Science.gov

Sample records for mitochondrial dna sequence

  1. Inferring ethnicity from mitochondrial DNA sequence

    PubMed Central

    2011-01-01

    Background The assignment of DNA samples to coarse population groups can be a useful but difficult task. One such example is the inference of coarse ethnic groupings for forensic applications. Ethnicity plays an important role in forensic investigation and can be inferred with the help of genetic markers. Being maternally inherited, of high copy number, and robust persistence in degraded samples, mitochondrial DNA may be useful for inferring coarse ethnicity. In this study, we compare the performance of methods for inferring ethnicity from the sequence of the hypervariable region of the mitochondrial genome. Results We present the results of comprehensive experiments conducted on datasets extracted from the mtDNA population database, showing that ethnicity inference based on support vector machines (SVM) achieves an overall accuracy of 80-90%, consistently outperforming nearest neighbor and discriminant analysis methods previously proposed in the literature. We also evaluate methods of handling missing data and characterize the most informative segments of the hypervariable region of the mitochondrial genome. Conclusions Support vector machines can be used to infer coarse ethnicity from a small region of mitochondrial DNA sequence with surprisingly high accuracy. In the presence of missing data, utilizing only the regions common to the training sequences and a test sequence proves to be the best strategy. Given these results, SVM algorithms are likely to also be useful in other DNA sequence classification applications. PMID:21554759

  2. Molecular Poltergeists: Mitochondrial DNA Copies (numts) in Sequenced Nuclear Genomes

    PubMed Central

    Hazkani-Covo, Einat; Zeller, Raymond M.; Martin, William

    2010-01-01

    The natural transfer of DNA from mitochondria to the nucleus generates nuclear copies of mitochondrial DNA (numts) and is an ongoing evolutionary process, as genome sequences attest. In humans, five different numts cause genetic disease and a dozen human loci are polymorphic for the presence of numts, underscoring the rapid rate at which mitochondrial sequences reach the nucleus over evolutionary time. In the laboratory and in nature, numts enter the nuclear DNA via non-homolgous end joining (NHEJ) at double-strand breaks (DSBs). The frequency of numt insertions among 85 sequenced eukaryotic genomes reveal that numt content is strongly correlated with genome size, suggesting that the numt insertion rate might be limited by DSB frequency. Polymorphic numts in humans link maternally inherited mitochondrial genotypes to nuclear DNA haplotypes during the past, offering new opportunities to associate nuclear markers with mitochondrial markers back in time. PMID:20168995

  3. PCR Primers for Metazoan Mitochondrial 12S Ribosomal DNA Sequences

    PubMed Central

    Machida, Ryuji J.; Kweskin, Matthew; Knowlton, Nancy

    2012-01-01

    Background Assessment of the biodiversity of communities of small organisms is most readily done using PCR-based analysis of environmental samples consisting of mixtures of individuals. Known as metagenetics, this approach has transformed understanding of microbial communities and is beginning to be applied to metazoans as well. Unlike microbial studies, where analysis of the 16S ribosomal DNA sequence is standard, the best gene for metazoan metagenetics is less clear. In this study we designed a set of PCR primers for the mitochondrial 12S ribosomal DNA sequence based on 64 complete mitochondrial genomes and then tested their efficacy. Methodology/Principal Findings A total of the 64 complete mitochondrial genome sequences representing all metazoan classes available in GenBank were downloaded using the NCBI Taxonomy Browser. Alignment of sequences was performed for the excised mitochondrial 12S ribosomal DNA sequences, and conserved regions were identified for all 64 mitochondrial genomes. These regions were used to design a primer pair that flanks a more variable region in the gene. Then all of the complete metazoan mitochondrial genomes available in NCBI's Organelle Genome Resources database were used to determine the percentage of taxa that would likely be amplified using these primers. Results suggest that these primers will amplify target sequences for many metazoans. Conclusions/Significance Newly designed 12S ribosomal DNA primers have considerable potential for metazoan metagenetic analysis because of their ability to amplify sequences from many metazoans. PMID:22536450

  4. Mitochondrial DNA sequence evolution in the Arctoidea.

    PubMed Central

    Zhang, Y P; Ryder, O A

    1993-01-01

    Some taxa in the superfamily Arctoidea, such as the giant panda and the lesser panda, have presented puzzles to taxonomists. In the present study, approximately 397 bases of the cytochrome b gene, 364 bases of the 12S rRNA gene, and 74 bases of the tRNA(Thr) and tRNA(Pro) genes from the giant panda, lesser panda, kinkajou, raccoon, coatimundi, and all species of the Ursidae were sequenced. The high transition/transversion ratios in cytochrome b and RNA genes prior to saturation suggest that the presumed transition bias may represent a trend for some mammalian lineages rather than strictly a primate phenomenon. Transversions in the 12S rRNA gene accumulate in arctoids at about half the rate reported for artiodactyls. Different arctoid lineages evolve at different rates: the kinkajou, a procyonid, evolves the fastest, 1.7-1.9 times faster than the slowest lineage that comprises the spectacled and polar bears. Generation-time effect can only partially explain the different rates of nucleotide substitution in arctoids. Our results based on parsimony analysis show that the giant panda is more closely related to bears than to the lesser panda; the lesser panda is neither closely related to bears nor to the New World procyonids. The kinkajou, raccoon, and coatimundi diverged from each other very early, even though they group together. The polar bear is closely related to the spectacled bear, and they began to diverge from a common mitochondrial ancestor approximately 2 million years ago. Relationships of the remaining five bear species are derived. PMID:8415740

  5. Directly repeated sequences associated with pathogenic mitochondrial DNA deletions.

    PubMed Central

    Johns, D R; Rutledge, S L; Stine, O C; Hurko, O

    1989-01-01

    We determined the nucleotide sequences of junctional regions associated with large deletions of mitochondrial DNA found in four unrelated individuals with a phenotype of chronic progressive external ophthalmoplegia. In each patient, the deletion breakpoint occurred within a directly repeated sequence of 13-18 base pairs, present in different regions of the normal mitochondrial genome-separated by 4.5-7.7 kilobases. In two patients, the deletions were identical. When all four repeated sequences are compared, a consensus sequence of 11 nucleotides emerges, similar to putative recombination signals, suggesting the involvement of a recombinational event. Partially deleted and normal mitochondrial DNAs were found in all tissues examined, but in very different proportions, indicating that these mutations originated before the primary cell layers diverged. Images PMID:2813377

  6. Haplogrouping mitochondrial DNA sequences in Legal Medicine/Forensic Genetics.

    PubMed

    Bandelt, Hans-Jürgen; van Oven, Mannis; Salas, Antonio

    2012-11-01

    Haplogrouping refers to the classification of (partial) mitochondrial DNA (mtDNA) sequences into haplogroups using the current knowledge of the worldwide mtDNA phylogeny. Haplogroup assignment of mtDNA control-region sequences assists in the focused comparison with closely related complete mtDNA sequences and thus serves two main goals in forensic genetics: first is the a posteriori quality analysis of sequencing results and second is the prediction of relevant coding-region sites for confirmation or further refinement of haplogroup status. The latter may be important in forensic casework where discrimination power needs to be as high as possible. However, most articles published in forensic genetics perform haplogrouping only in a rudimentary or incorrect way. The present study features PhyloTree as the key tool for assigning control-region sequences to haplogroups and elaborates on additional Web-based searches for finding near-matches with complete mtDNA genomes in the databases. In contrast, none of the automated haplogrouping tools available can yet compete with manual haplogrouping using PhyloTree plus additional Web-based searches, especially when confronted with artificial recombinants still present in forensic mtDNA datasets. We review and classify the various attempts at haplogrouping by using a multiplex approach or relying on automated haplogrouping. Furthermore, we re-examine a few articles in forensic journals providing mtDNA population data where appropriate haplogrouping following PhyloTree immediately highlights several kinds of sequence errors.

  7. Mitochondrial DNA sequences from a 7000-year old brain.

    PubMed Central

    Pääbo, S; Gifford, J A; Wilson, A C

    1988-01-01

    Pieces of mitochondrial DNA from a 7000-year-old human brain were amplified by the polymerase chain reaction and sequenced. Albumin and high concentrations of polymerase were required to overcome a factor in the brain extract that inhibits amplification. For this and other sources of ancient DNA, we find an extreme inverse dependence of the amplification efficiency on the length of the sequence to be amplified. This property of ancient DNA distinguishes it from modern DNA and thus provides a new criterion of authenticity for use in research on ancient DNA. The brain is from an individual recently excavated from Little Salt Spring in southwestern Florida and the anthropologically informative sequences it yielded are the first obtained from archaeologically retrieved remains. The sequences show that this ancient individual belonged to a mitochondrial lineage that is rare in the Old World and not previously known to exist among Native Americans. Our finding brings to three the number of maternal lineages known to have been involved in the prehistoric colonization of the New World. Images PMID:3186445

  8. Nuclear and mitochondrial DNA sequences from two Denisovan individuals

    PubMed Central

    Sawyer, Susanna; Renaud, Gabriel; Viola, Bence; Hublin, Jean-Jacques; Gansauge, Marie-Theres; Shunkov, Michael V.; Derevianko, Anatoly P.; Prüfer, Kay; Pääbo, Svante

    2015-01-01

    Denisovans, a sister group of Neandertals, have been described on the basis of a nuclear genome sequence from a finger phalanx (Denisova 3) found in Denisova Cave in the Altai Mountains. The only other Denisovan specimen described to date is a molar (Denisova 4) found at the same site. This tooth carries a mtDNA sequence similar to that of Denisova 3. Here we present nuclear DNA sequences from Denisova 4 and a morphological description, as well as mitochondrial and nuclear DNA sequence data, from another molar (Denisova 8) found in Denisova Cave in 2010. This new molar is similar to Denisova 4 in being very large and lacking traits typical of Neandertals and modern humans. Nuclear DNA sequences from the two molars form a clade with Denisova 3. The mtDNA of Denisova 8 is more diverged and has accumulated fewer substitutions than the mtDNAs of the other two specimens, suggesting Denisovans were present in the region over an extended period. The nuclear DNA sequence diversity among the three Denisovans is comparable to that among six Neandertals, but lower than that among present-day humans. PMID:26630009

  9. Mitochondrial DNA Sequence Divergence among Lycopersicon and Related Solanum Species

    PubMed Central

    McClean, Phillip E.; Hanson, Maureen R.

    1986-01-01

    Sequence divergence among the mitochondrial (mt) DNA of nine Lycopersicon and two closely related Solanum species was estimated using the shared fragment method. A portion of each mt genome was highlighted by probing total DNA with a series of plasmid clones containing mt-specific DNA fragments from Lycopersicon pennellii. A total of 660 fragments were compared. As calculated by the shared fragment method, sequence divergence among the mtDNAs ranged from 0.4% for the L. esculentum-L. esculentum var. cerasiforme pair to 2.7% for the Solanum rickii-L. pimpinellifolium and L. cheesmanii-L. chilense pairs. The mtDNA divergence is higher than that reported for Lycopersicon chloroplast (cp) DNA, which indicates that the DNAs of the two plant organelles are evolving at different rates. The percentages of shared fragments were used to construct a phenogram that illustrates the present-day relationships of the mtDNAs. The mtDNA-derived phenogram places L. hirsutum closer to L. esculentum than taxonomic and cpDNA comparisons. Further, the recent assignment of L. pennellii to the genus Lycopersicon is supported by the mtDNA analysis. PMID:17246320

  10. Genetic variability of Taenia saginata inferred from mitochondrial DNA sequences.

    PubMed

    Rostami, Sima; Salavati, Reza; Beech, Robin N; Babaei, Zahra; Sharbatkhori, Mitra; Harandi, Majid Fasihi

    2015-04-01

    Taenia saginata is an important tapeworm, infecting humans in many parts of the world. The present study was undertaken to identify inter- and intraspecific variation of T. saginata isolated from cattle in different parts of Iran using two mitochondrial CO1 and 12S rRNA genes. Up to 105 bovine specimens of T. saginata were collected from 20 slaughterhouses in three provinces of Iran. DNA were extracted from the metacestode Cysticercus bovis. After PCR amplification, sequencing of CO1 and 12S rRNA genes were carried out and two phylogenetic analyses of the sequence data were generated by Bayesian inference on CO1 and 12S rRNA sequences. Sequence analyses of CO1 and 12S rRNA genes showed 11 and 29 representative profiles respectively. The level of pairwise nucleotide variation between individual haplotypes of CO1 gene was 0.3-2.4% while the overall nucleotide variation among all 11 haplotypes was 4.6%. For 12S rRNA sequence data, level of pairwise nucleotide variation was 0.2-2.5% and the overall nucleotide variation was determined as 5.8% among 29 haplotypes of 12S rRNA gene. Considerable genetic diversity was found in both mitochondrial genes particularly in 12S rRNA gene.

  11. Analysis of sequence variation in Gnathostoma spinigerum mitochondrial DNA by single-strand conformation polymorphism analysis and DNA sequence.

    PubMed

    Ngarmamonpirat, Charinthon; Waikagul, Jitra; Petmitr, Songsak; Dekumyoy, Paron; Rojekittikhun, Wichit; Anantapruti, Malinee T

    2005-03-01

    Morphological variations were observed in the advance third stage larvae of Gnathostoma spinigerum collected from swamp eel (Fluta alba), the second intermediate host. Larvae with typical and three atypical types were chosen for partial cytochrome c oxidase subunit I (COI) gene sequence analysis. A 450 bp polymerase chain reaction product of the COI gene was amplified from mitochondrial DNA. The variations were analyzed by single-strand conformation polymorphism and DNA sequencing. The nucleotide variations of the COI gene in the four types of larvae indicated the presence of an intra-specific variation of mitochondrial DNA in the G. spinigerum population.

  12. Complete genome sequence of mitochondrial DNA (mtDNA) of Chlorella sorokiniana.

    PubMed

    Orsini, Massimiliano; Costelli, Cristina; Malavasi, Veronica; Cusano, Roberto; Concas, Alessandro; Angius, Andrea; Cao, Giacomo

    2016-01-01

    The complete sequence of mitochondrial genome of the Chlorella sorokiniana strain (SAG 111-8 k) is presented in this work. Within the Chlorella genus, it represents the second species with a complete sequenced and annotated mitochondrial genome (GenBank accession no. KM241869). The genome consists of circular chromosomes of 52,528 bp and encodes a total of 31 protein coding genes, 3 rRNAs and 26 tRNAs. The overall AT contents of the C. sorokiniana mtDNA is 70.89%, while the coding sequence is of 97.4%.

  13. Mitochondrial DNA sequences of five squamates: phylogenetic affiliation of snakes.

    PubMed

    Kumazawa, Yoshinori

    2004-04-30

    Complete or nearly complete mitochondrial DNA sequences were determined from four lizards (Western fence lizard, Warren's spinytail lizard, Terrestrial arboreal alligator lizard, and Chinese crocodile lizard) and a snake (Texas blind snake). These genomes had a typical gene organization found in those of most mammals and fishes, except for a translocation of the glutamine tRNA gene in the blind snake and a tandem duplication of the threonine and proline tRNA genes in the spinytail lizard. Although previous work showed the existence of duplicate control regions in mitochondrial DNAs of several snakes, the blind snake did not have this characteristic. Phylogenetic analyses based on different tree-building methods consistently supported that the blind snake and a colubrid snake (akamata) make a sister clade relative to all the lizard taxa from six different families. An alternative hypothesis that snakes evolved from a lineage of varanoids was not favored and nearly statistically rejected by the Kishino-Hasegawa test. It is therefore likely that the apparent similarity of the tongue structure between snakes and varanoids independently evolved and that the duplication of the control region occurred on a snake lineage after divergence of the blind snake.

  14. Deep sequencing unearths nuclear mitochondrial sequences under Leber's hereditary optic neuropathy-associated false heteroplasmic mitochondrial DNA variants.

    PubMed

    Petruzzella, Vittoria; Carrozzo, Rosalba; Calabrese, Claudia; Dell'Aglio, Rosa; Trentadue, Raffaella; Piredda, Roberta; Artuso, Lucia; Rizza, Teresa; Bianchi, Marzia; Porcelli, Anna Maria; Guerriero, Silvana; Gasparre, Giuseppe; Attimonelli, Marcella

    2012-09-01

    Leber's hereditary optic neuropathy (LHON) is associated with mitochondrial DNA (mtDNA) ND mutations that are mostly homoplasmic. However, these mutations are not sufficient to explain the peculiar features of penetrance and the tissue-specific expression of the disease and are believed to be causative in association with unknown environmental or other genetic factors. Discerning between clear-cut pathogenetic variants, such as those that appear to be heteroplasmic, and less penetrant variants, such as the homoplasmic, remains a challenging issue that we have addressed here using next-generation sequencing approach. We set up a protocol to quantify MTND5 heteroplasmy levels in a family in which the proband manifests a LHON phenotype. Furthermore, to study this mtDNA haplotype, we applied the cybridization protocol. The results demonstrate that the mutations are mostly homoplasmic, whereas the suspected heteroplasmic feature of the observed mutations is due to the co-amplification of Nuclear mitochondrial Sequences.

  15. Next-generation sequencing reveals DGUOK mutations in adult patients with mitochondrial DNA multiple deletions

    PubMed Central

    Garone, Caterina; Bordoni, Andreina; Gutierrez Rios, Purificacion; Calvo, Sarah E.; Ripolone, Michela; Ranieri, Michela; Rizzuti, Mafalda; Villa, Luisa; Magri, Francesca; Corti, Stefania; Bresolin, Nereo; Mootha, Vamsi K.; Moggio, Maurizio; DiMauro, Salvatore; Comi, Giacomo P.; Sciacco, Monica

    2012-01-01

    The molecular diagnosis of mitochondrial disorders still remains elusive in a large proportion of patients, but advances in next generation sequencing are significantly improving our chances to detect mutations even in sporadic patients. Syndromes associated with mitochondrial DNA multiple deletions are caused by different molecular defects resulting in a wide spectrum of predominantly adult-onset clinical presentations, ranging from progressive external ophthalmoplegia to multi-systemic disorders of variable severity. The mutations underlying these conditions remain undisclosed in half of the affected subjects. We applied next-generation sequencing of known mitochondrial targets (MitoExome) to probands presenting with adult-onset mitochondrial myopathy and harbouring mitochondrial DNA multiple deletions in skeletal muscle. We identified autosomal recessive mutations in the DGUOK gene (encoding mitochondrial deoxyguanosine kinase), which has previously been associated with an infantile hepatocerebral form of mitochondrial DNA depletion. Mutations in DGUOK occurred in five independent subjects, representing 5.6% of our cohort of patients with mitochondrial DNA multiple deletions, and impaired both muscle DGUOK activity and protein stability. Clinical presentations were variable, including mitochondrial myopathy with or without progressive external ophthalmoplegia, recurrent rhabdomyolysis in a young female who had received a liver transplant at 9 months of age and adult-onset lower motor neuron syndrome with mild cognitive impairment. These findings reinforce the concept that mutations in genes involved in deoxyribonucleotide metabolism can cause diverse clinical phenotypes and suggest that DGUOK should be screened in patients harbouring mitochondrial DNA deletions in skeletal muscle. PMID:23043144

  16. Mitochondrial DNA.

    ERIC Educational Resources Information Center

    Wright, Russell G.; Bottino, Paul J.

    1986-01-01

    Provides background information for teachers on mitochondrial DNA, pointing out that it may have once been a free-living organism. Includes a ready-to-duplicate exercise titled "Using Microchondrial DNA to Measure Evolutionary Distance." (JN)

  17. Amerindian mitochondrial DNA haplogroups predominate in the population of Argentina: towards a first nationwide forensic mitochondrial DNA sequence database.

    PubMed

    Bobillo, Maria Cecilia; Zimmermann, Bettina; Sala, Andrea; Huber, Gabriela; Röck, Alexander; Bandelt, Hans-Jürgen; Corach, Daniel; Parson, Walther

    2010-07-01

    The study presents South American mitochondrial DNA (mtDNA) data from selected north (N = 98), central (N = 193) and south (N = 47) Argentinean populations. Sequence analysis of the complete mtDNA control region (CR, 16024-576) resulted in 288 unique haplotypes ignoring C-insertions around positions 16193, 309, and 573; the additional analysis of coding region single nucleotide polymorphisms enabled a fine classification of the described lineages. The Amerindian haplogroups were most frequent in the north and south representing more than 60% of the sequences. A slightly different situation was observed in central Argentina where the Amerindian haplogroups represented less than 50%, and the European contribution was more relevant. Particular clades of the Amerindian subhaplogroups turned out to be nearly region-specific. A minor contribution of African lineages was observed throughout the country. This comprehensive admixture of worldwide mtDNA lineages and the regional specificity of certain clades in the Argentinean population underscore the necessity of carefully selecting regional samples in order to develop a nationwide mtDNA database for forensic and anthropological purposes. The mtDNA sequencing and analysis were performed under EMPOP guidelines in order to attain high quality for the mtDNA database.

  18. Homogeneity in mitochondrial DNA control region sequences in Swedish subpopulations.

    PubMed

    Tillmar, Andreas O; Coble, Michael D; Wallerström, Thomas; Holmlund, Gunilla

    2010-03-01

    In order to promote mitochondrial DNA (mtDNA) testing in Sweden we have typed 296 Swedish males, which will serve as a Swedish mtDNA frequency database. The tested males were taken from seven geographically different regions representing the contemporary Swedish population. The complete mtDNA control region was typed and the Swedish population was shown to have high haplotype diversity with a random match probability of 0.5%. Almost 47% of the tested samples belonged to haplogroup H and further haplogroup comparison with worldwide populations clustered the Swedish mtDNA data together with other European populations. AMOVA analysis of the seven Swedish subregions displayed no significant maternal substructure in Sweden (F (ST) = 0.002). Our conclusion from this study is that the typed Swedish individuals serve as good representatives for a Swedish forensic mtDNA database. Some caution should, however, be taken for individuals from the northernmost part of Sweden (provinces of Norrbotten and Lapland) due to specific demographic conditions. Furthermore, our analysis of a small sample set of a Swedish Saami population confirmed earlier findings that the Swedish Saami population is an outlier among European populations.

  19. Entire Mitochondrial DNA Sequencing on Massively Parallel Sequencing for the Korean Population

    PubMed Central

    2017-01-01

    Mitochondrial DNA (mtDNA) genome analysis has been a potent tool in forensic practice as well as in the understanding of human phylogeny in the maternal lineage. The traditional mtDNA analysis is focused on the control region, but the introduction of massive parallel sequencing (MPS) has made the typing of the entire mtDNA genome (mtGenome) more accessible for routine analysis. The complete mtDNA information can provide large amounts of novel genetic data for diverse populations as well as improved discrimination power for identification. The genetic diversity of the mtDNA sequence in different ethnic populations has been revealed through MPS analysis, but the Korean population not only has limited MPS data for the entire mtGenome, the existing data is mainly focused on the control region. In this study, the complete mtGenome data for 186 Koreans, obtained using Ion Torrent Personal Genome Machine (PGM) technology and retrieved from rather common mtDNA haplogroups based on the control region sequence, are described. The results showed that 24 haplogroups, determined with hypervariable regions only, branched into 47 subhaplogroups, and point heteroplasmy was more frequent in the coding regions. In addition, sequence variations in the coding regions observed in this study were compared with those presented in other reports on different populations, and there were similar features observed in the sequence variants for the predominant haplogroups among East Asian populations, such as Haplogroup D and macrohaplogroups M9, G, and D. This study is expected to be the trigger for the development of Korean specific mtGenome data followed by numerous future studies. PMID:28244283

  20. Complete sequence and characterization of mitochondrial DNA genome of Channa asiatica (Perciformes: Channidae).

    PubMed

    Meng, Yan; Zhang, Yan

    2016-01-01

    The complete nucleotide sequence of Channa asiatica mitochondrial (mtDNA) genome was determined in this study. The genome sequence (GenBank accession number KJ930190) was 16,550 base pairs in length, and the gene content and organization on the mitochondrial genome were similar to the other Channa fishes. The overall base composition of C. asiatica mitogenome is 29.4% A, 26.3% T, 15.3% G, 29.0% C, with a high A + T content of 55.7%. The mitochondrial sequence could provide useful genetic information for studying the molecular identification, population genetics, phylogenetic analysis and conservation genetics.

  1. Isolation and nucleotide sequence of a cDNA clone encoding rat mitochondrial malate dehydrogenase.

    PubMed Central

    Grant, P M; Tellam, J; May, V L; Strauss, A W

    1986-01-01

    We have determined the complete sequence of the rat mitochondrial malate dehydrogenase (mMDH) precursor derived from nucleotide sequence of the cDNA. A single synthetic oligodeoxynucleotide probe was used to screen a rat atrial cDNA library constructed in lambda gt10. A 1.2 kb full-length cDNA clone provided the first complete amino acid sequence of pre-mMDH. The 1014 nucleotide-long open reading frame encodes the 314 residue long mature mMDH protein and a 24 amino acid NH2-terminal extension which directs mitochondrial import and is cleaved from the precursor after import to generate mature mMDH. The amino acid composition of the transit peptide is polar and basic. The pre-mMDH transit peptide shows marked homology with those of two other enzymes targeted to the rat mitochondrial matrix. Images PMID:3755817

  2. Identification of two homologous mitochondrial DNA sequences, which bind strongly and specifically to a mitochondrial protein of Paracentrotus lividus.

    PubMed Central

    Roberti, M; Mustich, A; Gadaleta, M N; Cantatore, P

    1991-01-01

    Using a combination of band shift and DNasel protection experiments, two Paracentrotus lividus mitochondrial sequences, able to bind tightly and selectively to a mitochondrial protein from sea urchin embryos, have been found. The two sequences, which compete with each other for binding to the protein, are located in two genome regions which are thought to contain regulatory signals for mitochondrial replication and transcription. A computer analysis suggests that the sequence TTTTRTANNTCYYATCAYA, common to the two binding regions, is the minimal recognition signal for the binding to the protein. We discuss the hypothesis that the protein binding capacity of these two sequences is involved in the control of sea urchin mtDNA replication during developmental stages. Images PMID:1956785

  3. Mitochondrial DNA Sequencing of Cat Hair: An Informative Forensic Tool*

    PubMed Central

    Tarditi, Christy R.; Grahn, Robert A.; Evans, Jeffrey J.; Kurushima, Jennifer D.; Lyons, Leslie A.

    2010-01-01

    Approximately 81.7 million cats are in 37.5 million USA households. Shed fur can be criminal evidence due to transfer to victims, suspects, and / or their belongings. To improve cat hairs as forensic evidence, the mtDNA control region from single hairs, with and without root tags, was sequenced. A dataset of a 402 bp CR segment from 174 random-bred cats representing four USA geographic areas was generated to determine the informativeness of the mtDNA region. Thirty-two mtDNA mitotypes were observed ranging in frequencies from 0.6-27%. Four common types occurred in all populations. Low heteroplasmy, 1.7%, was determined. Unique mitotypes were found in 18 individuals, 10.3% of the population studied. The calculated discrimination power implied that 8.3 of 10 randomly selected individuals can be excluded by this region. The genetic characteristics of the region and the generated dataset support the use of this cat mtDNA region in forensic applications. PMID:21077873

  4. Molecular diversification of Trichuris spp. from Sigmodontinae (Cricetidae) rodents from Argentina based on mitochondrial DNA sequences.

    PubMed

    Callejón, Rocío; Robles, María Del Rosario; Panei, Carlos Javier; Cutillas, Cristina

    2016-08-01

    A molecular phylogenetic hypothesis is presented for the genus Trichuris based on sequence data from mitochondrial cytochrome c oxidase 1 (cox1) and cytochrome b (cob). The taxa consisted of nine populations of whipworm from five species of Sigmodontinae rodents from Argentina. Bayesian Inference, Maximum Parsimony, and Maximum Likelihood methods were used to infer phylogenies for each gene separately but also for the combined mitochondrial data and the combined mitochondrial and nuclear dataset. Phylogenetic results based on cox1 and cob mitochondrial DNA (mtDNA) revealed three clades strongly resolved corresponding to three different species (Trichuris navonae, Trichuris bainae, and Trichuris pardinasi) showing phylogeographic variation, but relationships among Trichuris species were poorly resolved. Phylogenetic reconstruction based on concatenated sequences had greater phylogenetic resolution for delimiting species and populations intra-specific of Trichuris than those based on partitioned genes. Thus, populations of T. bainae and T. pardinasi could be affected by geographical factors and co-divergence parasite-host.

  5. Sequencing mitochondrial DNA from a tooth and application to forensic odontology.

    PubMed

    Yamada, Y; Ohira, H; Iwase, H; Takatori, T; Nagao, M; Ohtani, S

    1997-06-01

    Genetic identification can be complicated by long intervals between the time of death and examination of tissues, and sometimes only bone and teeth may be available for analysis. Several investigators have described the isolation of nuclear DNA from these materials, but all have indicated that the DNA is significantly degraded. Recently, the polymerase chain reaction (PCR) and direct DNA sequencing have enabled rapid and reliable characterization of specific highly polymorphic DNA sequences from different individuals. Above all, mitochondrial DNA sequences offer several unique advantages for the identification of human remains. The isolation of mtDNA from a tooth and the symmetrical PCR amplification and direct DNA sequencing of its most polymorphic regions are reported.

  6. DNA sequences proximal to human mitochondrial DNA deletion breakpoints prevalent in human disease form G-quadruplexes, a class of DNA structures inefficiently unwound by the mitochondrial replicative Twinkle helicase.

    PubMed

    Bharti, Sanjay Kumar; Sommers, Joshua A; Zhou, Jun; Kaplan, Daniel L; Spelbrink, Johannes N; Mergny, Jean-Louis; Brosh, Robert M

    2014-10-24

    Mitochondrial DNA deletions are prominent in human genetic disorders, cancer, and aging. It is thought that stalling of the mitochondrial replication machinery during DNA synthesis is a prominent source of mitochondrial genome instability; however, the precise molecular determinants of defective mitochondrial replication are not well understood. In this work, we performed a computational analysis of the human mitochondrial genome using the "Pattern Finder" G-quadruplex (G4) predictor algorithm to assess whether G4-forming sequences reside in close proximity (within 20 base pairs) to known mitochondrial DNA deletion breakpoints. We then used this information to map G4P sequences with deletions characteristic of representative mitochondrial genetic disorders and also those identified in various cancers and aging. Circular dichroism and UV spectral analysis demonstrated that mitochondrial G-rich sequences near deletion breakpoints prevalent in human disease form G-quadruplex DNA structures. A biochemical analysis of purified recombinant human Twinkle protein (gene product of c10orf2) showed that the mitochondrial replicative helicase inefficiently unwinds well characterized intermolecular and intramolecular G-quadruplex DNA substrates, as well as a unimolecular G4 substrate derived from a mitochondrial sequence that nests a deletion breakpoint described in human renal cell carcinoma. Although G4 has been implicated in the initiation of mitochondrial DNA replication, our current findings suggest that mitochondrial G-quadruplexes are also likely to be a source of instability for the mitochondrial genome by perturbing the normal progression of the mitochondrial replication machinery, including DNA unwinding by Twinkle helicase.

  7. Mitochondrial DNA sequencing of beetle larvae (Nitidulidae: Omosita) recovered from human bone.

    PubMed

    DiZinno, Joseph A; Lord, Wayne D; Collins-Morton, Mary B; Wilson, Mark R; Goff, M Lee

    2002-11-01

    The isolation, amplification, and characterization of human DNA from hematophagous (blood feeding) and necrophagous (carrion feeding) arthropods have been advanced significantly by the development of polymerase chain reaction (PCR) DNA sequencing methodologies. Historically, DNA technology has been successfully utilized to identify individual hosts upon which species of hematophagous arthropods have fed. The analysis of hematophagous insects' gut content blood meals has led to major advances in medical entomology and vector-borne disease epidemiology. In the forensic arena, the ability to apply similar techniques to insects recovered from badly decomposed remains has been greatly enhanced through the advent of mitochondrial DNA (mtDNA) techniques. Mitochondrial DNA analyses have been utilized to identify both the human remains upon which fly larvae (maggots) have fed and the species of the larvae themselves. The preliminary work detailed here demonstrates, for the first time, the successful application of mtDNA sequencing techniques to the analysis of necrophagous beetle larvae. A small sample of sap beetle larvae, Omosita spp. (Coleoptera: Nitidulidae), was collected from human skeletal remains during anthropological examination and analyzed for human DNA using mtDNA sequencing. The beetle larvae yielded mtDNA matching that of the host human bone. The results detailed here further demonstrate the robust nature of human mtDNA and the ability to recover valuable mtDNA evidence from forensically important, late decompositional stage insect species.

  8. Mitochondrial DNA sequence and phylogenetic evaluation of geographically disparate Sus scrofa breeds.

    PubMed

    Cannon, M V; Brandebourg, T D; Kohn, M C; Ðikić, D; Irwin, M H; Pinkert, C A

    2015-01-01

    Next generation sequencing of mitochondrial DNA (mtDNA) facilitates studies into the metabolic characteristics of production animals and their relation to production traits. Sequence analysis of mtDNA from pure-bred swine with highly disparate production characteristics (Mangalica Blonde, Mangalica Swallow-bellied, Meishan, Turopolje, and Yorkshire) was initiated to evaluate the influence of mtDNA polymorphisms on mitochondrial function. Herein, we report the complete mtDNA sequences of five Sus scrofa breeds and evaluate their position within the phylogeny of domestic swine. Phenotypic traits of Yorkshire, Mangalica Blonde, and Swallow-belly swine are presented to demonstrate their metabolic characteristics. Our data support the division of European and Asian breeds noted previously and confirm European ancestry of Mangalica and Turopolje breeds. Furthermore, mtDNA differences between breeds suggest function-altering changes in proteins involved in oxidative phosphorylation such as ATP synthase 6 (MT-ATP6), cytochrome oxidase I (MT-CO1), cytochrome oxidase III (MT-CO3), and cytochrome b (MT-CYB), supporting the hypothesis that mtDNA polymorphisms contribute to differences in metabolic traits between swine breeds. Our sequence data form the basis for future research into the roles of mtDNA in determining production traits in domestic animals. Additionally, such studies should provide insight into how mtDNA haplotype influences the extreme adiposity observed in Mangalica breeds.

  9. mtDNAprofiler: a Web application for the nomenclature and comparison of human mitochondrial DNA sequences.

    PubMed

    Yang, In Seok; Lee, Hwan Young; Yang, Woo Ick; Shin, Kyoung-Jin

    2013-07-01

    Mitochondrial DNA (mtDNA) is a valuable tool in the fields of forensic, population, and medical genetics. However, recording and comparing mtDNA control region or entire genome sequences would be difficult if researchers are not familiar with mtDNA nomenclature conventions. Therefore, mtDNAprofiler, a Web application, was designed for the analysis and comparison of mtDNA sequences in a string format or as a list of mtDNA single-nucleotide polymorphisms (mtSNPs). mtDNAprofiler which comprises four mtDNA sequence-analysis tools (mtDNA nomenclature, mtDNA assembly, mtSNP conversion, and mtSNP concordance-check) supports not only the accurate analysis of mtDNA sequences via an automated nomenclature function, but also consistent management of mtSNP data via direct comparison and validity-check functions. Since mtDNAprofiler consists of four tools that are associated with key steps of mtDNA sequence analysis, mtDNAprofiler will be helpful for researchers working with mtDNA. mtDNAprofiler is freely available at http://mtprofiler.yonsei.ac.kr.

  10. Complete mitochondrial DNA sequence analysis of Bison bison and bison-cattle hybrids: function and phylogeny.

    PubMed

    Douglas, Kory C; Halbert, Natalie D; Kolenda, Claire; Childers, Christopher; Hunter, David L; Derr, James N

    2011-01-01

    Complete mitochondrial DNA (mtDNA) genomes from 43 bison and bison-cattle hybrids were sequenced and compared with other bovids. Selected animals reflect the historical range and current taxonomic structure of bison. This study identified regions of potential nuclear-mitochondrial incompatibilities in hybrids, provided a complete mtDNA phylogenetic tree for this species, and uncovered evidence of bison population substructure. Seventeen bison haplotypes defined by 66 polymorphic sites were discovered, whereas 728 fixed differences and 86 non-synonymous mutations were identified between bison and bison-cattle hybrid sequences. The potential roles of the mtDNA genome in the function of hybrid animals and bison taxonomy are discussed.

  11. Complete genome sequence of the mitochondrial DNA of the river lamprey, Lethenteron japonicum.

    PubMed

    Kawai, Yuri L; Yura, Kei; Shindo, Miyuki; Kusakabe, Rie; Hayashi, Keiko; Hata, Kenichiro; Nakabayashi, Kazuhiko; Okamura, Kohji

    2015-01-01

    Lampreys are eel-like jawless fishes evolutionarily positioned between invertebrates and vertebrates, and have been used as model organisms to explore vertebrate evolution. In this study we determined the complete genome sequence of the mitochondrial DNA of the Japanese river lamprey, Lethenteron japonicum, using next-generation sequencers. The sequence was 16,272 bp in length. The gene content and order were identical to those of the sea lamprey, Petromyzon marinus, which has been the reference among lamprey species. However, the sequence similarity was less than 90%, suggesting the need for the whole-genome sequencing of L. japonicum.

  12. What Is Mitochondrial DNA?

    MedlinePlus

    ... DNA What is mitochondrial DNA? What is mitochondrial DNA? Although most DNA is packaged in chromosomes within ... proteins. For more information about mitochondria and mitochondrial DNA: Molecular Expressions, a web site from the Florida ...

  13. Complete sequence of the mitochondrial DNA in the sea urchin Arbacia lixula: conserved features of the echinoid mitochondrial genome.

    PubMed

    De Giorgi, C; Martiradonna, A; Lanave, C; Saccone, C

    1996-04-01

    The complete nucleotide sequence (15,719 nucleotides) of the mitochondrial DNA (mtDNA) from the sea urchin Arbacia lixula is presented. The comparison of gene arrangement between different echinoderm orders of the same class provides evidence that the gene organization is conserved within the same echinoderm class. The peculiarities of sea urchin mtDNA features, already described, are confirmed by the A. lixula mtDNA sequence. The comparison of the entire sequences of mtDNA among A. lixula, Paracentrotus lividus, and Strongylocentrotus purpuratus allowed us to detect peculiar features, common to the three sea urchin species, that can represent the molecular signature of the mt genome in the sea urchin group. Analysis of the nucleotide composition indicates that A. lixula mtDNA, in contrast with the mtDNA of other sea urchins, shows a bias in the use of T and tends to avoid the use of C, most evident in the neutral part of the molecule, such as the third codon positions. This observation indicates that the three sea urchin mtDNAs evolve under different mutation pressure. Analysis of the sequence evolution allowed us to confirm the phylogenetic tree. However, the absolute divergence time, calculated on the basis of paleontological estimates, largely diverged from the expected one.

  14. Phylogeny and genetic diversity of Bridgeoporus nobilissimus inferred using mitochondrial and nuclear rDNA sequences

    USGS Publications Warehouse

    Redberg, G.L.; Hibbett, D.S.; Ammirati, J.F.; Rodriguez, R.J.

    2003-01-01

    The genetic diversity and phylogeny of Bridgeoporus nobilissimus have been analyzed. DNA was extracted from spores collected from individual fruiting bodies representing six geographically distinct populations in Oregon and Washington. Spore samples collected contained low levels of bacteria, yeast and a filamentous fungal species. Using taxon-specific PCR primers, it was possible to discriminate among rDNA from bacteria, yeast, a filamentous associate and B. nobilissimus. Nuclear rDNA internal transcribed spacer (ITS) region sequences of B. nobilissimus were compared among individuals representing six populations and were found to have less than 2% variation. These sequences also were used to design dual and nested PCR primers for B. nobilissimus-specific amplification. Mitochondrial small-subunit rDNA sequences were used in a phylogenetic analysis that placed B. nobilissimus in the hymenochaetoid clade, where it was associated with Oxyporus and Schizopora.

  15. Seventeen New Complete mtDNA Sequences Reveal Extensive Mitochondrial Genome Evolution within the Demospongiae

    PubMed Central

    Wang, Xiujuan; Lavrov, Dennis V.

