyzed P. jirovecii isolates from HIV-infected patients from three geographically distant populations: Uganda, the United States, and Spain. Among the 8 neutral markers, we observed high levels of allelic heterozygosity (average He, 0.586 to 0.842). Consistent with past reports, we observed limited global population structuring, with only the Ugandan isolates showing minor differentiation from the other two populations. In Ugandan isolates that harbored mutations in dhps, the microsatellite locus linked to dhps demonstrated a depressed He, consistent with positive directional selection for sulfa resistance mutations. Using a subset of these microsatellites, analyses of individual and paired samples from infections in San Francisco, CA, showed reliable typeability within a single infection and high discriminatory power between infections. These features suggest that this novel microsatellite typing approach will be an effective tool for molecular-epidemiological investigations into P. jirovecii population structure, transmission, and drug resistance. PMID:24523468

  5. Microfluidic droplet enrichment for targeted sequencing

    PubMed Central

    Eastburn, Dennis J.; Huang, Yong; Pellegrino, Maurizio; Sciambi, Adam; Ptáček, Louis J.; Abate, Adam R.

    2015-01-01

    Targeted sequence enrichment enables better identification of genetic variation by providing increased sequencing coverage for genomic regions of interest. Here, we report the development of a new target enrichment technology that is highly differentiated from other approaches currently in use. Our method, MESA (Microfluidic droplet Enrichment for Sequence Analysis), isolates genomic DNA fragments in microfluidic droplets and performs TaqMan PCR reactions to identify droplets containing a desired target sequence. The TaqMan positive droplets are subsequently recovered via dielectrophoretic sorting, and the TaqMan amplicons are removed enzymatically prior to sequencing. We demonstrated the utility of this approach by generating an average 31.6-fold sequence enrichment across 250 kb of targeted genomic DNA from five unique genomic loci. Significantly, this enrichment enabled a more comprehensive identification of genetic polymorphisms within the targeted loci. MESA requires low amounts of input DNA, minimal prior locus sequence information and enriches the target region without PCR bias or artifacts. These features make it well suited for the study of genetic variation in a number of research and diagnostic applications. PMID:25873629

  6. Microsatellite-centromere mapping in Japanese scallop ( Patinopecten yessoensis) through half-tetrad analysis in gynogenetic diploid families

    NASA Astrophysics Data System (ADS)

    Li, Qi; Qi, Mingjun; Nie, Hongtao; Kong, Lingfeng; Yu, Hong

    2016-06-01

    Gene-centromere mapping is an essential prerequisite for understanding the composition and structure of genomes. Half-tetrad analysis is a powerful tool for mapping genes and understanding chromosomal behavior during meiosis. The Japanese scallop ( Patinopecten yessoensis), a cold-tolerant species inhabiting the northwestern Pacific coast, is a commercially important marine bivalve in Asian countries. In this study, inheritance of 32 informative microsatellite loci was examined in 70-h D-shaped larvae of three induced meiogynogenetic diploid families of P. yessoensis for centromere mapping using half-tetrad analysis. The ratio of gynogenetic diploids was proven to be 100%, 100% and 96% in the three families, respectively. Inheritance analysis in the control crosses showed that 51 of the 53 genotypic ratios observed were in accordance with Mendelian expectations at the 5% level after Bonferroni correction. Seven of the 32 microsatellite loci showed the existence of null alleles in control crosses. The second division segregation frequency ( y) of the microsatellite loci ranged from 0.07 to 0.85 with a mean of 0.38, suggesting the existence of positive interference after a single chiasma formation in some chromosomes in the scallop. Microsatellite-centromere distances ranged from 4 cM to 42 cM under the assumption of complete interference. Information on the positions of centromeres in relation to the microsatellite loci will represent a contribution towards the assembly of genetic maps in the commercially important scallop species.