    2008-01-01

    Two major transitions in animal evolution–the origins of multicellularity and bilaterality–correlate with major changes in mitochondrial DNA (mtDNA) organization. Demosponges, the largest class in the phylum Porifera, underwent only the first of these transitions and their mitochondrial genomes display a peculiar combination of ancestral and animal-specific features. To get an insight into the evolution of mitochondrial genomes within the Demospongiae, we determined 17 new mtDNA sequences from this group and analyzing them with five previously published sequences. Our analysis revealed that all demosponge mtDNAs are 16- to 25-kbp circular molecules, containing 13–15 protein genes, 2 rRNA genes, and 2–27 tRNA genes. All but four pairs of sampled genomes had unique gene orders, with the number of shared gene boundaries ranging from 1 to 41. Although most demosponge species displayed low rates of mitochondrial sequence evolution, a significant acceleration in evolutionary rates occurred in the G1 group (orders Dendroceratida, Dictyoceratida, and Verticillitida). Large variation in mtDNA organization was also observed within the G0 group (order Homosclerophorida) including gene rearrangements, loss of tRNA genes, and the presence of two introns in Plakortis angulospiculatus. While introns are rare in modern-day demosponge mtDNA, we inferred that at least one intron was present in cox1 of the common ancestor of all demosponges. Our study uncovered an extensive mitochondrial genomic diversity within the Demospongiae. Although all sampled mitochondrial genomes retained some ancestral features, including a minimally modified genetic code, conserved structures of tRNA genes, and presence of multiple non-coding regions, they vary considerably in their size, gene content, gene order, and the rates of sequence evolution. Some of the changes in demosponge mtDNA, such as the loss of tRNA genes and the appearance of hairpin-containing repetitive elements, occurred in

  16. Mitochondrial DNA heteroplasmy in the emerging field of massively parallel sequencing

    PubMed Central

    Just, Rebecca S.; Irwin, Jodi A.; Parson, Walther

    2015-01-01

    Long an important and useful tool in forensic genetic investigations, mitochondrial DNA (mtDNA) typing continues to mature. Research in the last few years has demonstrated both that data from the entire molecule will have practical benefits in forensic DNA casework, and that massively parallel sequencing (MPS) methods will make full mitochondrial genome (mtGenome) sequencing of forensic specimens feasible and cost-effective. A spate of recent studies has employed these new technologies to assess intraindividual mtDNA variation. However, in several instances, contamination and other sources of mixed mtDNA data have been erroneously identified as heteroplasmy. Well vetted mtGenome datasets based on both Sanger and MPS sequences have found authentic point heteroplasmy in approximately 25% of individuals when minor component detection thresholds are in the range of 10–20%, along with positional distribution patterns in the coding region that differ from patterns of point heteroplasmy in the well-studied control region. A few recent studies that examined very low-level heteroplasmy are concordant with these observations when the data are examined at a common level of resolution. In this review we provide an overview of considerations related to the use of MPS technologies to detect mtDNA heteroplasmy. In addition, we examine published reports on point heteroplasmy to characterize features of the data that will assist in the evaluation of future mtGenome data developed by any typing method. PMID:26009256

  17. Mitochondrial DNA sequence variation in human evolution and disease.

    PubMed Central

    Wallace, D C

    1994-01-01

    Germ-line and somatic mtDNA mutations are hypothesized to act together to shape our history and our health. Germ-line mtDNA mutations, both ancient and recent, have been associated with a variety of degenerative diseases. Mildly to moderately deleterious germ-line mutations, like neutral polymorphisms, have become established in the distant past through genetic drift but now may predispose certain individuals to late-onset degenerative diseases. As an example, a homoplasmic, Caucasian, tRNA(Gln) mutation at nucleotide pair (np) 4336 has been observed in 5% of Alzheimer disease and Parkinson disease patients and may contribute to the multifactorial etiology of these diseases. Moderately to severely deleterious germ-line mutations, on the other hand, appear repeatedly but are eliminated by selection. Hence, all extant mutations of this class are recent and associated with more devastating diseases of young adults and children. Representative of these mutations is a heteroplasmic mutation in MTND6 at np 14459 whose clinical presentations range from adult-onset blindness to pediatric dystonia and basal ganglial degeneration. To the inherited mutations are added somatic mtDNA mutations which accumulate in random arrays within stable tissues. These mutations provide a molecular clock that measures our age and may cause a progressive decline in tissue energy output that could precipitate the onset of degenerative diseases in individuals harboring inherited deleterious mutations. Images PMID:8090716

  18. The complete mitochondrial DNA sequence of Crotalus horridus (timber rattlesnake).

    PubMed

    Hall, Jacob B; Cobb, Vincent A; Cahoon, A Bruce

    2013-04-01

    The complete mitogenome of the timber rattlesnake (Crotalus horridus) was completed using Sanger sequencing. It is 17,260 bp with 13 protein-coding genes, 21 tRNAs, two rRNAs and two control regions. Gene synteny is consistent with other snakes with the exception of a missing redundant tRNA (Ser) . This mitogenome should prove to be a useful addition of a well-known member of the Viperidae snake family.

  19. Sequence-specific modification of mitochondrial DNA using a chimeric zinc finger methylase

    PubMed Central

    Minczuk, Michal; Papworth, Monika A.; Kolasinska, Paulina; Murphy, Michael P.; Klug, Aaron

    2006-01-01

    We used engineered zinc finger peptides (ZFPs) to bind selectively to predetermined sequences in human mtDNA. Surprisingly, we found that engineered ZFPs cannot be reliably routed to mitochondria by using only conventional mitochondrial targeting sequences. We here show that addition of a nuclear export signal allows zinc finger chimeric enzymes to be imported into human mitochondria. The selective binding of mitochondria-specific ZFPs to mtDNA was exemplified by targeting the T8993G mutation, which causes two mitochondrial diseases, neurogenic muscle weakness, ataxia, and retinitis pigmentosa (NARP) and also maternally inherited Leigh's syndrome. To develop a system that allows the monitoring of site-specific alteration of mtDNA we combined a ZFP with the easily assayed DNA-modifying activity of hDNMT3a methylase. Expression of the mutation-specific chimeric methylase resulted in the selective methylation of cytosines adjacent to the mutation site. This is a proof of principle that it is possible to target and alter mtDNA in a sequence-specific manner by using zinc finger technology. PMID:17170133

  20. Complete Sequence of the Mitochondrial DNA of the Annelid Worm Lumbricus Terrestris

    PubMed Central

    Boore, J. L.; Brown, W. M.

    1995-01-01

    We have determined the complete nucleotide (nt) sequence of the mitochondrial genome of an oligochaete annelid, the earthworm Lumbricus terrestris. This genome contains the 37 genes typical of metazoan mitochondrial DNA (mtDNA), including ATPase8, which is missing from some invertebrate mtDNAs. ATPase8 is not immediately upstream of ATPase6, a condition found previously only in the mtDNA of snails. All genes are transcribed from the same DNA strand. The largest noncoding region is 384 nt and is characterized by several homopolymer runs, a tract of alternating TA pairs, and potential secondary structures. All protein-encoding genes either overlap the adjacent downstream gene or end at an abbreviated stop codon. In Lumbricus mitochondria, the variation of the genetic code that is typical of most invertebrate mitochondrial genomes is used. Only the codon ATG is used for translation initiation. Lumbricus mtDNA is A + T rich, which appears to affect the codon usage pattern. The DHU arm appears to be unpaired not only in tRNA(ser(AGN)), as is typical for metazoans, but perhaps also in tRNA(ser(UCN)), a condition found previously only in a chiton and among nematodes. Relating the Lumbricus gene organization to those of other major protostome groups requires numerous rearrangements. PMID:8536978

  1. Complete mitochondrial genome sequence of a Middle Pleistocene cave bear reconstructed from ultrashort DNA fragments.

    PubMed

    Dabney, Jesse; Knapp, Michael; Glocke, Isabelle; Gansauge, Marie-Theres; Weihmann, Antje; Nickel, Birgit; Valdiosera, Cristina; García, Nuria; Pääbo, Svante; Arsuaga, Juan-Luis; Meyer, Matthias

    2013-09-24

    Although an inverse relationship is expected in ancient DNA samples between the number of surviving DNA fragments and their length, ancient DNA sequencing libraries are strikingly deficient in molecules shorter than 40 bp. We find that a loss of short molecules can occur during DNA extraction and present an improved silica-based extraction protocol that enables their efficient retrieval. In combination with single-stranded DNA library preparation, this method enabled us to reconstruct the mitochondrial genome sequence from a Middle Pleistocene cave bear (Ursus deningeri) bone excavated at Sima de los Huesos in the Sierra de Atapuerca, Spain. Phylogenetic reconstructions indicate that the U. deningeri sequence forms an early diverging sister lineage to all Western European Late Pleistocene cave bears. Our results prove that authentic ancient DNA can be preserved for hundreds of thousand years outside of permafrost. Moreover, the techniques presented enable the retrieval of phylogenetically informative sequences from samples in which virtually all DNA is diminished to fragments shorter than 50 bp.

  2. Complete mitochondrial genome sequence of a Middle Pleistocene cave bear reconstructed from ultrashort DNA fragments

    PubMed Central

    Dabney, Jesse; Knapp, Michael; Glocke, Isabelle; Gansauge, Marie-Theres; Weihmann, Antje; Nickel, Birgit; Valdiosera, Cristina; García, Nuria; Pääbo, Svante; Arsuaga, Juan-Luis; Meyer, Matthias

    2013-01-01

    Although an inverse relationship is expected in ancient DNA samples between the number of surviving DNA fragments and their length, ancient DNA sequencing libraries are strikingly deficient in molecules shorter than 40 bp. We find that a loss of short molecules can occur during DNA extraction and present an improved silica-based extraction protocol that enables their efficient retrieval. In combination with single-stranded DNA library preparation, this method enabled us to reconstruct the mitochondrial genome sequence from a Middle Pleistocene cave bear (Ursus deningeri) bone excavated at Sima de los Huesos in the Sierra de Atapuerca, Spain. Phylogenetic reconstructions indicate that the U. deningeri sequence forms an early diverging sister lineage to all Western European Late Pleistocene cave bears. Our results prove that authentic ancient DNA can be preserved for hundreds of thousand years outside of permafrost. Moreover, the techniques presented enable the retrieval of phylogenetically informative sequences from samples in which virtually all DNA is diminished to fragments shorter than 50 bp. PMID:24019490

  3. Mitochondrial DNA sequence variation in Iranian native dogs.

    PubMed

    Amiri Ghanatsaman, Zeinab; Adeola, Adeniyi C; Asadi Fozi, Masood; Ma, Ya-Ping; Peng, Min-Sheng; Wang, Guo-Dong; Esmailizadeh, Ali; Zhang, Ya-Ping

    2017-03-17

    The dog mtDNA diversity picture from wide geographical sampling but from a small number of individuals per region or breed, displayed little geographical correlation and high degree of haplotype sharing between very distant breeds. For a clear picture, we extensively surveyed Iranian native dogs (n = 305) in comparison with published European (n = 443) and Southwest Asian (n = 195) dogs. Twelve haplotypes related to haplogroups A, B and C were shared by Iranian, European, Southwest Asian and East Asian dogs. In Iran, haplotype and nucleotide diversities were highest in east, southeast and northwest populations while western population had the least. Sarabi and Saluki dog populations can be assigned into haplogroups A, B, C and D; Qahderijani and Kurdi to haplogroups A, B and C, Torkaman to haplogroups A, B and D while Sangsari and Fendo into haplogroups A and B, respectively. Evaluation of population differentiation using pairwise FST generally revealed no clear population structure in most Iranian dog populations. The genetic signal of a recent demographic expansion was detected in East and Southeast populations. Further, in accordance with previous studies on dog-wolf hybridization for haplogroup d2 origin, the highest number of d2 haplotypes in Iranian dog as compared to other areas of Mediterranean basin suggests Iran as the probable center of its origin. Historical evidence showed that Silk Road linked Iran to countries in South East Asia and other parts of the world, which might have probably influenced effective gene flow within Iran and these regions. The medium nucleotide diversity observed in Iranian dog calls for utilization of appropriate management techniques in increasing effective population size.

  4. Repetitive sequences in Eurasian lynx (Lynx lynx L.) mitochondrial DNA control region.

    PubMed

    Sindičić, Magda; Gomerčić, Tomislav; Galov, Ana; Polanc, Primož; Huber, Duro; Slavica, Alen

    2012-06-01

    Mitochondrial DNA (mtDNA) control region (CR) of numerous species is known to include up to five different repetitive sequences (RS1-RS5) that are found at various locations, involving motifs of different length and extensive length heteroplasmy. Two repetitive sequences (RS2 and RS3) on opposite sides of mtDNA central conserved region have been described in domestic cat (Felis catus) and some other felid species. However, the presence of repetitive sequence RS3 has not been detected in Eurasian lynx (Lynx lynx) yet. We analyzed mtDNA CR of 35 Eurasian lynx (L. lynx L.) samples to characterize repetitive sequences and to compare them with those found in other felid species. We confirmed the presence of 80 base pairs (bp) repetitive sequence (RS2) at the 5' end of the Eurasian lynx mtDNA CR L strand and for the first time we described RS3 repetitive sequence at its 3' end, consisting of an array of tandem repeats five to ten bp long. We found that felid species share similar RS3 repetitive pattern and fundamental repeat motif TACAC.

  5. Cytogenetic and Sequence Analyses of Mitochondrial DNA Insertions in Nuclear Chromosomes of Maize

    PubMed Central

    Lough, Ashley N.; Faries, Kaitlyn M.; Koo, Dal-Hoe; Hussain, Abid; Roark, Leah M.; Langewisch, Tiffany L.; Backes, Teresa; Kremling, Karl A. G.; Jiang, Jiming; Birchler, James A.; Newton, Kathleen J.

    2015-01-01

    The transfer of mitochondrial DNA (mtDNA) into nuclear genomes is a regularly occurring process that has been observed in many species. Few studies, however, have focused on the variation of nuclear-mtDNA sequences (NUMTs) within a species. This study examined mtDNA insertions within chromosomes of a diverse set of Zea mays ssp. mays (maize) inbred lines by the use of fluorescence in situ hybridization. A relatively large NUMT on the long arm of chromosome 9 (9L) was identified at approximately the same position in four inbred lines (B73, M825, HP301, and Oh7B). Further examination of the similarly positioned 9L NUMT in two lines, B73 and M825, indicated that the large size of these sites is due to the presence of a majority of the mitochondrial genome; however, only portions of this NUMT (∼252 kb total) were found in the publically available B73 nuclear sequence for chromosome 9. Fiber-fluorescence in situ hybridization analysis estimated the size of the B73 9L NUMT to be ∼1.8 Mb and revealed that the NUMT is methylated. Two regions of mtDNA (2.4 kb and 3.3 kb) within the 9L NUMT are not present in the B73 mitochondrial NB genome; however, these 2.4-kb and 3.3-kb segments are present in other Zea mitochondrial genomes, including that of Zea mays ssp. parviglumis, a progenitor of domesticated maize. PMID:26333837

  6. Mitochondrial DNA sequence diversity in two groups of Italian Veneto speakers from Veneto.

    PubMed

    Mogentale-Profizi, N; Chollet, L; Stévanovitch, A; Dubut, V; Poggi, C; Pradié, M P; Spadoni, J L; Gilles, A; Béraud-Colomb, E

    2001-03-01

    Although frequencies of mitochondrial DNA (mtDNA) haplogroups in the different European populations are rather homogenous, there are a few European populations or linguistic isolates that show different mtDNA haplogroup distributions; examples are the Saami and Ladin speakers from the eastern Italian Alps. MtDNA sequence diversity was analysed from subjects from two villages in Veneto. The first, Posina, is situated in the Venetian Alps near Vicenza. The second, Barco di Pravisdomini is a village on the plains near Venice. In spite of their common Veneto dialect, the two group populations have not preserved a genetic homogeneity; particularly, they show differences in T and J haplogroups frequencies. MtDNA diversity in these two groups seems to depend more on their geographic situation.

  7. Transcription of mitochondrial DNA.

    PubMed

    Tabak, H F; Grivell, L A; Borst, P

    1983-01-01

    While mitochondrial DNA (mtDNA) is the simplest DNA in nature, coding for rRNAs and tRNAs, results of DNA sequence, and transcript analysis have demonstrated that both the synthesis and processing of mitochondrial RNAs involve remarkably intricate events. At one extreme, genes in animal mtDNAs are tightly packed, both DNA strands are completely transcribed (symmetric transcription), and the appearance of specific mRNAs is entirely dependent on processing at sites signalled by the sequences of the tRNAs, which abut virtually every gene. At the other extreme, gene organization in yeast (Saccharomyces) is anything but compact, with long stretches of AT-rich DNA interspaced between coding sequences and no obvious logic to the order of genes. Transcription is asymmetric and several RNAs are initiated de novo. Nevertheless, extensive RNA processing occurs due largely to the presence of split genes. RNA splicing is complex, is controlled by both mitochondrial and nuclear genes, and in some cases is accompanied by the formation of RNAs that behave as covalently closed circles. The present article reviews current knowledge of mitochondrial transcription and RNA processing in relation to possible mechanisms for the regulation of mitochondrial gene expression.

  8. Monophyletic origin of Lake Victoria cichlid fishes suggested by mitochondrial DNA sequences.

    PubMed

    Meyer, A; Kocher, T D; Basasibwaki, P; Wilson, A C

    1990-10-11

    Lake Victoria, together with its satellite lakes, harbours roughly 200 endemic forms of cichlid fishes that are classified as 'haplochromines' and yet the lake system is less than a million years old. This 'flock' has attracted attention because of the possibility that it evolved within the lake from one ancestral species and that biologists are thus presented with a case of explosive evolution. Within the past decade, however, morphology has increasingly emphasized the view that the flock may be polyphyletic. We sequenced up to 803 base pairs of mitochondrial DNA from 14 representative Victorian species and 23 additional African species. The flock seems to be monophyletic, and is more akin to that from Lake Malawi than to species from Lake Tanganyika; in addition, it contains less genetic variation than does the human species, and there is virtually no sharing of mitochondrial DNA types among species. These results confirm that the founding event was recent.

  9. Complete sequence of human mitochondrial DNA obtained by combining multiple displacement amplification and next-generation sequencing on a single oocyte.

    PubMed

    Ancora, Massimo; Orsini, Massimiliano; Colosimo, Alessia; Marcacci, Maurilia; Russo, Valentina; De Santo, Maria; D'Aurora, Marco; Stuppia, Liborio; Barboni, Barbara; Cammà, Cesare; Gatta, Valentina

    2017-03-01

    Mitochondrial DNA (mtDNA) plays a key role in the development of a competent oocyte. In this study, the complete mtDNA sequence obtained for the first time by multiple displacement amplification approach in combination with next-generation sequencing from a single human oocyte is reported (GenBank accession no. KT364276). The analysis of oocyte mitochondrial mutations could provide a better understanding of the genetic variants correlated with the oocyte quality.

  10. Complete DNA sequence of the mitochondrial genome of the black chiton, Katharina tunicata.

    PubMed

    Boore, J L; Brown, W M

    1994-10-01

    The DNA sequence of the 15,532-base pair (bp) mitochondrial DNA (mtDNA) of the chiton Katharina tunicata has been determined. The 37 genes typical of metazoan mtDNA are present: 13 for protein subunits involved in oxidative phosphorylation, 2 for rRNAs and 22 for tRNAs. The gene arrangement resembles those of arthropods much more than that of another mollusc, the bivalve Mytilus edulis. Most genes abut directly or overlap, and abbreviated stop codons are inferred for four genes. Four junctions between adjacent pairs of protein genes lack intervening tRNA genes; however, at each of these junctions there is a sequence immediately adjacent to the start codon of the downstream gene that is capable of forming a stem-and-loop structure. Analysis of the tRNA gene sequences suggests that the D arm is unpaired in tRNA(ser)(AGN), which is typical of metazoan mtDNAs, and also in tRNA(ser)(UCN), a condition found previously only in nematode mtDNAs. There are two additional sequences in Katharina mtDNA that can be folded into structures resembling tRNAs; whether these are functional genes is unknown. All possible codons except the stop codons TAA and TAG are used in the protein-encoding genes, and Katharina mtDNA appears to use the same variation of the mitochondrial genetic code that is used in Drosophila and Mytilus. Translation initiates at the codons ATG, ATA and GTG. A + T richness appears to have affected codon usage patterns and, perhaps, the amino acid composition of the encoded proteins. A 142-bp non-coding region between tRNA(glu) and CO3 contains a 72-bp tract of alternating A and T.

  11. Complete DNA Sequence of the Mitochondrial Genome of the Black Chiton, Katharina Tunicata

    PubMed Central

    Boore, J. L.; Brown, W. M.

    1994-01-01

    The DNA sequence of the 15,532-base pair (bp) mitochondrial DNA (mtDNA) of the chiton Katharina tunicata has been determined. The 37 genes typical of metazoan mtDNA are present: 13 for protein subunits involved in oxidative phosphorylation, 2 for rRNAs and 22 for tRNAs. The gene arrangement resembles those of arthropods much more than that of another mollusc, the bivalve Mytilus edulis. Most genes abut directly or overlap, and abbreviated stop codons are inferred for four genes. Four junctions between adjacent pairs of protein genes lack intervening tRNA genes; however, at each of these junctions there is a sequence immediately adjacent to the start codon of the downstream gene that is capable of forming a stem-and-loop structure. Analysis of the tRNA gene sequences suggests that the D arm is unpaired in tRNA(ser(AGN)), which is typical of metazoan mtDNAs, and also in tRNA(ser(UCN)), a condition found previously only in nematode mtDNAs. There are two additional sequences in Katharina mtDNA that can be folded into structures resembling tRNAs; whether these are functional genes is unknown. All possible codons except the stop codons TAA and TAG are used in the protein-encoding genes, and Katharina mtDNA appears to use the same variation of the mitochondrial genetic code that is used in Drosophila and Mytilus. Translation initiates at the codons ATG, ATA and GTG. A + T richness appears to have affected codon usage patterns and, perhaps, the amino acid composition of the encoded proteins. A 142-bp non-coding region between tRNA(glu) and CO3 contains a 72-bp tract of alternating A and T. PMID:7828825

  12. SAM: String-based sequence search algorithm for mitochondrial DNA database queries

    PubMed Central

    Röck, Alexander; Irwin, Jodi; Dür, Arne; Parsons, Thomas; Parson, Walther

    2011-01-01

    The analysis of the haploid mitochondrial (mt) genome has numerous applications in forensic and population genetics, as well as in disease studies. Although mtDNA haplotypes are usually determined by sequencing, they are rarely reported as a nucleotide string. Traditionally they are presented in a difference-coded position-based format relative to the corrected version of the first sequenced mtDNA. This convention requires recommendations for standardized sequence alignment that is known to vary between scientific disciplines, even between laboratories. As a consequence, database searches that are vital for the interpretation of mtDNA data can suffer from biased results when query and database haplotypes are annotated differently. In the forensic context that would usually lead to underestimation of the absolute and relative frequencies. To address this issue we introduce SAM, a string-based search algorithm that converts query and database sequences to position-free nucleotide strings and thus eliminates the possibility that identical sequences will be missed in a database query. The mere application of a BLAST algorithm would not be a sufficient remedy as it uses a heuristic approach and does not address properties specific to mtDNA, such as phylogenetically stable but also rapidly evolving insertion and deletion events. The software presented here provides additional flexibility to incorporate phylogenetic data, site-specific mutation rates, and other biologically relevant information that would refine the interpretation of mitochondrial DNA data. The manuscript is accompanied by freeware and example data sets that can be used to evaluate the new software (http://stringvalidation.org). PMID:21056022

  13. A mitochondrial DNA sequence is associated with abnormal pollen development in cytoplasmic male sterile bean plants.

    PubMed Central

    Johns, C; Lu, M; Lyznik, A; Mackenzie, S

    1992-01-01

    Cytoplasmic male sterility (CMS) in common bean is associated with the presence of a 3-kb unique mitochondrial sequence designated pvs. The pvs sequence encodes at least two open reading frames (297 and 720 bp in length) with portions derived from the chloroplast genome. Fertility restoration by the nuclear restorer gene Fr results in the loss of this transcriptionally active unique region. We examined the effect of CMS (pvs present) and fertility restoration by Fr (pvs absent) on the pattern of pollen development in bean. In the CMS line, pollen aborted in the tetrad stage late in microgametogenesis. Microspores maintained cytoplasmic connections throughout pollen development, indicating aberrant or incomplete cytokinesis. Pollen-specific events associated with pollen abortion and fertility restoration imply that a gametophytic factor or event may be involved in CMS. In situ hybridization experiments suggested that significant reduction or complete loss of the mitochondrial sterility-associated sequence occurred in fertile pollen of F2 populations segregating for fertility. These observations support a model of fertility restoration by the loss of a mitochondrial DNA sequence prior to or during microsporogenesis/gametogenesis. PMID:1498602

  14. Identifications of Captive and Wild Tilapia Species Existing in Hawaii by Mitochondrial DNA Control Region Sequence

    PubMed Central

    Wu, Liang; Yang, Jinzeng

    2012-01-01

    Background The tilapia family of the Cichlidae includes many fish species, which live in freshwater and saltwater environments. Several species, such as O. niloticus, O. aureus, and O. mossambicus, are excellent for aquaculture because these fish are easily reproduced and readily adapt to diverse environments. Historically, tilapia species, including O. mossambicus, S. melanotheron, and O. aureus, were introduced to Hawaii many decades ago, and the state of Hawaii uses the import permit policy to prevent O. niloticus from coming into the islands. However, hybrids produced from O. niloticus may already be present in the freshwater and marine environments of the islands. The purpose of this study was to identify tilapia species that exist in Hawaii using mitochondrial DNA analysis. Methodology/Principal Findings In this study, we analyzed 382 samples collected from 13 farm (captive) and wild tilapia populations in Oahu and the Hawaii Islands. Comparison of intraspecies variation between the mitochondrial DNA control region (mtDNA CR) and cytochrome c oxidase I (COI) gene from five populations indicated that mtDNA CR had higher nucleotide diversity than COI. A phylogenetic tree of all sampled tilapia was generated using mtDNA CR sequences. The neighbor-joining tree analysis identified seven distinctive tilapia species: O. aureus, O. mossambicus, O. niloticus, S. melanotheron, O. urolepies, T. redalli, and a hybrid of O. massambicus and O. niloticus. Of all the populations examined, 10 populations consisting of O. aureus, O. mossambicus, O. urolepis, and O. niloticus from the farmed sites were relatively pure, whereas three wild populations showed some degree of introgression and hybridization. Conclusions/Significance This DNA-based tilapia species identification is the first report that confirmed tilapia species identities in the wild and captive populations in Hawaii. The DNA sequence comparisons of mtDNA CR appear to be a valid method for tilapia species

  15. Whole mitochondrial DNA sequencing in Alpine populations and the genetic history of the Neolithic Tyrolean Iceman.

    PubMed

    Coia, V; Cipollini, G; Anagnostou, P; Maixner, F; Battaggia, C; Brisighelli, F; Gómez-Carballa, A; Destro Bisol, G; Salas, A; Zink, A

    2016-01-14

    The Tyrolean Iceman is an extraordinarily well-preserved natural mummy that lived south of the Alpine ridge ~5,200 years before present (ybp), during the Copper Age. Despite studies that have investigated his genetic profile, the relation of the Iceman´s maternal lineage with present-day mitochondrial variation remains elusive. Studies of the Iceman have shown that his mitochondrial DNA (mtDNA) belongs to a novel lineage of haplogroup K1 (K1f) not found in extant populations. We analyzed the complete mtDNA sequences of 42 haplogroup K bearing individuals from populations of the Eastern Italian Alps - putatively in genetic continuity with the Tyrolean Iceman-and compared his mitogenome with a large dataset of worldwide K1 sequences. Our results allow a re-definition of the K1 phylogeny, and indicate that the K1f haplogroup is absent or rare in present-day populations. We suggest that mtDNA Iceman´s lineage could have disappeared during demographic events starting in Europe from ~5,000 ybp. Based on the comparison of our results with published data, we propose a scenario that could explain the apparent contrast between the phylogeographic features of maternal and paternal lineages of the Tyrolean Iceman within the context of the demographic dynamics happening in Europe from 8,000 ybp.

  16. Whole mitochondrial DNA sequencing in Alpine populations and the genetic history of the Neolithic Tyrolean Iceman

    PubMed Central

    Coia, V.; Cipollini, G.; Anagnostou, P.; Maixner, F.; Battaggia, C.; Brisighelli, F.; Gómez-Carballa, A; Destro Bisol, G.; Salas, A.; Zink, A.

    2016-01-01

    The Tyrolean Iceman is an extraordinarily well-preserved natural mummy that lived south of the Alpine ridge ~5,200 years before present (ybp), during the Copper Age. Despite studies that have investigated his genetic profile, the relation of the Iceman´s maternal lineage with present-day mitochondrial variation remains elusive. Studies of the Iceman have shown that his mitochondrial DNA (mtDNA) belongs to a novel lineage of haplogroup K1 (K1f) not found in extant populations. We analyzed the complete mtDNA sequences of 42 haplogroup K bearing individuals from populations of the Eastern Italian Alps – putatively in genetic continuity with the Tyrolean Iceman—and compared his mitogenome with a large dataset of worldwide K1 sequences. Our results allow a re-definition of the K1 phylogeny, and indicate that the K1f haplogroup is absent or rare in present-day populations. We suggest that mtDNA Iceman´s lineage could have disappeared during demographic events starting in Europe from ~5,000 ybp. Based on the comparison of our results with published data, we propose a scenario that could explain the apparent contrast between the phylogeographic features of maternal and paternal lineages of the Tyrolean Iceman within the context of the demographic dynamics happening in Europe from 8,000 ybp. PMID:26764605

  17. Cloning and sequencing of the PIF gene involved in repair and recombination of yeast mitochondrial DNA.

    PubMed Central

    Foury, F; Lahaye, A

    1987-01-01

    The nuclear gene PIF of Saccharomyces cerevisiae is required for both repair of mitochondrial DNA (mtDNA) and recognition of a recombinogenic signal characterized by a 26-bp palindromic AT sequence in the ery region of mtDNA. This gene has been cloned in yeast by genetic complementation of pif mutants. Its chromosomal disruption does not destroy the genetic function of mitochondria. The nucleotide sequence of the 3.5-kb insert from a complementing plasmid reveals an open reading frame encoding a potential protein of 857 amino acids and Mr = 97,500. An ATP-binding domain is present in the central part of the gene and in the carboxy-terminal region a putative DNA-binding site is present. Its alpha helix-turn-alpha helix motif is found in DNA-binding proteins such as lambda and lactose repressors which recognize symmetric sequences. Significant amino acid homology is observed with yeast RAD3 and E. coli UvrD (helicase II) proteins which are required for excision repair of damaged DNA. Images Fig. 1. Fig. 2. PMID:3038524

  18. Intraspecific nucleotide sequence differences in the major noncoding region of human mitochondrial DNA.

    PubMed Central

    Horai, S; Hayasaka, K

    1990-01-01

    Nucleotide sequences of the major noncoding region of human mitochondrial DNA (mtDNA) from 95 human placentas have been determined. These sequences include at least a 482-bp-long region encompassing most of the D-loop-forming region. Comparisons of these sequences with those previously determined have revealed remarkable features of nucleotide substitutions and insertion/deletion events. The nucleotide diversity among the sequences is estimated as 1.45%, which is three- to fourfold higher than the corresponding value estimated from restriction-enzyme analysis of whole mtDNA genome. A hypervariable region has also been defined. In this 14-bp region, 17 different sequences were detected. More than 97% of the base changes are transitions. A significantly nonrandom distribution of nucleotide substitutions and sequence length variations were also noted. The phylogenetic analysis indicates that diversity among the negroids is much larger than that among the caucasoids or the mongoloids. In fact, part of the negroids first diverged from other humans in the phylogenetic tree. A striking finding in the phylogenetic analysis is that the mongoloids can be separated into two distinct groups. Divergence of part of the mongoloids follows the earliest divergence of part of the negroids. The remainder of the mongoloids subsequently diverged together with the caucasoids. This observation confirmed our earlier study, which clearly demonstrated, by the restriction-enzyme analysis, existence of two distinct groups in the Japanese. Images Figure 3 PMID:2316527

  19. Sequence polymorphism in a novel noncoding region of Pacific oyster mitochondrial DNA.

    PubMed

    Aranishi, Futoshi; Okimoto, Takane

    2005-01-01

    Nucleotide sequence polymorphism in a 641-bp novel major noncoding region of mitochondrial DNA (mtDNA-NC) of the Pacific oyster Crassostrea gigas was analysed for 29 cultured individuals within the Goseong population. A total of 30 variable sites were detected, and the relative frequency of nucleotide alteration was determined to be 4.68. Alterations were mostly single nucleotide substitutions. Transition, transversion, both transition and transversion, and both transversion and nucleotide deletion were observed at 18, 9, 2 and 1 sites, respectively. Among 29 specimens, 22 haplotypes were identified, and pairwise genetic diversity of haplotypes was calculated to be 0.988 from multiple sequence substitutions using the two-parameter model. A phylogenetic tree, obtained for haplotypes by the neighbor-joining method, showed a single cluster of linkages. The cluster comprised 11 haplotypes associating with 14 specimens, while the other 11 haplotypes associating with 15 specimens were scattered. This mtDNA-NC presenting a high nucleotide sequence polymorphism is a potential mtDNA control region. It therefore can serve as a genetic marker for intraspecies phylogenetic analysis of the Pacific oyster and is more useful than the less polymorphic mtDNA coding genes.

  20. Mitochondrial DNA in the sea urchin Arbacia lixula: evolutionary inferences from nucleotide sequence analysis.

    PubMed

    De Giorgi, C; Lanave, C; Musci, M D; Saccone, C

    1991-07-01

    From the stirodont Arbacia lixula we determined the sequence of 5,127 nucleotides of mitochondrial DNA (mtDNA) encompassing 18 tRNAs, two complete coding genes, parts of three other coding genes, and part of the 12S ribosomal RNA (rRNA). The sequence confirms that the organization of mtDNA is conserved within echinoids. Furthermore, it underlines the following peculiar features of sea urchin mtDNA: the clustering of tRNAs, the short noncoding regulatory sequence, and the separation by the ND1 and ND2 genes of the two rRNA genes. Comparison with the orthologous sequences from the camarodont species Paracentrotus lividus and Strongylocentrotus purpuratus revealed that (1) echinoids have an extra piece on the amino terminus of the ND5 gene that is probably the remnant of an old leucine tRNA gene; (2) third-position codon nucleotide usage has diverged between A. lixula and the camarodont species to a significant extent, implying different directional mutational pressures; and (3) the stirodont-camarodont divergence occurred twice as long ago as did the P. lividus-S. purpuratus divergence.

  1. Population subdivision in Europe's great bustard inferred from mitochondrial and nuclear DNA sequence variation.

    PubMed

    Pitra, C; Lieckfeldt, D; Alonso, J C

    2000-08-01

    A continent-wide survey of sequence variation in mitochondrial (mt) and nuclear (n) DNA of the endangered great bustard (Otis tarda) was conducted to assess the extent of phylogeographic structure in a morphologically monotypic bird. DNA sequence variation in a combined 809 bp segment of the mtDNA genome from 66 individuals from the last six breeding regions showed relatively low levels of intraspecific sequence diversity (n = 0.32%) but significant differences in the regional distribution of 11 haplotypes (phiST = 0.49). Despite their exceptional potential for dispersal, a complete and long-term historical separation between the populations from the Iberian Peninsula (Spain) and mainland Europe (Hungary, Slovakia, Germany, and Russia) was demonstrated. Divergence between populations based on a 3-bp insertion-deletion polymorphism within the intron region of the nuclear CHD-Z gene was geographically concordant with the primary subdivision identified within the mtDNA sequences. Inferred aspects of phylogeography were used to formulate conservation recommendations for this endangered species.

  2. Phylogeny and evolution of the auks (subfamily Alcinae) based on mitochondrial DNA sequences

    USGS Publications Warehouse

    Moum, Truls; Johansen, Steinar; Erikstad, Kjell Einar; Piatt, John F.

    1994-01-01

    The genetic divergence and phylogeny of the auks was assessed by mitochondrial DNA sequence comparisons in a study using 19 of the 22 auk species and two outgroup representatives. We compared more than 500 nucleotides from each of two mitochondrial genes encoding 12S rRNA and the NADH dehydrogenase subunit 6. Divergence times were estimated from transversional substitutions. The dovekie (Alle alle) is related to the razorbill (Alca torda) and the murres (Uria spp). Furthermore, the Xantus's murrelet (Synthliboramphus hypoleucus) and the ancient (Synthliboramphus antiquus) and Japanese murrelets (Synthliboramphus wumizusume) are genetically distinct members of the same main lineage, whereas brachyramphine and synthliboramphine murrelets are not closely related. An early adaptive radiation of six main species groups of auks seems to trace back to Middle Miocene. Later speciation probably involved ecological differentiations and geographical isolations.

  3. Population genetic structure and historical demography of Oratosquilla oratoria revealed by mitochondrial DNA sequences.

    PubMed

    Zhang, D; Ding, Ge; Ge, B; Zhang, H; Tang, B

    2012-12-01

    Genetic diversity, population genetic structure and molecular phylogeographic pattern of mantis shrimp Oratosquilla oratoria in Bohai Sea and South China Sea were analyzed by mitochondrial DNA sequences. Nucleotide and haplotype diversities were 0.00409-0.00669 and 0.894-0.953 respectively. Neighbor-Joining phylogenetic tree clustered two distinct lineages. Both phylogenetic tree and median-joining network showed the consistent genetic structure corresponding to geographical distribution. Mismatch distributions, negative neutral test and "star-like" network supported a sudden population expansion event. And the time was estimated about 44000 and 50000 years ago.

  4. Primer effect in the detection of mitochondrial DNA point heteroplasmy by automated sequencing.

    PubMed

    Calatayud, Marta; Ramos, Amanda; Santos, Cristina; Aluja, Maria Pilar

    2013-06-01

    The correct detection of mitochondrial DNA (mtDNA) heteroplasmy by automated sequencing presents methodological constraints. The main goals of this study are to investigate the effect of sense and distance of primers in heteroplasmy detection and to test if there are differences in the accurate determination of heteroplasmy involving transitions or transversions. A gradient of the heteroplasmy levels was generated for mtDNA positions 9477 (transition G/A) and 15,452 (transversion C/A). Amplification and subsequent sequencing with forward and reverse primers, situated at 550 and 150 bp from the heteroplasmic positions, were performed. Our data provide evidence that there is a significant difference between the use of forward and reverse primers. The forward primer is the primer that seems to give a better approximation to the real proportion of the variants. No significant differences were found concerning the distance at which the sequencing primers were placed neither between the analysis of transitions and transversions. The data collected in this study are a starting point that allows to glimpse the importance of the sequencing primers in the accurate detection of point heteroplasmy, providing additional insight into the overall automated sequencing strategy.

  5. Import of desired nucleic acid sequences using addressing motif of mitochondrial ribosomal 5S-rRNA for fluorescent in vivo hybridization of mitochondrial DNA and RNA.

    PubMed

    Zelenka, Jaroslav; Alán, Lukáš; Jabůrek, Martin; Ježek, Petr

    2014-04-01

    Based on the matrix-addressing sequence of mitochondrial ribosomal 5S-rRNA (termed MAM), which is naturally imported into mitochondria, we have constructed an import system for in vivo targeting of mitochondrial DNA (mtDNA) or mt-mRNA, in order to provide fluorescence hybridization of the desired sequences. Thus DNA oligonucleotides were constructed, containing the 5'-flanked T7 RNA polymerase promoter. After in vitro transcription and fluorescent labeling with Alexa Fluor(®) 488 or 647 dye, we obtained the fluorescent "L-ND5 probe" containing MAM and exemplar cargo, i.e., annealing sequence to a short portion of ND5 mRNA and to the light-strand mtDNA complementary to the heavy strand nd5 mt gene (5'-end 21 base pair sequence). For mitochondrial in vivo fluorescent hybridization, HepG2 cells were treated with dequalinium micelles, containing the fluorescent probes, bringing the probes proximally to the mitochondrial outer membrane and to the natural import system. A verification of import into the mitochondrial matrix of cultured HepG2 cells was provided by confocal microscopy colocalizations. Transfections using lipofectamine or probes without 5S-rRNA addressing MAM sequence or with MAM only were ineffective. Alternatively, the same DNA oligonucleotides with 5'-CACC overhang (substituting T7 promoter) were transcribed from the tetracycline-inducible pENTRH1/TO vector in human embryonic kidney T-REx®-293 cells, while mitochondrial matrix localization after import of the resulting unlabeled RNA was detected by PCR. The MAM-containing probe was then enriched by three-order of magnitude over the natural ND5 mRNA in the mitochondrial matrix. In conclusion, we present a proof-of-principle for mitochondrial in vivo hybridization and mitochondrial nucleic acid import.

  6. Simultaneous detection of human mitochondrial DNA and nuclear-inserted mitochondrial-origin sequences (NumtS) using forensic mtDNA amplification strategies and pyrosequencing technology.

    PubMed

    Bintz, Brittania J; Dixon, Groves B; Wilson, Mark R

    2014-07-01

    Next-generation sequencing technologies enable the identification of minor mitochondrial DNA variants with higher sensitivity than Sanger methods, allowing for enhanced identification of minor variants. In this study, mixtures of human mtDNA control region amplicons were subjected to pyrosequencing to determine the detection threshold of the Roche GS Junior(®) instrument (Roche Applied Science, Indianapolis, IN). In addition to expected variants, a set of reproducible variants was consistently found in reads from one particular amplicon. A BLASTn search of the variant sequence revealed identity to a segment of a 611-bp nuclear insertion of the mitochondrial control region (NumtS) spanning the primer-binding sites of this amplicon (Nature 1995;378:489). Primers (Hum Genet 2012;131:757; Hum Biol 1996;68:847) flanking the insertion were used to confirm the presence or absence of the NumtS in buccal DNA extracts from twenty donors. These results further our understanding of human mtDNA variation and are expected to have a positive impact on the interpretation of mtDNA profiles using deep-sequencing methods in casework.

  7. Mitochondrial DNA sequence variation is associated with free-living activity energy expenditure in the elderly.

    PubMed

    Tranah, Gregory J; Lam, Ernest T; Katzman, Shana M; Nalls, Michael A; Zhao, Yiqiang; Evans, Daniel S; Yokoyama, Jennifer S; Pawlikowska, Ludmila; Kwok, Pui-Yan; Mooney, Sean; Kritchevsky, Stephen; Goodpaster, Bret H; Newman, Anne B; Harris, Tamara B; Manini, Todd M; Cummings, Steven R

    2012-09-01

    The decline in activity energy expenditure underlies a range of age-associated pathological conditions, neuromuscular and neurological impairments, disability, and mortality. The majority (90%) of the energy needs of the human body are met by mitochondrial oxidative phosphorylation (OXPHOS). OXPHOS is dependent on the coordinated expression and interaction of genes encoded in the nuclear and mitochondrial genomes. We examined the role of mitochondrial genomic variation in free-living activity energy expenditure (AEE) and physical activity levels (PAL) by sequencing the entire (~16.5 kilobases) mtDNA from 138 Health, Aging, and Body Composition Study participants. Among the common mtDNA variants, the hypervariable region 2 m.185G>A variant was significantly associated with AEE (p=0.001) and PAL (p=0.0005) after adjustment for multiple comparisons. Several unique nonsynonymous variants were identified in the extremes of AEE with some occurring at highly conserved sites predicted to affect protein structure and function. Of interest is the p.T194M, CytB substitution in the lower extreme of AEE occurring at a residue in the Qi site of complex III. Among participants with low activity levels, the burden of singleton variants was 30% higher across the entire mtDNA and OXPHOS complex I when compared to those having moderate to high activity levels. A significant pooled variant association across the hypervariable 2 region was observed for AEE and PAL. These results suggest that mtDNA variation is associated with free-living AEE in older persons and may generate new hypotheses by which specific mtDNA complexes, genes, and variants may contribute to the maintenance of activity levels in late life.

  8. Analysis of the complete mitochondrial DNA sequence of the brachiopod terebratulina retusa places Brachiopoda within the protostomes.

    PubMed Central

    Stechmann, A; Schlegel, M

    1999-01-01

    Brachiopod phylogeny is still a controversial subject. Analyses using nuclear 18SrRNA and mitochondrial 12SrDNA sequences place them within the protostomes but some recent interpretations of morphological data support a relationship with deuterostomes. In order to investigate brachiopod affinities within the metazoa further, we compared the gene arrangement on the brachiopod mitochondrial genome with several metazoan taxa. The complete (15 451 bp) mitochondrial DNA (mtDNA) sequence of the articulate brachiopod Terebratulina retusa was determined from two overlapping long polymerase chain reaction products. All the genes are encoded on the same strand and gene order comparisons showed that.only one major rearrangement is required to interconvert the T. retusa and Katharina tunicata (Mollusca: Polvplacophora) mitochondrial genomes. The partial mtDNA sequence of the prosobranch mollusc Littorina saxatilis shows complete congruence with the T. rehtusa gene arrangement with regard to the ribosomal and protein coding genes. This high similarity in gene arrangement is the first to be reported within the protostomes. Sequence analyses of mitochondrial protein coding genes also support a close relationship of the brachiopod with molluscs and annelids, thus supporting the clade Lophotrochozoa. Though being highly informative, sequence analyses of the mitochondrial protein coding genes failed to resolve the branching order within the lophotrochozoa. PMID:10902540

  9. New complete mitochondrial DNA sequence of the lancelet Branchiostoma lanceolatum (Cephalochordata) and the identity of this species' sequences.

    PubMed

    Nohara, Masahiro; Nishida, Mutsumi; Nishikawa, Teruaki

    2005-06-01

    Three mitochondrial (mt) genes were sequenced for two Atlantic lancelet species, Branchiostoma lanceolatum and B. floridae, to examine a serious discrepancy among previously published results of molecular studies: substantial sequence difference in a nuclear gene vs. virtual identity in the mt genome sequence. The results revealed that three mt genes of B. lanceolatum, collected from Helgoland in the North Sea and Naples in the Mediterranean, were quite diverged from those of B. floridae, collected from Tampa Bay, Florida. Therefore, the previously recognized identity in the mt genome between the two species is attributable to misidentification of materials used. To correct this misleading information, the complete mtDNA sequence of B. lanceolatum was determined for an individual from Helgoland.

  10. Global matrilineal population structure in sperm whales as indicated by mitochondrial DNA sequences.

    PubMed Central

    Lyrholm, T; Gyllensten, U

    1998-01-01

    The genetic variability and population structure of worldwide populations of the sperm whale was investigated by sequence analysis of the first 5'L 330 base pairs in the mitochondrial DNA (mtDNA) control region. The study included a total of 231 individuals from three major oceanic regions, the North Atlantic, the North Pacific and the Southern Hemisphere. Fifteen segregating nucleotide sites defined 16 mtDNA haplotypes (lineages). The most common mtDNA types were present in more than one oceanic region, whereas ocean-specific types were rare. Analyses of heterogeneity of mtDNA type frequencies between oceans indicated moderate (GST = 0.03) but statistically significant (p = 0.0007) genetic differentiation on a global scale. In addition, strong genetic differentiation was found between potential social groups (GST = 0.03-0.6), indicating matrilineal relatedness within groups. The global nucleotide diversity was quite low (pi = 0.004) implying a recent common mtDNA ancestry (< 100,000) years ago) and a young global population structure. However, within this time period, female dispersal has apparently been limited enough to allow the development of global mtDNA differentiation. The results are consistent with those from observational studies and whaling data indicating stable social affiliations, some degree of area fidelity and latitudinal range limitations in groups of females and juveniles. PMID:9753788

  11. mtDNA-Server: next-generation sequencing data analysis of human mitochondrial DNA in the cloud.

    PubMed

    Weissensteiner, Hansi; Forer, Lukas; Fuchsberger, Christian; Schöpf, Bernd; Kloss-Brandstätter, Anita; Specht, Günther; Kronenberg, Florian; Schönherr, Sebastian

    2016-07-08

    Next generation sequencing (NGS) allows investigating mitochondrial DNA (mtDNA) characteristics such as heteroplasmy (i.e. intra-individual sequence variation) to a higher level of detail. While several pipelines for analyzing heteroplasmies exist, issues in usability, accuracy of results and interpreting final data limit their usage. Here we present mtDNA-Server, a scalable web server for the analysis of mtDNA studies of any size with a special focus on usability as well as reliable identification and quantification of heteroplasmic variants. The mtDNA-Server workflow includes parallel read alignment, heteroplasmy detection, artefact or contamination identification, variant annotation as well as several quality control metrics, often neglected in current mtDNA NGS studies. All computational steps are parallelized with Hadoop MapReduce and executed graphically with Cloudgene. We validated the underlying heteroplasmy and contamination detection model by generating four artificial sample mix-ups on two different NGS devices. Our evaluation data shows that mtDNA-Server detects heteroplasmies and artificial recombinations down to the 1% level with perfect specificity and outperforms existing approaches regarding sensitivity. mtDNA-Server is currently able to analyze the 1000G Phase 3 data (n = 2,504) in less than 5 h and is freely accessible at https://mtdna-server.uibk.ac.at.

  12. mtDNA-Server: next-generation sequencing data analysis of human mitochondrial DNA in the cloud

    PubMed Central

    Weissensteiner, Hansi; Forer, Lukas; Fuchsberger, Christian; Schöpf, Bernd; Kloss-Brandstätter, Anita; Specht, Günther; Kronenberg, Florian; Schönherr, Sebastian

    2016-01-01

    Next generation sequencing (NGS) allows investigating mitochondrial DNA (mtDNA) characteristics such as heteroplasmy (i.e. intra-individual sequence variation) to a higher level of detail. While several pipelines for analyzing heteroplasmies exist, issues in usability, accuracy of results and interpreting final data limit their usage. Here we present mtDNA-Server, a scalable web server for the analysis of mtDNA studies of any size with a special focus on usability as well as reliable identification and quantification of heteroplasmic variants. The mtDNA-Server workflow includes parallel read alignment, heteroplasmy detection, artefact or contamination identification, variant annotation as well as several quality control metrics, often neglected in current mtDNA NGS studies. All computational steps are parallelized with Hadoop MapReduce and executed graphically with Cloudgene. We validated the underlying heteroplasmy and contamination detection model by generating four artificial sample mix-ups on two different NGS devices. Our evaluation data shows that mtDNA-Server detects heteroplasmies and artificial recombinations down to the 1% level with perfect specificity and outperforms existing approaches regarding sensitivity. mtDNA-Server is currently able to analyze the 1000G Phase 3 data (n = 2,504) in less than 5 h and is freely accessible at https://mtdna-server.uibk.ac.at. PMID:27084948

  13. A pedigree-based study of mitochondrial D-loop DNA sequence variation among Arabian horses.

    PubMed

    Bowling, A T; Del Valle, A; Bowling, M

    2000-02-01

    Through DNA sequence comparisons of a mitochondrial D-loop hypervariable region, we investigated matrilineal diversity for Arabian horses in the United States. Sixty-two horses were tested. From published pedigrees they traced in the maternal line to 34 mares acquired primarily in the mid to late 19th century from nomadic Bedouin tribes. Compared with the reference sequence (GenBank X79547), these samples showed 27 haplotypes with altogether 31 base substitution sites within 397 bp of sequence. Based on examination of pedigrees from a random sampling of 200 horses in current studbooks of the Arabian Horse Registry of America, we estimated that this study defined the expected mtDNA haplotypes for at least 89% of Arabian horses registered in the US. The reliability of the studbook recorded maternal lineages of Arabian pedigrees was demonstrated by haplotype concordance among multiple samplings in 14 lines. Single base differences observed within two maternal lines were interpreted as representing alternative fixations of past heteroplasmy. The study also demonstrated the utility of mtDNA sequence studies to resolve historical maternity questions without access to biological material from the horses whose relationship was in question, provided that representatives of the relevant female lines were available for comparison. The data call into question the traditional assumption that Arabian horses of the same strain necessarily share a common maternal ancestry.

  14. Belgian canine population and purebred study for forensics by improved mitochondrial DNA sequencing.

    PubMed

    Desmyter, Stijn; Gijsbers, Leonie

    2012-01-01

    In canine population studies for forensics, the mitochondrial DNA is profiled by sequencing the two hyper variable regions, HV1 and HV2 of the control region. In a first effort to create a Belgian population database some samples showed partially poor sequence quality. We demonstrated that a nuclear pseudogene was co-amplified with the mtDNA control region. Using a new combination of primers this adverse result was no longer observed and sequencing quality was improved. All former samples with poor sequence data were reanalyzed. Furthermore, the forensic canine population study was extended to 208 breed and mixed dogs. In total, 58 haplotypes were identified, resulting in an exclusion capacity of 0.92. The profile distribution of the Belgian population sample was not significantly different from those observed in population studies of three other countries. In addition to the total population study 107 Belgian registered pedigree dogs of six breeds were profiled. Per breed, the obtained haplotypes were supplemented with those from population and purebred studies. The combined data revealed that some haplotypes were more or less prominent present in particular dog breeds. The statistically significant differences in haplotype distribution between breeds and population sample can have consequences on mtDNA databasing and matching probabilities in forensics.

  15. Mitochondrial DNA sequences support allozyme evidence for cryptic radiation of New Zealand Peripatoides (Onychophora).

    PubMed

    Trewick, S A

    2000-03-01

    A combination of single-strand conformation polymorphism analysis (SSCP) and sequencing were used to survey cytochrome oxidase I (COI) mitochondrial DNA (mtDNA) diversity among New Zealand ovoviviparous Onychophora. Most of the sites and individuals had previously been analysed using allozyme electrophoresis. A total of 157 peripatus collected at 54 sites throughout New Zealand were screened yielding 62 different haplotypes. Comparison of 540-bp COI sequences from Peripatoides revealed mean among-clade genetic distances of up to 11. 4% using Kimura 2-parameter (K2P) analysis or 17.5% using general time-reversible (GTR + I + Gamma) analysis. Phylogenetic analysis revealed eight well-supported clades that were consistent with the allozyme analysis. Five of the six cryptic peripatus species distinguished by allozymes were confirmed by mtDNA analysis. The sixth taxon appeared to be paraphyletic, but genetic and geographical evidence suggested recent speciation. Two additional taxa were evident from the mtDNA data but neither occurred within the areas surveyed using allozymes. Among the peripatus surveyed with both mtDNA and allozymes, only one clear instance of recent introgression was evident, even though several taxa occurred in sympatry. This suggests well-developed mate recognition despite minimal morphological variation and low overall genetic diversity.

  16. Direct sequencing of mitochondrial DNA detects highly divergent haplotypes in blue marlin (Makaira nigricans).

    PubMed

    Finnerty, J R; Block, B A

    1992-06-01

    We were able to differentiate between species of billfish (Istiophoridae family) and to detect considerable intraspecific variation in the blue marlin (Makaira nigricans) by directly sequencing a polymerase chain reaction (PCR)-amplified, 612-bp fragment of the mitochondrial cytochrome b gene. Thirteen variable nucleotide sites separated blue marlin (n = 26) into 7 genotypes. On average, these genotypes differed by 5.7 base substitutions. A smaller sample of swordfish from an equally broad geographic distribution displayed relatively little intraspecific variation, with an average of 1.3 substitutions separating different genotypes. A cladistic analysis of blue marlin cytochrome b variants indicates two major divergent evolutionary lines within the species. The frequencies of these two major evolutionary lines differ significantly between Atlantic and Pacific ocean basins. This finding is important given that the Atlantic stocks of blue marlin are considered endangered. Migration from the Pacific can help replenish the numbers of blue marlin in the Atlantic, but the loss of certain mitochondrial DNA haplotypes in the Atlantic due to overfishing probably could not be remedied by an influx of Pacific fish because of their absence in the Pacific population. Fishery management strategies should attempt to preserve the genetic diversity within the species. The detection of DNA sequence polymorphism indicates the utility of PCR technology in pelagic fishery genetics.

  17. DNA capture and next-generation sequencing can recover whole mitochondrial genomes from highly degraded samples for human identification

    PubMed Central

    2013-01-01

    Background Mitochondrial DNA (mtDNA) typing can be a useful aid for identifying people from compromised samples when nuclear DNA is too damaged, degraded or below detection thresholds for routine short tandem repeat (STR)-based analysis. Standard mtDNA typing, focused on PCR amplicon sequencing of the control region (HVS I and HVS II), is limited by the resolving power of this short sequence, which misses up to 70% of the variation present in the mtDNA genome. Methods We used in-solution hybridisation-based DNA capture (using DNA capture probes prepared from modern human mtDNA) to recover mtDNA from post-mortem human remains in which the majority of DNA is both highly fragmented (<100 base pairs in length) and chemically damaged. The method ‘immortalises’ the finite quantities of DNA in valuable extracts as DNA libraries, which is followed by the targeted enrichment of endogenous mtDNA sequences and characterisation by next-generation sequencing (NGS). Results We sequenced whole mitochondrial genomes for human identification from samples where standard nuclear STR typing produced only partial profiles or demonstrably failed and/or where standard mtDNA hypervariable region sequences lacked resolving power. Multiple rounds of enrichment can substantially improve coverage and sequencing depth of mtDNA genomes from highly degraded samples. The application of this method has led to the reliable mitochondrial sequencing of human skeletal remains from unidentified World War Two (WWII) casualties approximately 70 years old and from archaeological remains (up to 2,500 years old). Conclusions This approach has potential applications in forensic science, historical human identification cases, archived medical samples, kinship analysis and population studies. In particular the methodology can be applied to any case, involving human or non-human species, where whole mitochondrial genome sequences are required to provide the highest level of maternal lineage discrimination

  18. Mitochondrial DNA sequence analysis of four Alzheimer`s and Parkinson`s disease patients

    SciTech Connect

    Brown, M.D.; Shoffner, J.M.; Wallace, D.C.

    1996-01-22

    The mitochondrial DNA (mtDNA) sequence was determined on 3 patients with Alzheimer`s disease (AD) exhibiting AD plus Parkinson`s disease (PD) neuropathologic changes and one patient with PD. Patient mtDNA sequences were compared to the standard Cambridge sequence to identify base changes. In the first AD + PD patient, 2 of the 15 nucleotide substitutions may contribute to the neuropathology, a nucleotide pair (np) 4336 transition in the tRNA{sup Gln} gene found 7.4 times more frequently in patients than in controls, and a unique np 721 transition in the 12S rRNA gene which was not found in 70 other patients or 905 controls. In the second AD + PD patient, 27 nucleotide substitutions were detected, including an np 3397 transition in the ND1 gene which converts a conserved methionine to a valine. In the third AD + PD patient, 2 polymorphic base substitutions frequently found at increased frequency in Leber`s hereditary optic neuropathy patients were observed, an np 4216 transition in ND1 and an np 13708 transition in the ND5 gene. For the PD patient, 2 novel variants were observed among 25 base substitutions, an np 1709 substitution in the 16S rRNA gene and an np 15851 missense mutation in the cytb gene. Further studies will be required to demonstrate a casual role for these base substitutions in neurodegenerative disease. 68 refs., 2 tabs.

  19. Complete DNA sequence of the mitochondrial genome of the ascidian Halocynthia roretzi (Chordata, Urochordata).

    PubMed Central

    Yokobori, S i; Ueda, T; Feldmaier-Fuchs, G; Pääbo, S; Ueshima, R; Kondow, A; Nishikawa, K; Watanabe, K

    1999-01-01

    The complete nucleotide sequence of the 14,771-bp-long mitochondrial (mt) DNA of a urochordate (Chordata)-the ascidian Halocynthia roretzi-was determined. All the Halocynthia mt-genes were found to be located on a single strand, which is rich in T and G rather than in A and C. Like nematode and Mytilus edulis mtDNAs, that of Halocynthia encodes no ATP synthetase subunit 8 gene. However, it does encode an additional tRNA gene for glycine (anticodon TCT) that enables Halocynthia mitochondria to use AGA and AGG codons for glycine. The mtDNA carries an unusual tRNA(Met) gene with a TAT anticodon instead of the usual tRNA(Met)(CAT) gene. As in other metazoan mtDNAs, there is not any long noncoding region. The gene order of Halocynthia mtDNA is completely different from that of vertebrate mtDNAs except for tRNA(His)-tRNA(Ser)(GCU), suggesting that evolutionary change in the mt-gene structure is much accelerated in the urochordate line compared with that in vertebrates. The amino acid sequences of Halocynthia mt-proteins deduced from their gene sequences are quite different from those in other metazoans, indicating that the substitution rate in Halocynthia mt-protein genes is also accelerated. PMID:10581290

  20. Complete DNA sequence of the mitochondrial genome of the ascidian Halocynthia roretzi (Chordata, Urochordata).

    PubMed

    Yokobori, S i; Ueda, T; Feldmaier-Fuchs, G; Pääbo, S; Ueshima, R; Kondow, A; Nishikawa, K; Watanabe, K

    1999-12-01

    The complete nucleotide sequence of the 14,771-bp-long mitochondrial (mt) DNA of a urochordate (Chordata)-the ascidian Halocynthia roretzi-was determined. All the Halocynthia mt-genes were found to be located on a single strand, which is rich in T and G rather than in A and C. Like nematode and Mytilus edulis mtDNAs, that of Halocynthia encodes no ATP synthetase subunit 8 gene. However, it does encode an additional tRNA gene for glycine (anticodon TCT) that enables Halocynthia mitochondria to use AGA and AGG codons for glycine. The mtDNA carries an unusual tRNA(Met) gene with a TAT anticodon instead of the usual tRNA(Met)(CAT) gene. As in other metazoan mtDNAs, there is not any long noncoding region. The gene order of Halocynthia mtDNA is completely different from that of vertebrate mtDNAs except for tRNA(His)-tRNA(Ser)(GCU), suggesting that evolutionary change in the mt-gene structure is much accelerated in the urochordate line compared with that in vertebrates. The amino acid sequences of Halocynthia mt-proteins deduced from their gene sequences are quite different from those in other metazoans, indicating that the substitution rate in Halocynthia mt-protein genes is also accelerated.

  1. Phylogeny of "Philoceanus complex" seabird lice (Phthiraptera: Ischnocera) inferred from mitochondrial DNA sequences.

    PubMed

    Page, Roderic D M; Cruickshank, Robert H; Dickens, Megan; Furness, Robert W; Kennedy, Martyn; Palma, Ricardo L; Smith, Vincent S

    2004-03-01

    The Philoceanus complex is a large assemblage of lice that parasitise procellariiform seabirds (petrels, albatrosses, and their relatives). We obtained mitochondrial 12S rRNA and cytochrome oxidase I DNA sequences from 39 species from diverse hosts and localities. Resolution of deeper relationships between genera was limited, however there is evidence for two major clades, one hosted by albatrosses, the other by petrels. Based on our results, the genera hosted by albatrosses are excellent candidates for detailed analysis of cospeciation. Our results also suggest that a previous estimate of a 5-fold difference in the relative rate of sequence evolution in lice and their avian hosts is an artefact of limited taxonomic sampling.

  2. Mitochondrial DNA sequence-based phylogenetic relationship of Trichiurus lepturus (Perciformes: Trichiuridae) from the Persian Gulf

    PubMed Central

    Tamadoni Jahromi, S.; Mohd Noor, S. A.; Pirian, K.; Dehghani, R.; Nazemi, M.; Khazaali, A.

    2016-01-01

    In this study, mitochondrial DNA analysis using 16S ribosomal DNA (rDNA) was performed to investigate the phylogeny relationship of Trichiurus lepturus in the Persian Gulf compared to the other investigated area. The amplification of 16S rDNA resulted in a product of 600 bp in all samples. The results showed that the isolated strain belongs to T. lepturus showing 42 divergence sites among the same reported partial sequences of 16S rRNA gene from the other area (West Atlantic and Indo-Pacific area). Phylogeny results showed that all 18 haplotypes of the species clustered into five clades with reasonably high bootstrap support of values (>64%). Overall, the tree topology for both phylogenetic and phenetic trees for 16S rDNA was similar. Both trees exposed two major clusters, one wholly containing the haplotypes of the T. lepturus species belonging to Indo-Pacific area with two major sister groups including Persian Gulf specimen and the other cleared the Western Atlantic and Japan individuals clustered in another distinct clade supporting the differentiation between the two areas. Phylogenic relationship observed between the Persian Gulf and the other Indo-Pacific Individuals suggested homogeneity between two mentioned areas. PMID:27822250

  3. Mitochondrial DNA Sequence and Lack of Response to Anoxia in the Annual Killifish Austrofundulus limnaeus

    PubMed Central

    Wagner, Josiah T.; Herrejon Chavez, Florisela; Podrabsky, Jason E.

    2016-01-01

    The annual killifish Austrofundulus limnaeus inhabits ephemeral ponds in regions of Venezuela, South America. Permanent populations of A. limnaeus are maintained by production of stress-tolerant embryos that are able to persist in the desiccated sediment. Previous work has demonstrated that A. limnaeus have a remarkable ability to tolerate extended periods of anoxia and desiccating conditions. After considering temperature, A. limnaeus embryos have the highest known tolerance to anoxia when compared to any other vertebrate yet studied. Oxygen is completely essential for the process of oxidative phosphorylation by mitochondria, the intracellular organelle responsible for the majority of adenosine triphosphate production. Thus, understanding the unique properties of A. limnaeus mitochondria is of great interest. In this work, we describe the first complete mitochondrial genome (mtgenome) sequence of a single adult A. limnaeus individual and compare both coding and non-coding regions to several other closely related fish mtgenomes. Mitochondrial features were predicted using MitoAnnotator and polyadenylation sites were predicted using RNAseq mapping. To estimate the responsiveness of A. limnaeus mitochondria to anoxia treatment, we measure relative mitochondrial DNA copy number and total citrate synthase activity in both relatively anoxia-tolerant and anoxia-sensitive embryonic stages. Our cross-species comparative approach identifies unique features of ND1, ND5, ND6, and ATPase-6 that may facilitate the unique phenotype of A. limnaeus embryos. Additionally, we do not find evidence for mitochondrial degradation or biogenesis during anoxia/reoxygenation treatment in A. limnaeus embryos, suggesting that anoxia-tolerant mitochondria do not respond to anoxia in a manner similar to anoxia-sensitive mitochondria. PMID:27630577

  4. Evolution of Repeated Sequence Arrays in the D-Loop Region of Bat Mitochondrial DNA

    PubMed Central

    Wilkinson, G. S.; Mayer, F.; Kerth, G.; Petri, B.

    1997-01-01

    Analysis of mitochondrial DNA control region sequences from 41 species of bats representing 11 families revealed that repeated sequence arrays near the tRNA-Pro gene are present in all vespertilionine bats. Across 18 species tandem repeats varied in size from 78 to 85 bp and contained two to nine repeats. Heteroplasmy ranged from 15% to 63%. Fewer repeats among heteroplasmic than homoplasmic individuals in a species with up to nine repeats indicates selection may act against long arrays. A lower limit of two repeats and more repeats among heteroplasmic than homoplasmic individuals in two species with few repeats suggests length mutations are biased. Significant regressions of heteroplasmy, θ and π, on repeat number further suggest that repeat duplication rate increases with repeat number. Comparison of vespertilionine bat consensus repeats to mammal control region sequences revealed that tandem repeats of similar size, sequence and number also occur in shrews, cats and bighorn sheep. The presence of two conserved protein-binding sequences in all repeat units indicates that convergent evolution has occurred by duplication of functional units. We speculate that D-loop region tandem repeats may provide signal redundancy and a primitive repair mechanism in the event of somatic mutations to these binding sites. PMID:9215906

  5. DNA sequence variation in the mitochondrial control region of red-backed voles (Clethrionomys).

    PubMed

    Matson, C W; Baker, R J

    2001-08-01

    The complete mitochondrial DNA (mtDNA) control region was sequenced for 71 individuals from five species of the rodent genus Clethrionomys both to understand patterns of variation and to explore the existence of previously described domains and other elements. Among species, the control region ranged from 942 to 971 bp in length. Our data were compatible with the proposal of three domains (extended terminal associated sequences [ETAS], central, conserved sequence blocks [CSB]) within the control region. The most conserved region in the control region was the central domain (12% of nucleotide positions variable), whereas in the ETAS and CSB domains, 22% and 40% of nucleotide positions were variable, respectively. Tandem repeats were encountered only in the ETAS domain of Clethrionomys rufocanus. This tandem repeat found in C. rufocanus was 24 bp in length and was located at the 5' end of the control region. Only two of the proposed CSB and ETAS elements appeared to be supported by our data; however, a "CSB1-like" element was also documented in the ETAS domain.

  6. Mitochondrial DNA sequence variation among populations and host races of Lambdina fiscellaria (Gn.) (Lepidoptera: Geometridae).

    PubMed

    Sperling, F A; Raske, A G; Otvos, I S

    1999-02-01

    The hemlock looper, Lambdina fiscellaria (Gn.), is a recurring major forest pest that is widely distributed in North America. Three subspecies (L. f. fiscellaria, L. f. lugubrosa (Hulst) and L. f. somniaria (Hulst)) have been recognized based on larval host or adult pheromone differences, but no consistent morphological differences have been reported. To clarify their taxonomic status, we surveyed mitochondrial DNA (mtDNA) sequence and restriction site variation in two protein coding genes, cytochrome oxidase I and II (COI and COII), in populations across the range of L. fiscellaria. In addition to variation in COI and COII, we found an intergenic spacer region of 20-23 bp located between the tRNA tyrosine gene and the start of COI. Of the 141 specimens of L. fiscellaria assayed, 137 were grouped into two distinct mtDNA lineages, one of which was disproportionately associated with eastern populations and one with western populations. However, single specimens and two populations in eastern Canada had mtDNA resembling that of western populations. Three divergent and rare haplotypes had basal affinities to the two common lineages. The two major lineages of L. fiscellaria were diverged by approximately 2% from each other, as well as from the mtDNA of two outgroup species, L. athasaria (Walker) and L. pellucidaria(G. & R.). The two outgroup species had essentially the same mtDNA and may be conspecific. We interpret the pattern of mtDNA variation within L. fiscellaria as indicating genetic polymorphism within a single species without clear subspecific divisions, rather than evidence of multiple cryptic species.

  7. Sequence analysis of the mitochondrial DNA control region of ciscoes (genus Coregonus): taxonomic implications for the Great Lakes species flock.

    PubMed

    Reed, K M; Dorschner, M O; Todd, T N; Phillips, R B

    1998-09-01

    Sequence variation in the control region (D-loop) of the mitochondrial DNA (mtDNA) was examined to assess the genetic distinctiveness of the shortjaw cisco (Coregonus zenithicus). Individuals from within the Great Lakes Basin as well as inland lakes outside the basin were sampled. DNA fragments containing the entire D-loop were amplified by PCR from specimens of C. zenithicus and the related species C. artedi, C. hoyi, C. kiyi, and C. clupeaformis. DNA sequence analysis revealed high similarity within and among species and shared polymorphism for length variants. Based on this analysis, the shortjaw cisco is not genetically distinct from other cisco species.

  8. Phylogeny of the owlet-nightjars (Aves: Aegothelidae) based on mitochondrial DNA sequence

    USGS Publications Warehouse

    Dumbacher, J.P.; Pratt, T.K.; Fleischer, R.C.

    2003-01-01

    The avian family Aegothelidae (Owlet-nightjars) comprises nine extant species and one extinct species, all of which are currently classified in a single genus, Aegotheles. Owlet-nightjars are secretive nocturnal birds of the South Pacific. They are relatively poorly studied and some species are known from only a few specimens. Furthermore, their confusing morphological variation has made it difficult to cluster existing specimens unambiguously into hierarchical taxonomic units. Here we sample all extant owlet-nightjar species and all but three currently recognized subspecies. We use DNA extracted primarily from museum specimens to obtain mitochondrial gene sequences and construct a molecular phylogeny. Our phylogeny suggests that most species are reciprocally monophyletic, however A. albertisi appears paraphyletic. Our data also suggest splitting A. bennettii into two species and splitting A. insignis and A. tatei as suggested in another recent paper. ?? 2003 Elsevier Science (USA). All rights reserved.

  9. Phylogenetic position of mammoth and Steller's sea cow within Tethytheria demonstrated by mitochondrial DNA sequences.

    PubMed

    Ozawa, T; Hayashi, S; Mikhelson, V M

    1997-04-01

    Here we report DNA sequences from mitochondrial cytochrome b gene segments (1,005 base pairs per species) for the extinct woolly mammoth (Mammuthus primigenius) and Steller's sea cow (Hydrodamalis gigas) and the extant Asian elephant (Elephas maximus), the Western Indian manatee (Trichechus manatus), and the hyrax (Procavia capensis). These molecular data have allowed us to construct the phylogeny for the Tethytheria. Our molecular data resolve the trichotomy between the two species of living elephants and the mammoth and confirm that the mammoth was more closely related to the Asian elephant than to the African elephant. Our data also suggest that the sea cow-dugong divergence was likely as ancient as the dugong-manatee split, and it appears to have been much earlier (22 million years ago) than had been previously estimated (4-8 million years ago) by immunological comparison.

  10. Does behavior reflect phylogeny in swiftlets (Aves: Apodidae)? A test using cytochrome b mitochondrial DNA sequences.

    PubMed Central

    Lee, P L; Clayton, D H; Griffiths, R; Page, R D

    1996-01-01

    Swiftlets are small insectivorous birds, many of which nest in caves and are known to echolocate. Due to a lack of distinguishing morphological characters, the taxonomy of swiftlets is primarily based on the presence or absence of echolocating ability, together with nest characters. To test the reliability of these behavioral characters, we constructed an independent phylogeny using cytochrome b mitochondrial DNA sequences from swiftlets and their relatives. This phylogeny is broadly consistent with the higher classification of swifts but does not support the monophyly of swiftlets. Echolocating swiftlets (Aerodramus) and the nonecholocating "giant swiftlet" (Hydrochous gigas) group together, but the remaining nonecholocating swiftlets belonging to Collocalia are not sister taxa to these swiftlets. While echolocation may be a synapomorphy of Aerodramus (perhaps secondarily lost in Hydrochous), no character of Aerodramus nests showed a statistically significant fit to the molecular phylogeny, indicating that nest characters are not phylogenetically reliable in this group. Images Fig. 1 PMID:8692950

  11. A phylogeny of cockroaches and related insects based on DNA sequence of mitochondrial ribosomal RNA genes.

    PubMed Central

    Kambhampati, S

    1995-01-01

    Cockroaches are among the most ancient winged insects, the earliest fossils dating back to about 400 million years. Several conflicting phylogenies for cockroach families, subfamilies, and genera have been proposed in the past. In addition, the relationship of Cryptocercidae to other cockroach families and the relationship between the cockroach, Cryptocercus punctulatus, and the termite, Mastotermes darwiniensis, have generated debate. In this paper, a phylogeny for cockroaches, mantids, and termites based on DNA sequence of the mitochondrial ribosomal RNA genes is presented. The results indicated that cockroaches are a monophyletic group, whose sister group is Mantoidea. The inferred relationship among cockroach families was in agreement with the presently accepted phylogeny. However, there was only partial congruence at the subfamily and the generic levels. The phylogeny inferred here does not support a close relationship between C. punctulatus and M. darwiniensis. The apparent synapomorphies of these two species are likely a manifestation of convergent evolution because there are similarities in biology and habitat. PMID:7534409

  12. Determination of the melon chloroplast and mitochondrial genome sequences reveals that the largest reported mitochondrial genome in plants contains a significant amount of DNA having a nuclear origin

    PubMed Central

    2011-01-01

    Background The melon belongs to the Cucurbitaceae family, whose economic importance among vegetable crops is second only to Solanaceae. The melon has a small genome size (454 Mb), which makes it suitable for molecular and genetic studies. Despite similar nuclear and chloroplast genome sizes, cucurbits show great variation when their mitochondrial genomes are compared. The melon possesses the largest plant mitochondrial genome, as much as eight times larger than that of other cucurbits. Results The nucleotide sequences of the melon chloroplast and mitochondrial genomes were determined. The chloroplast genome (156,017 bp) included 132 genes, with 98 single-copy genes dispersed between the small (SSC) and large (LSC) single-copy regions and 17 duplicated genes in the inverted repeat regions (IRa and IRb). A comparison of the cucumber and melon chloroplast genomes showed differences in only approximately 5% of nucleotides, mainly due to short indels and SNPs. Additionally, 2.74 Mb of mitochondrial sequence, accounting for 95% of the estimated mitochondrial genome size, were assembled into five scaffolds and four additional unscaffolded contigs. An 84% of the mitochondrial genome is contained in a single scaffold. The gene-coding region accounted for 1.7% (45,926 bp) of the total sequence, including 51 protein-coding genes, 4 conserved ORFs, 3 rRNA genes and 24 tRNA genes. Despite the differences observed in the mitochondrial genome sizes of cucurbit species, Citrullus lanatus (379 kb), Cucurbita pepo (983 kb) and Cucumis melo (2,740 kb) share 120 kb of sequence, including the predicted protein-coding regions. Nevertheless, melon contained a high number of repetitive sequences and a high content of DNA of nuclear origin, which represented 42% and 47% of the total sequence, respectively. Conclusions Whereas the size and gene organisation of chloroplast genomes are similar among the cucurbit species, mitochondrial genomes show a wide variety of sizes, with a non

  13. Genetic structure of Florida green turtle rookeries as indicated by mitochondrial DNA control region sequences

    USGS Publications Warehouse

    Shamblin, Brian M.; Bagley, Dean A.; Ehrhart, Llewellyn M.; Desjardin, Nicole A.; Martin, R. Erik; Hart, Kristen M.; Naro-Maciel, Eugenia; Rusenko, Kirt; Stiner, John C.; Sobel, Debra; Johnson, Chris; Wilmers, Thomas; Wright, Laura J.; Nairn, Campbell J.

    2014-01-01

    Green turtle (Chelonia mydas) nesting has increased dramatically in Florida over the past two decades, ranking the Florida nesting aggregation among the largest in the Greater Caribbean region. Individual beaches that comprise several hundred kilometers of Florida’s east coast and Keys support tens to thousands of nests annually. These beaches encompass natural to highly developed habitats, and the degree of demographic partitioning among rookeries was previously unresolved. We characterized the genetic structure of ten Florida rookeries from Cape Canaveral to the Dry Tortugas through analysis of 817 base pair mitochondrial DNA (mtDNA) control region sequences from 485 nesting turtles. Two common haplotypes, CM-A1.1 and CM-A3.1, accounted for 87 % of samples, and the haplotype frequencies were strongly partitioned by latitude along Florida’s Atlantic coast. Most genetic structure occurred between rookeries on either side of an apparent genetic break in the vicinity of the St. Lucie Inlet that separates Hutchinson Island and Jupiter Island, representing the finest scale at which mtDNA structure has been documented in marine turtle rookeries. Florida and Caribbean scale analyses of population structure support recognition of at least two management units: central eastern Florida and southern Florida. More thorough sampling and deeper sequencing are necessary to better characterize connectivity among Florida green turtle rookeries as well as between the Florida nesting aggregation and others in the Greater Caribbean region.

  14. Phylogenetic relationships between Hapalemur species and subspecies based on mitochondrial DNA sequences

    PubMed Central

    Fausser, Jean-Luc; Prosper, Prosper; Donati, Giuseppe; Ramanamanjato, Jean-Baptiste; Rumpler, Yves

    2002-01-01

    Background Phylogenetic relationships of the genus Hapalemur remains controversial, particularly within the Hapalemur griseus species group. In order to obtain more information on the taxonomic status within this genus, and particularly in the cytogenetic distinct subspecies group of Hapalemur griseus, 357 bp sequence of cytochrome b and 438 bp of 12S mitochondrial DNAs were analyzed on a sample of animals captured in areas extending from the north to the south-east of Madagascar. This sample covers all cytogenetically defined types recognized of the genus Hapalemur. Results Phylogenetic trees and distances analyses demonstrate a first emergence of Hapalemur simus followed by H. aureus which is the sister clade of the H. griseus subspecies. Hapalemur griseus is composed of 4 subspecies separated into two clades. The first contains H. g. griseus, H. g. alaotrensis and H. g. occidentalis. The second consists of H. g. meridionalis. A new chromosomal polymorphic variant from the region of Ranomafana, H. griseus ssp, has been analysed and was found in both clades. Conclusions Our results support the raising of H. g. meridionalis to the specific rank H. meridionalis, while neither cytogenetic nor molecular evidences support the raising of H. g. alaotrensis to a species rank despite its morphological characteristics. The new cytotype H. g. ssp which has been previously characterized by cytogenetic studies contains animals clustering either with the group of Hapalemur griseus griseus or with that of Hapalemur meridionalis. This suggests the existence of an ancestral polymorphism or an introgression of mitochondrial DNA between subspecies. PMID:11914128

  15. Assessing Mitochondrial DNA Variation and Copy Number in Lymphocytes of ~2,000 Sardinians Using Tailored Sequencing Analysis Tools

    PubMed Central

    Ding, Jun; Sidore, Carlo; Butler, Thomas J.; Wing, Mary Kate; Qian, Yong; Meirelles, Osorio; Busonero, Fabio; Tsoi, Lam C.; Maschio, Andrea; Angius, Andrea; Kang, Hyun Min; Nagaraja, Ramaiah; Cucca, Francesco; Abecasis, Gonçalo R.; Schlessinger, David

    2015-01-01

    DNA sequencing identifies common and rare genetic variants for association studies, but studies typically focus on variants in nuclear DNA and ignore the mitochondrial genome. In fact, analyzing variants in mitochondrial DNA (mtDNA) sequences presents special problems, which we resolve here with a general solution for the analysis of mtDNA in next-generation sequencing studies. The new program package comprises 1) an algorithm designed to identify mtDNA variants (i.e., homoplasmies and heteroplasmies), incorporating sequencing error rates at each base in a likelihood calculation and allowing allele fractions at a variant site to differ across individuals; and 2) an estimation of mtDNA copy number in a cell directly from whole-genome sequencing data. We also apply the methods to DNA sequence from lymphocytes of ~2,000 SardiNIA Project participants. As expected, mothers and offspring share all homoplasmies but a lesser proportion of heteroplasmies. Both homoplasmies and heteroplasmies show 5-fold higher transition/transversion ratios than variants in nuclear DNA. Also, heteroplasmy increases with age, though on average only ~1 heteroplasmy reaches the 4% level between ages 20 and 90. In addition, we find that mtDNA copy number averages ~110 copies/lymphocyte and is ~54% heritable, implying substantial genetic regulation of the level of mtDNA. Copy numbers also decrease modestly but significantly with age, and females on average have significantly more copies than males. The mtDNA copy numbers are significantly associated with waist circumference (p-value = 0.0031) and waist-hip ratio (p-value = 2.4×10-5), but not with body mass index, indicating an association with central fat distribution. To our knowledge, this is the largest population analysis to date of mtDNA dynamics, revealing the age-imposed increase in heteroplasmy, the relatively high heritability of copy number, and the association of copy number with metabolic traits. PMID:26172475

  16. Mitochondrial DNA Sequence Divergence among Meloidogyne incognita, Romanomermis culicivorax, Ascaris suum, and Caenorhabditis elegans

    PubMed Central

    Powers, T. O.; Harris, T. S.; Hyman, B. C.