  7. Microsatellite primers in Agave utahensis (Asparagaceae), a keystone species in the Mojave Desert and Colorado Plateau1

    PubMed Central

    Byers, Charlee; Maughan, Peter J.; Clouse, Jared; Stewart, J. Ryan

    2014-01-01

    • Premise of the study: Utah agave (Agave utahensis) and its putative subspecies, A. utahensis subsp. kaibabensis and A. utahensis subsp. utahensis, are keystone species of the Mojave Desert and Colorado Plateau in the southwestern United States. Here we developed microsatellite markers to study population structure and genetic diversity of the two subspecies of A. utahensis. • Methods and Results: We analyzed 22,386 454-pyrosequencing large contigs (>400 bp), derived from a genome reduction experiment consisting of A. utahensis accessions, for putative microsatellites. The use of unique multiplex barcodes for each of the Agave accessions allowed for the identification of putatively polymorphic microsatellites based solely on sequence alignment analysis. We report the characteristics of 11 polymorphic microsatellite loci based on a panel of 104 individuals from the two subspecies. The number of alleles per locus varied from three to eight, with an average of 5.5 alleles per locus. Observed and expected heterozygosity values ranged from 0.038 to 0.777 and 0.038 to 0.707, respectively. • Conclusions: The microsatellites identified here will be invaluable for future studies of population structure, polyploidy, and genetic diversity across the species. PMID:25225631

  8. Microsatellite Markers of Willow Species and Characterization of 11 Polymorphic Microsatellites for Salix eriocephala (Salicaceae), a Potential Native Species for Biomass Production in Canada

    PubMed Central

    Lauron-Moreau, Aurélien; Pitre, Frédéric E.; Brouillet, Luc; Labrecque, Michel

    2013-01-01

    Biomass produced from dedicated plantations constitutes a source of renewable energy and is expected to play an important role in several countries in the coming decades. The cultivation of woody crops such as willows therefore raises several environmental issues. In North America, several native willows are potentially interesting for biomass producers. Willow trees are diverse but few species used for environmental applications have been the object of molecular genetic studies. Based on the sequenced poplar genome, 24 microsatellite markers were assayed on five native North American willow species: Salix amygdaloides, S. discolor, S. eriocephala, S. interior and S. nigra. Polymorphic microsatellite markers were used to characterize the allele data on the shrub Salix eriocephala, a North American species with economic potential. Eleven markers amplified and confirmed the potential of this species. Analysis of samples from six populations in eastern Canada showed that all markers were variable as well as polymorphic in at least one population. The number of alleles per locus ranged from 1 to 9 (mean 2.95) and showed that these microsatellite markers can be used to assess genetic diversity of North American willow species. PMID:27137372

  9. Variation in sequences containing microsatellite motifs in the perennial biomass and forage grass, Phalaris arundinacea (Poaceae).

    PubMed

    Barth, Susanne; Jankowska, Marta Jolanta; Hodkinson, Trevor Roland; Vellani, Tia; Klaas, Manfred

    2016-01-01

    Forty three microsatellite markers were developed for further genetic characterisation of a forage and biomass grass crop, for which genomic resources are currently scarce. The microsatellite markers were developed from a normalized EST-SSR library. All of the 43 markers gave a clear banding pattern on 3% Metaphor agarose gels. Eight selected SSR markers were tested in detail for polymorphism across eleven DNA samples of large geographic distribution across Europe. The new set of 43 SSR markers will help future research to characterise the genetic structure and diversity of Phalaris arundinacea, with a potential to further understand its invasive character in North American wetlands, as well as aid in breeding work for desired biomass and forage traits. P. arundinacea is particularly valued in the northern latitude as a crop with high biomass potential, even more so on marginal lands. PMID:27005474

  10. Isolation and characterization of polymorphic microsatellite loci in Spondias radlkoferi (Anacardiaceae)1

    PubMed Central

    Aguilar-Barajas, Esther; Sork, Victoria L.; González-Zamora, Arturo; Rocha-Ramírez, Víctor; Arroyo-Rodríguez, Víctor; Oyama, Ken

    2014-01-01

    • Premise of the study: Microsatellite markers were developed for Spondias radlkoferi to assess the impact of primate seed dispersal on the genetic diversity and structure of this important tree species of Anacardiaceae. • Methods and Results: Fourteen polymorphic loci were isolated from S. radlkoferi through 454 GS-FLX Titanium pyrosequencing of genomic DNA. The number of alleles ranged from three to 12. The observed and expected heterozygosities ranged from 0.382 to 1.00 and from 0.353 to 0.733, respectively. The amplification was also successful in S. mombin and two genera of Anacardiaceae: Rhus aromatica and Toxicodendron radicans. • Conclusions: These microsatellite loci will be useful to assess the genetic diversity and population structure of S. radlkoferi and related species, and will allow us to investigate the effects of seed dispersal by spider monkeys (Ateles geoffroyi) on the genetic structure and diversity of S. radlkoferi populations in a fragmented rainforest. PMID:25383270

  11. Isolation and characterization of 10 microsatellite loci for Pallas' long-tongued bat Glossophaga soricina (Phyllostomidae).