    1993-01-01

    Mitochondrial DNA sequences were obtained from the NADH dehydrogenase subunit 3 (ND3), large rRNA, and cytochrome b genes from Meloidogyne incognita and Romanomermis culicivorax. Both species show considerable genetic distance within these same genes when compared with Caenorhabditis elegans or Ascaris suum, two species previously analyzed. Caenorhabditis, Ascaris, and Meloidogyne were selected as representatives of three subclasses in the nematode class Secernentea: Rhabditia, Spiruria, and Diplogasteria, respectively. Romanomermis served as a representative out-group of the class Adenophorea. The divergence between the phytoparasitic lineage (represented by Meloidogyne) and the three other species is so great that virtually every variable position in these genes appears to have accumulated multiple mutations, obscuring the phylogenetic information obtainable from these comparisons. The 39 and 42% amino acid similarity between the M. incognita and C. elegans ND3 and cytochrome b coding sequences, respectively, are approximately the same as those of C. elegans-mouse comparisons for the same genes (26 and 44%). This discovery calls into question the feasibility of employing cloned C. elegans probes as reagents to isolate phytoparasitic nematode genes. The genetic distance between the phytoparasitic nematode lineage and C. elegans markedly contrasts with the 79% amino acid similarity between C. elegans and A. suum for the same sequences. The molecular data suggest that Caenorhabditis and Ascaris belong to the same subclass. PMID:19279810

  17. Phylogeography and Pleistocene refugia of the adder (Vipera berus) as inferred from mitochondrial DNA sequence data.

    PubMed

    Ursenbacher, S; Carlsson, M; Helfer, V; Tegelström, H; Fumagalli, L

    2006-10-01

    In order to contribute to the debate about southern glacial refugia used by temperate species and more northern refugia used by boreal or cold-temperate species, we examined the phylogeography of a widespread snake species (Vipera berus) inhabiting Europe up to the Arctic Circle. The analysis of the mitochondrial DNA (mtDNA) sequence variation in 1043 bp of the cytochrome b gene and in 918 bp of the noncoding control region was performed with phylogenetic approaches. Our results suggest that both the duplicated control region and cytochrome b evolve at a similar rate in this species. Phylogenetic analysis showed that V. berus is divided into three major mitochondrial lineages, probably resulting from an Italian, a Balkan and a Northern (from France to Russia) refugial area in Eastern Europe, near the Carpathian Mountains. In addition, the Northern clade presents an important substructure, suggesting two sequential colonization events in Europe. First, the continent was colonized from the three main refugial areas mentioned above during the Lower-Mid Pleistocene. Second, recolonization of most of Europe most likely originated from several refugia located outside of the Mediterranean peninsulas (Carpathian region, east of the Carpathians, France and possibly Hungary) during the Mid-Late Pleistocene, while populations within the Italian and Balkan Peninsulas fluctuated only slightly in distribution range, with larger lowland populations during glacial times and with refugial mountain populations during interglacials, as in the present time. The phylogeographical structure revealed in our study suggests complex recolonization dynamics of the European continent by V. berus, characterized by latitudinal as well as altitudinal range shifts, driven by both climatic changes and competition with related species.

  18. Extreme-Depth Re-sequencing of Mitochondrial DNA Finds No Evidence of Paternal Transmission in Humans.

    PubMed

    Pyle, Angela; Hudson, Gavin; Wilson, Ian J; Coxhead, Jonathan; Smertenko, Tania; Herbert, Mary; Santibanez-Koref, Mauro; Chinnery, Patrick F

    2015-05-01

    Recent reports have questioned the accepted dogma that mammalian mitochondrial DNA (mtDNA) is strictly maternally inherited. In humans, the argument hinges on detecting a signature of inter-molecular recombination in mtDNA sequences sampled at the population level, inferring a paternal source for the mixed haplotypes. However, interpreting these data is fraught with difficulty, and direct experimental evidence is lacking. Using extreme-high depth mtDNA re-sequencing up to ~1.2 million-fold coverage, we find no evidence that paternal mtDNA haplotypes are transmitted to offspring in humans, thus excluding a simple dilution mechanism for uniparental transmission of mtDNA present in all healthy individuals. Our findings indicate that an active mechanism eliminates paternal mtDNA which likely acts at the molecular level.

  19. Extreme-Depth Re-sequencing of Mitochondrial DNA Finds No Evidence of Paternal Transmission in Humans

    PubMed Central

    Pyle, Angela; Hudson, Gavin; Wilson, Ian J.; Coxhead, Jonathan; Smertenko, Tania; Herbert, Mary; Santibanez-Koref, Mauro; Chinnery, Patrick F.

    2015-01-01

    Recent reports have questioned the accepted dogma that mammalian mitochondrial DNA (mtDNA) is strictly maternally inherited. In humans, the argument hinges on detecting a signature of inter-molecular recombination in mtDNA sequences sampled at the population level, inferring a paternal source for the mixed haplotypes. However, interpreting these data is fraught with difficulty, and direct experimental evidence is lacking. Using extreme-high depth mtDNA re-sequencing up to ~1.2 million-fold coverage, we find no evidence that paternal mtDNA haplotypes are transmitted to offspring in humans, thus excluding a simple dilution mechanism for uniparental transmission of mtDNA present in all healthy individuals. Our findings indicate that an active mechanism eliminates paternal mtDNA which likely acts at the molecular level. PMID:25973765

  20. Mitochondrial DNA sequence variation and phylogeography of Pimelia darkling beetles on the island of Tenerife (Canary Islands).

    PubMed

    Juan, C; Ibrahim, K M; Oromi, P; Hewitt, G M

    1996-12-01

    Four morphological taxa of the beetle genus Pimelia (Coleoptera, Tenebrionidae) are known to exist on the Atlantic island of Tenerife. We have obtained DNA sequences for 61 individuals from these taxa across the island for a 200 bp long fragment of the mitochondrial COI gene. In addition, a restriction site polymorphism in the nuclear rRNA ITS-1 sequence was identified and screened in a sample of these individuals using the enzyme Kpn2I. The results were analysed using approaches which allow inferences to be made about the population genetic structure and the mitochondrial genealogy of these closely related beetles. The mtDNA haplotype distribution and the estimates of sequence divergence revealed the presence of two ancient mtDNA lineages which coincide with the disjunct volcanic evolution of the island. The ITS-1 polymorphism was found to be diagnostic of these two lineages. However, the morphological and mitochondrial phylogenies were found to be discordant. We argue that this is possibly the result of rapid morphological change, produced by selection in different habitats, which has been recently superimposed on an older mitochondrial DNA divergence.

  1. Phylogenetic relationships among major species of japanese coleoid cephalopods (Mollusca: Cephalopoda) using three mitochondrial DNA sequences.

    PubMed

    Takumiya, Mikio; Kobayashi, Mari; Tsuneki, Kazuhiko; Furuya, Hidetaka

    2005-02-01

    Phylogenetic relationships among 36 species of major coleoid cephalopods from Japanese waters were studied using partial sequences of three mitochondrial genes, 16S rDNA, 12S rDNA, and cytochrome c oxidase subunit I gene. Octopoda and Decapoda were monophylic groups. Within Sepioidea, Sepiadariidae and Sepiolidae were not closely related to Sepiidae, but rather related to Teuthoidea. Sepiidae with a distinct calcareous shell formed a single cluster. Myopsida was closely related to Oegopsida. Within Octopoda, Opisthoteuthis depressa and Argonauta argo diverged earlier than Octopodiidae. The common octopuses in Japanese waters were separated into three clusters. The first cluster occupied a basal position, and includes large-sized octopuses, such as Enteroctopus dofleini and Octopus (Paroctopus) conispadiceus from the continental shelf and upper slope. The second cluster consisted of long-armed octopuses, such as O. ornatus, O. minor, and O. sasakii. The third cluster contained small- to medium-sized octopus, such as Amphioctopus fangsiao, A. areolatus, O. cyaneus, and O. vulgaris, in which several species possess ocelli on the web. The second cluster formed the sister group to the third cluster.

  2. Complete mitochondrial DNA genome sequences of extinct birds: ratite phylogenetics and the vicariance biogeography hypothesis.

    PubMed

    Haddrath, O; Baker, A J

    2001-05-07

    The ratites have stimulated much debate as to how such large flightless birds came to be distributed across the southern continents, and whether they are a monophyletic group or are composed of unrelated lineages that independently lost the power of flight. Hypotheses regarding the relationships among taxa differ for morphological and molecular data sets, thus hindering attempts to test whether plate tectonic events can explain ratite biogeography. Here, we present the complete mitochondrial DNA genomes of two extinct moas from New Zealand, along with those of five extant ratites (the lesser rhea, the ostrich, the great spotted kiwi, the emu and the southern cassowary and two tinamous from different genera. The non-stationary base composition in these sequences violates the assumptions of most tree-building methods. When this bias is corrected using neighbour-joining with log-determinant distances and non-homogeneous maximum likelihood, the ratites are found to be monophlyletic, with moas basal, as in morphological trees. The avian sequences also violate a molecular clock, so we applied a non-parametric rate smoothing algorithm, which minimizes ancestor-descendant local rate changes, to date nodes in the tree. Using this method, most of the major ratite lineages fit the vicariance biogeography hypothesis, the exceptions being the ostrich and the kiwi, which require dispersal to explain their present distribution.

  3. Molecular phylogenetic and dating analyses using mitochondrial DNA sequences of eyelid geckos (Squamata: Eublepharidae).

    PubMed

    Jonniaux, Pierre; Kumazawa, Yoshinori

    2008-01-15

    Mitochondrial DNA sequences of approximately 2.3 kbp including the complete NADH dehydrogenase subunit 2 gene and its flanking genes, as well as parts of 12S and 16S rRNA genes were determined from major species of the eyelid gecko family Eublepharidae sensu [Kluge, A.G. 1987. Cladistic relationships in the Gekkonoidea (Squamata, Sauria). Misc. Publ. Mus. Zool. Univ. Michigan 173, 1-54.]. In contrast to previous morphological studies, phylogenetic analyses based on these sequences supported that Eublepharidae and Gekkonidae form a sister group with Pygopodidae, raising the possibility of homoplasious character change in some key features of geckos, such as reduction of movable eyelids and innovation of climbing toe pads. The phylogenetic analyses also provided a well-resolved tree for relationships between the eublepharid species. The Bayesian estimation of divergence times without assuming the molecular clock suggested the Jurassic divergence of Eublepharidae from Gekkonidae and radiations of most eublepharid genera around the Cretaceous. These dating results appeared to be robust against some conditional changes for time estimation, such as gene regions used, taxon representation, and data partitioning. Taken together with geological evidence, these results support the vicariant divergence of Eublepharidae and Gekkonidae by the breakup of Pangea into Laurasia and Gondwanaland, and recent dispersal of two African eublepharid genera from Eurasia to Africa after these landmasses were connected in the Early Miocene.

  4. Complete mitochondrial DNA sequence of the endangered fish (Bahaba taipingensis): Mitogenome characterization and phylogenetic implications

    PubMed Central

    Zhao, Linlin; Gao, Tianxiang; Lu, Weihua

    2015-01-01

    Abstract To understand the systematic status of Bahaba taipingensis within Sciaenidae, the complete mitochondrial genome (mitogenome) sequence of Chinese bahaba has recently been determined by long PCR and primer walking methods. The complete mitochondrial genome is 16500 bp in length and contains 37 mitochondrial genes (13 protein-coding genes, 2 ribosomal RNA genes and 22 transfer RNA genes) as well as a control region (CR) as other bony fishes. Within the control region, we identified the extended termination associated sequence domain (ETAS), the central conserved sequence block domain (CSB-D, SCB-E and CSB-F) and the conserved sequence block domain (CSB-1, CSB-2 and CSB-3). Phylogenetic analyses revealed that Bahaba taipingensis is more closely related to Pseudosciaeniae than Argyrosominae and Sciaeninae. Additionally, Bahaba taipingensis is the sister taxon of Miichthys miiuy, and those two are sister to Collichthys plus Larimichthys. PMID:26798311

  5. Complete mitochondrial DNA sequence of the endangered fish (Bahaba taipingensis): Mitogenome characterization and phylogenetic implications.

    PubMed

    Zhao, Linlin; Gao, Tianxiang; Lu, Weihua

    2015-01-01

    To understand the systematic status of Bahaba taipingensis within Sciaenidae, the complete mitochondrial genome (mitogenome) sequence of Chinese bahaba has recently been determined by long PCR and primer walking methods. The complete mitochondrial genome is 16500 bp in length and contains 37 mitochondrial genes (13 protein-coding genes, 2 ribosomal RNA genes and 22 transfer RNA genes) as well as a control region (CR) as other bony fishes. Within the control region, we identified the extended termination associated sequence domain (ETAS), the central conserved sequence block domain (CSB-D, SCB-E and CSB-F) and the conserved sequence block domain (CSB-1, CSB-2 and CSB-3). Phylogenetic analyses revealed that Bahaba taipingensis is more closely related to Pseudosciaeniae than Argyrosominae and Sciaeninae. Additionally, Bahaba taipingensis is the sister taxon of Miichthys miiuy, and those two are sister to Collichthys plus Larimichthys.

  6. [Origin and genetic diversity of Mongolian and Chinese sheep using mitochondrial DNA D-loop sequences].

    PubMed

    Luo, Yu-Zhu; Cheng, Shu-Ru; Batsuuri, Lkhagva; Badamdorj, D; Olivier, Hanotte; Han, Jian-Lin

    2005-12-01

    To determine the origin and gene diversity of the Chinese and Mongolian domestic sheep, a partial fragment of mitochondrial DNA D-loop was sequenced for total number of 314 individuals from nine Chinese sheep populations and 11 Mongolian sheep populations. The results show no difference in nucleotide composition between Chinese and Mongolian sheep mtDNA D-loop sequences. However, more variables were identified in Mongolian sheep (26.85% of the sites) than that in Chinese sheep (24.22%). In China, mtDNA haplotype diversity was the highest in Qinghai Tibetan sheep, followed then by Gansu Tibetan sheep, Gansu Alpine Merino, Qinghai Merino, Gannan Tibetan sheep, Small-tailed Han sheep, Tan sheep, Hu sheep and Minxian Black Fur sheep. In Mongolian sheep, mtDNA haplotype diversity was the highest in Bayad and Baidrag populations and the lowest in the Gobi-Altai population. In general, Mongolian sheep have a richer genetic diversity than the Chinese ones with larger number of haplotypes (86.06% (142/165) versus 78.83% (108/137)), higher haplotype diversity (Hd; 0.976 versus 0.936), higher nucleotide diversity (Pi (pi); 0. 036 versus 0.034) and higher average number of nucleotide differences (k; 23.50 versus 22.48). Phylogenetic analysis of the 217 haplotypes identified in both Mongolian and Chinese sheep supported the same origin of their domestication with three distinct maternal lineages defined as major haplotypes A, B and C, of which haplotype A are the commonest in all Chinese sheep populations and in the majority of Mongolian sheep populations (9/11) with an average frequency of 58.73%, followed by haplotype B present in eight of Chinese population and in all Mongolian sheep populations with an average frequency of 24.68%, and haplotype C present in eight Chinese and in 10 Mongolian sheep populations with an average frequency of 16.59%. Further network analysis of the phylogenetic relationship of the 87 haplotypes identified from 91 sequences retrieved from Gen

  7. [Variability of nucleotide sequences of the mitochondrial DNA cytochrome c gene in dolly varden and taranetz char].

    PubMed

    Radchenko, O A; Derenko, M V; Maliarchuk, B A

    2000-07-01

    Nucleotide sequence of the 307-bp fragment of the mitochondrial DNA cytochrome b gene was determined in representatives of the three species of the Salvelinus genus, specifically, dolly varden char (S. malma), taranetz char (S. taranetzi), and white-spotted char (S. leucomaenis). These results pointed to a high level of mitochondrial DNA (mtDNA) divergence between white-spotted char and dolly varden char, on the one hand, and taranetz char, on the other (the mean d value was 5.45%). However, the divergence between the dolly varden char and taranetz char was only 0.81%, which is comparable with the level of intraspecific divergence in the dolly varden char (d = 0.87%). It was shown that the dolly varden char mitochondrial gene pool contained DNA lineages differing from the main mtDNA pool at least in the taranetz char-specific mitochondrial lineages. One of these dolly varden char mtDNA lineages was characterized by the presence of the restriction endonuclease MspI-D variant of the cytochrome b gene. This lineage was widely distributed in the Chukotka populations but it was not detected in the Yana River (Okhotsk sea) populations. These findings suggest that dolly varden char has a more ancient evolutionary lineage, diverging from the common ancestor earlier than did taranetz char.

  8. Complete nucleotide and derived amino acid sequence of cDNA encoding the mitochondrial uncoupling protein of rat brown adipose tissue: lack of a mitochondrial targeting presequence.

    PubMed Central

    Ridley, R G; Patel, H V; Gerber, G E; Morton, R C; Freeman, K B

    1986-01-01

    A cDNA clone spanning the entire amino acid sequence of the nuclear-encoded uncoupling protein of rat brown adipose tissue mitochondria has been isolated and sequenced. With the exception of the N-terminal methionine the deduced N-terminus of the newly synthesized uncoupling protein is identical to the N-terminal 30 amino acids of the native uncoupling protein as determined by protein sequencing. This proves that the protein contains no N-terminal mitochondrial targeting prepiece and that a targeting region must reside within the amino acid sequence of the mature protein. Images PMID:3012461

  9. A new hypothesis of squamate evolutionary relationships from nuclear and mitochondrial DNA sequence data

    SciTech Connect

    Townsend, Ted M.; Larson, Allan; Louis, Edward; Macey, J. Robert

    2004-05-19

    Squamate reptiles serve as model systems for evolutionary studies of a variety of morphological and behavioral traits, and phylogeny is crucial to many generalizations derived from such studies. Specifically, the traditional dichotomy between Iguania and Scleroglossa has been correlated with major evolutionary shifts within Squamata. We present a molecular phylogenetic study of squamates using DNA sequence data from the nuclear genes RAG-1 and c-mos and the mitochondrial ND2 region, sampling all major clades and most major subclades. Monophyly of Iguania, Anguimorpha, and almost all currently recognized squamate families is strongly supported. However, monophyly is rejected for Scleroglossa, Varanoidea, and several other higher taxa, and Iguania is highly nested within Squamata. Limblessness evolved independently in snakes, dibamids, and amphisbaenians, suggesting widespread morphological convergence or parallelism in limbless, burrowing forms. Amphisbaenians are the sister group of lacertids, and snakes are grouped with iguanians and anguimorphs. Dibamids diverged early in squamate evolutionary history. Xantusiidae is the sister taxon of Cordylidae. Studies of functional tongue morphology and feeding mode have found significant differences between Scleroglossa and Iguania, and our finding of a nonmonophyletic Scleroglossa and a highly nested Iguania suggest that similar states evolved separately in Sphenodon and Iguania, and that jaw prehension is the ancestral feeding mode in squamates.

  10. Mitochondrial DNA in the sea urchin Arbacia lixula: nucleotide sequence differences between two polymorphic molecules indicate asymmetry of mutations.

    PubMed

    De Giorgi, C; De Luca, F; Saccone, C

    1991-07-22

    Two polymorphic forms of mitochondrial DNA (mtDNA) extracted from Arbacia lixula eggs were cloned and the nucleotide sequences of specific regions determined. A comparison of the sequences of the sense strand of the two molecules demonstrates that all the differences are transitions and only of the A----G type. A change such as G----A (or A----G) on the sense mtDNA strand results from either a direct G----A (or A----G) mutation on that strand or a C----T (or T----C) on the complementary strand. None of the C----T (or T----C) changes were detected on the sense strand, which implies that the A----G mutation bias on the sense strand is not reversed for the other strand. Our observation indicates the existence of mechanisms acting asymmetrically on the two mtDNA strands, possibly during mtDNA replication.

  11. The complete mitochondrial DNA sequences of Nephroselmis olivacea and Pedinomonas minor. Two radically different evolutionary patterns within green algae.

    PubMed Central

    Turmel, M; Lemieux, C; Burger, G; Lang, B F; Otis, C; Plante, I; Gray, M W

    1999-01-01

    Green plants appear to comprise two sister lineages, Chlorophyta (classes Chlorophyceae, Ulvophyceae, Trebouxiophyceae, and Prasinophyceae) and Streptophyta (Charophyceae and Embryophyta, or land plants). To gain insight into the nature of the ancestral green plant mitochondrial genome, we have sequenced the mitochondrial DNAs (mtDNAs) of Nephroselmis olivacea and Pedinomonas minor. These two green algae are presumptive members of the Prasinophyceae. This class is thought to include descendants of the earliest diverging green algae. We find that Nephroselmis and Pedinomonas mtDNAs differ markedly in size, gene content, and gene organization. Of the green algal mtDNAs sequenced so far, that of Nephroselmis (45,223 bp) is the most ancestral (minimally diverged) and occupies the phylogenetically most basal position within the Chlorophyta. Its repertoire of 69 genes closely resembles that in the mtDNA of Prototheca wickerhamii, a later diverging trebouxiophycean green alga. Three of the Nephroselmis genes (nad10, rpl14, and rnpB) have not been identified in previously sequenced mtDNAs of green algae and land plants. In contrast, the 25,137-bp Pedinomonas mtDNA contains only 22 genes and retains few recognizably ancestral features. In several respects, including gene content and rate of sequence divergence, Pedinomonas mtDNA resembles the reduced mtDNAs of chlamydomonad algae, with which it is robustly affiliated in phylogenetic analyses. Our results confirm the existence of two radically different patterns of mitochondrial genome evolution within the green algae. PMID:10488238

  12. Major patterns of higher teleostean phylogenies: a new perspective based on 100 complete mitochondrial DNA sequences.

    PubMed

    Miya, Masaki; Takeshima, Hirohiko; Endo, Hiromitsu; Ishiguro, Naoya B; Inoue, Jun G; Mukai, Takahiko; Satoh, Takashi P; Yamaguchi, Motoomi; Kawaguchi, Akira; Mabuchi, Kohji; Shirai, Shigeru M; Nishida, Mutsumi

    2003-01-01

    A recent preliminary study using complete mitochondrial DNA sequences from 48 species of teleosts has suggested that higher teleostean phylogenies should be reinvestigated on the basis of more intensive taxonomic sampling. As a second step towards the resolution of higher teleostean phylogenies, which have been described as the "(unresolved) bush at the top of the tree," we reanalyzed their relationships using mitogenomic data from 100 purposefully chosen species that fully represented all of the higher teleostean orders, except for the Batrachoidiformes. Unweighted and weighted maximum parsimony analyses were conducted with the data set that comprised concatenated nucleotide sequences from 12 protein-coding genes (excluding 3rd codon positions) and 21 transfer RNA (tRNA) genes (stem regions only) from each species. The resultant trees were well resolved and largely congruent, with most internal branches being supported by high statistical values. All major, comprehensive groups above ordinal level as currently defined in higher teleosts (with the exception of the Neoteleostei and several monotypic groups), such as the Eurypterygii, Ctenosquamata, Acanthomorpha, Paracanthopterygii, Acanthopterygii, and Percomorpha, appeared to be nonmonophyletic in the present tree. Such incongruities largely resulted from differences in the placement and/or limits of the orders Ateleopodiformes, Lampridiformes, Polymixiiformes, Ophidiiformes, Lophiiformes, Beryciformes, Stephanoberyciformes, and Zeiformes, long-standing problematic taxa in systematic ichthyology. Of these, the resulting phylogenetic positions of the Ophidiiformes and Lophiiformes were totally unexpected, because, although they have consistently been considered relatively primitive groups within higher teleosts (Paracanthopterygii), they were confidently placed within a crown group of teleosts, herein called the Percomorpha. It should be noted that many unexpected, but highly supported relationships were found

  13. Repetitive transpositions of mitochondrial DNA sequences to the nucleus during the radiation of horseshoe bats (Rhinolophus, Chiroptera).

    PubMed

    Shi, Huizhen; Dong, Ji; Irwin, David M; Zhang, Shuyi; Mao, Xiuguang

    2016-05-01

    Transposition of mitochondrial DNA into the nucleus, which gives rise to nuclear mitochondrial DNAs (NUMTs), has been well documented in eukaryotes. However, very few studies have assessed the frequency of these transpositions during the evolutionary history of a specific taxonomic group. Here we used the horseshoe bats (Rhinolophus) as a case study to determine the frequency and relative timing of nuclear transfers of mitochondrial control region sequences. For this, phylogenetic and coalescent analyzes were performed on NUMTs and authentic mtDNA sequences generated from eight horseshoe bat species. Our results suggest at least three independent transpositions, including two ancient and one more recent, during the evolutionary history of Rhinolophus. The two ancient transpositions are represented by the NUMT-1 and -2 clades, with each clade consisting of NUMTs from almost all studied species but originating from different portions of the mtDNA genome. Furthermore, estimates of the most recent common ancestor for each clade corresponded to the time of the initial diversification of this genus. The recent transposition is represented by NUMT-3, which was discovered only in a specific subgroup of Rhinolophus and exhibited a close relationship to its mitochondrial counterpart. Our similarity searches of mtDNA in the R. ferrumequinum genome confirmed the presence of NUMT-1 and NUMT-2 clade sequences and, for the first time, assessed the extent of NUMTs in a bat genome. To our knowledge, this is the first study to report on the frequency of transpositions of mtDNA occurring before the common ancestry of a genus.

  14. Sequence analysis of the mitochondrial DNA control region of ciscoes (genus Coregonus): Taxonomic implications for the Great Lakes species flock

    USGS Publications Warehouse

    Reed, Kent M.; Dorschner, Michael O.; Todd, Thomas N.; Phillips, Ruth B.

    1998-01-01

    Sequence variation in the control region (D-loop) of the mitochondrial DNA (mtDNA) was examined to assess the genetic distinctiveness of the shortjaw cisco (Coregonus zenithicus). Individuals from within the Great Lakes Basin as well as inland lakes outside the basin were sampled. DNA fragments containing the entire D-loop were amplified by PCR from specimens ofC. zenithicus and the related species C. artedi, C. hoyi, C. kiyi, and C. clupeaformis. DNA sequence analysis revealed high similarity within and among species and shared polymorphism for length variants. Based on this analysis, the shortjaw cisco is not genetically distinct from other cisco species.

  15. Dna Sequencing

    DOEpatents

    Tabor, Stanley; Richardson, Charles C.

    1995-04-25

    A method for sequencing a strand of DNA, including the steps off: providing the strand of DNA; annealing the strand with a primer able to hybridize to the strand to give an annealed mixture; incubating the mixture with four deoxyribonucleoside triphosphates, a DNA polymerase, and at least three deoxyribonucleoside triphosphates in different amounts, under conditions in favoring primer extension to form nucleic acid fragments complementory to the DNA to be sequenced; labelling the nucleic and fragments; separating them and determining the position of the deoxyribonucleoside triphosphates by differences in the intensity of the labels, thereby to determine the DNA sequence.

  16. Sequence analysis of the canine mitochondrial DNA control region from shed hair samples in criminal investigations.

    PubMed

    Berger, C; Berger, B; Parson, W

    2012-01-01

    In recent years, evidence from domestic dogs has increasingly been analyzed by forensic DNA testing. Especially, canine hairs have proved most suitable and practical due to the high rate of hair transfer occurring between dogs and humans. Starting with the description of a contamination-free sample handling procedure, we give a detailed workflow for sequencing hypervariable segments (HVS) of the mtDNA control region from canine evidence. After the hair material is lysed and the DNA extracted by Phenol/Chloroform, the amplification and sequencing strategy comprises the HVS I and II of the canine control region and is optimized for DNA of medium-to-low quality and quantity. The sequencing procedure is based on the Sanger Big-dye deoxy-terminator method and the separation of the sequencing reaction products is performed on a conventional multicolor fluorescence detection capillary electrophoresis platform. Finally, software-aided base calling and sequence interpretation are addressed exemplarily.

  17. Extensive mitochondrial genome rearrangements between Cerithioidea and Hypsogastropoda (Mollusca; Caenogastropoda) as determined from the partial nucleotide sequences of the mitochondrial DNA of Cerithidea djadjariensis and Batillaria cumingi.

    PubMed

    Kojima, Shigeaki

    2010-06-01

    Partial nucleotide sequences ( approximately 8000 bp) of the mitochondrial DNA of two cerithioidean gastropod species-Cerithidea djadjariensis and Batillaria cumingi-were determined. The order of mitochondrial genes (eight protein genes, two ribosomal RNA genes, and nine transfer RNA genes) was identical between these two species. and remarkably different from the previously reported order in other gastropods. The results indicate that the genome structure of the common ancestor of Cerithioidea and its sister group, Hypsogastropoda, is almost identical to that of the common ancestor of Gastropoda; moreover, independent mitochondrial genome rearrangements were identified between the lineages of Cerithioidea and Hypsogastropoda. The rearrangements within Cerithioidea can be explained by the inversion of a single tRNA gene, two translocations of a single tRNA gene, and three translocations of a genome fragment containing a tRNA gene and protein-coding gene(s).

  18. Length heterogeneity at conserved sequence block 2 in human mitochondrial DNA acts as a rheostat for RNA polymerase POLRMT activity

    PubMed Central

    Tan, Benedict G.; Wellesley, Frederick C.; Savery, Nigel J.; Szczelkun, Mark D.

    2016-01-01

    The guanine (G)-tract of conserved sequence block 2 (CSB 2) in human mitochondrial DNA can result in transcription termination due to formation of a hybrid G-quadruplex between the nascent RNA and the nontemplate DNA strand. This structure can then influence genome replication, stability and localization. Here we surveyed the frequency of variation in sequence identity and length at CSB 2 amongst human mitochondrial genomes and used in vitro transcription to assess the effects of this length heterogeneity on the activity of the mitochondrial RNA polymerase, POLRMT. In general, increased G-tract length correlated with increased termination levels. However, variation in the population favoured CSB 2 sequences which produced efficient termination while particularly weak or strong signals were avoided. For all variants examined, the 3′ end of the transcripts mapped to the same downstream sequences and were prevented from terminating by addition of the transcription factor TEFM. We propose that CSB 2 length heterogeneity allows variation in the efficiency of transcription termination without affecting the position of the products or the capacity for regulation by TEFM. PMID:27436287

  19. Eight new mtDNA sequences of glass sponges reveal an extensive usage of +1 frameshifting in mitochondrial translation.

    PubMed

    Haen, Karri M; Pett, Walker; Lavrov, Dennis V

    2014-02-10

    Three previously studied mitochondrial genomes of glass sponges (phylum Porifera, class Hexactinellida) contained single nucleotide insertions in protein coding genes inferred as sites of +1 translational frameshifting. To investigate the distribution and evolution of these sites and to help elucidate the mechanism of frameshifting, we determined eight new complete or nearly complete mtDNA sequences from glass sponges and examined individual mitochondrial genes from three others. We found nine new instances of single nucleotide insertions in these sequences and analyzed them both comparatively and phylogenetically. The base insertions appear to have been gained and lost repeatedly in hexactinellid mt protein genes, suggesting no functional significance for the frameshifting sites. A high degree of sequence conservation, the presence of unusual tRNAs, and a distinct pattern of codon usage suggest the "out-of-frame pairing" model of translational frameshifting. Additionally, we provide evidence that relaxed selection pressure on glass sponge mtDNA - possibly a result of their low growth rates and deep-water lifestyle - has allowed frameshift insertions to be tolerated for hundreds of millions of years. Our study provides the first example of a phylogenetically diverse and extensive usage of translational frameshifting in animal mitochondrial coding sequences.

  20. [Mitochondrial DNA sequence variation, demographic history, and population structure of Amur sturgeon Acipenser schrenckii Brandt, 1869].

    PubMed

    Shedko, S V; Miroshnichenko, I L; Nemkova, G A; Koshelev, V N; Shedko, M B

    2015-02-01

    The variability of the mtDNA control region (D-loop) was examined in Amur sturgeon endemic to the Amur River. This species is also classified as critically endangered by the IUCN Red List of Threatened species. Sequencing of 796- to 812-bp fragments of the D-loop in 112 sturgeon collected in the Lower Amur revealed 73 different genotypes. The sample was characterized by a high level of haplotypic (0.976) and nucleotide (0.0194) diversity. The identified haplotypes split into two well-defined monophyletic groups, BG (n = 39) and SM (n = 34), differing (HKY distance) on average by 3.41% of nucleotide positions upon an average level of intragroup differences of 0.54 and 1.23%, respectively. Moreover, the haplotypes of the SM groups differed by the presence of a 13-14 bp deletion. Most ofthe samples (66 out of 112) carried BG haplotypes. Overall, the pattern of pairwise nucleotide differences and the results of neutrality tests, as well as the results of tests for compliance with the model of sudden demographic expansion or with the model of exponential growth pointed to a past significant increase in the number of Amur sturgeon, which was most clearly manifested in the analysis of data on the BG haplogroup. The constructed Bayesian skyline plots showed that this growth began about 18 to 16 thousand years ago. At present, the effective size of the strongly reduced (due to overharvesting) population of Amur sturgeon may be equal to or even lower than it was before the beginning of this growth during the Last Glacial Maximum. The presence in the mitochondrial gene pool ofAmur sturgeon of two haplogroups, their unequal evolutionary dynamics, and, judging by scanty data, their unequal representation in the Russian and Chinese parts of the Amur River basin point to the possible existence of at least two distinct populations of Amur sturgeon in the past.

  1. Full mitochondrial genome sequences of two endemic Philippine hornbill species (Aves: Bucerotidae) provide evidence for pervasive mitochondrial DNA recombination

    PubMed Central

    2011-01-01

    Background Although nowaday it is broadly accepted that mitochondrial DNA (mtDNA) may undergo recombination, the frequency of such recombination remains controversial. Its estimation is not straightforward, as recombination under homoplasmy (i.e., among identical mt genomes) is likely to be overlooked. In species with tandem duplications of large mtDNA fragments the detection of recombination can be facilitated, as it can lead to gene conversion among duplicates. Although the mechanisms for concerted evolution in mtDNA are not fully understood yet, recombination rates have been estimated from "one per speciation event" down to 850 years or even "during every replication cycle". Results Here we present the first complete mt genome of the avian family Bucerotidae, i.e., that of two Philippine hornbills, Aceros waldeni and Penelopides panini. The mt genomes are characterized by a tandemly duplicated region encompassing part of cytochrome b, 3 tRNAs, NADH6, and the control region. The duplicated fragments are identical to each other except for a short section in domain I and for the length of repeat motifs in domain III of the control region. Due to the heteroplasmy with regard to the number of these repeat motifs, there is some size variation in both genomes; with around 21,657 bp (A. waldeni) and 22,737 bp (P. panini), they significantly exceed the hitherto longest known avian mt genomes, that of the albatrosses. We discovered concerted evolution between the duplicated fragments within individuals. The existence of differences between individuals in coding genes as well as in the control region, which are maintained between duplicates, indicates that recombination apparently occurs frequently, i.e., in every generation. Conclusions The homogenised duplicates are interspersed by a short fragment which shows no sign of recombination. We hypothesize that this region corresponds to the so-called Replication Fork Barrier (RFB), which has been described from the chicken

  2. Amphioxus mitochondrial DNA, chordate phylogeny, and the limits of inference based on comparisons of sequences.

    PubMed

    Naylor, G J; Brown, W M

    1998-03-01

    Analyses of both the nucleotide and amino acid sequences derived from all 13 mitochondrial protein-encoding genes (12,234 bp) of 19 metazoan species, including that of the lancelet Branchiostoma floridae ("amphioxus"), fail to yield the widely accepted phylogeny for chordates and, within chordates, for vertebrates. Given the breadth and the compelling nature of the data supporting that phylogeny, relationships supported by the mitochondrial sequence comparisons are almost certainly incorrect, despite their being supported by equally weighted parsimony, distance, and maximum-likelihood analyses. The incorrect groupings probably result in part from convergent base-compositional similarities among some of the taxa, similarities that are strong enough to overwhelm the historical signal. Comparisons among very distantly related taxa are likely to be particularly susceptible to such artifacts, because the historical signal is already greatly attenuated. Empirical results underscore the need for approaches to phylogenetic inference that go beyond simple site-by-site comparison of aligned sequences. This study and others indicate that, once a sequence sample of reasonable size has been obtained, accurate phylogenetic estimation may be better served by incorporating knowledge of molecular structures and processes into inference models and by seeking additional higher order characters embedded in those sequences, than by gathering ever larger sequence samples from the same organisms in he hope that the historical signal will eventually prevail.

  3. Comparison of base composition analysis and Sanger sequencing of mitochondrial DNA for four U.S. population groups.

    PubMed

    Kiesler, Kevin M; Coble, Michael D; Hall, Thomas A; Vallone, Peter M

    2014-01-01

    A set of 711 samples from four U.S. population groups was analyzed using a novel mass spectrometry based method for mitochondrial DNA (mtDNA) base composition profiling. Comparison of the mass spectrometry results with Sanger sequencing derived data yielded a concordance rate of 99.97%. Length heteroplasmy was identified in 46% of samples and point heteroplasmy was observed in 6.6% of samples in the combined mass spectral and Sanger data set. Using discrimination capacity as a metric, Sanger sequencing of the full control region had the highest discriminatory power, followed by the mass spectrometry base composition method, which was more discriminating than Sanger sequencing of just the hypervariable regions. This trend is in agreement with the number of nucleotides covered by each of the three assays.

  4. The Complete DNA Sequence of the Mitochondrial Genome of a ``living Fossil,'' the Coelacanth (Latimeria Chalumnae)

    PubMed Central

    Zardoya, R.; Meyer, A.

    1997-01-01

    The complete nucleotide sequence of the 16,407-bp mitochondrial genome of the coelacanth (Latimeria chalumnae) was determined. The coelacanth mitochondrial genome order is identical to the consensus vertebrate gene order which is also found in all ray-finned fishes, the lungfish, and most tetrapods. Base composition and codon usage also conform to typical vertebrate patterns. The entire mitochondrial genome was PCR-amplified with 24 sets of primers that are expected to amplify homologous regions in other related vertebrate species. Analyses of the control region of the coelacanth mitochondrial genome revealed the existence of four 22-bp tandem repeats close to its 3' end. The phylogenetic analyses of a large data set combining genes coding for rRNAs, tRNAs, and proteins (16,140 characters) confirmed the phylogenetic position of the coelacanth as a lobe-finned fish; it is more closely related to tetrapods than to ray-finned fishes. However, different phylogenetic methods applied to this largest available molecular data set were unable to resolve unambiguously the relationship of the coelacanth to the two other groups of extant lobe-finned fishes, the lungfishes and the tetrapods. Maximum parsimony favored a lungfish/coelacanth or a lungfish/tetrapod sistergroup relationship depending on which transversion:transition weighting is assumed. Neighbor-joining and maximum likelihood supported a lungfish/tetrapod sistergroup relationship. PMID:9215903

  5. The complete DNA sequence of the mitochondrial genome of a "living fossil," the coelacanth (Latimeria chalumnae).

    PubMed

    Zardoya, R; Meyer, A

    1997-07-01

    The complete nucleotide sequence of the 16,407-bp mitochondrial genome of the coelacanth (Latimeria chalumnae) was determined. The coelacanth mitochondrial genome order is identical to the consensus vertebrate gene order which is also found in all ray-finned fishes, the lungfish, and most tetrapods. Base composition and codon usage also conform to typical vertebrate patterns. The entire mitochondrial genome was PCR-amplified with 24 sets of primers that are expected to amplify homologous regions in other related vertebrate species. Analyses of the control region of the coelacanth mitochondrial genome revealed the existence of four 22-bp tandem repeats close to its 3' end. The phylogenetic analyses of a large data set combining genes coding for rRNAs, tRNAs, and proteins (16,140 characters) confirmed the phylogenetic position of the coelacanth as a lobe-finned fish; it is more closely related to tetrapods than to ray-finned fishes. However, different phylogenetic methods applied to this largest available molecular data set were unable to resolve unambiguously the relationship of the coelacanth to the two other groups of extant lobe-finned fishes, the lungfishes and the tetrapods. Maximum parsimony favored a lungfish/coelacanth or a lungfish/tetrapod sistergroup relationship depending on which transversion:transition weighting is assumed. Neighbor-joining and maximum likelihood supported a lungfish/tetrapod sistergroup relationship.

  6. Mitochondrial DNA sequence variation and phylogeography of Neotropic pumas (Puma concolor).

    PubMed

    Caragiulo, Anthony; Dias-Freedman, Isabela; Clark, J Alan; Rabinowitz, Salisa; Amato, George

    2014-08-01

    Pumas occupy the largest latitudinal range of any New World terrestrial mammal. Human population growth and associated habitat reduction has reduced their North American range by nearly two-thirds, but the impact of human expansion in Central and South America on puma populations is not clear. We examined mitochondrial DNA diversity of pumas across the majority of their range, with a focus on Central and South America. Four mitochondrial gene regions (1140 base pairs) revealed 16 unique haplotypes differentiating pumas into three geographic groupings: North America, Central America and South America. These groups were highly differentiated as indicated by significant pairwise FST values. North American samples were genetically homogenous compared to Central and South American samples, and South American pumas were the most diverse and ancestral. These findings support an earlier hypothesis that North America was recolonized by founding pumas from Central and South America.

  7. Ultra-Deep Sequencing of Mouse Mitochondrial DNA: Mutational Patterns and Their Origins

    PubMed Central

    Freyer, Christoph; Hagström, Erik; Ingman, Max; Larsson, Nils-Göran; Gyllensten, Ulf

    2011-01-01

    Somatic mutations of mtDNA are implicated in the aging process, but there is no universally accepted method for their accurate quantification. We have used ultra-deep sequencing to study genome-wide mtDNA mutation load in the liver of normally- and prematurely-aging mice. Mice that are homozygous for an allele expressing a proof-reading–deficient mtDNA polymerase (mtDNA mutator mice) have 10-times-higher point mutation loads than their wildtype siblings. In addition, the mtDNA mutator mice have increased levels of a truncated linear mtDNA molecule, resulting in decreased sequence coverage in the deleted region. In contrast, circular mtDNA molecules with large deletions occur at extremely low frequencies in mtDNA mutator mice and can therefore not drive the premature aging phenotype. Sequence analysis shows that the main proportion of the mutation load in heterozygous mtDNA mutator mice and their wildtype siblings is inherited from their heterozygous mothers consistent with germline transmission. We found no increase in levels of point mutations or deletions in wildtype C57Bl/6N mice with increasing age, thus questioning the causative role of these changes in aging. In addition, there was no increased frequency of transversion mutations with time in any of the studied genotypes, arguing against oxidative damage as a major cause of mtDNA mutations. Our results from studies of mice thus indicate that most somatic mtDNA mutations occur as replication errors during development and do not result from damage accumulation in adult life. PMID:21455489

  8. Isolation, amplification, and sequencing of human mitochondrial DNA obtained from human crab louse, Pthirus pubis (L.), blood meals.

    PubMed

    Lord, W D; DiZinno, J A; Wilson, M R; Budowle, B; Taplin, D; Meinking, T L

    1998-09-01

    The ability to identify individual human hosts based on analyses of blood recovered from the digestive tract of hematophagous arthropods has been a long-term pursuit in both medical and forensic entomology. Blood meal individualization techniques can bring important advancements to studies of vector-borne disease epidemiology. Forensically, these analyses may aid in assailant identification in violent crime cases where blood-feeding insects or their excreta are recovered from victims or at crime scenes. Successful isolation, amplification, and sequencing of human mitochondrial DNA obtained from adult human crab lice fed on human volunteers are reported. Adult lice were removed from recruited volunteers frequenting inner city health clinics. Live lice were killed by freezing and subsequently air dried at ambient temperature. A saliva sample was obtained from each volunteer and served as a DNA reference sample. Volunteers were afforded free, approved pediculosis treatment. Individual lice were subsequently processed using procedures developed for the extraction of mitochondrial DNA from human hair, teeth, and bone. The resulting DNA was amplified by the polymerase chain reaction and sequenced. Our results point to valuable avenues for future entomological research.

  9. Simultaneous Whole Mitochondrial Genome Sequencing with Short Overlapping Amplicons Suitable for Degraded DNA Using the Ion Torrent Personal Genome Machine

    PubMed Central

    Chaitanya, Lakshmi; Ralf, Arwin; van Oven, Mannis; Kupiec, Tomasz; Chang, Joseph; Lagacé, Robert

    2015-01-01

    ABSTRACT Whole mitochondrial (mt) genome analysis enables a considerable increase in analysis throughput, and improves the discriminatory power to the maximum possible phylogenetic resolution. Most established protocols on the different massively parallel sequencing (MPS) platforms, however, invariably involve the PCR amplification of large fragments, typically several kilobases in size, which may fail due to mtDNA fragmentation in the available degraded materials. We introduce a MPS tiling approach for simultaneous whole human mt genome sequencing using 161 short overlapping amplicons (average 200 bp) with the Ion Torrent Personal Genome Machine. We illustrate the performance of this new method by sequencing 20 DNA samples belonging to different worldwide mtDNA haplogroups. Additional quality control, particularly regarding the potential detection of nuclear insertions of mtDNA (NUMTs), was performed by comparative MPS analysis using the conventional long‐range amplification method. Preliminary sensitivity testing revealed that detailed haplogroup inference was feasible with 100 pg genomic input DNA. Complete mt genome coverage was achieved from DNA samples experimentally degraded down to genomic fragment sizes of about 220 bp, and up to 90% coverage from naturally degraded samples. Overall, we introduce a new approach for whole mt genome MPS analysis from degraded and nondegraded materials relevant to resolve and infer maternal genetic ancestry at complete resolution in anthropological, evolutionary, medical, and forensic applications. PMID:26387877

  10. Simultaneous Whole Mitochondrial Genome Sequencing with Short Overlapping Amplicons Suitable for Degraded DNA Using the Ion Torrent Personal Genome Machine.

    PubMed

    Chaitanya, Lakshmi; Ralf, Arwin; van Oven, Mannis; Kupiec, Tomasz; Chang, Joseph; Lagacé, Robert; Kayser, Manfred

    2015-12-01

    Whole mitochondrial (mt) genome analysis enables a considerable increase in analysis throughput, and improves the discriminatory power to the maximum possible phylogenetic resolution. Most established protocols on the different massively parallel sequencing (MPS) platforms, however, invariably involve the PCR amplification of large fragments, typically several kilobases in size, which may fail due to mtDNA fragmentation in the available degraded materials. We introduce a MPS tiling approach for simultaneous whole human mt genome sequencing using 161 short overlapping amplicons (average 200 bp) with the Ion Torrent Personal Genome Machine. We illustrate the performance of this new method by sequencing 20 DNA samples belonging to different worldwide mtDNA haplogroups. Additional quality control, particularly regarding the potential detection of nuclear insertions of mtDNA (NUMTs), was performed by comparative MPS analysis using the conventional long-range amplification method. Preliminary sensitivity testing revealed that detailed haplogroup inference was feasible with 100 pg genomic input DNA. Complete mt genome coverage was achieved from DNA samples experimentally degraded down to genomic fragment sizes of about 220 bp, and up to 90% coverage from naturally degraded samples. Overall, we introduce a new approach for whole mt genome MPS analysis from degraded and nondegraded materials relevant to resolve and infer maternal genetic ancestry at complete resolution in anthropological, evolutionary, medical, and forensic applications.

  11. Complete mitochondrial DNA sequence of the fat dormouse, Glis glis: further evidence of rodent paraphyly.

    PubMed

    Reyes, A; Pesole, G; Saccone, C

    1998-05-01

    The complete mitochondrial genome of the fat dormouse, Glis glis, has been sequenced (16,602 bp). A total of 23 complete mitochondrial mammalian genomes have been taken into account for phylogenetic reconstruction. Phylogenetic analyses were performed with parsimony, distance (stationary Markov model), and maximum-likelihood methods. In all cases, data strongly support the paraphyly of rodents, with dormouse and guinea pig in a different clade from rat and mouse, reaching bootstrap values of 95%. Rodent monophyly and the existence of Glires (Rodentia and Lagomorpha) are weakly supported, with maximum bootstrap values of 11% and 8.6%, respectively. This result agrees with the analyses of isochore patterns in the nuclear genome and the B2 and B2-like retroposons, which show a close relationship between dormice and guinea pigs rather than between dormice and rats and mice.

  12. Phylogenetic relationships in Demodex mites (Acari: Demodicidae) based on mitochondrial 16S rDNA partial sequences.

    PubMed

    Zhao, Ya-E; Wu, Li-Ping

    2012-09-01

    To confirm phylogenetic relationships in Demodex mites based on mitochondrial 16S rDNA partial sequences, mtDNA 16S partial sequences of ten isolates of three Demodex species from China were amplified, recombined, and sequenced and then analyzed with two Demodex folliculorum isolates from Spain. Lastly, genetic distance was computed, and phylogenetic tree was reconstructed. MEGA 4.0 analysis showed high sequence identity among 16S rDNA partial sequences of three Demodex species, which were 95.85 % in D. folliculorum, 98.53 % in Demodex canis, and 99.71 % in Demodex brevis. The divergence, genetic distance, and transition/transversions of the three Demodex species reached interspecies level, whereas there was no significant difference of the divergence (1.1 %), genetic distance (0.011), and transition/transversions (3/1) of the two geographic D. folliculorum isolates (Spain and China). Phylogenetic trees reveal that the three Demodex species formed three separate branches of one clade, where D. folliculorum and D. canis gathered first, and then gathered with D. brevis. The two Spain and five China D. folliculorum isolates did not form sister clades. In conclusion, 16S mtDNA are suitable for phylogenetic relationship analysis in low taxa (genus or species), but not for intraspecies determination of Demodex. The differentiation among the three Demodex species has reached interspecies level.

  13. Isolation of a species-specific mitochondrial DNA sequence for identification of Tilletia indica, the Karnal bunt of wheat fungus.

    PubMed Central

    Ferreira, M A; Tooley, P W; Hatziloukas, E; Castro, C; Schaad, N W

    1996-01-01

    Mitochondrial DNA (mtDNA) from five isolates of Tilletia indica was isolated and digested with several restriction enzymes. A 2.3-kb EcoRI fragment was chosen, cloned, and shown to hybridize with total DNA restricted with EcoRI from T. indica and not from a morphologically similar smut fungus, Tilletia barclayana. The clone was partially sequenced, and primers were designed and tested under high-stringency conditions in PCR assays. The primer pair Ti1/Ti4 amplified a 2.3-kb fragment from total DNA of 17 T. indica isolates from India, Pakistan, and Mexico. DNA from 25 isolates of other smut fungi (T. barclayana, Tilletia foetida, Tilletia caries, Tilletia fusca, and Tilletia controversa) did not produce any bands, as detected by ethidium bromide-stained agarose gels and Southern hybridizations. The sensitivity of the assay was determined and increased by using a single nested primer in a second round of amplification, so that 1 pg of total mycelial DNA could be detected. The results indicated that the primers which originated from a cloned mtDNA sequence can be used to differentiate T. indica from other Tilletia species and have the potential to identify teliospores contaminating wheat seeds. PMID:8572716

  14. Deep Sequencing of Mixed Total DNA without Barcodes Allows Efficient Assembly of Highly Plastic Ascidian Mitochondrial Genomes

    PubMed Central

    Rubinstein, Nimrod D.; Feldstein, Tamar; Shenkar, Noa; Botero-Castro, Fidel; Griggio, Francesca; Mastrototaro, Francesco; Delsuc, Frédéric; Douzery, Emmanuel J.P.; Gissi, Carmela; Huchon, Dorothée

    2013-01-01

    Ascidians or sea squirts form a diverse group within chordates, which includes a few thousand members of marine sessile filter-feeding animals. Their mitochondrial genomes are characterized by particularly high evolutionary rates and rampant gene rearrangements. This extreme variability complicates standard polymerase chain reaction (PCR) based techniques for molecular characterization studies, and consequently only a few complete Ascidian mitochondrial genome sequences are available. Using the standard PCR and Sanger sequencing approach, we produced the mitochondrial genome of Ascidiella aspersa only after a great effort. In contrast, we produced five additional mitogenomes (Botrylloides aff. leachii, Halocynthia spinosa, Polycarpa mytiligera, Pyura gangelion, and Rhodosoma turcicum) with a novel strategy, consisting in sequencing the pooled total DNA samples of these five species using one Illumina HiSeq 2000 flow cell lane. Each mitogenome was efficiently assembled in a single contig using de novo transcriptome assembly, as de novo genome assembly generally performed poorly for this task. Each of the new six mitogenomes presents a different and novel gene order, showing that no syntenic block has been conserved at the ordinal level (in Stolidobranchia and in Phlebobranchia). Phylogenetic analyses support the paraphyly of both Ascidiacea and Phlebobranchia, with Thaliacea nested inside Phlebobranchia, although the deepest nodes of the Phlebobranchia–Thaliacea clade are not well resolved. The strategy described here thus provides a cost-effective approach to obtain complete mitogenomes characterized by a highly plastic gene order and a fast nucleotide/amino acid substitution rate. PMID:23709623

  15. Deep sequencing of mixed total DNA without barcodes allows efficient assembly of highly plastic ascidian mitochondrial genomes.

    PubMed

    Rubinstein, Nimrod D; Feldstein, Tamar; Shenkar, Noa; Botero-Castro, Fidel; Griggio, Francesca; Mastrototaro, Francesco; Delsuc, Frédéric; Douzery, Emmanuel J P; Gissi, Carmela; Huchon, Dorothée

    2013-01-01

    Ascidians or sea squirts form a diverse group within chordates, which includes a few thousand members of marine sessile filter-feeding animals. Their mitochondrial genomes are characterized by particularly high evolutionary rates and rampant gene rearrangements. This extreme variability complicates standard polymerase chain reaction (PCR) based techniques for molecular characterization studies, and consequently only a few complete Ascidian mitochondrial genome sequences are available. Using the standard PCR and Sanger sequencing approach, we produced the mitochondrial genome of Ascidiella aspersa only after a great effort. In contrast, we produced five additional mitogenomes (Botrylloides aff. leachii, Halocynthia spinosa, Polycarpa mytiligera, Pyura gangelion, and Rhodosoma turcicum) with a novel strategy, consisting in sequencing the pooled total DNA samples of these five species using one Illumina HiSeq 2000 flow cell lane. Each mitogenome was efficiently assembled in a single contig using de novo transcriptome assembly, as de novo genome assembly generally performed poorly for this task. Each of the new six mitogenomes presents a different and novel gene order, showing that no syntenic block has been conserved at the ordinal level (in Stolidobranchia and in Phlebobranchia). Phylogenetic analyses support the paraphyly of both Ascidiacea and Phlebobranchia, with Thaliacea nested inside Phlebobranchia, although the deepest nodes of the Phlebobranchia-Thaliacea clade are not well resolved. The strategy described here thus provides a cost-effective approach to obtain complete mitogenomes characterized by a highly plastic gene order and a fast nucleotide/amino acid substitution rate.

  16. RE-EVALUATION OF THE GEOGRAPHIC DISTRIBUTION AND PHYLOGEOGRAPHY OF THE SIGMODON HISPIDUS COMPLEX BASED ON MITOCHONDRIAL DNA SEQUENCES

    PubMed Central

    Bradley, Robert D.; Henson, Dallas D.; Durish, Nevin D.

    2010-01-01

    Geographic distribution among members of the Sigmodon hispidus complex (Sigmodon hirsutus, S. hispidus, and S. toltecus) were examined using DNA sequences from the mitochondrial cytochrome-b gene. Geographic distribution of each taxon was defined based on DNA sequences obtained from 69 samples (19 newly obtained and 50 from previous studies) collected from North, Central, and South America. These data indicated that S. hispidus is restricted to the southern one-half of the United States and northeastern Mexico (Nuevo León and Tamaulipas), S. toltecus occupies the eastern one-third of Mexico (central Tamaulipas) to northern Honduras, and S. hirsutus is distributed from central Chiapas and southeastern Oaxaca to northern South America (Venezuela). The newly collected data extend distributions of S. hispidus from the southern United States southward into northeastern Mexico and that of S. toltecus from Chiapas, Mexico, southward to Honduras. Genetic divergence and patterns of phylogeography were examined within each taxon. PMID:20613884

  17. RE-EVALUATION OF THE GEOGRAPHIC DISTRIBUTION AND PHYLOGEOGRAPHY OF THE SIGMODON HISPIDUS COMPLEX BASED ON MITOCHONDRIAL DNA SEQUENCES.

    PubMed

    Bradley, Robert D; Henson, Dallas D; Durish, Nevin D

    2008-09-01

    Geographic distribution among members of the Sigmodon hispidus complex (Sigmodon hirsutus, S. hispidus, and S. toltecus) were examined using DNA sequences from the mitochondrial cytochrome-b gene. Geographic distribution of each taxon was defined based on DNA sequences obtained from 69 samples (19 newly obtained and 50 from previous studies) collected from North, Central, and South America. These data indicated that S. hispidus is restricted to the southern one-half of the United States and northeastern Mexico (Nuevo León and Tamaulipas), S. toltecus occupies the eastern one-third of Mexico (central Tamaulipas) to northern Honduras, and S. hirsutus is distributed from central Chiapas and southeastern Oaxaca to northern South America (Venezuela). The newly collected data extend distributions of S. hispidus from the southern United States southward into northeastern Mexico and that of S. toltecus from Chiapas, Mexico, southward to Honduras. Genetic divergence and patterns of phylogeography were examined within each taxon.

  18. [Genetic variation of Manchurian pheasant (Phasianus colchicus pallasi Rotshild, 1903) inferred from mitochondrial DNA control region sequences].

    PubMed

    Kozyrenko, M M; Fisenko, P V; Zhuravlev, Iu N

    2009-04-01

    Sequence variation of the mitochondrial DNA control region was studied in Manchurian pheasants (Phasianus colchicus pallasi Rotshild, 1903) representing three geographic populations from the southern part of the Russian Far East. Extremely low population genetic differentiation (F(ST) = 0.0003) pointed to a very high gene exchange between the populations. Combination of such characters as high haplotype diversity (0.884 to 0.913), low nucleotide diversity (0.0016 to 0.0022), low R2 values (0.1235 to 0.1337), certain patterns of pairwise-difference distributions, and the absence of phylogenetic structure suggested that the phylogenetic history of Ph. C. pallasi included passing through a bottleneck with further expansion in the postglacial period. According to the data obtained, it was suggested that differentiation between the mitochondrial lineages started approximately 100 000 years ago.

  19. Dicrocoelium chinensis and Dicrocoelium dendriticum (Trematoda: Digenea) are distinct lancet fluke species based on mitochondrial and nuclear ribosomal DNA sequences.

    PubMed

    Liu, Guo-Hua; Yan, Hong-Bin; Otranto, Domenico; Wang, Xing-Ye; Zhao, Guang-Hui; Jia, Wan-Zhong; Zhu, Xing-Quan

    2014-10-01

    Lancet flukes parasitize the bile ducts and gall bladder of a range of mammals, including humans, causing dicrocoeliosis. In the present study, we sequenced and characterized the complete mitochondrial (mt) genomes as well as the first and second internal transcribed spacers (ITS-1 and ITS-2=ITS) of nuclear ribosomal DNA (rDNA) of two lancet flukes, Dicrocoelium chinensis and D. dendriticum. Sequence comparison of a conserved mt gene and nuclear rDNA sequences among multiple individual lancet flukes revealed substantial nucleotide differences between the species but limited sequence variation within each of them. Phylogenetic analysis of the concatenated amino acid and multiple mt rrnS sequences using Bayesian inference supported the separation of D. chinensis and D. dendriticum into two distinct species-specific clades. Results of the present study support the proposal that D. dendriticum and D. chinensis represent two distinct lancet flukes. While providing the first mt genomes from members of the superfamily Plagiorchioidea, the novel mt markers described herein will be useful for further studies of the diagnosis, epidemiology and systematics of the lancet flukes and other trematodes of human and animal health significance.

  20. Phylogenetically Informative Length Polymorphism and Sequence Variability in Mitochondrial DNA of Australian Songbirds (Pomatostomus)

    PubMed Central

    Edwards, S. V.; Wilson, A. C.

    1990-01-01

    A combination of restriction analysis and direct sequencing via the polymerase chain reaction (PCR) was used to build trees relating mitochondrial DNAs (mtDNAs) from 50 individuals belonging to five species of Australian babblers (Pomatostomus). The trees served as a quantitative framework for analyzing the direction and tempo of evolution of an intraspecific length polymorphism from a third mitochondrial ancestor. The length polymorphism lies between the cytochrome b and 12S rRNA (srRNA) genes. Screening of mtDNAs within and between the five species with restriction enzymes showed that Pomatosomus temporalis was polymorphic for two smaller size classes (M and S) that are completely segregated geographically, whereas mtDNAs from the other four species were exclusively of a third, larger size (L). Inter- and intraspecific phylogenetic trees relating mtDNAs based on restriction maps, cytochrome b sequences obtained via PCR, and the two data sets combined were compared to one another statistically and were broadly similar except for the phylogenetic position of Pomatosomus halli. Both sets of phylogenies imply that only two deletion events can account for the observed intraspecific distribution of the three length types. High levels of base-substitutional divergence were detected within and between northern and southern lineages of P. temporalis, which implies a low level of gene flow between northern and southern regions as well as a low rate of length mutation. These conclusions were confirmed by applying coalescent theory to the statistical framework provided by the phylogenetic analyses. PMID:1979038

  1. Mitochondrial DNA polymorphism in mitochondrial myopathy.

    PubMed

    Holt, I J; Harding, A E; Morgan-Hughes, J A

    1988-05-01

    In order to test the hypothesis that mitochondrial myopathy may be caused by mutation of the mitochondrial (mt) genome, restriction fragment length polymorphism in leucocyte mt DNA has been studied in 38 patients with mitochondrial myopathy, 44 of their unaffected matrilineal relatives, and 35 normal control subjects. Previously unreported mt DNA polymorphisms were identified in both patients and controls. No differences in restriction fragment patterns were observed between affected and unaffected individuals in the same maternal line, and there was no evidence of major deletion of mt DNA in patients. This study provides no positive evidence of mitochondrial inheritance in mitochondrial myopathy, but this has not been excluded.

  2. Phylogenetic analysis of Demodex caprae based on mitochondrial 16S rDNA sequence.

    PubMed

    Zhao, Ya-E; Hu, Li; Ma, Jun-Xian

    2013-11-01

    Demodex caprae infests the hair follicles and sebaceous glands of goats worldwide, which not only seriously impairs goat farming, but also causes a big economic loss. However, there are few reports on the DNA level of D. caprae. To reveal the taxonomic position of D. caprae within the genus Demodex, the present study conducted phylogenetic analysis of D. caprae based on mt16S rDNA sequence data. D. caprae adults and eggs were obtained from a skin nodule of the goat suffering demodicidosis. The mt16S rDNA sequences of individual mite were amplified using specific primers, and then cloned, sequenced, and aligned. The sequence divergence, genetic distance, and transition/transversion rate were computed, and the phylogenetic trees in Demodex were reconstructed. Results revealed the 339-bp partial sequences of six D. caprae isolates were obtained, and the sequence identity was 100% among isolates. The pairwise divergences between D. caprae and Demodex canis or Demodex folliculorum or Demodex brevis were 22.2-24.0%, 24.0-24.9%, and 22.9-23.2%, respectively. The corresponding average genetic distances were 2.840, 2.926, and 2.665, and the average transition/transversion rates were 0.70, 0.55, and 0.54, respectively. The divergences, genetic distances, and transition/transversion rates of D. caprae versus the other three species all reached interspecies level. The five phylogenetic trees all presented that D. caprae clustered with D. brevis first, and then with D. canis, D. folliculorum, and Demodex injai in sequence. In conclusion, D. caprae is an independent species, and it is closer to D. brevis than to D. canis, D. folliculorum, or D. injai.

  3. Mitochondrial DNA sequence analyses and phylogenetic relationships among two Nigerian goat breeds and the South African Kalahari Red.

    PubMed

    Awotunde, Esther O; Bemji, Martha N; Olowofeso, Olajide; James, Ikechukwu J; Ajayi, O O; Adebambo, Ayotunde O

    2015-01-01

    The first hypervariable (HV1) region of mitochondrial DNA (mtDNA) of two popular Nigerian goat breeds: West African Dwarf (WAD) (n=35) and Red Sokoto (RS) (n=37) and one exotic breed: Kalahari Red (KR) (n=38) imported from South Africa were sequenced to investigate sequence diversity, genetic structure, origin, and demographic history of the populations. A total of 68 polymorphic sites were found in 110 sequences that grouped into 68 haplotypes. Average haplotype and nucleotide diversities for all breeds were 0.982±0.005 and 0.02350±0.00213, respectively. Phylogenetic analysis revealed two mtDNA lineages (A and B). Lineage A was predominant and included all haplotypes from WAD and RS and 5 out of 11 haplotypes of KR goats. The remaining haplotypes (6) of KR belong to lineage B. The analysis of molecular variance revealed a high-within breed genetic variance of 82.4% and a low-between breed genetic variance of 17.6%. The three breeds clustered with Capra aegagrus as their wild ancestor. Mismatch distribution analysis showed that WAD, RS and haplogroup A have experienced population expansion events. The study has revealed very high diversity within the three breeds which are not strongly separated from each other based on mtDNA analysis. The information obtained on the genetic structure of the breeds will be useful in planning improvement and conservation programs for the local populations.

  4. Origin and phylogenetic analysis of Tibetan Mastiff based on the mitochondrial DNA sequence.

    PubMed

    Li, Qifa; Liu, Zhenshan; Li, Yinxia; Zhao, Xingbo; Dong, Liyan; Pan, Zengxiang; Sun, Yuanrong; Li, Ning; Xu, Yinxue; Xie, Zhuang

    2008-06-01

    At present, the Tibetan Mastiff is the oldest and most ferocious dog in the world. However, the origin of the Tibetan Mastiff and its phylogenetic relationship with other large breed dogs such as Saint Bernard are unclear. In this study, the primers were designed according to the mitochondrial genome sequence of the domestic dog, and the 2,525 bp mitochondrial sequence, containing the whole sequence of Cytochrome b, tRNA-Thr, tRNA-Pro, and control region of the Tibetan Mastiff, was obtained. Using grey wolves and coyotes as outgroups, the Tibetan Mastiff and 12 breeds of domestic dogs were analyzed in phylogenesis. Tibetan Mastiff, domestic dog breeds, and grey wolves were clustered into a group and coyotes were clustered in a group separately. This indicated that the Tibetan Mastiff and the other domestic dogs originated from the grey wolf, and the Tibetan Mastiff belonged to Carnivora, Canidae, Canis, Canis lupus, Canis lupus familiaris on the animal taxonomy. In domestic dogs, the middle and small breed dogs were clustered at first; German Sheepdog, Swedish Elkhound, and Black Russian Terrier were clustered into one group, and the Tibetan Mastiff, Old English Sheepdog, Leonberger, and Saint Bernard were clustered in another group. This confirmed the viewpoint that many of the famous large breed dogs worldwide such as Saint Bernard possibly had the blood lineage of the Tibetan Mastiff, based on the molecular data. According to the substitution rate, we concluded that the approximate divergence time between Tibetan Mastiff and grey wolf was 58,000 years before the present (YBP), and the approximate divergence time between other domestic dogs and grey wolf was 42,000 YBP, demonstrating that the time of origin of the Tibetan Mastiff was earlier than that of the other domestic dogs.

  5. Neotomine-peromyscine rodent systematics based on combined analyses of nuclear and mitochondrial DNA sequences.

    PubMed

    Reeder, Serena A; Carroll, Darin S; Edwards, Cody W; Kilpatrick, C William; Bradley, Robert D

    2006-07-01

    Recently, sequences from two nuclear genes (exon 6 of the dentin matrix protein 1 gene and intron 7 of the beta-fibrinogen gene) and one mitochondrial gene (cytochrome b gene) were used independently in an attempt to resolve phylogenetic relationships within the neotomine-peromyscine complex. Although these studies provided testable hypotheses regarding this group of rodents, the affinities of certain tribes and genera remain uncertain. To elucidate these relationships, the three data partitions were tested for heterogeneity and then concatenated according to conditional data combination and total evidence approaches. Support was found for five clades, four of which correspond to well recognized tribes (the Neotomini, Peromyscini=Reithrodontomyini, Baiomyini, and Tylomyini). Recommendations are made regarding the recognition of Ochrotomys as a tribe of its own, the Ochrotomyini, paralleling other recent findings. The Peromyscini, Baiomyini, and Ochrotomyini are unresolved in relation to each other, but as a whole are sister to the Neotomini. The Tylomyini is basal to all clades. It appears that combined data from the nuclear and mitochondrial genes (analyzing all three partitions simultaneously) resulted in the best phylogenetic hypothesis regarding the complex.

  6. Genome-wide mapping of nuclear mitochondrial DNA sequences links DNA replication origins to chromosomal double-strand break formation in Schizosaccharomyces pombe.

    PubMed

    Lenglez, Sandrine; Hermand, Damien; Decottignies, Anabelle

    2010-09-01

    Chromosomal double-strand breaks (DSBs) threaten genome integrity and repair of these lesions is often mutagenic. How and where DSBs are formed is a major question conveniently addressed in simple model organisms like yeast. NUMTs, nuclear DNA sequences of mitochondrial origin, are present in most eukaryotic genomes and probably result from the capture of mitochondrial DNA (mtDNA) fragments into chromosomal breaks. NUMT formation is ongoing and was reported to cause de novo human genetic diseases. Study of NUMTs is likely to contribute to the understanding of naturally occurring chromosomal breaks. We show that Schizosaccharomyces pombe NUMTs are exclusively located in noncoding regions with no preference for gene promoters and, when located into promoters, do not affect gene transcription level. Strikingly, most noncoding regions comprising NUMTs are also associated with a DNA replication origin (ORI). Chromatin immunoprecipitation experiments revealed that chromosomal NUMTs are probably not acting as ORI on their own but that mtDNA insertions occurred directly next to ORIs, suggesting that these loci may be prone to DSB formation. Accordingly, induction of excessive DNA replication origin firing, a phenomenon often associated with human tumor formation, resulted in frequent nucleotide deletion events within ORI3001 subtelomeric chromosomal locus, illustrating a novel aspect of DNA replication-driven genomic instability. How mtDNA is fragmented is another important issue that we addressed by sequencing experimentally induced NUMTs. This highlighted regions of S. pombe mtDNA prone to breaking. Together with an analysis of human NUMTs, we propose that these fragile sites in mtDNA may correspond to replication pause sites.

  7. Phylogenetic relationships of extant zokors (Myospalacinae) (Rodentia, Spalacidae) inferred from mitochondrial DNA sequences.

    PubMed

    Su, Junhu; Ji, Weihong; Wang, Jing; Gleeson, Dianne M; Zhou, Janwei; Hua, Limin; Wei, Yanming

    2014-04-01

    In this study, we use three mitochondrial markers, cytochrome b gene (Cyt b), NADH dehydrogenase subunit 4 (ND4) and control region (D-loop) to investigate the phylogenetic relationships of extant zokor species in Mysopalacinae. The phylogenetic tree constructed based on Cyt b strongly supports the monophyly genera Eospalax and Myospalax with E. fontanierii being the most ancient species in Eospalax. Further phylogenetic analyses of four species of Eospalax based on ND4 and D-loop sequences revealed two clades that correspond to two geographical distributions. The basal clade includes E. cansus which is mainly found on Loess Plateau (LP) and another clade including E. baileyi, E. smithii and E. rufescens that inhabits areas above 2000 m on Qinghai-Tibetan Plateau (QTP) and Qinling Mountains. Geographical events of QTP and LP may have played a major role in the diversification and evolution of Mysopalacinae.

  8. Sequence motifs associated with paternal transmission of mitochondrial DNA in the horse mussel, Modiolus modiolus (Bivalvia: Mytilidae).

    PubMed

    Robicheau, Brent M; Breton, Sophie; Stewart, Donald T

    2017-03-20

    In the majority of metazoans paternal mitochondria represent evolutionary dead-ends. In many bivalves, however, this paradigm does not hold true; both maternal and paternal mitochondria are inherited. Herein, we characterize maternal and paternal mitochondrial control regions of the horse mussel, Modiolus modiolus (Bivalvia: Mytilidae). The maternal control region is 808bp long, while the paternal control region is longer at 2.3kb. We hypothesize that the size difference is due to a combination of repeated duplications within the control region of the paternal mtDNA genome, as well as an evolutionarily ancient recombination event between two sex-associated mtDNA genomes that led to the insertion of a second control region sequence in the genome that is now transmitted via males. In a comparison to other mytilid male control regions, we identified two evolutionarily Conserved Motifs, CMA and CMB, associated with paternal transmission of mitochondrial DNA. CMA is characterized by a conserved purine/pyrimidine pattern, while CMB exhibits a specific 13bp nucleotide string within a stem and loop structure. The identification of motifs CMA and CMB in M. modiolus extends our understanding of Sperm Transmission Elements (STEs) that have recently been identified as being associated with the paternal transmission of mitochondria in marine bivalves.

  9. Electrophoretic analysis of sequence variability in three mitochondrial DNA regions for ascaridoid parasites of human and animal health significance.

    PubMed

    Li, Ming-Wei; Lin, Rui-Qing; Song, Hui-Qun; Sani, Rehana A; Wu, Xiang-Yun; Zhu, Xing-Quan

    2008-07-01

    Sequence variability in three mitochondrial DNA (mtDNA) regions, namely cytochrome c oxidase subunit 1 (cox1), NADH dehydrogenase subunits 1 and 4 (nad1 and nad4), among and within Toxocara canis, T. cati, T. malaysiensis, T. vitulorum and Toxascaris leonina from different geographical origins was examined by a mutation-scanning approach. A portion of the cox1 gene (pcox1), a portion of the nad1 and nad4 genes (pnad1 and pnad4) were amplified separately from individual ascaridoid nematodes by polymerase chain reaction and the amplicons analyzed by single-strand conformation polymorphism (SSCP). Representative samples displaying sequence variation in SSCP profiles were subjected to sequencing in order to define genetic markers for their specific identification and differentiation. While the intra-specific sequence variations within each of the five ascaridoid species were 0.2-3.7% for pcox1, 0-2.8% for pnad1 and 0-2.3% for pnad4, the inter-specific sequence differences were significantly higher, being 7.9-12.9% for pcox1, 10.7-21.1% for pnad1 and 12.9-21.7% for pnad4, respectively. Phylogenetic analyses based on the combined sequences of pcox1, pnad1 and pnad4 revealed that the recently described species T. malaysiensis was more closely related to T. cati than to T. canis. These findings provided mtDNA evidence for the validity of T. malaysiensis and also demonstrated clearly the usefulness and attributes of the mutation-scanning sequencing approach for studying the population genetic structures of these and other nematodes of socio-economic importance.

  10. Genetic identification of istiophorid larvae from the Gulf of Mexico based on the analysis of mitochondrial DNA control region sequences.

    PubMed

    McKenzie, J L; Alvarado Bremer, J R

    2017-03-01

    Assigning relative importance of spawning and nursery habitats for threatened and endangered teleosts, such as those seen in the Gulf of Mexico (GoM), relies on the proper identification of the early life-history stages of the species of concern. Here, sequencing a portion of the mitochondrial DNA (mtDNA) control region (CR) I as barcodes is recommended to identify istiophorid (billfish) larvae in the Atlantic Ocean because of its high resolution and the intrinsic value of the levels of genetic variation that can be extracted from these data. The universality of the primers employed here demonstrates their utility for not only the positive identification of istiophorids in the GoM, but for any larval teleost occurring in areas recognized as larval hotspots worldwide.

  11. Human Mitochondrial DNA Replication

    PubMed Central

    Holt, Ian J.; Reyes, Aurelio

    2012-01-01

    Elucidation of the process of DNA replication in mitochondria is in its infancy. For many years, maintenance of the mitochondrial genome was regarded as greatly simplified compared to the nucleus. Mammalian mitochondria were reported to lack all DNA repair systems, to eschew DNA recombination, and to possess but a single DNA polymerase, polymerase γ. Polγ was said to replicate mitochondrial DNA exclusively via one mechanism, involving only two priming events and a handful of proteins. In this “strand-displacement model,” leading strand DNA synthesis begins at a specific site and advances approximately two-thirds of the way around the molecule before DNA synthesis is initiated on the “lagging” strand. Although the displaced strand was long-held to be coated with protein, RNA has more recently been proposed in its place. Furthermore, mitochondrial DNA molecules with all the features of products of conventional bidirectional replication have been documented, suggesting that the process and regulation of replication in mitochondria is complex, as befits a genome that is a core factor in human health and longevity. PMID:23143808

  12. Associations between sequence variations in the mitochondrial DNA D-loop region and outcome of hepatocellular carcinoma

    PubMed Central

    LI, SHILAI; WAN, PEIQI; PENG, TAO; XIAO, KAIYIN; SU, MING; SHANG, LIMING; XU, BANGHAO; SU, ZHIXIONG; YE, XINPING; PENG, NING; QIN, QUANLIN; LI, LEQUN

    2016-01-01

    The association between mitochondrial DNA (mtDNA) polymorphisms or mutations and the prognoses of cancer have been investigated previously, but the results have been ambiguous. In the present study, the associations between sequence variations in the mtDNA D-loop region and the outcomes of patients with hepatocellular carcinoma (HCC) were analysed. A total of 140 patients with HCC (123 males and 17 females), who were hospitalised to undergo radical resection, were studied. Polymerase chain reaction and direct sequencing were performed to detect the sequence variations in the mtDNA D-loop region. Multivariate and univariate analyses were conducted to determine important factors in the prognosis of HCC. A total of 150 point sequence variations were observed in the 140 cases (13 point mutations, 8 insertions, 20 deletions and 116 polymorphisms). The variation rate was 13.4% (150/1, 122). mtDNA nucleotide 150 (C/T) was an independent factor in the logistic regression for early/late recurrence of HCC. Patients with 150T appeared to have later recurrences. In a Cox proportional hazards regression model, hepatitis B virus DNA, Child-Pugh class, differentiation degree, tumour-node-metastasis (TNM) stage, nucleotide 16263 (T/C) and nucleotide 315 (N/insertion C) were independent factors for tumour-free survival time. Patients with the 16263T allele had a greater tumour-free survival time than patients with the 16263C allele. Similarly, patients with 315 insertion C had a superior tumour-free survival time when compared with patients with 315 N (normal). In the Cox proportional hazards regression model, recurrence type (early/late), Child-Pugh class, TNM stage and adjuvant treatment after tumour recurrence (none or one/more than one treatment) were independent factors for overall survival. None of the mtDNA variations served as independent factors. Patients with late recurrence, Child-Pugh class A, and low TNM stages and/or those who received more than one adjuvant treatment

  13. Phylogenetic relationships among Octopodidae species in coastal waters of China inferred from two mitochondrial DNA gene sequences.

    PubMed

    Lü, Z M; Cui, W T; Liu, L Q; Li, H M; Wu, C W

    2013-09-19

    Octopus in the family Octopodidae (Mollusca: Cephalopoda) has been generally recognized as a "catch-all" genus. The monophyly of octopus species in China's coastal waters has not yet been studied. In this paper, we inferred the phylogeny of 11 octopus species (family Octopodidae) in China's coastal waters using nucleotide sequences of two mitochondrial DNA genes: cytochrome c oxidase subunit I (COI) and 16S rRNA. Sequence analysis of both genes revealed that the 11 species of Octopodidae fell into four distinct groups, which were genetically distant from one another and exhibited identical phylogenetic resolution. The phylogenies indicated strongly that the genus Octopus in China's coastal waters is also not monophyletic, and it is therefore clear that the Octopodidae systematics in this area requires major revision. It is demonstrated that partial sequence information of both the mitochondrial genes 16S rRNA and COI could be used as diagnostic molecular markers in the identification and resolution of the taxonomic ambiguity of Octopodidae species.

  14. cDNA, genomic sequence cloning and overexpression of giant panda (Ailuropoda melanoleuca) mitochondrial ATP synthase ATP5G1.

    PubMed

    Hou, W-R; Hou, Y-L; Ding, X; Wang, T

    2012-09-03

    The ATP5G1 gene is one of the three genes that encode mitochondrial ATP synthase subunit c of the proton channel. We cloned the cDNA and determined the genomic sequence of the ATP5G1 gene from the giant panda (Ailuropoda melanoleuca) using RT-PCR technology and touchdown-PCR, respectively. The cloned cDNA fragment contains an open reading frame of 411 bp encoding 136 amino acids; the length of the genomic sequence is of 1838 bp, containing three exons and two introns. Alignment analysis revealed that the nucleotide sequence and the deduced protein sequence are highly conserved compared to Homo sapiens, Mus musculus, Rattus norvegicus, Bos taurus, and Sus scrofa. The homologies for nucleotide sequences of the giant panda ATP5G1 to those of these species are 93.92, 92.21, 92.46, 93.67, and 92.46%, respectively, and the homologies for amino acid sequences are 90.44, 95.59, 93.38, 94.12, and 91.91%, respectively. Topology prediction showed that there is one protein kinase C phosphorylation site, one casein kinase II phosphorylation site, five N-myristoylation sites, and one ATP synthase c subunit signature in the ATP5G1 protein of the giant panda. The cDNA of ATP5G1 was transfected into Escherichia coli, and the ATP5G1 fused with the N-terminally GST-tagged protein gave rise to accumulation of an expected 40-kDa polypeptide, which had the characteristics of the predicted protein.

  15. Relationships within aphids Cinara (Cupressobium) (Hemiptera) based on mitochondrial and nuclear DNA sequences.

    PubMed

    Durak, Roma; Lachowska-Cierlik, Dorota; Bartoszewski, Sławomir

    2014-02-01

    The relationships between Cinara (Cupressobium) aphids inhabiting woody parts and leaves of conifers belonging to Cupressaceae have been studied using a mitochondrial gene (COI) and a nuclear gene (EF1-α). Based on the COI sequences, genetic distances between species ranged from 5.6 % between Cinara (C.) tujafilina (del Guercio) and Cinara (C.) juniperi (De Geer) to 10.5 % between C. (C.) tujafilina and Cinara (C.) mordvilkoi (Pašek). Genetic distances among EF1-α sequences were lower and showed from 0.1 % between C. cupressi and C. juniperi to 2.3 % between C. tujafilina and C. mordvilkoi. Molecular phylogenetic trees were constructed using the Bayesian inference (BI) phylogenetic analysis and maximum parsimony (MP) criterion. Phylogenetic trees obtained based on COI and EF1-α marker genes created two sister clades. Our results indicate that Cinara (Cupressobium) are a monophyletic group of aphids. Phylogenetic relationships amongst Cupressobium aphids do not result from the association with the host plant, but from the feeding site on the host plant or an ability to change the microhabitat on the plant. As closely related species inhabit similar microhabitats on different host plants, it suggests that the host switching is the main mode of speciation in this subgenus.

  16. Phylogeography of Douglas-fir based on mitochondrial and chloroplast DNA sequences: testing hypotheses from the fossil record.

    PubMed

    Gugger, Paul F; Sugita, Shinya; Cavender-Bares, Jeannine

    2010-05-01

    The integration of fossil and molecular data can provide a synthetic understanding of the ecological and evolutionary history of an organism. We analysed range-wide maternally inherited mitochondrial DNA and paternally inherited chloroplast DNA sequence data with coalescent simulations and traditional population genetic methods to test hypotheses of population divergence generated from the fossil record of Douglas-fir (Pseudotsuga menziesii), an ecologically and economically important western North American conifer. Specifically, we tested (i) the hypothesis that the Pliocene orogeny of the Cascades and Sierra Nevada caused the divergence of coastal and Rocky Mountain Douglas-fir varieties; and (ii) the hypothesis that multiple glacial refugia existed on the coast and in the Rocky Mountains. We found that Douglas-fir varieties diverged about 2.11 Ma (4.37 Ma-755 ka), which could be consistent with a Pliocene divergence. Rocky Mountain Douglas-fir probably resided in three or more glacial refugia. More variable molecular markers would be required to detect the two coastal refugia suggested in the fossil record. Comparison of mitochondrial DNA and chloroplast DNA variation revealed that gene flow via pollen linked populations isolated from seed exchange. Postglacial colonization of Canada from coastal and Rocky Mountain refugia near the ice margin at the Last Glacial Maximum produced a wide hybrid zone among varieties that formed almost exclusively by pollen exchange and chloroplast DNA introgression, not seed exchange. Postglacial migration rates were 50-165 m/year, insufficient to track projected 21st century warming in some regions. Although fossil and genetic data largely agree, each provides unique insights.