    PubMed

    Oprea, M; Peixoto, F P; Resende, L V; Collevatti, R G; Telles, M P C

    2012-01-01

    Glossophaga soricina is a widespread Neotropical nectarivorous bat. We characterized 10 microsatellite loci isolated from a shotgun genomic library. We analyzed tissues from wing membrane of 67 individuals collected from two populations of Central Brazil (Brasília and Alto Paraíso). The number of alleles per locus ranged from 2 to 20, and the observed and expected heterozygosities ranged from 0.015 to 0.666 and from 0.016 to 0.915, respectively. The high combined probability of genetic identity (4.369 x 10(-8)) and probability of paternity exclusion (0.996) showed that these microsatellite loci would be useful for population genetic structure and parentage studies in natural populations of G. soricina. PMID:23079846

  12. Genome wide survey and analysis of small repetitive sequences in caulimoviruses.

    PubMed

    George, Biju; Gnanasekaran, Prabu; Jain, S K; Chakraborty, Supriya

    2014-10-01

    Microsatellites are known to exhibit ubiquitous presence across all kingdoms of life including viruses. Members of the Caulimoviridae family severely affect growth of vegetable and fruit plants and reduce economic yield in diverse cropping systems worldwide. Here, we analyzed the nature and distribution of both simple and complex microsatellites present in complete genome of 44 species of Caulimoviridae. Our results showed, in all analyzed genomes, genome size and GC content had a weak influence on number, relative abundance and relative density of microsatellites, respectively. For each genome, mono- and dinucleotide repeats were found to be highly predominant and are overrepresented in genome of majority of caulimoviruses. AT/TA and GAA/AAG/AGA was the most abundant di- and trinucleotide repeat motif, respectively. Repeats larger than trinucleotide were rarely found in these genomes. Comparative study of occurrence, abundance and density of microsatellite among available RNA and DNA viral genomes indicated that simple repeats were least abundant in genomes of caulimoviruses. Polymorphic repeats even though rare were observed in the large intergenic region of the genome, indicating strand slippage and/or unequal recombination processes do occur in caulimoviruses. To our knowledge, this is the first analysis of microsatellites occurring in any dsDNA viral genome. Characterization of such variations in repeat sequences would be important in deciphering the origin, mutational processes, and role of repeat sequences in viral genomes. PMID:24999243

  13. MitoSatPlant: mitochondrial microsatellites database of viridiplantae.

    PubMed

    Kumar, Manjeet; Kapil, Aditi; Shanker, Asheesh

    2014-11-01

    Microsatellites also known as simple sequence repeats (SSRs) consist of 1-6 nucleotide long repeating units. The importance of mitochondrial SSRs (mtSSRs) in fields like population genetics, plant phylogenetics and genome mapping motivated us to develop MitoSatPlant, a repository of plant mtSSRs. It contains information for perfect, imperfect and compound SSRs mined from 92 mitochondrial genomes of green plants, available at NCBI (as of 1 Feb 2014). A total of 72,798 SSRs were found, of which PCR primers were designed for 72,495 SSRs. Among all sequences, tetranucleotide repeats (26,802) were found to be most abundant whereas hexanucleotide repeats (2751) were detected with least frequency. MitoSatPlant was developed using SQL server 2008 and can be accessed through a front end designed in ASP.Net. It is an easy to use, user-friendly database and will prove to be a useful resource for plant scientists. To the best of our knowledge MitoSatPlant is the only database available for plant mtSSRs and can be freely accessed at http://compubio.in/mitosatplant/. PMID:24561221

  14. Variable microsatellite loci for population genetic analysis of Old World monkey lice (Pedicinus sp.).

    PubMed

    Scholl, Katlyn; Allen, Julie M; Leendertz, Fabian H; Chapman, Colin A; Reed, David L