  17. Monitoring of Fasciola Species Contamination in Water Dropwort by cox1 Mitochondrial and ITS-2 rDNA Sequencing Analysis.

    PubMed

    Choi, In-Wook; Kim, Hwang-Yong; Quan, Juan-Hua; Ryu, Jae-Gee; Sun, Rubing; Lee, Young-Ha

    2015-10-01

    Fascioliasis, a food-borne trematode zoonosis, is a disease primarily in cattle and sheep and occasionally in humans. Water dropwort (Oenanthe javanica), an aquatic perennial herb, is a common second intermediate host of Fasciola, and the fresh stems and leaves are widely used as a seasoning in the Korean diet. However, no information regarding Fasciola species contamination in water dropwort is available. Here, we collected 500 samples of water dropwort in 3 areas in Korea during February and March 2015, and the water dropwort contamination of Fasciola species was monitored by DNA sequencing analysis of the Fasciola hepatica and Fasciola gigantica specific mitochondrial cytochrome c oxidase subunit 1 (cox1) and nuclear ribosomal internal transcribed spacer 2 (ITS-2). Among the 500 samples assessed, the presence of F. hepatica cox1 and 1TS-2 markers were detected in 2 samples, and F. hepatica contamination was confirmed by sequencing analysis. The nucleotide sequences of cox1 PCR products from the 2 F. hepatica-contaminated samples were 96.5% identical to the F. hepatica cox1 sequences in GenBank, whereas F. gigantica cox1 sequences were 46.8% similar with the sequence detected from the cox1 positive samples. However, F. gigantica cox1 and ITS-2 markers were not detected by PCR in the 500 samples of water dropwort. Collectively, in this survey of the water dropwort contamination with Fasciola species, very low prevalence of F. hepatica contamination was detected in the samples.

  18. Mitochondrial COII sequences and modern human origins.

    PubMed

    Ruvolo, M; Zehr, S; von Dornum, M; Pan, D; Chang, B; Lin, J

    1993-11-01

    The aim of this study is to measure human mitochondrial sequence variability in the relatively slowly evolving mitochondrial gene cytochrome oxidase subunit II (COII) and to estimate when the human common ancestral mitochondrial type existed. New COII gene sequences were determined for five humans (Homo sapiens), including some of the most mitochondrially divergent humans known; for two pygmy chimpanzees (Pan paniscus); and for a common chimpanzee (P. troglodytes). COII sequences were analyzed with those from another relatively slowly evolving mitochondrial region (ND4-5). From class 1 (third codon position) sequence data, a relative divergence date for the human mitochondrial ancestor is estimated as 1/27 th of the human-chimpanzee divergence time. If it is assumed that humans and chimpanzees diverged 6 Mya, this places a human mitochondrial ancestor at 222,000 years, significantly different from 1 Myr (the presumed time of an H. erectus emergence from Africa). The mean coalescent time estimated from all 1,580 sites of combined mitochondrial data, when a 6-Mya human-chimpanzee divergence is assumed, is 298,000 years, with 95% confidence interval of 129,000-536,000 years. Neither estimate is compatible with a 1-Myr-old human mitochondrial ancestor. The mitochondrial DNA sequence data from COII and ND4-5 regions therefore do not support this multiregional hypothesis for the emergence of modern humans.

  19. Molecular phylogeography of the brown bear (Ursus arctos) in Northeastern Asia based on analyses of complete mitochondrial DNA sequences.

    PubMed

    Hirata, Daisuke; Mano, Tsutomu; Abramov, Alexei V; Baryshnikov, Gennady F; Kosintsev, Pavel A; Vorobiev, Alexandr A; Raichev, Evgeny G; Tsunoda, Hiroshi; Kaneko, Yayoi; Murata, Koichi; Fukui, Daisuke; Masuda, Ryuichi

    2013-07-01

    To further elucidate the migration history of the brown bears (Ursus arctos) on Hokkaido Island, Japan, we analyzed the complete mitochondrial DNA (mtDNA) sequences of 35 brown bears from Hokkaido, the southern Kuril Islands (Etorofu and Kunashiri), Sakhalin Island, and the Eurasian Continent (continental Russia, Bulgaria, and Tibet), and those of four polar bears. Based on these sequences, we reconstructed the maternal phylogeny of the brown bear and estimated divergence times to investigate the timing of brown bear migrations, especially in northeastern Eurasia. Our gene tree showed the mtDNA haplotypes of all 73 brown and polar bears to be divided into eight divergent lineages. The brown bear on Hokkaido was divided into three lineages (central, eastern, and southern). The Sakhalin brown bear grouped with eastern European and western Alaskan brown bears. Etorofu and Kunashiri brown bears were closely related to eastern Hokkaido brown bears and could have diverged from the eastern Hokkaido lineage after formation of the channel between Hokkaido and the southern Kuril Islands. Tibetan brown bears diverged early in the eastern lineage. Southern Hokkaido brown bears were closely related to North American brown bears.

  20. What Is Peromyscus? Evidence from nuclear and mitochondrial DNA sequences suggests the need for a new classification

    PubMed Central

    Platt, Roy N.; Amman, Brian R.; Keith, Megan S.; Thompson, Cody W.; Bradley, Robert D.

    2015-01-01

    The evolutionary relationships between Peromyscus, Habromys, Isthmomys, Megadontomys, Neotomodon, Osgoodomys, and Podomys are poorly understood. In order to further explore the evolutionary boundaries of Peromyscus and compare potential taxonomic solutions for this diverse group and its relatives, we conducted phylogenetic analyses of DNA sequence data from alcohol dehydrogenase (Adh1-I2), beta fibrinogen (Fgb-I7), interphotoreceptor retinoid-binding protein (Rbp3), and cytochrome-b (Cytb). Phylogenetic analyses of mitochondrial and nuclear genes produced similar topologies although levels of nodal support varied. The best-supported topology was obtained by combining nuclear and mitochondrial sequences. No monophyletic Peromyscus clade was supported. Instead, support was found for a clade containing Habromys, Megadontomys, Neotomodon, Osgoodomys, Podomys, and Peromyscus suggesting paraphyly of Peromyscus and confirming previous observations. Our analyses indicated an early divergence of Isthmomys from Peromyscus (approximately 8 million years ago), whereas most other peromyscine taxa emerged within the last 6 million years. To recover a monophyletic taxonomy from Peromyscus and affiliated lineages, we detail 3 taxonomic options in which Habromys, Megadontomys, Neotomodon, Osgoodomys, and Podomys are retained as genera, subsumed as subgenera, or subsumed as species groups within Peromyscus. Each option presents distinct taxonomic challenges, and the appropriate taxonomy must reflect the substantial levels of morphological divergence that characterize this group while maintaining the monophyletic relationships obtained from genetic data. PMID:26937047

  1. What Is Peromyscus? Evidence from nuclear and mitochondrial DNA sequences suggests the need for a new classification.

    PubMed

    Platt, Roy N; Amman, Brian R; Keith, Megan S; Thompson, Cody W; Bradley, Robert D

    2015-08-03

    The evolutionary relationships between Peromyscus, Habromys, Isthmomys, Megadontomys, Neotomodon, Osgoodomys, and Podomys are poorly understood. In order to further explore the evolutionary boundaries of Peromyscus and compare potential taxonomic solutions for this diverse group and its relatives, we conducted phylogenetic analyses of DNA sequence data from alcohol dehydrogenase (Adh1-I2), beta fibrinogen (Fgb-I7), interphotoreceptor retinoid-binding protein (Rbp3), and cytochrome-b (Cytb). Phylogenetic analyses of mitochondrial and nuclear genes produced similar topologies although levels of nodal support varied. The best-supported topology was obtained by combining nuclear and mitochondrial sequences. No monophyletic Peromyscus clade was supported. Instead, support was found for a clade containing Habromys, Megadontomys, Neotomodon, Osgoodomys, Podomys, and Peromyscus suggesting paraphyly of Peromyscus and confirming previous observations. Our analyses indicated an early divergence of Isthmomys from Peromyscus (approximately 8 million years ago), whereas most other peromyscine taxa emerged within the last 6 million years. To recover a monophyletic taxonomy from Peromyscus and affiliated lineages, we detail 3 taxonomic options in which Habromys, Megadontomys, Neotomodon, Osgoodomys, and Podomys are retained as genera, subsumed as subgenera, or subsumed as species groups within Peromyscus. Each option presents distinct taxonomic challenges, and the appropriate taxonomy must reflect the substantial levels of morphological divergence that characterize this group while maintaining the monophyletic relationships obtained from genetic data.

  2. Maternal Origin of Turkish and Iranian Native Chickens Inferred from Mitochondrial DNA D-loop Sequences

    PubMed Central

    Meydan, Hasan; Jang, Cafer Pish; Yıldız, Mehmet Ali; Weigend, Steffen

    2016-01-01

    To assess genetic diversity and maternal origin of Turkish and Iranian native chicken breeds, we analyzed the mtDNA D-loop sequences of 222 chickens from 2 Turkish (Denizli and Gerze) and 7 Iranian (White Marandi, Black Marandi, Naked Neck, Common Breed, Lari, West Azarbaijan, and New Hampshire) native chicken breeds, together with the available reference sequences of G. gallus gallus in GenBank. The haplotype diversity was estimated as 0.24±0.01 and 0.36±0.02 for Turkish and Iranian populations, respectively. In total, 19 haplotypes were observed from 24 polymorphic sites in Turkish and Iranian native chicken populations. Two different clades or haplogroups (A and E) were found in Turkish and Iranian chickens. Clade A haplotypes were found only in White Marandi, Common Breed and New Hampshire populations. Clade E haplotypes, which are quite common, were observed in Turkish and Iranian populations with 18 different haplotypes, of which Turkish and Iranian chickens, Clade E, haplotype 1 (TRIRE1) was a major haplotype with the frequency of 81.5% (181/222) across all breeds. Compared to red jungle fowl, Turkish and Iranian chicken breeds are closely related to each other. These results suggest that Turkish and Iranian chickens originated from the same region, the Indian subcontinent. Our results will provide reliable basic information for mtDNA haplotypes of Turkish and Iranian chickens and for studying the origin of domestic chickens. PMID:27189637

  3. Comparison of mitochondrial DNA control region sequence and microsatellite DNA analyses in estimating population structure and gene flow rates in Atlantic sturgeon Acipenser oxyrinchus

    USGS Publications Warehouse

    Wirgin, I.; Waldman, J.; Stabile, J.; Lubinski, B.; King, T.

    2002-01-01

    Atlantic sturgeon Acipenser oxyrinchus is large, long-lived, and anadromous with subspecies distributed along the Atlantic (A. oxyrinchus oxyrinchus) and Gulf of Mexico (A. o. desotoi) coasts of North America. Although it is not certain if extirpation of some population units has occurred, because of anthropogenic influences abundances of all populations are low compared with historical levels. Informed management of A. oxyrinchus demands a detailed knowledge of its population structure, levels of genetic diversity, and likelihood to home to natal rivers. We compared the use of mitochondrial DNA (mtDNA) control region sequence and microsatellite nuclear DNA (nDNA) analyses in identifying the stock structure and homing fidelity of Atlantic and Gulf coast populations of A. oxyrinchus. The approaches were concordant in that they revealed moderate to high levels of genetic diversity and suggested that populations of Atlantic sturgeon are highly structured. At least six genetically distinct management units were detected using the two approaches among the rivers surveyed. Mitochondrial DNA sequences revealed a significant cline in haplotype diversity along the Atlantic coast with monomorphism observed in Canadian populations. High levels of nDNA diversity were also observed among populations along the Atlantic coast, including the two Canadian populations, probably resulting from the more rapid rate of mutational and evolutionary change at microsatellite loci. Estimates of gene flow among populations were similar between both approaches with the exception that because of mtDNA monomorphism in Canadian populations, gene flow estimates between them were unobtainable. Analyses of both genomes provided high resolution and confidence in characterizing the population structure of Atlantic sturgeon. Microsatellite analysis was particularly informative in delineating population structure in rivers that were recently glaciated and may prove diagnostic in rivers that are

  4. Phylogenetic relationships among cirrate octopods (Mollusca: Cephalopoda) resolved using mitochondrial 16S ribosomal DNA sequences.

    PubMed

    Piertney, Stuart B; Hudelot, Cendrine; Hochberg, F G; Collins, Martin A

    2003-05-01

    PHYLOGENETIC RELATIONSHIPS AMONG THE CIRRATE OCTOPODS (MOLLUSCA: Cephalopoda) were investigated using partial sequences of the 16S rRNA mitochondrial gene. The derived phylogeny supports the traditional separation of cirrate families based on web form. Genera with a single web (Opisthoteuthis, Grimpoteuthis, Luteuthis, and Cirroctopus) are clearly distinct from those with an intermediate or secondary web (Cirroteuthis, Cirrothauma, and Stauroteuthis). The cirrates with a single web are separated into three groups. The first group is represented by Opisthoteuthis species, the second by Grimpoteuthis and Luteuthis, and the third by members of the genus Cirroctopus. There is no support for the isolation of Luteuthis in a separate family (Luteuthidae). There is, however, evidence of two groupings within the genus Opisthoteuthis. The data suggest the following revisions in the systematic classification of the cirrates: (1) Cirrothauma, Cirroteuthis, and Stauroteuthis be united in the Cirroteuthidae; (2) Grimpoteuthis and Luteuthis be placed in the Grimpoteuthidae; (3) Opisthoteuthis in the Opisthoteuthidae, and; (4) Cirroctopus be considered sufficiently distinct from both Opisthoteuthidae and Grimpoteuthidae to warrant placement in a new family.

  5. Molecular phylogeny of the large carpenter bees, genus Xylocopa (Hymenoptera: apidae), based on mitochondrial DNA sequences.

    PubMed

    Leys, R; Cooper, S J; Schwarz, M P

    2000-12-01

    Carpenter bees, genus Xylocopa Latreille, a group of bees found on all continents, are of particular interest to behavioral ecologists because of their utility for studies of the evolution of mating strategies and sociality. This paper presents phylogenetic analyses based on sequences of two mitochondrial genes cytochrome oxidase 1 and cytochrome b for 22 subgenera of Xylocopa. Maximum-parsimony and maximum-likelihood methods were used to infer phylogenetic relationships. The analyses resulted in three resolved clades of subgenera: a South American group (including the subgenera Stenoxylocopa, Megaxylocopa, and Neoxylocopa), a group including the subgenera Xylocopa s.s. and Ctenoxylocopa, and an Ethiopean group (including the subgenera Afroxylocopa, Mesotrichia, Alloxylocopa, Platynopoda, Hoploxylocopa, and Koptortosoma). The relationships between the 11 other subgenera and the resolved clades are unclear. Within the Ethiopian group we found a clear separation of the African and the Oriental taxa and apparent polyphyly of the subgenus Koptortosoma. Using an evolutionary rate for ants, we investigated whether Gondwana vicariance or more recent dispersal events could best explain the present-day distribution of subgenera. Although some taxa show divergences that approach Gondwanan breakup times, most divergences between geographic groups are too recent to support a vicariance hypothesis.

  6. A phylogenetic analysis of Pseudonaja (Hydrophiinae, Elapidae, Serpentes) based on mitochondrial DNA sequences.

    PubMed

    Skinner, Adam; Donnellan, Stephen C; Hutchinson, Mark N; Hutchinson, Rhonda G

    2005-11-01

    A phylogenetic analysis of mitochondrial ND4 and adjacent tRNA sequences for a geographically extensive series of specimens reveals nine major clades within Pseudonaja, of which six are largely coincident with nominal taxa (P. affinis, P. guttata, P. inframacula, P. ingrami, P. modesta, and P. textilis). The remaining three clades are composed of specimens presently referred to P. nuchalis. Two of these clades correspond with the "Darwin" and "Southern" morphs of previous authors, while the third clade incorporates the "Orange with black head" and "Pale head, grey nape" morphs. We are unable to confirm the presence of consistent karyotypic differences between "Orange with black head" and "Pale head, grey nape" specimens, however, P. inframacula, P. textilis, and P. nuchalis "Darwin" are found to exhibit distinctive karyotypes, as previously reported. These results, in conjunction with additional observations of karyotpic and morphological variation, are consistent with nine historically-independent lineages (i.e., species) within Pseudonaja. There is strong support for a clade composed of P. affinis, P. inframacula, P. ingrami, P. textilis, and the three P. nuchalis lineages, and for the relationships (P. inframacula, P. nuchalis "Southern") and (P. nuchalis "Darwin", P. nuchalis "Orange with black head"--"Pale head, grey nape" ).

  7. Phylogenetic relationships among the family Ommastrephidae (Mollusca: Cephalopoda) inferred from two mitochondrial DNA gene sequences.

    PubMed

    Wakabayashi, T; Suzuki, N; Sakai, M; Ichii, T; Chow, S

    2012-09-01

    Squids of the family Ommastrephidae are distributed worldwide, and the family includes many species of commercial importance. To investigate phylogenetic relationships among squid species of the family Ommastrephidae, partial nucleotide sequences of two mitochondrial gene loci (cytochrome c oxidase subunit I [1277bp] and 16S rRNA [443bp]) of 15 ommastrephid species and two outgroup species from the families Loliginidae and Enoploteuthidae were determined and used to construct parsimony and distance based phylogenetic trees. The molecular data provided several new phylogenetic inferences. The monophyletic status of three subfamilies (Illicinae, Todarodinae and Ommastrephinae) was well supported, although phylogenetic relationships between the subfamilies were not resolved. Inclusion of a problematic species, Ornithoteuthis volatilis, to Todarodinae was indicated. Within Todarodinae, the Japanese common squid Todarodes pacificus was observed to have much closer relationship to the species of the genus Nototodarus than to its congener (Todarodes filippovae). These results indicate that re-evaluation of several morphological key characters for ommastrephid taxonomy may be necessary.

  8. Phylogenetic relationships in European Ceriporiopsis species inferred from nuclear and mitochondrial ribosomal DNA sequences.

    PubMed

    Tomšovský, Michal; Menkis, Audrius; Vasaitis, Rimvydas

    2010-04-01

    The aim of this work was to clarify taxonomy and examine evolutionary relationships within European Ceriporiopsis species using a combined analysis of the large subunit (nLSU) nuclear rRNA and small subunit (mtSSU) mitochondrial rRNA gene sequences. Data from the ITS region were applied to enhance the view of the phylogenetic relationships among different species. The studied samples grouped into four complex clades, suggesting that the genus Ceriporiopsis is polyphyletic. The generic type Ceriporiopsis gilvescens formed a separate group together with Ceriporiopsis guidella and Phlebia spp. in the phlebioid clade. In this clade, the closely related species Ceriporiopsis resinascens and Ceriporiopsis pseudogilvescens grouped together with Ceriporiopsis aneirina. C. resinascens and C. pseudogilvescens have identical LSU and SSU sequences but differ in ITS. Ceriporiopsis pannocincta also fell in the phlebioid clade, but showed closer proximity to Gloeoporus dichrous than to C. gilvescens or C. aneirina-C. pseudogilvescens-C. resinascens group. Another clade was composed of a Ceriporiopsis balaenae-Ceriporiopsis consobrina group and was found to be closely related to Antrodiella and Frantisekia, with the overall clade highly reminiscent of the residual polyporoid clade. The monotypic genus Pouzaroporia, erected in the past for Ceriporiopsis subrufa due to its remarkable morphological differences, also fell within the residual polyporoid clade. Ceriporiopsis subvermispora held an isolated position from the other species of the genus. Therefore, the previously proposed name Gelatoporia subvermispora has been adopted for this species. Physisporinus rivulosus appeared unrelated to two other European Physisporinus species. Moreover, Ceriporiopsis (=Skeletocutis) jelicii grouped in a separate clade, distinct from Ceriporiopsis species. Finally, the ITS data demonstrated the proximity of some Ceriporiopsis species (Ceriporiopsis portcrosensis and Ceriporiopsis

  9. Interference of Co-amplified nuclear mitochondrial DNA sequences on the determination of human mtDNA heteroplasmy by Using the SURVEYOR nuclease and the WAVE HS system.

    PubMed

    Yen, Hsiu-Chuan; Li, Shiue-Li; Hsu, Wei-Chien; Tang, Petrus

    2014-01-01

    High-sensitivity and high-throughput mutation detection techniques are useful for screening the homoplasmy or heteroplasmy status of mitochondrial DNA (mtDNA), but might be susceptible to interference from nuclear mitochondrial DNA sequences (NUMTs) co-amplified during polymerase chain reaction (PCR). In this study, we first evaluated the platform of SURVEYOR Nuclease digestion of heteroduplexed DNA followed by the detection of cleaved DNA by using the WAVE HS System (SN/WAVE-HS) for detecting human mtDNA variants and found that its performance was slightly better than that of denaturing high-performance liquid chromatography (DHPLC). The potential interference from co-amplified NUMTs on screening mtDNA heteroplasmy when using these 2 highly sensitive techniques was further examined by using 2 published primer sets containing a total of 65 primer pairs, which were originally designed to be used with one of the 2 techniques. We confirmed that 24 primer pairs could amplify NUMTs by conducting bioinformatic analysis and PCR with the DNA from 143B-ρ0 cells. Using mtDNA extracted from the mitochondria of human 143B cells and a cybrid line with the nuclear background of 143B-ρ0 cells, we demonstrated that NUMTs could affect the patterns of chromatograms for cell DNA during SN-WAVE/HS analysis of mtDNA, leading to incorrect judgment of mtDNA homoplasmy or heteroplasmy status. However, we observed such interference only in 2 of 24 primer pairs selected, and did not observe such effects during DHPLC analysis. These results indicate that NUMTs can affect the screening of low-level mtDNA variants, but it might not be predicted by bioinformatic analysis or the amplification of DNA from 143B-ρ0 cells. Therefore, using purified mtDNA from cultured cells with proven purity to evaluate the effects of NUMTs from a primer pair on mtDNA detection by using PCR-based high-sensitivity methods prior to the use of a primer pair in real studies would be a more practical strategy.

  10. Phylogenetic relationships among the Caribbean members of the Cliona viridis complex (Porifera, Demospongiae, Hadromerida) using nuclear and mitochondrial DNA sequences.

    PubMed

    Escobar, Dairo; Zea, Sven; Sánchez, Juan A

    2012-08-01

    Species complexes - groups of closely related species in which intraspecific and interspecific variability overlap - have generated considerable interest and study. Frequently, members of a species complex do not have complete reproductive isolation; therefore, the complex may go through extensive gene flow. In the Caribbean Sea, some encrusting and excavating sponges of the genus Cliona (Porifera, Hadromerida, Clionaidae) are grouped within the great "Cliona viridis" complex because of their morphological similarities. This study examined the evolutionary relationships of the Caribbean members of this complex (C. caribbaea, C. tenuis, C. aprica and C. varians) and related taxa based on nuclear (ITS1 and ITS2) and mitochondrial (3' end of ND6) DNA sequences. The intragenomic ITS variation and its secondary structures were evaluated using a mixed approach of Denaturing Gradient Gel Electrophoresis (DGGE), DNA sequencing and secondary structure prediction. Considerable intragenomic variation was found in all the species, with apparently functional ITS1 and ITS2 secondary structures. Despite the subtle but clear morphological differentiation in these excavating sponges, the intragenomic copies of C. caribbaea, C. tenuis and C. aprica had a polyphyletic placement in the ITS1 and ITS2 genealogies and very low divergence. Therefore, it is clear that these species constitute a species complex (herein called Ct-complex). Genetic distances within the Ct-complex revealed that an important part of the interspecific variation overlapped with intraspecific variation, suggesting either incomplete lineage sorting or extensive gene flow. In contrast, C. varians and an unidentified "Pione" species emerged as monophyletic clades, being the closest sister groups to the Ct-complex. Additionally, our results support that C. laticavicola and C. delitrix conform a monophyletic group, but absence of reciprocal monophyly in these species suggests they may be life stages or ecophenotypes of

  11. Evolutionary relationships among the true vipers (Reptilia: Viperidae) inferred from mitochondrial DNA sequences.

    PubMed

    Lenk, P; Kalyabina, S; Wink, M; Joger, U

    2001-04-01

    Nucleotide sequences of mitochondrial cytochrome b and 16S rRNA genes, totaling 946 bp, were used to reconstruct a molecular phylogeny of 42 species of the subfamily Viperinae representing 12 of the 13 recognized genera. Maximum-parsimony and maximum-likelihood were used as methods for phylogeny reconstruction with and without a posteriori weighting. When representatives of the Causinae were taken as outgroup, five major monophyletic groups were consistently identified: Bitis, Cerastes, Echis, the Atherini (Atheris s.l.), and the Eurasian viperines. Proatheris was affiliated with Atheris, and Adenorhinos clustered within Atheris. The African Bitis consisted of at least three monophyletic groups: (i) the B. gabonica group, (ii) the B. caudalis group, and (iii) the B. cornuta group. B. worthingtoni and B. arietans are not included in any of these lineages. Eurasian viperines could be unambiguously devided into four monophyletic groups: (i) Pseudocerastes and Eristicophis, (ii) European vipers (Vipera s.str.), (iii) Middle East Macrovipera plus Montivipera (Vipera xanthina group), and (iv) North African Macrovipera plus Vipera palaestinae and Daboia russelii. These evolutionary lineages are consistent with historical biogeographical patterns. According to our analyses, the viperines originated in the Oligocene in Africa and successively underwent a first radiation leading to the five basal groups. The radiation might have been driven by the possession of an effective venom apparatus and a foraging startegy (sit-wait-strike) superior in most African biomes and might have been adaptive. The next diversifications led to the Proatheris-Atheris furcation, the basal Bitis splitting, and the emergence of the basal lineages within the Eurasian stock. Thereafter, lineages within Echis, Atheris, and Cerastes evolved. The emergence of three groups within Vipera s.l. might have been forced by the existence of three land masses during the early Miocene in the area of the

  12. Retrieval of four adaptive lineages in duiker antelope: evidence from mitochondrial DNA sequences and fluorescence in situ hybridization.

    PubMed

    van Vuuren, B J; Robinson, T J

    2001-09-01

    Independent molecular markers (mitochondrial DNA sequences from two genes and fluorescence in situ hybridization with satellite DNA sequences as hybridization probes) were employed to investigate phylogenetic relationships among duiker antelope. When analyzed singly or taken together, the molecular and cytogenetic data allowed for the delimitation of four adaptive groups: the conservative dwarfs which are basal, a savanna specialist which groups apart from the forest duikers, the giant duikers, and the red duikers. Within the latter, a further subdivision comprising an east African and a west African red duiker clade is evident. The placement of the endangered zebra duiker and Aders' duiker remains problematic. Several of the nomenclatural divisions in current use are questioned by our results. These include the recognition of Philantomba as genus name for the blue and Maxwell's duiker and that Harvey's duiker be relegated to a subspecies of the Natal red duiker. We place our results in a biogeographic context and argue that duiker speciation has been driven predominantly by habitat fragmentation which probably led to the disruption of gene flow between geographic populations.

  13. Mitochondrial DNA sequence analysis of the Mexican Creole sheep (Ovis aries) reveals a narrow Iberian maternal origin.

    PubMed

    Alonso, Rogelio A; Ulloa-Arvizu, Raul; Gayosso-Vázquez, Amanda

    2017-01-31

    The Creole sheep in America is supposed to have originated specifically from the Iberian Peninsula and introduced by the Spaniards during the colonization. However, it is not clear their genetic relationship with Iberian breeds. The genetic origin and diversity of the Mexican Creole sheep (MCS) were investigated by mitochondrial DNA control region nucleotide sequences. DNA sequence from 33 MCS samples from three regions of México revealed 21 different haplotypes. Phylogenetic analysis including European and Iberian sheep haplotypes showed that the MCS population belongs to a differentiated and defined genetic lineage. This finding suggests that the MCS populations may be the result of a founder effect originating from a discrete Iberian population. MCS haplotypes were related to haplotypes found in the Churro Trunk and the Entrefino Trunk groups of Iberian breeds, supporting historical reports. In the Mexican genetic branch, there were also haplotypes reported from Lacaune and Awassi sheep breeds. Although it is uncertain whether a particular breed was involved as a founder of the MCS, these populations have a common phylogenetic origin.

  14. Mitochondrial DNA diversity in the acanthocephalan Prosthenorchis elegans in Colombia based on cytochrome c oxidase I (COI) gene sequence.

    PubMed

    Falla, Ana Carolina; Brieva, Claudia; Bloor, Paul

    2015-12-01

    Prosthenorchis elegans is a member of the Phylum Acanthocephala and is an important parasite affecting New World Primates in the wild in South America and in captivity around the world. It is of significant management concern due to its pathogenicity and mode of transmission through intermediate hosts. Current diagnosis of P. elegans is based on the detection of eggs by coprological examination. However, this technique lacks both specificity and sensitivity, since eggs of most members of the genus are morphologically indistinguishable and shed intermittently, making differential diagnosis difficult, and coprological examinations are often negative in animals severely infected at death. We examined sequence variation in 633 bp of mitochondrial DNA (mtDNA) cytochrome c oxidase I (COI) sequence in 37 isolates of P. elegans from New World monkeys (Saguinus leucopus and Cebus albifrons) in Colombia held in rescue centers and from the wild. Intraspecific divergence ranged from 0.0 to 1.6% and was comparable with corresponding values within other species of acanthocephalans. Furthermore, comparisons of patterns of sequence divergence within the Acanthocephala suggest that Prosthenorchis represents a separate genus within the Oligacanthorhynchida. Six distinct haplotypes were identified within P. elegans which grouped into one of two well-supported mtDNA haplogroups. No association between haplogroup/haplotype, holding facility and species was found. This information will help pave the way to the development of molecular-based diagnostic tools for the detection of P. elegans as well as furthering research into the life cycle, intermediate hosts and epidemiological aspects of the species.

  15. Mitochondrial DNA diversity in the acanthocephalan Prosthenorchis elegans in Colombia based on cytochrome c oxidase I (COI) gene sequence

    PubMed Central

    Falla, Ana Carolina; Brieva, Claudia; Bloor, Paul

    2015-01-01

    Prosthenorchis elegans is a member of the Phylum Acanthocephala and is an important parasite affecting New World Primates in the wild in South America and in captivity around the world. It is of significant management concern due to its pathogenicity and mode of transmission through intermediate hosts. Current diagnosis of P. elegans is based on the detection of eggs by coprological examination. However, this technique lacks both specificity and sensitivity, since eggs of most members of the genus are morphologically indistinguishable and shed intermittently, making differential diagnosis difficult, and coprological examinations are often negative in animals severely infected at death. We examined sequence variation in 633 bp of mitochondrial DNA (mtDNA) cytochrome c oxidase I (COI) sequence in 37 isolates of P. elegans from New World monkeys (Saguinus leucopus and Cebus albifrons) in Colombia held in rescue centers and from the wild. Intraspecific divergence ranged from 0.0 to 1.6% and was comparable with corresponding values within other species of acanthocephalans. Furthermore, comparisons of patterns of sequence divergence within the Acanthocephala suggest that Prosthenorchis represents a separate genus within the Oligacanthorhynchida. Six distinct haplotypes were identified within P. elegans which grouped into one of two well-supported mtDNA haplogroups. No association between haplogroup/haplotype, holding facility and species was found. This information will help pave the way to the development of molecular-based diagnostic tools for the detection of P. elegans as well as furthering research into the life cycle, intermediate hosts and epidemiological aspects of the species. PMID:26759793

  16. Complete mitochondrial DNA sequence of the endangered giant sable antelope (Hippotragus niger variani): insights into conservation and taxonomy.

    PubMed

    Espregueira Themudo, Gonçalo; Rufino, Ana C; Campos, Paula F

    2015-02-01

    The giant sable antelope is one of the most endangered African bovids. Populations of this iconic animal, the national symbol of Angola, were recently rediscovered, after many decades of presumed extinction. Even so, their numbers are scarce and hence conservation plans are essential. However, fundamental information such as its taxonomic position, time of divergence and degree of genetic variation are still lacking. Here, we used a museum preserved horn as a source of DNA to describe, for the first time, the complete mitochondrial genome of the giant sable antelope, and provide insights into its evolutionary history. Reads generated by shotgun sequencing were mapped against the mitochondrial genome of common sable antelope and the nuclear genomes of cow and sheep. Phylogenetic reconstruction and divergence time estimate give support to the monophyly of the giant sable and a maximum divergence time of 170 thousand years to the closest subspecies. About 7% of the nuclear genome was mapped against the reference. The genetic resources reported here are now available for future work in the field of conservation genetics and phylogeny, in this and related species.

  17. Complete nucleotide sequences of the domestic cat (Felis catus) mitochondrial genome and a transposed mtDNA tandem repeat (Numt) in the nuclear genome

    SciTech Connect

    Lopez, J.V.; Cevario, S.; O`Brien, S.J.

    1996-04-15

    The complete 17,009-bp mitochondrial genome of the domestic cat, Felis catus, has been sequenced and conforms largely to the typical organization of previously characterized mammalian mtDNAs. Codon usage and base composition also followed canonical vertebrate patterns, except for an unusual ATC (non-AUG) codon initiating the NADH dehydrogenase subunit 2 (ND2) gene. Two distinct repetitive motifs at opposite ends of the control region contribute to the relatively large size (1559 bp) of this carnivore mtDNA. Alignment of the feline mtDNA genome to a homologous 7946-bp nuclear mtDNA tandem repeat DNA sequence in the cat, Numt, indicates simple repeat motifs associated with insertion/deletion mutations. Overall DNA sequence divergence between Numt and cytoplasmic mtDNA sequence was only 5.1%. Substitutions predominate at the third codon position of homologous feline protein genes. Phylogenetic analysis of mitochondrial gene sequences confirms the recent transfer of the cytoplasmic mtDNA sequences to the domestic cat nucleus and recapitulates evolutionary relationships between mammal species. 86 refs., 4 figs., 3 tabs.

  18. Phylogeography of shy and white-capped albatrosses inferred from mitochondrial DNA sequences: implications for population history and taxonomy.

    PubMed

    Abbott, Cathryn L; Double, Michael C

    2003-10-01

    The evolutionary relationship between shy (Thalassarche cauta) and white-capped (T. steadi) albatrosses was examined using mitochondrial control region sequences. Results were interpreted in the context of a recent and contentious taxonomic revision that recommended full species status for shy and white-capped albatrosses. Low sequence divergence between shy and white-capped albatrosses (1.8%) and between their close relatives, Salvin's and Chatham albatrosses (2.9%), was observed. Much higher sequence divergence was found between the shy/white-capped pair and the Salvin's/Chatham pair (7.0%). Phylogenetic analyses confirmed the separation of the shy/white-capped pair from the Salvin's/Chatham pair but did not provide species-level resolution. Phylogeographic analyses, including a nested clade analysis, FST estimates and an analysis of molecular variance, indicated unambiguous genetic structuring between shy and white-capped albatrosses, thus confirming the demographic isolation of the species, but showed little to no structuring within each species. The geographical distribution of mtDNA haplotypes and other evidence suggest that shy albatrosses arose through range expansion by white-capped albatrosses.

  19. Phylogeography of the endangered Cathaya argyrophylla (Pinaceae) inferred from sequence variation of mitochondrial and nuclear DNA.

    PubMed

    Wang, Hong-Wei; Ge, Song

    2006-11-01

    Cathaya argyrophylla is an endangered conifer restricted to subtropical mountains of China. To study phylogeographical pattern and demographic history of C. argyrophylla, species-wide genetic variation was investigated using sequences of maternally inherited mtDNA and biparentally inherited nuclear DNA. Of 15 populations sampled from all four distinct regions, only three mitotypes were detected at two loci, without single region having a mixed composition (G(ST) = 1). Average nucleotide diversity (theta(ws) = 0.0024; pi(s) = 0.0029) across eight nuclear loci is significantly lower than those found for other conifers (theta(ws) = 0.003 approximately 0.015; pi(s) = 0.002 approximately 0.012) based on estimates of multiple loci. Because of its highest diversity among the eight nuclear loci and evolving neutrally, one locus (2009) was further used for phylogeographical studies and eight haplotypes resulting from 12 polymorphic sites were obtained from 98 individuals. All the four distinct regions had at least four haplotypes, with the Dalou region (DL) having the highest diversity and the Bamian region (BM) the lowest, paralleling the result of the eight nuclear loci. An AMOVA revealed significant proportion of diversity attributable to differences among regions (13.4%) and among populations within regions (8.9%). F(ST) analysis also indicated significantly high differentiation among populations (F(ST) = 0.22) and between regions (F(ST) = 0.12-0.38). Non-overlapping distribution of mitotypes and high genetic differentiation among the distinct geographical groups suggest the existence of at least four separate glacial refugia. Based on network and mismatch distribution analyses, we do not find evidence of long distance dispersal and population expansion in C. argyrophylla. Ex situ conservation and artificial crossing are recommended for the management of this endangered species.

  20. Mitochondrial DNA D-loop sequences suggest a Southeast Asian and Indian origin of Zimbabwean village chickens.

    PubMed

    Muchadeyi, F C; Eding, H; Simianer, H; Wollny, C B A; Groeneveld, E; Weigend, S

    2008-12-01

    This study sought to assess mitochondrial DNA (mtDNA) diversity and phylogeographic structure of chickens from five agro-ecological zones of Zimbabwe. Furthermore, chickens from Zimbabwe were compared with populations from other geographical regions (Malawi, Sudan and Germany) and other management systems (broiler and layer purebred lines). Finally, haplotypes of these animals were aligned to chicken sequences, taken from GenBank, that reflected populations of presumed centres of domestication. A 455-bp fragment of the mtDNA D-loop region was sequenced in 283 chickens of 14 populations. Thirty-two variable sites that defined 34 haplotypes were observed. In Zimbabwean chickens, diversity within ecotypes accounted for 96.8% of the variation, indicating little differentiation between ecotypes. The 34 haplotypes clustered into three clades that corresponded to (i) Zimbabwean and Malawian chickens, (ii) broiler and layer purebred lines and Northwest European chickens, and (iii) a mixture of chickens from Zimbabwe, Sudan, Northwest Europe and the purebred lines. Diversity among clades explained more than 80% of the total variation. Results indicated the existence of two distinct maternal lineages evenly distributed among the five Zimbabwean chicken ecotypes. For one of these lineages, chickens from Zimbabwe and Malawi shared major haplotypes with chicken populations that have a Southeast Asian background. The second maternal lineage, probably from the Indian subcontinent, was common to the five Zimbabwean chicken ecotypes, Sudanese and Northwest European chickens as well as purebred broiler and layer chicken lines. A third maternal lineage excluded Zimbabwean and other African chickens and clustered with haplotypes presumably originating from South China.

  1. Single Nucleotides in the mtDNA Sequence Modify Mitochondrial Molecular Function and Are Associated with Sex-Specific Effects on Fertility and Aging.

    PubMed

    Camus, M Florencia; Wolf, Jochen B W; Morrow, Edward H; Dowling, Damian K

    2015-10-19

    Mitochondria underpin energy conversion in eukaryotes. Their small genomes have been the subject of increasing attention, and there is evidence that mitochondrial genetic variation can affect evolutionary trajectories and shape the expression of life-history traits considered to be key human health indicators [1, 2]. However, it is not understood how genetic variation across a diminutive genome, which in most species harbors only about a dozen protein-coding genes, can exert broad-scale effects on the organismal phenotype [2, 3]. Such effects are particularly puzzling given that the mitochondrial genes involved are under strong evolutionary constraint and that mitochondrial gene expression is highly conserved across diverse taxa [4]. We used replicated genetic lines in the fruit fly, Drosophila melanogaster, each characterized by a distinct and naturally occurring mitochondrial haplotype placed alongside an isogenic nuclear background. We demonstrate that sequence variation within the mitochondrial DNA (mtDNA) affects both the copy number of mitochondrial genomes and patterns of gene expression across key mitochondrial protein-coding genes. In several cases, haplotype-mediated patterns of gene expression were gene-specific, even for genes from within the same transcriptional units. This invokes post-transcriptional processing of RNA in the regulation of mitochondrial genetic effects on organismal phenotypes. Notably, the haplotype-mediated effects on gene expression could be traced backward to the level of individual nucleotides and forward to sex-specific effects on fertility and longevity. Our study thus elucidates how small-scale sequence changes in the mitochondrial genome can achieve broad-scale regulation of health-related phenotypes and even contribute to sex-related differences in longevity.

  2. Evolutionary history and phylogeography of the schistosome-vector freshwater snail Biomphalaria glabrata based on nuclear and mitochondrial DNA sequences.

    PubMed

    Mavárez, J; Steiner, C; Pointier, J-P; Jarne, P

    2002-10-01

    The phylogeography of the freshwater snail Biomphalaria glabrata remains poorly known, although this species is the major vector of schistosomiasis in the New World. It was here investigated in South America and the Lesser Antilles, based on partial mitochondrial large ribosomal subunit (16S rDNA) and nuclear internal transcribed spacer-2 (ITS-2) gene sequences. Sampling included 17 populations from a large part of the current geographic range of the species (Brazil, Venezuela and Lesser Antilles). Substantial variability was detected, as well as a high amount of phylogenetically informative signal. The molecular phylogeny inferred splits B. glabrata into Northern and Southern clades separated by the Amazon river, and may even suggest a supra-specific status for B. glabrata. Brazilian populations were the most diverse and appeared basal to the other populations. Venezuelan haplotypes formed a single clade, albeit not strongly supported. Two Venezuelan haplotypes appear rather similar to Brazilian haplotypes. Similarly, Lesser Antilles haplotypes clustered in the same monophyletic clade, which suggests that the recent colonisation of the Antilles has a northern South American origin. However, the estimated divergence time between Antilles and Venezuelan sequences is extremely large (conservatively higher than 10(5) years). These results are discussed in the light of (i) phylogeographic patterns at South American scale, and (ii) recurrent introduction of molluscs, especially in the Antilles, as a consequence of human activities.

  3. Identification of mitochondrial DNA sequence variation and development of single nucleotide polymorphic markers for CMS-D8 in cotton.

    PubMed

    Suzuki, Hideaki; Yu, Jiwen; Wang, Fei; Zhang, Jinfa

    2013-06-01

    Cytoplasmic male sterility (CMS), which is a maternally inherited trait and controlled by novel chimeric genes in the mitochondrial genome, plays a pivotal role in the production of hybrid seed. In cotton, no PCR-based marker has been developed to discriminate CMS-D8 (from Gossypium trilobum) from its normal Upland cotton (AD1, Gossypium hirsutum) cytoplasm. The objective of the current study was to develop PCR-based single nucleotide polymorphic (SNP) markers from mitochondrial genes for the CMS-D8 cytoplasm. DNA sequence variation in mitochondrial genes involved in the oxidative phosphorylation chain including ATP synthase subunit 1, 4, 6, 8 and 9, and cytochrome c oxidase 1, 2 and 3 subunits were identified by comparing CMS-D8, its isogenic maintainer and restorer lines on the same nuclear genetic background. An allelic specific PCR (AS-PCR) was utilized for SNP typing by incorporating artificial mismatched nucleotides into the third or fourth base from the 3' terminus in both the specific and nonspecific primers. The result indicated that the method modifying allele-specific primers was successful in obtaining eight SNP markers out of eight SNPs using eight primer pairs to discriminate two alleles between AD1 and CMS-D8 cytoplasms. Two of the SNPs for atp1 and cox1 could also be used in combination to discriminate between CMS-D8 and CMS-D2 cytoplasms. Additionally, a PCR-based marker from a nine nucleotide insertion-deletion (InDel) sequence (AATTGTTTT) at the 59-67 bp positions from the start codon of atp6, which is present in the CMS and restorer lines with the D8 cytoplasm but absent in the maintainer line with the AD1 cytoplasm, was also developed. A SNP marker for two nucleotide substitutions (AA in AD1 cytoplasm to CT in CMS-D8 cytoplasm) in the intron (1,506 bp) of cox2 gene was also developed. These PCR-based SNP markers should be useful in discriminating CMS-D8 and AD1 cytoplasms, or those with CMS-D2 cytoplasm as a rapid, simple, inexpensive, and

  4. The case for the continuing use of the revised Cambridge Reference Sequence (rCRS) and the standardization of notation in human mitochondrial DNA studies.

    PubMed

    Bandelt, Hans-Jürgen; Kloss-Brandstätter, Anita; Richards, Martin B; Yao, Yong-Gang; Logan, Ian

    2014-02-01

    Since the determination in 1981 of the sequence of the human mitochondrial DNA (mtDNA) genome, the Cambridge Reference Sequence (CRS), has been used as the reference sequence to annotate mtDNA in molecular anthropology, forensic science and medical genetics. The CRS was eventually upgraded to the revised version (rCRS) in 1999. This reference sequence is a convenient device for recording mtDNA variation, although it has often been misunderstood as a wild-type (WT) or consensus sequence by medical geneticists. Recently, there has been a proposal to replace the rCRS with the so-called Reconstructed Sapiens Reference Sequence (RSRS). Even if it had been estimated accurately, the RSRS would be a cumbersome substitute for the rCRS, as the new proposal fuses--and thus confuses--the two distinct concepts of ancestral lineage and reference point for human mtDNA. Instead, we prefer to maintain the rCRS and to report mtDNA profiles by employing the hitherto predominant circumfix style. Tree diagrams could display mutations by using either the profile notation (in conventional short forms where appropriate) or in a root-upwards way with two suffixes indicating ancestral and derived nucleotides. This would guard against misunderstandings about reporting mtDNA variation. It is therefore neither necessary nor sensible to change the present reference sequence, the rCRS, in any way. The proposed switch to RSRS would inevitably lead to notational chaos, mistakes and misinterpretations.

  5. cDNA sequence of a human skeletal muscle ADP/ATP translocator: lack of a leader peptide, divergence from a fibroblast translocator cDNA, and coevolution with mitochondrial DNA genes

    SciTech Connect

    Neckelmann, N.; Li, K.; Wade, R.P.; Shuster, R.; Wallace, D.C.

    1987-11-01

    The authors have characterized a 1400-nucleotide cDNA for the human skeletal muscle ADP/ATP translocator. The deduced amino acid sequence is 94% homologous to the beef heart ADP/ATP translocator protein and contains only a single additional amino-terminal methionine. This implies that the human translocator lacks an amino-terminal targeting peptide, a conclusion substantiated by measuring the molecular weight of the protein synthesized in vitro. A 1400-nucleotide transcript encoding the skeletal muscle translocator was detected on blots of total RNA from human heart, kidney, skeletal muscle, and HeLa cells by hybridization with oligonucleotide probes homologous to the coding region and 3' noncoding region of the cDNA. However, the level of this mRNA varied substantially among tissues. Comparison of our skeletal muscle translocator sequence with that of a recently published human fibroblast translocator cognate revealed that the two proteins are 88% identical and diverged about 275 million years ago. Hence, tissues vary both in the level of expression of individual translocator genes and in differential expression of cognate translocator genes. Comparison of the base substitution rates of the ADP/ATP translocator and the oxidative phosphorylation genes encoded by mitochondrial DNA revealed that the mitochondrial DNA genes fix 10 times more synonymous substitutions and 12 times more replacement substitutions; yet, these nuclear and cytoplasmic respiration genes experience comparable evolutionary constraints. This suggest that the mitochondrial DNA genes are highly prone to deleterious mutations.

  6. Sequence variation in two mitochondrial DNA regions and internal transcribed spacer among isolates of the nematode Oesophagostomum asperum originating from goats in Hunan Province, China.

    PubMed

    Li, F; Hu, T; Duan, N C; Li, W Y; Teng, Q; Li, H; Liu, W; Liu, Y; Cheng, T Y

    2016-01-01

    The present study examined sequence variability in two mitochondrial DNA (mtDNA) regions, namely cytochrome c oxidase subunit 1 (cox1) and NADH dehydrogenase subunit 1 (nad1), and internal transcribed spacer (ITS) of nuclear ribosomal DNA (rDNA) among Oesophagostomum asperum isolates from goats in Hunan Province, China. A portion of the cox1 (pcox1), nad1 (pnad1) genes and the ITS (ITS1+5.8S rDNA+ITS2) rDNA were amplified by polymerase chain reaction (PCR) separately from adult O. asperum individuals and the representative amplicons were subjected to sequencing from both directions. The lengths of pcox1, pnad1 and ITS rDNA were 366 bp, 681 bp and 785 bp, respectively. The A+T contents of gene sequences were 71.5-72% for pcox1, 73.7-74.2% for pnad1 and 58-58.8% for ITS rDNA. Intra-specific sequence variations within O. asperum were 0-1.6% for pcox1, 0-1.9% for pnad1 and 0-1.7% for ITS rDNA, while inter-specific sequence differences among members of the genus Oesophagostomum were significantly higher, being 11.1-12.5%, 13.3-17.7% and 8.5-18.6% for pcox1, pnad1 and ITS rDNA, respectively. Phylogenetic analyses using combined sequences of pcox1 and pnad1, with three different computational algorithms (Bayesian inference, maximum likelihood and maximum parsimony), revealed distinct groups with high statistical support. These findings demonstrated the existence of intra-specific variation in mtDNA and rDNA sequences among O. asperum isolates from goats in Hunan Province, China, and have implications for studying molecular epidemiology and population genetics of O. asperum.

  7. Phylogeny of the sea hares in the aplysia clade based on mitochondrial DNA sequence data

    SciTech Connect

    Medina, Monica; Collins, Timothy; Walsh, Patrick J.

    2004-02-20

    Sea hare species within the Aplysia clade are distributed worldwide. Their phylogenetic and biogeographic relationships are, however, still poorly known. New molecular evidence is presented from a portion of the mitochondrial cytochrome oxidase c subunit 1 gene (cox1) that improves our understanding of the phylogeny of the group. Based on these data a preliminary discussion of the present distribution of sea hares in a biogeographic context is put forward. Our findings are consistent with only some aspects of the current taxonomy and nomenclatural changes are proposed. The first, is the use of a rank free classification for the different Aplysia clades and subclades as opposed to previously used genus and subgenus affiliations. The second, is the suggestion that Aplysia brasiliana (Rang, 1828) is a junior synonym of Aplysia fasciata (Poiret, 1789). The third, is the elimination of Neaplysia since its only member is confirmed to be part of the large Varria clade.

  8. Phylogenetic studies of two Anas platyrhynchos (Anatini: Anatinae) in Hunan province of China based on complete mitochondrial DNA sequences.

    PubMed

    He, Xi; Lin, Qian; Cao, Rong; Yuan, Ya-Ting; Pan, Di-Zi; Yun, Long; Zhang, Shi-Rui; Hou, De-Xing

    2016-07-01

    In this study, we cloned and sequenced the complete mitochondrial DNAs of Chinese duck, Anas platyrhynchos, population from two different areas of Hunan province in China. The Anas platyrhynchos breed Linwu duck (LW) sample was taken from the Linwu county of Chenzhou city, and the Anas platyrhynchos breed Youxian duck (YX) sample was taken from the Youxian county of Zhuzhou city. The lengths of their complete mitochondrial genome were 16,604 bp (LW) and 16,606 bp (YX), respectively. The organization of the two Anas platyrhynchos breed mitochondrial genomes was similar to those reported from other duck mitochondrial genomes. Phylogenetic analyses using N-J computational algorithms showed that the analyzed species are divided into four major clades: Anatinae, Anserinae, Dendrocygninae and Anseranatidae. Also, the Linwu duck and Youxian duck have highly similar phylogenetic relationship.

  9. The complete mitochondrial DNA sequence of the short mackerel (Rastrelliger brachysoma), and its phylogenetic position within Scombroidei, Perciformes.

    PubMed

    Jondeung, Amnuay; Karinthanyakit, Wirangrong

    2010-04-01

    In order to support studies of short mackerel population genetic structure in the Gulf of Thailand and phylogenetic relationships, the mitochondrial genome of the short mackerel, Rastrelliger brachysoma, has recently been determined by a partial cloning technique, long PCR with three pairs of newly designed primers and primer walking sequencing. The complete mitochondrial genome is 16,539 bp in length and contains 37 mitochondrial genes (13 protein-coding genes, 2 ribosomal RNA genes and 22 transfer RNA genes) and a control region (CR) as in other bony fishes. Within the 845-bp CR, we identified several conserved motifs. The phylogeny obtained by Bayesian analyses based on two nucleotide datasets corresponding to the cytb and nd2 mitochondrial genes strongly support the inclusion of R. brachysoma within the monophyletic tribe of Scombrini in the family Scombridae. The obtained phylogeny also reveals high-statistical support for the existence of two distinct groups indicating that Scombroidei and Xiphioidei are two separate suborders.

  10. Phylogeny of hard- and soft-tick taxa (Acari: Ixodida) based on mitochondrial 16S rDNA sequences.

    PubMed Central

    Black, W C; Piesman, J

    1994-01-01

    Ticks are parasitiform mites that are obligate hematophagous ectoparasites of amphibians, reptiles, birds, and mammals. A phylogeny for tick families, subfamilies, and genera has been described based on morphological characters, life histories, and host associations. To test the existing phylogeny, we sequenced approximately 460 bp from the 3' end of the mitochondrial 16S rRNA gene (rDNA) in 36 hard- and soft-tick species; a mesostigmatid mite, Dermanyssus gallinae, was used as an outgroup. Phylogenies derived using distance, maximum-parsimony, or maximum-likelihood methods were congruent. The existing phylogeny was largely supported with four exceptions. In hard ticks (Ixodidae), members of Haemaphysalinae were monophyletic with the primitive Amblyomminae and members of Hyalomminae grouped within the Rhipicephalinae. In soft ticks (Argasidae), the derived phylogeny failed to support a monophyletic relationship among members of Ornithodorinae and supported placement of Argasinae as basal to the Ixodidae, suggesting that hard ticks may have originated from an Argas-like ancestor. Because most Argas species are obligate bird octoparasites, this result supports earlier suggestions that hard ticks did not evolve until the late Cretaceous. PMID:7937832

  11. Mitochondrial and nuclear DNA sequences support a Cretaceous origin of Columbiformes and a dispersal-driven radiation in the Paleocene .

    PubMed

    Pereira, Sergio L; Johnson, Kevin P; Clayton, Dale H; Baker, Allan J

    2007-08-01

    Phylogenetic relationships among genera of pigeons and doves (Aves, Columbiformes) have not been fully resolved because of limited sampling of taxa and characters in previous studies. We therefore sequenced multiple nuclear and mitochondrial DNA genes totaling over 9000 bp from 33 of 41 genera plus 8 outgroup taxa, and, together with sequences from 5 other pigeon genera retrieved from GenBank, recovered a strong phylogenetic hypothesis for the Columbiformes. Three major clades were recovered with the combined data set, comprising the basally branching New World pigeons and allies (clade A) that are sister to Neotropical ground doves (clade B), and the Afro-Eurasian and Australasian taxa (clade C). None of these clades supports the monophyly of current families and subfamilies. The extinct, flightless dodo and solitaires (Raphidae) were embedded within pigeons and doves (Columbidae) in clade C, and monophyly of the subfamily Columbinae was refuted because the remaining subfamilies were nested within it. Divergence times estimated using a Bayesian framework suggest that Columbiformes diverged from outgroups such as Apodiformes and Caprimulgiformes in the Cretaceous before the mass extinction that marks the end of this period. Bayesian and maximum likelihood inferences of ancestral areas, accounting for phylogenetic uncertainty and divergence times, respectively, favor an ancient origin of Columbiformes in the Neotropical portion of what was then Gondwana. The radiation of modern genera of Columbiformes started in the Early Eocene to the Middle Miocene, as previously estimated for other avian groups such as ratites, tinamous, galliform birds, penguins, shorebirds, parrots, passerine birds, and toucans. Multiple dispersals of more derived Columbiformes between Australasian and Afro-Eurasian regions are required to explain current distributions.

  12. Phylogenetic assessment of the earthworm Aporrectodea caliginosa species complex (Oligochaeta: Lumbricidae) based on mitochondrial and nuclear DNA sequences.

    PubMed

    Pérez-Losada, Marcos; Ricoy, Maigualida; Marshall, Jonathon C; Domínguez, Jorge

    2009-08-01

    The Aporrectodea caliginosa species complex includes the most abundant earthworms in grasslands and agricultural ecosystems of the Paleartic region. Historically this complex consisted of the following taxa: A. caliginosa s.s.Savigny, 1826, A. trapezoides Dugés (1828), A. tuberculata (Eisen, 1874), and A. nocturna Evans (1946). These four taxa are morphologically very similar and difficult to differentiate because of their morphological variability. Consequently, their taxonomic status and their phylogenetic relationships have been a matter of discussion for more than a century. To study these questions, we sequenced the COII (686 bp), 12S (362 bp), 16S (1200 bp), ND1 (917 bp), and tRNAs(Asn-Asp-Val-Leu-Ala-Ser-Leu) (402 bp) mitochondrial and 28S (809 bp) nuclear gene regions for 85 European earthworms from 27 different localities belonging to the A. caliginosa species complex and four outgroup taxa. DNA sequences were analyzed using maximum parsimony, maximum likelihood, and Bayesian approaches of phylogenetic inference. The resulting trees were combined with morphological, ecological, and genomic evidence to test species boundaries (i.e., integrative approach). Our molecular analyses showed that A. caliginosa s.s. and A. tuberculata form a sister clade to A. trapezoides, A. longa, and A. nocturna, which indicates that A. longa is part of the A. caliginosa species complex. We confirm the species status of all these taxa and identify two hitherto unrecognized Aporrectodea species in Corsica (France). Moreover our analyses also showed the presence of highly divergent lineages within A. caliginosa, A. trapezoides, and A. longa, suggesting the existence of cryptic diversity within these taxa.

  13. Maternal inheritance of mitochondrial DNA (mtDNA) in the Pacific oyster (Crassostrea gigas): a preliminary study using mtDNA sequence analysis with evidence of random distribution of MitoTracker-stained sperm mitochondria in fertilized eggs.

    PubMed

    Obata, Mayu; Shimizu, Michiyo; Sano, Natsumi; Komaru, Akira

    2008-03-01

    In many bivalve species, paternal and maternal mitochondrial DNA (mtDNA) from sperm and eggs is transmitted to the offspring. This phenomenon is known as doubly uniparental inheritance (DUI). In these species, sperm mtDNA (M type) is inherited by the male gonad of the offspring. Egg mtDNA (F type) is inherited by both male and female somatic cells and female gonadal cells. In Mytilidae, sperm mitochondria are distributed in the cytoplasm of differentiating male germ cells because they are transmitted to the male gonad. In the present study, we investigated maternal inheritance of mtDNA in the Pacific oyster, Crassostrea gigas. Sequence analysis of two mitochondrial non-coding regions revealed an identical sequence pattern in the gametes and adductor muscle samples taken from six males and five females. To observe whether sperm mitochondria were specifically located in the cytoplasm of differentiating germ cells, their distribution was recorded in C. gigas fertilized eggs by vital staining with MitoTracker Green. Although the 1D blastomere was identified in the cytoplasm of differentiating germ cells, sperm mitochondria were located at the 1D blastomere in only 32% of eggs during the 8-cell stage. Thus, in C. gigas, sperm mitochondria do not specifically locate in the germ cell region at the 1D blastomere. We suggest that the distribution of sperm mitochondria is not associated with germ cell formation in C. gigas. Furthermore, as evidenced by the mtDNA sequences of two non-coding regions, we conclude that mitochondrial DNA is maternally inherited in this species.

  14. Taxonomic and genetic status of lancelet in Weihai coastal waters based on mitochondrial DNA sequence

    NASA Astrophysics Data System (ADS)

    Zhao, Qi; Zhu, Qian

    2011-05-01

    Lancelets (subphylum Cephalochordata) are a transitional species between invertebrates and vertebrates. They are currently listed in the Second Order of Protected Animals in China. Lancelets were first documented in the waters around the city of Weihai (Shandong, China) in 2002. However, little is known about the phylogeny of this population. We analyzed the sequences of cytochrome b (Cyt b) and cytochrome oxidase c subunit I (CO I) genes from samples collected from coastal waters in the cities of Weihai and Qingdao (˜150 km to the south). We analyzed 176 sequences, of which 150 were novel sequences and 26 were obtained from GenBank. Our results suggest that (1) lancelets in the two cities belong to the species Branchiostoma japonicus and have a high level of genetic diversity; (2) there is a high level of gene flow and low level of genetic differentiation between lancelets from the two cities; (3) demographic expansion occurred an estimated 1.1 million years (Ma) ago (mid Pleistocene) for lancelets in Weihai-Qingdao; and (4) the divergence between B. belcheri and B. japonicus was estimated at between 37.75 Ma (early Oligocene)-46.5 Ma (late Eocene).

  15. Regulation of DNA replication at the end of the mitochondrial D-loop involves the helicase TWINKLE and a conserved sequence element

    PubMed Central

    Jemt, Elisabeth; Persson, Örjan; Shi, Yonghong; Mehmedovic, Majda; Uhler, Jay P.; Dávila López, Marcela; Freyer, Christoph; Gustafsson, Claes M.; Samuelsson, Tore; Falkenberg, Maria

    2015-01-01

    The majority of mitochondrial DNA replication events are terminated prematurely. The nascent DNA remains stably associated with the template, forming a triple-stranded displacement loop (D-loop) structure. However, the function of the D-loop region of the mitochondrial genome remains poorly understood. Using a comparative genomics approach we here identify two closely related 15 nt sequence motifs of the D-loop, strongly conserved among vertebrates. One motif is at the D-loop 5′-end and is part of the conserved sequence block 1 (CSB1). The other motif, here denoted coreTAS, is at the D-loop 3′-end. Both these sequences may prevent transcription across the D-loop region, since light and heavy strand transcription is terminated at CSB1 and coreTAS, respectively. Interestingly, the replication of the nascent D-loop strand, occurring in a direction opposite to that of heavy strand transcription, is also terminated at coreTAS, suggesting that coreTAS is involved in termination of both transcription and replication. Finally, we demonstrate that the loading of the helicase TWINKLE at coreTAS is reversible, implying that this site is a crucial component of a switch between D-loop formation and full-length mitochondrial DNA replication. PMID:26253742

  16. Molecular phylogeny of the speciose vole genus Microtus (Arvicolinae, Rodentia) inferred from mitochondrial DNA sequences.

    PubMed

    Jaarola, Maarit; Martínková, Natália; Gündüz, Islam; Brunhoff, Cecilia; Zima, Jan; Nadachowski, Adam; Amori, Giovanni; Bulatova, Nina S; Chondropoulos, Basil; Fraguedakis-Tsolis, Stella; González-Esteban, Jorge; José López-Fuster, María; Kandaurov, Andrei S; Kefelioğlu, Haluk; da Luz Mathias, Maria; Villate, Idoia; Searle, Jeremy B

    2004-12-01

    Voles of the genus Microtus represent one of the most speciose mammalian genera in the Holarctic. We established a molecular phylogeny for Microtus to resolve contentious issues of systematic relationships and evolutionary history in this genus. A total of 81 specimens representing ten Microtus species endemic to Europe as well as eight Eurasian, six Asian and one Holarctic species were sequenced for the entire cytochrome b gene (1140 bp). A further 25 sequences were retrieved from GenBank, providing data on an additional 23, mainly Nearctic, Microtus species. Phylogenetic analysis of these 48 species generated four well-supported monophyletic lineages. The genus Chionomys, snow voles, formed a distinct and well-supported lineage separate from the genus Microtus. The subgenus Microtus formed the strongest supported lineage with two sublineages displaying a close relationship between the arvalis species group (common voles) and the socialis species group (social voles). Monophyly of the Palearctic pitymyid voles, subgenus Terricola, was supported, and this subgenus was also subdivided into two monophyletic species groups. Together, these groupings clarify long-standing taxonomic uncertainties in Microtus. In addition, the "Asian" and the Nearctic lineages reported previously were identified although the latter group was not supported. However, relationships among the main Microtus branches were not resolved, suggesting a rapid and potentially simultaneous radiation of a widespread ancestor early in the history of the genus. This and subsequent radiations discernible in the cytochrome b phylogeny, show the considerable potential of Microtus for analysis of historical and ecological determinants of speciation in small mammals. It is evident that speciation is an ongoing process in the genus and that the molecular data provides a vital insight into current species limits as well as cladogenic events of the past.

  17. Analysis of complete mitochondrial DNA sequences of three members of the Montastraea annularis coral species complex (Cnidaria, Anthozoa, Scleractinia)

    NASA Astrophysics Data System (ADS)

    Fukami, Hironobu; Knowlton, Nancy

    2005-11-01

    Complete mitochondrial nucleotide sequences of two individuals each of Montastraea annularis, Montastraea faveolata, and Montastraea franksi were determined. Gene composition and order differed substantially from the sea anemone Metridium senile, but were identical to that of the phylogenetically distant coral genus Acropora. However, characteristics of the non-coding regions differed between the two scleractinian genera. Among members of the M. annularis complex, only 25 of 16,134 base pair positions were variable. Sixteen of these occurred in one colony of M. franksi, which (together with additional data) indicates the existence of multiple divergent mitochondrial lineages in this species. Overall, rates of evolution for these mitochondrial genomes were extremely slow (0.03 0.04% per million years based on the fossil record of the M. annularis complex). At higher taxonomic levels, patterns of genetic divergence and synonymous/nonsynonymous substitutions suggest non-neutral and unequal rates of evolution between the two lineages to which Montastraea and Acropora belong.

  18. Evolution of mitochondrial SSU-rDNA variable domain sequences and rRNA secondary structures, and phylogeny of the Agrocybe aegerita multispecies complex.

    PubMed

    Uhart, Marina; Sirand-Pugnet, Pascal; Labarère, Jacques

    2007-04-01

    Mitochondrial small subunit (mtSSU) rDNA variable (V1, V2, V4, V6, V8 and V9) domain sequences and rRNA secondary structures evidenced eight molecular groups within 32 strains of the Agrocybe aegerita multispecies complex from different continents. mtSSU-rRNA secondary structure evolution occurred mainly by insertion/deletion of sequences from 8 to 57nt long. Preferential insertion/deletion sites correlated with loops of the mtSSU-rRNA secondary structures, and suggested that these events occurred in regions without interactions in the ribosomal-protein assembly. Indels modified the stem length (V1 and V4 domains) or the size and loop number (V6 and V9 domains). Three indels inserted in the V1 and V4 domains had 76.5% to 94.7% identity with short sequences of the mitochondrial cytochrome c oxidase gene; this fact and the presence of inverted repeated motifs within indel sequences suggested a mechanism of evolution based on insertion/deletion of sequences from another region of the mitochondrial genome. Phylogenetic relationships inferred using both ribosomal DNA sequences and rRNA secondary structures were congruent and evidenced three clades within the A. aegerita complex: European, Argentinean, and a more distant Asian-American clade including A. aegerita and A. chaxingu strains. These results suggested that numerous genetic exchanges occurred between Asian-American strains after isolation of the European clade. V4-V6-V9 concatenated sequences of European and Argentinean clades had 86.1% identity, similar to the value calculated between two Agrocybe closely related species, suggesting that these clades could represent different species. A cleaved amplified polymorphic sequence test for rapid characterization of strains was developed.

  19. Phylogenetic relationships among phrynosomatid lizards as inferred from mitochondrial ribosomal DNA sequences: substitutional bias and information content of transitions relative to transversions.

    PubMed

    Reeder, T W

    1995-06-01

    The phylogenetic relationships among 40 species, representing all genera, within the North American lizard family Phrynosomatidae were inferred from mitochondrial ribosomal RNA gene sequences. Cladistic analysis of the DNA sequence data (779 bp; 162 informative characters) supported the monophyly of the sand lizards (Callisaurus, Cophosaurus, Holbrookia, and Uma), Petrosaurus, Phrynosoma, Urosaurus, and Uta. All the species of Sceloporus, except S. variabilis and S. chrysostictus, formed a clade. Except for a sand lizard + Phrynosoma clade, the intergeneric relationships inferred from the mtDNA were largely incongruent with recent cladistic analyses based on morphology. Sceloporus group monophyly was not supported, with Petrosaurus being a member of a clade containing Sator, Sceloporus, and Urosaurus, to the exclusion of Uta. The phylogenetic placement of Uta was ambiguous. The substitutional bias in the phrynosomatid mitochondrial rDNA sequences was examined, as well as the phylogenetic information content of transitions relative to transversions. There appeared to be a lower transition bias than observed in other vertebrate sequences, with some classes of transversions occurring as frequently as G <-> A transitions. Transitions were no less informative for phylogeny reconstruction than transversions. Therefore, transitions should not be down-weighted in phylogenetic analysis, as is often done.

  20. Double trouble for grasshopper molecular systematics: intra-individual heterogeneity of both mitochondrial 12S-valine-16S and nuclear internal transcribed spacer ribosomal DNA sequences in Hesperotettix viridis

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Hesperotettix viridis grasshoppers (Orthoptera: Acrididae:Melanoplinae) exhibit intra-individual variation in both mitochondrial 12S-valine-16S and nuclear internal transcribed spacer (ITS) ribosomal DNA sequences. These findings violate core assumptions underlying DNA sequence data obtained via pol...

  1. Population genetic structure of the parasitic nematode Camallanus cotti inferred from DNA sequences of ITS1 rDNA and the mitochondrial COI gene.

    PubMed

    Wu, Shan G; Wang, Gui T; Xi, Bing W; Xiong, Fan; Liu, Tao; Nie, Pin

    2009-10-14

    The population genetic structure of fish parasitic nematode, Camallanus cotti, collected from the Yangtze River, Pearl River and Minjiang River in China was investigated. From these parasites, the approximately 730 bp of the first internal transcribed spacer of ribosomal DNA (ITS1 rDNA) and the 428bp of mitochondrial cytochrome c oxidase subunit I (COI) gene were sequenced. For the ITS1 rDNA data set, highly significant Fst values and low rates of migration were detected between the Pearl River group and both the Yangtze River (Fst=0.70, P<0.00001; Nm=0.21) and Minjiang River (Fst=0.73, P<0.00001; Nm=0.18) groups, while low Fst value (Fst=0.018, P>0.05) and high rate of migration (Nm=28.42) were found between the Minjiang and the Yangtze rivers. When different host/locality populations (subpopulations) within each river were considered, subpopulations between the Yangtze River and Minjiang River had low Fst values (3.72), while Pearl River subpopulations were significantly different from the Yangtze River and Minjiang River subpopulations (Fst>or=0.59; Nm<1). The COI gene data set revealed a similar genetic structure. Both phylogenetic analyses and a statistical parsimony network grouped the Pearl River haplotypes into one phylogroup, while the Yangtze River and Minjiang River haplotypes formed a second group. These results suggested that the Yangtze River and Minjiang River subpopulations constituted a single reproductive pool that was distinct from the Pearl River subpopulations. In addition, the present study did not find host-related genetic differentiation occurring in the same drainage.

  2. Complete Mitochondrial DNA Sequences of the Threadfin Cichlid (Petrochromis trewavasae) and the Blunthead Cichlid (Tropheus moorii) and Patterns of Mitochondrial Genome Evolution in Cichlid Fishes

    PubMed Central

    Fischer, Christoph; Koblmüller, Stephan; Gülly, Christian; Schlötterer, Christian; Sturmbauer, Christian; Thallinger, Gerhard G.

    2013-01-01

    The cichlid fishes of the East African Great Lakes represent a model especially suited to study adaptive radiation and speciation. With several African cichlid genome projects being in progress, a promising set of closely related genomes is emerging, which is expected to serve as a valuable data base to solve questions on genotype-phenotype relations. The mitochondrial (mt) genomes presented here are the first results of the assembly and annotation process for two closely related but eco-morphologically highly distinct Lake Tanganyika cichlids, Petrochromis trewavasae and Tropheus moorii. The genomic sequences comprise 16,588 bp (P. trewavasae) and 16,590 bp (T. moorii), and exhibit the typical mitochondrial structure, with 13 protein-coding genes, 2 rRNA genes, 22 tRNA genes, and a non-coding control region. Analyses confirmed that the two species are very closely related with an overall sequence similarity of 96%. We analyzed the newly generated sequences in the phylogenetic context of 21 published labroid fish mitochondrial genomes. Consistent with other vertebrates, the D-loop region was found to evolve faster than protein-coding genes, which in turn are followed by the rRNAs; the tRNAs vary greatly in the rate of sequence evolution, but on average evolve the slowest. Within the group of coding genes, ND6 evolves most rapidly. Codon usage is similar among examined cichlid tribes and labroid families; although a slight shift in usage patterns down the gene tree could be observed. Despite having a clearly different nucleotide composition, ND6 showed a similar codon usage. C-terminal ends of Cox1 exhibit variations, where the varying number of amino acids is related to the structure of the obtained phylogenetic tree. This variation may be of functional relevance for Cox1 synthesis. PMID:23826193

  3. Mitochondrial DNA diagnosis for taeniasis and cysticercosis.

    PubMed

    Yamasaki, Hiroshi; Nakao, Minoru; Sako, Yasuhito; Nakaya, Kazuhiro; Sato, Marcello Otake; Ito, Akira

    2006-01-01

    Molecular diagnosis for taeniasis and cysticercosis in humans on the basis of mitochondrial DNA analysis was reviewed. Development and application of three different methods, including restriction fragment length polymorphism analysis, base excision sequence scanning thymine-base analysis and multiplex PCR, were described. Moreover, molecular diagnosis of cysticerci found in specimens submitted for histopathology and the molecular detection of taeniasis using copro-DNA were discussed.

  4. Sequencing and comparing whole mitochondrial genomes ofanimals

    SciTech Connect

    Boore, Jeffrey L.; Macey, J. Robert; Medina, Monica

    2005-04-22

    Comparing complete animal mitochondrial genome sequences is becoming increasingly common for phylogenetic reconstruction and as a model for genome evolution. Not only are they much more informative than shorter sequences of individual genes for inferring evolutionary relatedness, but these data also provide sets of genome-level characters, such as the relative arrangements of genes, that can be especially powerful. We describe here the protocols commonly used for physically isolating mtDNA, for amplifying these by PCR or RCA, for cloning,sequencing, assembly, validation, and gene annotation, and for comparing both sequences and gene arrangements. On several topics, we offer general observations based on our experiences to date with determining and comparing complete mtDNA sequences.

  5. Mitochondrial DNA and retroviral RNA analyses of archival oral polio vaccine (OPV CHAT) materials: evidence of macaque nuclear sequences confirms substrate identity.

    PubMed

    Berry, Neil; Jenkins, Adrian; Martin, Javier; Davis, Clare; Wood, David; Schild, Geoffrey; Bottiger, Margareta; Holmes, Harvey; Minor, Philip; Almond, Neil

    2005-02-25

    Inoculation of live experimental oral poliovirus vaccines (OPV CHAT) during the 1950s in central Africa has been proposed to account for the introduction of HIV into human populations. For this to have occurred, it would have been necessary for chimpanzee rather than macaque kidney epithelial cells to have been included in the preparation of early OPV materials. Theoretically, this could have led to contamination with a progenitor of HIV-1 derived from a related simian immunodeficiency virus of chimpanzees (SIVCPZ). In this article we present further detailed analyses of two samples of OPV, CHAT 10A-11 and CHAT 6039/Yugo, which were used in early human trials of poliovirus vaccination. Recovery of poliovirus by culture techniques confirmed the biological viability of the vaccines and sequence analysis of poliovirus RNA specifically identified the presence of the CHAT strain. Independent nested sets of oligonucleotide primers specific for HIV-1/SIVCPZ and HIV-2/SIVMAC/SIVSM phylogenetic lineages, respectively, indicated no evidence of HIV/SIV RNA in either vaccine preparation, at a sensitivity of 100 RNA equivalents/ml. Analysis of cellular substrate by the amplification of two distinct regions of mitochondrial DNA (D-loop control region and 12S ribosomal sequences) revealed no evidence of chimpanzee cellular sequences. However, this approach positively identified rhesus and cynomolgus macaque DNA for the CHAT 10A-11 and CHAT 6039/Yugo vaccine preparations, respectively. Analysis of multiple clones of mtDNA 12S rDNA indicated a relatively high number of nuclear mitochondrial DNA sequences (numts) in the CHAT 10A-11 material, but confirmed the macaque origin of cellular substrate used in vaccine preparation. These data reinforce earlier findings on this topic providing no evidence to support the contention that poliovirus vaccination was responsible for the introduction of HIV into humans and sparking the AIDS pandemic.

  6. Long-distance colonization and radiation in gekkonid lizards, Tarentola (Reptilia: Gekkonidae), revealed by mitochondrial DNA sequences.

    PubMed Central

    Carranza, S; Arnold, E N; Mateo, J A; López-Jurado, L F

    2000-01-01

    Morphological systematics makes it clear that many non-volant animal groups have undergone extensive transmarine dispersal with subsequent radiation in new, often island, areas. However, details of such events are often lacking. Here we use partial DNA sequences derived from the mitochondrial cytochrome b and 12S rRNA genes (up to 684 and 320 bp, respectively) to trace migration and speciation in Tarentola geckos, a primarily North African clade which has invaded many of the warmer islands in the North Atlantic Ocean. There were four main invasions of archipelagos presumably by rafting. (i) The subgenus Neotarentola reached Cuba up to 23 million years (Myr) ago, apparently via the North Equatorial current, a journey of at least 6000 km. (ii) The subgenus Tarentola invaded the eastern Canary Islands relatively recently covering a minimum of 120 km. (iii) The subgenus Makariogecko got to Gran Canaria and the western Canary Islands 7-17.5 Myr ago, either directly from the mainland or via the Selvages or the archipelago of Madeira, an excursion of 200-1200 km. (iv) A single species of Makariogecko from Gomera or Tenerife in the western Canaries made the 1400 km journey to the Cape Verde Islands tip to 7 Myr ago by way of the south-running Canary current. Many journeys have also occurred within archipelagos, a minimum of five taking place in the Canaries and perhaps 16 in the Cape Verde Islands. Occupation of the Cape Verde archipelago first involved an island in the northern group, perhaps São Nicolau, with subsequent spread to its close neighbours. The eastern and southern islands were colonized from these northern islands, at least two invasions widely separated in time being involved. While there are just three allopatric species of Makariogecko in the Canaries, the single invader of the Cape Verde Islands radiated into five, most of the islands being inhabited by two of these which differ in size. While size difference may possibly be a product of character

  7. Mitochondrial replacement in human oocytes carrying pathogenic mitochondrial DNA mutations.

    PubMed

    Kang, Eunju; Wu, Jun; Gutierrez, Nuria Marti; Koski, Amy; Tippner-Hedges, Rebecca; Agaronyan, Karen; Platero-Luengo, Aida; Martinez-Redondo, Paloma; Ma, Hong; Lee, Yeonmi; Hayama, Tomonari; Van Dyken, Crystal; Wang, Xinjian; Luo, Shiyu; Ahmed, Riffat; Li, Ying; Ji, Dongmei; Kayali, Refik; Cinnioglu, Cengiz; Olson, Susan; Jensen, Jeffrey; Battaglia, David; Lee, David; Wu, Diana; Huang, Taosheng; Wolf, Don P; Temiakov, Dmitry; Belmonte, Juan Carlos Izpisua; Amato, Paula; Mitalipov, Shoukhrat

    2016-12-08

    Maternally inherited mitochondrial (mt)DNA mutations can cause fatal or severely debilitating syndromes in children, with disease severity dependent on the specific gene mutation and the ratio of mutant to wild-type mtDNA (heteroplasmy) in each cell and tissue. Pathogenic mtDNA mutations are relatively common, with an estimated 778 affected children born each year in the United States. Mitochondrial replacement therapies or techniques (MRT) circumventing mother-to-child mtDNA disease transmission involve replacement of oocyte maternal mtDNA. Here we report MRT outcomes in several families with common mtDNA syndromes. The mother's oocytes were of normal quality and mutation levels correlated with those in existing children. Efficient replacement of oocyte mutant mtDNA was performed by spindle transfer, resulting in embryos containing >99% donor mtDNA. Donor mtDNA was stably maintained in embryonic stem cells (ES cells) derived from most embryos. However, some ES cell lines demonstrated gradual loss of donor mtDNA and reversal to the maternal haplotype. In evaluating donor-to-maternal mtDNA interactions, it seems that compatibility relates to mtDNA replication efficiency rather than to mismatch or oxidative phosphorylation dysfunction. We identify a polymorphism within the conserved sequence box II region of the D-loop as a plausible cause of preferential replication of specific mtDNA haplotypes. In addition, some haplotypes confer proliferative and growth advantages to cells. Hence, we propose a matching paradigm for selecting compatible donor mtDNA for MRT.

  8. Mitochondrial DNA maintenance: an appraisal.

    PubMed

    Akhmedov, Alexander T; Marín-García, José

    2015-11-01

    Mitochondria play a crucial role in a variety of cellular processes ranging from energy metabolism, generation of reactive oxygen species (ROS), and Ca(2+) handling to stress responses, cell survival, and death. Malfunction of the organelle may contribute to the pathogenesis of neuromuscular disorders, cancer, premature aging, and cardiovascular diseases, including myocardial ischemia, cardiomyopathy, and heart failure. Mitochondria are unique as they contain their own genome organized into DNA-protein complexes, so-called mitochondrial nucleoids, along with multiprotein machineries, which promote mitochondrial DNA (mtDNA) replication, transcription, and repair. Although the organelle possesses almost all known nuclear DNA repair pathways, including base excision repair, mismatch repair, and recombinational repair, the proximity of mtDNA to the main sites of ROS production and the lack of protective histones may result in increased susceptibility to oxidative stress and other types of mtDNA damage. Defects in the components of these highly organized machineries, which mediate mtDNA maintenance (replication and repair), may result in accumulation of point mutations and/or deletions in mtDNA and decreased mtDNA copy number impairing mitochondrial function. This review will focus on the mechanisms of mtDNA maintenance with emphasis on the proteins implicated in these processes and their functional role in various disease conditions and aging.

  9. Implications of mitochondrial DNA mutations and mitochondrial dysfunction in tumorigenesis

    PubMed Central

    Lu, Jianxin; Sharma, Lokendra Kumar; Bai, Yidong

    2016-01-01

    Alterations in oxidative phosphorylation resulting from mitochondrial dysfunction have long been hypothesized to be involved in tumorigenesis. Mitochondria have recently been shown to play an important role in regulating both programmed cell death and cell proliferation. Furthermore, mitochondrial DNA (mtDNA) mutations have been found in various cancer cells. However, the role of these mtDNA mutations in tumorigenesis remains largely unknown. This review focuses on basic mitochondrial genetics, mtDNA mutations and consequential mitochondrial dysfunction associated with cancer. The potential molecular mechanisms, mediating the pathogenesis from mtDNA mutations and mitochondrial dysfunction to tumorigenesis are also discussed. PMID:19532122

  10. Genetic characterization of the Pacific sheath-tailed bat (Emballonura semicaudata rotensis) using mitochondrial DNA sequence data

    USGS Publications Warehouse

    Oyler-McCance, Sara J.; Valdez, Ernest W.; O'Shea, Thomas J.; Fike, Jennifer A.