    2012-10-01

    Parasitic lice have been valuable informants of their host's evolutionary history because they complete their entire life cycle on the host and move between hosts primarily through direct host-to-host contact. Therefore, lice are confined to their hosts both in ecological and evolutionary time. Lice on great apes have been studied to examine details of their host's evolutionary history; however, species of Pedicinus, which parasitize the Old World monkeys, are less well known. We sampled lice from 2 groups of red colobus (Procolobus spp.) in Kibale National Park in Uganda and from red colobus and black and white colobus (Procolobus polycomos) in Taï National Park in Côte d'Ivoire. We used next-generation sequencing data analysis and the human body louse (Pediculus humanus humanus) genome to search for microsatellites for population genetic studies of Pedicinus lice. The 96 primer sets for microsatellite loci designed from the human body louse genome failed to amplify microsatellites in Pedicinus sp., perhaps due to the fast rate of evolution in parasitic lice. Of 63 microsatellites identified by next-generation sequencing data analysis of Pedicinus sp., 12 were variable among populations and 9 were variable within a single population. Our results suggest that these loci will be useful across the genus Pedicinus. We found that the lice in Uganda are not structured according to their hosts' social group; rather, 2 non-interbreeding populations of lice were found on both groups of red colobus. Because direct host-to-host contact is usually required for lice to move among hosts, these lice could be useful for identification and study of behavioral interactions between primate species. PMID:22509906

  15. Development of microsatellites for population genetic analyses of Tabanus nigrovittatus (Diptera: Tabanidae).

    PubMed

    Husseneder, Claudia; Delatte, Jennifer R; Krumholt, Jeremy; Foil, Lane D

    2014-01-01

    The greenhead horse fly, Tabanus nigrovittatus Macquart (Diptera: Tabanidae), is frequently found in coastal marshes of the Eastern United States. The females are autogenous (i.e., able to develop eggs without a bloodmeal),but they become a considerable pest to both humans and animals when they pursue a source of blood protein to produce additional eggs. In this study, we identified microsatellite markers to provide first insight into the population genetic structure of this notorious pest species. Because no prior genomic information was available for T. nigrovittatus, we used direct shotgun pyrosequencing technology to characterize microsatellite loci. Approximately 10% of the 105,634 short sequence reads generated from random genome sampling contained microsatellites with at least four repeats ofdi-, tri-, tetra-, penta-, and hexamers. Primers were designed for 36 different microsatellite loci with di-, tri-, and tetramer repeat units. After optimization, 20 primer pairs yielded consistent PCR products and were validated for population genetic application in six populations in Western Louisiana Ten loci were polymorphic with 2-9 alleles per locus and an average observed heterozygosity of 0.20 across populations. The horse fly populations from different trap sites (distance 50-144 km) or years of collection (2010 vs 2011) were genetically distinct from each other (FST = 0.05-0.39) and genetically diverse (gene diversity: 0.24-0.37) but considerably inbred (FIS: 0.22-0.47), with high mean relatedness among individuals (r = 0.27), suggesting the capture of a high percentage of sisters at the same trap location who were progeny of incest. PMID:24605460

  16. Genetic evidence that both dNTP-stabilized and strand slippage mechanisms may dictate DNA polymerase errors within mononucleotide microsatellites.

    PubMed

    Baptiste, Beverly A; Jacob, Kimberly D; Eckert, Kristin A

    2015-05-01

    Mononucleotide microsatellites are tandem repeats of a single base pair, abundant within coding exons and frequent sites of mutation in the human genome. Because the repeated unit is one base pair, multiple mechanisms of insertion/deletion (indel) mutagenesis are possible, including strand-slippage, dNTP-stabilized, and misincorportion-misalignment. Here, we examine the effects of polymerase identity (mammalian Pols α, β, κ, and η), template sequence, dNTP pool size, and reaction temperature on indel errors during in vitro synthesis of mononucleotide microsatellites. We utilized the ratio of insertion to deletion errors as a genetic indicator of mechanism. Strikingly, we observed a statistically significant bias toward deletion errors within mononucleotide repeats for the majority of the 28 DNA template and polymerase combinations examined, with notable exceptions based on sequence and polymerase identity. Using mutator forms of Pol β did not substantially alter the error specificity, suggesting that mispairing-misalignment mechanism is not a primary mechanism. Based on our results for mammalian DNA polymerases representing three structurally distinct families, we suggest that dNTP-stabilized mutagenesis may be an alternative mechanism for mononucleotide microsatellite indel mutation. The change from a predominantly dNTP-stabilized mechanism to a strand-slippage mechanism with increasing microsatellite length may account for the differential rates of tandem repeat mutation that are observed genome-wide. PMID:25758780

  17. Gene amplification and microsatellite instability induced in tumorigenic human bronchial epithelial cells by alpha particles and heavy ions

    NASA Technical Reports Server (NTRS)

    Piao, C. Q.; Hei, T. K.; Hall, E. J. (Principal Investigator)

    2001-01-01

    Gene amplification and microsatellite alteration are useful markers of genomic instability in tumor and transformed cell lines. It has been suggested that