    2013-01-01

    Emballonura semicaudata occurs in the southwestern Pacific and populations on many islands have declined or disappeared. One subspecies (E. semicaudata rotensis) occurs in the Northern Mariana Islands, where it has been extirpated from all but 1 island (Aguiguan). We assessed genetic similarity between the last population of E. s. rotensis and 2 other subspecies, and examined genetic diversity on Aguiguan. We sampled 12 E. s. rotensis, sequenced them at 3 mitochondrial loci, and compared them with published sequences from 2 other subspecies. All 12 E. s. rotensis had identical sequences in each of the 3 regions. Using cytochrome-b (Cytb) data E. s. rotensis was sister to E. s. palauensis in a clade separate from E. s. semicaudata. 12S ribosomal RNA (12S) sequences grouped all E. s. semicaudata in 1 clade with E. s. rotensis in a clade by itself. Genetic distances among the 3 subspecies at Cytb were smallest between E. s. palauensis and E. s. rotensis. Distance between E. s. semicaudata and the other 2 subspecies was not different from the distance between E. s. semicaudata and the full species E. raffrayana. A similar relationship was found using the 12S data. These distances are larger than those typically reported for mammalian subspecies using Cytb sequence and within the range of sister species.

  11. The complete mitochondrial genome of a turbinid vetigastropod from MiSeq Illumina sequencing of genomic DNA and steps towards a resolved gastropod phylogeny.

    PubMed

    Williams, S T; Foster, P G; Littlewood, D T J

    2014-01-01

    A need to increase sampling of mitochondrial genomes for Vetigastropoda has been identified as an important step towards resolving relationships within the Gastropoda. We used shotgun sequencing of genomic DNA, using an Illumina MiSeq, to obtain the first mitochondrial genome for the vetigastropod family Turbinidae, doubling the number of genomes for the species-rich superfamily Trochoidea. This method avoids the necessity of finding suitable primers for long PCRs or primer-walking amplicons, resulting in a timely and cost-effective method for obtaining whole mitochondrial genomes from ethanol-preserved tissue samples. Bayesian analysis of amino acid variation for all available gastropod genomes including the new turbinid mtgenome produced a well resolved tree with high nodal support for most nodes. Major clades within Gastropoda were recovered with strong support, with the exception of Littorinimorpha, which was polyphyletic. We confirm here that mitogenomics is a useful tool for molluscan phylogenetics, especially when using powerful new models of amino acid evolution, but recognise that increased taxon sampling is still required to resolve existing differences between nuclear and mitochondrial gene trees.

  12. Markov chain for estimating human mitochondrial DNA mutation pattern

    NASA Astrophysics Data System (ADS)

    Vantika, Sandy; Pasaribu, Udjianna S.

    2015-12-01

    The Markov chain was proposed to estimate the human mitochondrial DNA mutation pattern. One DNA sequence was taken randomly from 100 sequences in Genbank. The nucleotide transition matrix and mutation transition matrix were estimated from this sequence. We determined whether the states (mutation/normal) are recurrent or transient. The results showed that both of them are recurrent.

  13. The Complete Mitochondrial DNA Sequence of the Bichir (Polypterus Ornatipinnis), a Basal Ray-Finned Fish: Ancient Establishment of the Consensus Vertebrate Gene Order

    PubMed Central

    Noack, K.; Zardoya, R.; Meyer, A.

    1996-01-01

    The evolutionary position of bichirs is disputed, and they have been variously aligned with ray-finned fish (Actinopterygii) or lobe-finned fish (Sarcopterygii), which also include tetrapods. Alternatively, they have been placed into their own group, the Brachiopterygii. The phylogenetic position of bichirs as possibly the most primitive living bony fish (Osteichthyes) made knowledge about their mitochondrial genome of considerable evolutionary interest. We determined the complete nucleotide sequence (16,624 bp) of the mitochondrial genome of a bichir, Polypterus ornatipinnis. Its genome contains 13 protein-coding genes, 22 tRNAs, two rRNAs and one major noncoding region. The genome's structure and organization show that this is the most basal vertebrate that conforms to the consensus vertebrate mtDNA gene order. Bichir mitochondrial protein-coding and ribosomal RNA genes have greater sequence similarity to ray-finned fish than to either lamprey or lungfish. Phylogenetic analyses suggest the bichir's placement as the most basal living member of the ray-finned fish and rule out its classification as a lobe-finned fish. Hence, its lobe-fins are probably not a shared-derived trait with those of lobe-finned fish (Sarcopterygii). PMID:8913758

  14. DNA sequence variation in the mitochondrial control region of subterranean mole rats, Spalax ehrenbergi superspecies, in Israel.

    PubMed

    Reyes, Aurelio; Nevo, Eviatar; Saccone, Cecilia

    2003-04-01

    The complete mitochondrial control region was sequenced for 60 individuals representing different populations for each of the four species of the subterranean mole rat Spalax ehrenbergi superspecies in Israel: Spalax galili (2n = 52), S. golani (2n = 54), S. carmeli (2n = 58), and S. judaei (2n = 60). The control region of all species and populations is very similar both in length (979 to 983 bp) and in base composition. As in agreement with previous surveys on mitochondrial control regions on mammals, the mole rat control region can be divided into a central domain and two flanking domains, ETAS (extended termination associated sequences) and CSB (conserved sequence blocks). Along with the common conserved blocks found in these domains (ETAS1, ETAS2, CSB1, CSB2, and CSB3), we have also detected in all individuals an ETAS1-like and a CSB1-like element, both in the ETAS domain. The most conserved region was the central domain, followed by the CSB and ETAS domains, showing important differences in the four species analyzed. Phylogenetic analysis supported the existence of two clades. One clade contained individuals belonging to Spalax galili (2n = 52) and S. golani (2n = 54), separated in two different branches depending on the species. The other clade contained individuals belonging to S. carmeli (2n = 58) and S. judaei (2n = 60) mixed together, suggesting a more recent event of speciation. Within species we have observed a southward trend of increasing variability. These results have been explained as a consequence of the adaptation of the species to ecological factors such as aridity and temperature stresses.

  15. Stock structure and homing fidelity in Gulf of Mexico sturgeon (Acipenser oxyrinchus desotoi) based on restriction fragment length polymorphism and sequence analyses of mitochondrial DNA.

    PubMed

    Stabile, J; Waldman, J R; Parauka, F; Wirgin, I

    1996-10-01

    Efforts have been proposed worldwide to restore sturgeon populations through the use of hatcheries to supplement natural reproduction and to reintroduce sturgeon where they have become extinct. We examined the population structure and inferred the extent of homing in the anadromous Gulf of Mexico (Gulf) sturgeon (Acipenser oxyrinchus desotoi). Restriction fragment length polymorphism and control region sequence analyses of mitochondrial DNA (mtDNA) were used to identify haplotypes of Gulf sturgeon specimens obtained from eight drainages spanning the subspecies' entire distribution from Louisiana to Florida. Significant differences in haplotype frequencies indicated substantial geographic structuring of populations. A minimum of four regional or river-specific populations were identified (from west to east): (1) Pearl River, LA and Pascagoula River, MS, (2) Escambia and Yellow rivers, FI, (3) Choctawbatchee River, FL and (4) Apalachicola Ochlockonee, and Suwannee rivers, FL. Estimates of maternally mediated gene flow between any pair of the four regional or river-specific stocks ranged between 0.15 to 1.2. Tandem repeats in the mtDNA control region of Gulf sturgeon were not perfectly conserved. This result, together with an absence of heteroplasmy and length variation in Gulf sturgeon mtDNA, indicates that the molecular mechanisms of mtDNA control region sequence evolution differ among acipenserids.

  16. Stock Structure and Homing Fidelity in Gulf of Mexico Sturgeon (Acipenser Oxyrinchus Desotoi) Based on Restriction Fragment Length Polymorphism and Sequence Analyses of Mitochondrial DNA

    PubMed Central

    Stabile, J.; Waldman, J. R.; Parauka, F.; Wirgin, I.

    1996-01-01

    Efforts have been proposed worldwide to restore sturgeon populations through the use of hatcheries to supplement natural reproduction and to reintroduce sturgeon where they have become extinct. We examined the population structure and inferred the extent of homing in the anadromous Gulf of Mexico (Gulf) sturgeon (Acipenser oxyrinchus desotoi). Restriction fragment length polymorphism and control region sequence analyses of mitochondrial DNA (mtDNA) were used to identify haplotypes of Gulf sturgeon specimens obtained from eight drainages spanning the subspecies' entire distribution from Louisiana to Florida. Significant differences in haplotype frequencies indicated substantial geographic structuring of populations. A minimum of four regional or river-specific populations were identified (from west to east): (1) Pearl River, LA and Pascagoula River, MS, (2) Escambia and Yellow rivers, FL, (3) Choctawhatchee River, FL, and (4) Apalachicola, Ochlockonee, and Suwannee rivers, FL. Estimates of maternally mediated gene flow between any pair of the four regional or river-specific stocks ranged between 0.15 to 1.2. Tandem repeats in the mtDNA control region of Gulf sturgeon were not perfectly conserved. This result, together with an absence of heteroplasmy and length variation in Gulf sturgeon mtDNA, indicates that the molecular mechanisms of mtDNA control region sequence evolution differ among acipenserids. PMID:8889537

  17. Phylogeny and Biogeography of Cedrus (Pinaceae) Inferred from Sequences of Seven Paternal Chloroplast and Maternal Mitochondrial DNA Regions

    PubMed Central

    Qiao, Cai-Yuan; Ran, Jin-Hua; Li, Yan; Wang, Xiao-Quan

    2007-01-01

    Background and Aims Cedrus (true cedars) is a very important horticultural plant group. It has a disjunct distribution in the Mediterranean region and western Himalaya. Its evolution and biogeography are of great interest to botanists. This study aims to investigate the phylogeny and biogeography of Cedrus based on sequence analyses of seven cytoplasmic DNA fragments. Methods The methods used were PCR amplification and sequencing of seven paternal cpDNA and maternal mtDNA fragments, parsimony and maximum likelihood analyses of the DNA dataset, and molecular clock estimate of divergence times of Cedrus species. Key Results Phylogenies of Cedrus constructed from cpDNA, mtDNA and the combined cp- and mt-DNA dataset are identical in topology. It was found that the Himalayan cedar C. deodara diverged first, and then the North African species C. atlantica separated from the common ancestor of C. libani and C. brevifolia, two species from the eastern Mediterranean area. Molecular clock estimates suggest that the divergence between C. atlantica and the eastern Mediterranean clade at 23·49 ± 3·55 to 18·81 ± 1·25 Myr and the split between C. libani and C. brevifolia at 7·83 ± 2·79 to 6·56 ± 1·20 Myr. Conclusions The results, combined with palaeogeographical and palaeoecological information, indicate that Cedrus could have an origin in the high latitude area of Eurasia, and its present distribution might result from vicariance of southerly migrated populations during climatic oscillations in the Tertiary and further fragmentation and dispersal of these populations. It is very likely that Cedrus migrated into North Africa in the very late Tertiary, while its arrival in the Himalayas would not have been before the Miocene, after which the phased or fast uplift of the Tibetan plateau happened. PMID:17611189

  18. Mitochondrial DNA and Cancer Epidemiology Workshop

    Cancer.gov

    A workshop to review the state-of-the science in the mitochondrial DNA field and its use in cancer epidemiology, and to develop a concept for a research initiative on mitochondrial DNA and cancer epidemiology.

  19. Phylogeny of hydrothermal-vent-endemic gastropods Alviniconcha spp. from the western Pacific revealed by mitochondrial DNA sequences.

    PubMed

    Kojima, S; Segawa, R; Fijiwara, Y; Fujikura, K; Ohta, S; Hashimoto, J

    2001-06-01

    Mitochondrial genes for cytochrome oxidase I (COI) from hydrothermal-vent-endemic gastropods of the genus Alviniconcha were sequenced to determine the phylogenetic relationships among specimens from three areas in the western Pacific. Individuals of Alviniconcha hessleri were collected at two vent fields (depths 1470 m and 3600 m) in the Mariana Trough. Specimens collected in the North Fiji Basin could be divided into two genetically distinct groups, both of which also differed from A. hessleri from the Mariana Trough. None of the specimens of the genus Alviniconcha collected in the Manus Basin differed genetically from the dominant group from the North Fiji Basin. We suggest that the specimens of the genus Alviniconcha analyzed in the present study can be tentatively classified into A. hessleri and two undescribed species.

  20. Mitochondrial DNA sequence evolution and phylogeny of the Atlantic Alcidae, including the extinct great auk (Pinguinus impennis).

    PubMed

    Moum, Truls; Arnason, Ulfur; Arnason, Einar

    2002-09-01

    The Atlantic auk assemblage includes four extant species, razorbill (Alca torda), dovekie (Alle alle), common murre (Uria aalge), and thick-billed murre (U. lomvia), and one recently extinct species, the flightless great auk (Pinguinus impennis). To determine the phylogenetic relationships among the species, a contiguous 4.2-kb region of the mitochondrial genome from the extant species was amplified using PCR. This region included one ribosomal RNA gene, four transfer RNA genes, two protein-coding genes, the control region, and intergenic spacers. Sets of PCR primers for amplifying the same region from great auk were designed from sequences of the extant species. The authenticity of the great auk sequence was ascertained by alternative amplifications, cloning, and separate analyses in an independent laboratory. Phylogenetic analyses of the entire assemblage, made possible by the great auk sequence, fully resolved the phylogenetic relationships and split it into two primary lineages, Uria versus Alle, Alca, and Pinguinus. A sister group relationship was identified between Alca and Pinguinus to the exclusion of ALLE: Phylogenetically, the flightless great auk originated late relative to other divergences within the assemblage. This suggests that three highly divergent species in terms of adaptive specializations, Alca, Alle, and Pinguinus, evolved from a single lineage in the Atlantic Ocean, in a process similar to the initial adaptive radiation of alcids in the Pacific Ocean.

  1. Prevalence of rare mitochondrial DNA mutations in mitochondrial disorders

    PubMed Central

    Bannwarth, Sylvie; Procaccio, Vincent; Lebre, Anne Sophie; Jardel, Claude; Chaussenot, Annabelle; Hoarau, Claire; Maoulida, Hassani; Charrier, Nathanaël; Gai, Xiaowu; Xie, Hongbo M; Ferre, Marc; Fragaki, Konstantina; Hardy, Gaëlle; Mousson de Camaret, Bénédicte; Marlin, Sandrine; Dhaenens, Claire Marie; Slama, Abdelhamid; Rocher, Christophe; Paul Bonnefont, Jean; Rötig, Agnès; Aoutil, Nadia; Gilleron, Mylène; Desquiret-Dumas, Valérie; Reynier, Pascal; Ceresuela, Jennifer; Jonard, Laurence; Devos, Aurore; Espil-Taris, Caroline; Martinez, Delphine; Gaignard, Pauline; Le Quan Sang, Kim-Hanh; Amati-Bonneau, Patrizia; Falk, Marni J; Florentz, Catherine; Chabrol, Brigitte; Durand-Zaleski, Isabelle; Paquis-Flucklinger, Véronique

    2013-01-01

    Abstract Background Mitochondrial DNA (mtDNA) diseases are rare disorders whose prevalence is estimated around 1 in 5000. Patients are usually tested only for deletions and for common mutations of mtDNA which account for 5–40% of cases, depending on the study. However, the prevalence of rare mtDNA mutations is not known. Methods We analysed the whole mtDNA in a cohort of 743 patients suspected of manifesting a mitochondrial disease, after excluding deletions and common mutations. Both heteroplasmic and homoplasmic variants were identified using two complementary strategies (Surveyor and MitoChip). Multiple correspondence analyses followed by hierarchical ascendant cluster process were used to explore relationships between clinical spectrum, age at onset and localisation of mutations. Results 7.4% of deleterious mutations and 22.4% of novel putative mutations were identified. Pathogenic heteroplasmic mutations were more frequent than homoplasmic mutations (4.6% vs 2.8%). Patients carrying deleterious mutations showed symptoms before 16 years of age in 67% of cases. Early onset disease (<1 year) was significantly associated with mutations in protein coding genes (mainly in complex I) while late onset disorders (>16 years) were associated with mutations in tRNA genes. MTND5 and MTND6 genes were identified as ‘hotspots’ of mutations, with Leigh syndrome accounting for the large majority of associated phenotypes. Conclusions Rare mitochondrial DNA mutations probably account for more than 7.4% of patients with respiratory chain deficiency. This study shows that a comprehensive analysis of mtDNA is essential, and should include young children, for an accurate diagnosis that is now accessible with the development of next generation sequencing technology. PMID:23847141

  2. Genetic variability of Echinococcus granulosus complex in various geographical populations of Iran inferred by mitochondrial DNA sequences.

    PubMed

    Spotin, Adel; Mahami-Oskouei, Mahmoud; Harandi, Majid Fasihi; Baratchian, Mehdi; Bordbar, Ali; Ahmadpour, Ehsan; Ebrahimi, Sahar

    2017-01-01

    To investigate the genetic variability and population structure of Echinococcus granulosus complex, 79 isolates were sequenced from different host species covering human, dog, camel, goat, sheep and cattle as of various geographical sub-populations of Iran (Northwestern, Northern, and Southeastern). In addition, 36 sequences of other geographical populations (Western, Southeastern and Central Iran), were directly retrieved from GenBank database for the mitochondrial cytochrome c oxidase subunit 1 (cox1) gene. The confirmed isolates were grouped as G1 genotype (n=92), G6 genotype (n=14), G3 genotype (n=8) and G2 genotype (n=1). 50 unique haplotypes were identified based on the analyzed sequences of cox1. A parsimonious network of the sequence haplotypes displayed star-like features in the overall population containing IR23 (22: 19.1%) as the most common haplotype. According to the analysis of molecular variance (AMOVA) test, the high value of haplotype diversity of E. granulosus complex was shown the total genetic variability within populations while nucleotide diversity was low in all populations. Neutrality indices of the cox1 (Tajima's D and Fu's Fs tests) were shown negative values in Western-Northwestern, Northern and Southeastern populations which indicating significant divergence from neutrality and positive but not significant in Central isolates. A pairwise fixation index (Fst) as a degree of gene flow was generally low value for all populations (0.00647-0.15198). The statistically Fst values indicate that Echinococcus sensu stricto (genotype G1-G3) populations are not genetically well differentiated in various geographical regions of Iran. To appraise the hypothetical evolutionary scenario, further study is needed to analyze concatenated mitogenomes and as well a panel of single locus nuclear markers should be considered in wider areas of Iran and neighboring countries.

  3. Detection of Mitochondrial COII DNA Sequences in Ant Guts as a Method for Assessing Termite Predation by Ants

    PubMed Central

    Fayle, Tom M.; Scholtz, Olivia; Dumbrell, Alex J.; Russell, Stephen; Segar, Simon T.; Eggleton, Paul

    2015-01-01

    Termites and ants contribute more to animal biomass in tropical rain forests than any other single group and perform vital ecosystem functions. Although ants prey on termites, at the community level the linkage between these groups is poorly understood. Thus, assessing the distribution and specificity of ant termitophagy is of considerable interest. We describe an approach for quantifying ant-termite food webs by sequencing termite DNA (cytochrome c oxidase subunit II, COII) from ant guts and apply this to a soil-dwelling ant community from tropical rain forest in Gabon. We extracted DNA from 215 ants from 15 species. Of these, 17.2 % of individuals had termite DNA in their guts, with BLAST analysis confirming the identity of 34.1 % of these termites to family level or better. Although ant species varied in detection of termite DNA, ranging from 63 % (5/7; Camponotus sp. 1) to 0 % (0/7; Ponera sp. 1), there was no evidence (with small sample sizes) for heterogeneity in termite consumption across ant taxa, and no evidence for species-specific ant-termite predation. In all three ant species with identifiable termite DNA in multiple individuals, multiple termite species were represented. Furthermore, the two termite species that were detected on multiple occasions in ant guts were in both cases found in multiple ant species, suggesting that ant-termite food webs are not strongly compartmentalised. However, two ant species were found to consume only Anoplotermes-group termites, indicating possible predatory specialisation at a higher taxonomic level. Using a laboratory feeding test, we were able to detect termite COII sequences in ant guts up to 2 h after feeding, indicating that our method only detects recent feeding events. Our data provide tentative support for the hypothesis that unspecialised termite predation by ants is widespread and highlight the use of molecular approaches for future studies of ant-termite food webs. PMID:25853549

  4. Detection of mitochondrial COII DNA sequences in ant guts as a method for assessing termite predation by ants.

    PubMed

    Fayle, Tom M; Scholtz, Olivia; Dumbrell, Alex J; Russell, Stephen; Segar, Simon T; Eggleton, Paul

    2015-01-01

    Termites and ants contribute more to animal biomass in tropical rain forests than any other single group and perform vital ecosystem functions. Although ants prey on termites, at the community level the linkage between these groups is poorly understood. Thus, assessing the distribution and specificity of ant termitophagy is of considerable interest. We describe an approach for quantifying ant-termite food webs by sequencing termite DNA (cytochrome c oxidase subunit II, COII) from ant guts and apply this to a soil-dwelling ant community from tropical rain forest in Gabon. We extracted DNA from 215 ants from 15 species. Of these, 17.2 % of individuals had termite DNA in their guts, with BLAST analysis confirming the identity of 34.1 % of these termites to family level or better. Although ant species varied in detection of termite DNA, ranging from 63 % (5/7; Camponotus sp. 1) to 0 % (0/7; Ponera sp. 1), there was no evidence (with small sample sizes) for heterogeneity in termite consumption across ant taxa, and no evidence for species-specific ant-termite predation. In all three ant species with identifiable termite DNA in multiple individuals, multiple termite species were represented. Furthermore, the two termite species that were detected on multiple occasions in ant guts were in both cases found in multiple ant species, suggesting that ant-termite food webs are not strongly compartmentalised. However, two ant species were found to consume only Anoplotermes-group termites, indicating possible predatory specialisation at a higher taxonomic level. Using a laboratory feeding test, we were able to detect termite COII sequences in ant guts up to 2 h after feeding, indicating that our method only detects recent feeding events. Our data provide tentative support for the hypothesis that unspecialised termite predation by ants is widespread and highlight the use of molecular approaches for future studies of ant-termite food webs.

  5. Production of mitochondrial DNA transgenic mice using zygotes.

    PubMed

    Inoue, Kimiko; Ogura, Atsuo; Hayashi, Jun-Ichi

    2002-04-01

    Several animal models of human disease, which have been developed by random or targeted modifications of genomic DNA sequences, have furthered our understanding of pathogenesis and the development of therapeutics. However, these models have not facilitated studies on mitochondrial diseases, since modifications to mitochondrial DNA (mtDNA) sequences are not possible using current recombination techniques. Consequently, information on human mitochondrial diseases is relatively sparse, and issues related to mitochondrial pathogenesis and inheritance remain unresolved. Recently, we reported the development of a new technique to generate mice carrying mutant mtDNA from a mouse cell line. In this report, we describe our techniques in detail, with emphasis on the preparation of donor cytoplasts and the micromanipulative procedures for electrofusion of cytoplasts and recipient zygotes. These steps are critically important for the successful introduction of exogenous mtDNA into embryos, and thereby into animals, so that the mutant mtDNA is efficiently propagated in subsequent generations.

  6. Isolation and DNA sequence of ADH3, a nuclear gene encoding the mitochondrial isozyme of alcohol dehydrogenase in Saccharomyces cerevisiae.

    PubMed Central

    Young, E T; Pilgrim, D

    1985-01-01

    The Saccharomyces cerevisiae nuclear gene, ADH3, that encodes the mitochondrial alcohol dehydrogenase isozyme ADH III was cloned by virtue of its nucleotide homology to ADH1 and ADH2. Both chromosomal and plasmid-encoded ADH III isozymes were repressed by glucose and migrated heterogeneously on nondenaturing gels. Nucleotide sequence analysis indicated 73 and 74% identity for ADH3 with ADH1 and ADH2, respectively. The amino acid identity between the predicted ADH III polypeptide and ADH I and ADH II was 79 and 80%, respectively. The open reading frame encoding ADH III has a highly basic 27-amino-acid amino-terminal extension relative to ADH I and ADH II. The nucleotide sequence of the presumed leader peptide has a high degree of identity with the untranslated leader regions of ADH1 and ADH2 mRNAs. A strain containing a null allele of ADH3 did not have a detectably altered phenotype. The cloned gene integrated at the ADH3 locus, indicating that this is the structural gene for ADH III. Images PMID:2943982

  7. The evolution and phylogeography of the African elephant inferred from mitochondrial DNA sequence and nuclear microsatellite markers.

    PubMed

    Eggert, Lori S; Rasner, Caylor A; Woodruff, David S

    2002-10-07

    Recent genetic results support the recognition of two African elephant species: Loxodonta africana, the savannah elephant, and Loxodonta cyclotis, the forest elephant. The study, however, did not include the populations of West Africa, where the taxonomic affinities of elephants have been much debated. We examined mitochondrial cytochrome b control region sequences and four microsatellite loci to investigate the genetic differences between the forest and savannah elephants of West and Central Africa. We then combined our data with published control region sequences from across Africa to examine patterns at the continental level. Our analysis reveals several deeply divergent lineages that do not correspond with the currently recognized taxonomy: (i) the forest elephants of Central Africa; the forest and savannah elephants of West Africa; and (iii) the savannah elephants of eastern, southern and Central Africa. We propose that the complex phylogeographic patterns we detect in African elephants result from repeated continental-scale climatic changes over their five-to-six million year evolutionary history. Until there is consensus on the taxonomy, we suggest that the genetic and ecological distinctness of these lineages should be an important factor in conservation management planning.

  8. The evolution and phylogeography of the African elephant inferred from mitochondrial DNA sequence and nuclear microsatellite markers.

    PubMed Central

    Eggert, Lori S; Rasner, Caylor A; Woodruff, David S

    2002-01-01

    Recent genetic results support the recognition of two African elephant species: Loxodonta africana, the savannah elephant, and Loxodonta cyclotis, the forest elephant. The study, however, did not include the populations of West Africa, where the taxonomic affinities of elephants have been much debated. We examined mitochondrial cytochrome b control region sequences and four microsatellite loci to investigate the genetic differences between the forest and savannah elephants of West and Central Africa. We then combined our data with published control region sequences from across Africa to examine patterns at the continental level. Our analysis reveals several deeply divergent lineages that do not correspond with the currently recognized taxonomy: (i) the forest elephants of Central Africa; the forest and savannah elephants of West Africa; and (iii) the savannah elephants of eastern, southern and Central Africa. We propose that the complex phylogeographic patterns we detect in African elephants result from repeated continental-scale climatic changes over their five-to-six million year evolutionary history. Until there is consensus on the taxonomy, we suggest that the genetic and ecological distinctness of these lineages should be an important factor in conservation management planning. PMID:12396498

  9. Molecular phylogeny of commercially important lobster species from Indian coast inferred from mitochondrial and nuclear DNA sequences.

    PubMed

    Jeena, N S; Gopalakrishnan, A; Radhakrishnan, E V; Kizhakudan, Joe K; Basheer, V S; Asokan, P K; Jena, J K

    2016-07-01

    Lobsters constitute low-volume high-value crustacean fishery resource along Indian coast. For the conservation and management of this declining resource, accurate identification of species and larvae is essential. The objectives of this work were to generate species-specific molecular signatures of 11 commercially important species of lobsters of families Palinuridae and Scyllaridae and to reconstruct a phylogeny to clarify the evolutionary relationships among genera and species included in this study. Partial sequences were generated for all the candidate species from sampling sites along the Indian coast using markers like Cytochrome oxidase I (COI), 16SrRNA, 12SrRNA, and 18SrRNA genes, and analyzed. The genetic identities of widely distributed Thenus species along the Indian coast to be Thenus unimaculatus and the sub-species of Panulirus homarus to be P. homarus homarus were confirmed. Phylogeny reconstruction using the individual gene and concatenated mtDNA data set were carried out. The overall results suggested independent monophyly of Scyllaridae and Stridentes of Palinuridae. The interspecific divergence was found to be highest for the 12SrRNA compared with other genes. Significant incongruence between mtDNA and nuclear 18SrRNA gene tree topologies was observed. The results hinted an earlier origin for Palinuridae compared with Scyllaridae. The DNA sequence data generated from this study will aid in the correct identification of lobster larvae and will find application in research related to larval transport and distribution.

  10. Mitochondrial Genome Sequence of the Legume Vicia faba.

    PubMed

    Negruk, Valentine

    2013-01-01

    The number of plant mitochondrial genomes sequenced exceeds two dozen. However, for a detailed comparative study of different phylogenetic branches more plant mitochondrial genomes should be sequenced. This article presents sequencing data and comparative analysis of mitochondrial DNA (mtDNA) of the legume Vicia faba. The size of the V. faba circular mitochondrial master chromosome of cultivar Broad Windsor was estimated as 588,000 bp with a genome complexity of 387,745 bp and 52 conservative mitochondrial genes; 32 of them encoding proteins, 3 rRNA, and 17 tRNA genes. Six tRNA genes were highly homologous to chloroplast genome sequences. In addition to the 52 conservative genes, 114 unique open reading frames (ORFs) were found, 36 without significant homology to any known proteins and 29 with homology to the Medicago truncatula nuclear genome and to other plant mitochondrial ORFs, 49 ORFs were not homologous to M. truncatula but possessed sequences with significant homology to other plant mitochondrial or nuclear ORFs. In general, the unique ORFs revealed very low homology to known closely related legumes, but several sequence homologies were found between V. faba, Beta vulgaris, Nicotiana tabacum, Vitis vinifera, and even the monocots Oryza sativa and Zea mays. Most likely these ORFs arose independently during angiosperm evolution (Kubo and Mikami, 2007; Kubo and Newton, 2008). Computational analysis revealed in total about 45% of V. faba mtDNA sequence being homologous to the Medicago truncatula nuclear genome (more than to any sequenced plant mitochondrial genome), and 35% of this homology ranging from a few dozen to 12,806 bp are located on chromosome 1. Apparently, mitochondrial rrn5, rrn18, rps10, ATP synthase subunit alpha, cox2, and tRNA sequences are part of transcribed nuclear mosaic ORFs.

  11. Mitochondrial DNA haplotype predicts deafness risk

    SciTech Connect

    Hutchin, T.; Cortopassi, G.

    1995-12-18

    Since mitochondrial DNA (mtDNA) does not recombine in humans, once deleterious variation arises within a particular mtDNA clone it remains linked to that clonal type. An A to G mutation at mtDNA position 1555 confers matrilineal deafness among Asians and others. Two major mtDNA types (I and II) have been defined in Asians by D-loop sequencing. We have determined the D-loop sequence of 8 unrelated deaf Asians bearing the 1555G mutation, and find that 7 are of type II, whereas only one is of type I. Thus the frequency of the 1555G mutation is higher in type II mtDNA than type I (P = 0.035, binomial test), and persons with type II mtDNA are more likely to become deaf. Type II mtDNAs are rare in the Caucasian population, which may explain the rarity of this form of deafness in the United States. Negative Darwinian selection is expected to rapidly eliminate mtDNAs bearing severely deleterious mutations; but mildly deleterious mutations whose phenotype is expressed after reproduction should persist on the mtDNA background in which they arose. Thus determination of mtDNA clonal type has the potential to predict human risk for diseases that are the result of mildly deleterious mtDNA mutations which confer a post-reproductive phenotype. 4 refs., 1 fig.

  12. Comparative phylogeography between the ermine Mustela erminea and the least weasel M. nivalis of Palaearctic and Nearctic regions, based on analysis of mitochondrial DNA control region sequences.

    PubMed

    Kurose, Naoko; Abramov, Alexei V; Masuda, Ryuichi

    2005-10-01

    Phylogeography of the ermine Mustela erminea and the least weasel M. nivalis from Palaearctic and Nearctic regions were investigated based on mitochondrial DNA control region sequences. Mustela erminea exhibited a very low level of genetic variation, and geographic structures among populations were unclear. This may indicate that M. erminea recently reoccupied a wide territory in Eurasia following the last glacial retreat. In comparison with M. erminea, genetic variations within and among populations of M. nivalis were much greater. Molecular phylogenetic relationships showed that two lineages of M. nivalis occurred in the Holarctic region: one spread from the Eurasian region to North America, and the other occurred in south-eastern Europe, the Caucasus and Central Asia. The results suggest either mitochondrial DNA introgression among populations of south-eastern Europe, the Caucasus and Central Asia, or ancestral polymorphisms remaining in those populations. Contrastive phylogeographic patterns between the two mustelid species could reflect differences of their migration histories in Eurasia after the last glacial age.

  13. Phylogeography of the New Zealand cicada Maoricicada campbelli based on mitochondrial DNA sequences: ancient clades associated with cenozoic environmental change.

    PubMed

    Buckley, T R; Simon, C; Chambers, G K

    2001-07-01

    New Zealand's isolation, its well-studied rapidly changing landscape, and its many examples of rampant speciation make it an excellent location for studying the process of genetic differentiation. Using 1520 base pairs of mitochondrial DNA from the cytochrome oxidase subunit I, ATPase subunits 6 and 8 and tRNA(Asp) genes, we detected two well-differentiated, parapatrically distributed clades within the widespread New Zealand cicada species Maoricicada campbelli that may prove to represent two species. The situation that we uncovered is unusual in that an ancient lineage with low genetic diversity is surrounded on three sides by two recently diverged lineages. Using a relaxed molecular clock model coupled with Bayesian statistics, we dated the earliest divergence within M. campbelli at 2.3 +/- 0.55 million years. Our data suggest that geological and climatological events of the late Pliocene divided a once-widespread species into northern and southern components and that near the middle of the Pleistocene the northern lineage began moving south eventually reaching the southern clade. The southern clade seems to have moved northward to only a limited extent. We discovered five potential zones of secondary contact through mountain passes that will be examined in future work. We predict that, as in North American periodical cicadas, contact between these highly differentiated lineages will exist but will not involve gene flow.

  14. The exome sequencing identified the mutation in YARS2 encoding the mitochondrial tyrosyl-tRNA synthetase as a nuclear modifier for the phenotypic manifestation of Leber's hereditary optic neuropathy-associated mitochondrial DNA mutation.

    PubMed

    Jiang, Pingping; Jin, Xiaofen; Peng, Yanyan; Wang, Meng; Liu, Hao; Liu, Xiaoling; Zhang, Zengjun; Ji, Yanchun; Zhang, Juanjuan; Liang, Min; Zhao, Fuxin; Sun, Yan-Hong; Zhang, Minglian; Zhou, Xiangtian; Chen, Ye; Mo, Jun Qin; Huang, Taosheng; Qu, Jia; Guan, Min-Xin

    2016-02-01

    Leber's hereditary optic neuropathy (LHON) is the most common mitochondrial disorder. Nuclear modifier genes are proposed to modify the phenotypic expression of LHON-associated mitochondrial DNA (mtDNA) mutations. By using an exome sequencing approach, we identified a LHON susceptibility allele (c.572G>T, p.191Gly>Val) in YARS2 gene encoding mitochondrial tyrosyl-tRNA synthetase, which interacts with m.11778G>A mutation to cause visual failure. We performed functional assays by using lymphoblastoid cell lines derived from members of Chinese families (asymptomatic individuals carrying m.11778G>A mutation, or both m.11778G>A and heterozygous p.191Gly>Val mutations and symptomatic subjects harboring m.11778G>A and homozygous p.191Gly>Val mutations) and controls lacking these mutations. The 191Gly>Val mutation reduced the YARS2 protein level in the mutant cells. The aminoacylated efficiency and steady-state level of tRNA(Tyr) were markedly decreased in the cell lines derived from patients both carrying homozygous YARS2 p.191Gly>Val and m.11778G>A mutations. The failure in tRNA(Tyr) metabolism impaired mitochondrial translation, especially for polypeptides with high content of tyrosine codon such as ND4, ND5, ND6 and COX2 in cells lines carrying homozygous YARS2 p.191Gly>Val and m.11778G>A mutations. The YARS2 p.191Gly>Val mutation worsened the respiratory phenotypes associated with m.11778G>A mutation, especially reducing activities of complexes I and IV. The respiratory deficiency altered the efficiency of mitochondrial ATP synthesis and increased the production of reactive oxygen species. Thus, mutated YARS2 aggravates mitochondrial dysfunctions associated with the m.11778G>A mutation, exceeding the threshold for the expression of blindness phenotype. Our findings provided new insights into the pathophysiology of LHON that were manifested by interaction between mtDNA mutation and mutated nuclear-modifier YARS2.

  15. Classification and phylogeny of sika deer (Cervus nippon) subspecies based on the mitochondrial control region DNA sequence using an extended sample set.

    PubMed

    Ba, Hengxing; Yang, Fuhe; Xing, Xiumei; Li, Chunyi

    2015-06-01

    To further refine the classification and phylogeny of sika deer subspecies, the well-annotated sequences of the complete mitochondrial DNA (mtDNA) control region of 13 sika deer subspecies from GenBank were downloaded, aligned and analyzed in this study. By reconstructing the phylogenetic tree with an extended sample set, the results revealed a split between Northern and Southern Mainland Asia/Taiwan lineages, and moreover, two subspecies, C.n.mantchuricus and C.n.hortulorum, were existed in Northern Mainland Asia. Unexpectedly, Dybowskii's sika deer that was thought to originate from Northern Mainland Asia joins the Southern Mainland Asia/Taiwan lineage. The genetic divergences were ranged from 2.1% to 4.7% between Dybowskii's sika deer and all the other established subspecies at the mtDNA sequence level, which suggests that the maternal lineage of uncertain sika subspecies in Europe had been maintained until today. This study also provides a better understanding for the classification, phylogeny and phylogeographic history of sika deer subspecies.

  16. Genetic relationships among some subspecies of the Peregrine Falcon (Falco peregrinus L.), inferred from mitochondrial DNA control-region sequences

    USGS Publications Warehouse

    White, Clayton M.; Sonsthagen, Sarah A.; Sage, George K.; Anderson, Clifford; Talbot, Sandra L.

    2013-01-01

    The ability to successfully colonize and persist in diverse environments likely requires broad morphological and behavioral plasticity and adaptability, and this may partly explain why the Peregrine Falcon (Falco peregrinus) exhibits a large range of morphological characteristics across their global distribution. Regional and local differences within Peregrine Falcons were sufficiently variable that ∼75 subspecies have been described; many were subsumed, and currently 19 are generally recognized. We used sequence information from the control region of the mitochondrial genome to test for concordance between genetic structure and representatives of 12 current subspecies and from two areas where subspecies distributions overlap. Haplotypes were broadly shared among subspecies, and all geographic locales shared a widely distributed common haplotype (FalconCR2). Haplotypes were distributed in a star-like phylogeny, consistent with rapid expansion of a recently derived species, with observed genetic patterns congruent with incomplete lineage sorting and/or differential rates of evolution on morphology and neutral genetic characters. Hierarchical analyses of molecular variance did not uncover genetic partitioning at the continental level, despite strong population-level structure (FST = 0.228). Similar analyses found weak partitioning, albeit significant, among subspecies (FCT = 0.138). All reconstructions placed the hierofalcons' (Gyrfalcon [F. rusticolus] and Saker Falcon [F. cherrug]) haplotypes in a well-supported clade either basal or unresolved with respect to the Peregrine Falcon. In addition, haplotypes representing Taita Falcon (F. fasciinucha) were placed within the Peregrine Falcon clade.

  17. DNA sequencing conference, 2

    SciTech Connect

    Cook-Deegan, R.M.; Venter, J.C.; Gilbert, W.; Mulligan, J.; Mansfield, B.K.

    1991-06-19

    This conference focused on DNA sequencing, genetic linkage mapping, physical mapping, informatics and bioethics. Several were used to study this sequencing and mapping. This article also discusses computer hardware and software aiding in the mapping of genes.

  18. Diagnosis of mitochondrial disorders by concomitant next-generation sequencing of the exome and mitochondrial genome

    PubMed Central

    Dinwiddie, Darrell L.; Smith, Laurie D.; Miller, Neil A.; Atherton, Andrea M.; Farrow, Emily G.; Strenk, Meghan E.; Soden, Sarah E.; Saunders, Carol J.; Kingsmore, Stephen F.

    2015-01-01

    Mitochondrial diseases are notoriously difficult to diagnose due to extreme locus and allelic heterogeneity, with both nuclear and mitochondrial genomes potentially liable. Using exome sequencing we demonstrate the ability to rapidly and cost effectively evaluate both the nuclear and mitochondrial genomes to obtain a molecular diagnosis for four patients with three distinct mitochondrial disorders. One patient was found to have Leigh syndrome due to a mutation in MT-ATP6, two affected siblings were discovered to be compound heterozygous for mutations in the NDUFV1 gene, which causes mitochondrial complex I deficiency, and one patient was found to have coenzyme Q10 deficiency due to compound heterozygous mutations in COQ2. In all cases conventional diagnostic testing failed to identify a molecular diagnosis. We suggest that additional studies should be conducted to evaluate exome sequencing as a primary diagnostic test for mitochondrial diseases, including those due to mtDNA mutations. PMID:23631824

  19. DNA sequence from Cretaceous period bone fragments.

    PubMed

    Woodward, S R; Weyand, N J; Bunnell, M

    1994-11-18

    DNA was extracted from 80-million-year-old bone fragments found in strata of the Upper Cretaceous Blackhawk Formation in the roof of an underground coal mine in eastern Utah. This DNA was used as the template in a polymerase chain reaction that amplified and sequenced a portion of the gene encoding mitochondrial cytochrome b. These sequences differ from all other cytochrome b sequences investigated, including those in the GenBank and European Molecular Biology Laboratory databases. DNA isolated from these bone fragments and the resulting gene sequences demonstrate that small fragments of DNA may survive in bone for millions of years.

  20. Development of a method for the genetic identification of flatfish species on the basis of mitochondrial DNA sequences.

    PubMed

    Espiñeira, Montserrat; González-Lavín, Nerea; Vieites, Juan M; Santaclara, Francisco J

    2008-10-08

    In the present study a method for genetic identification of flatfish species was developed. The technique is based on DNA sequencing of amplified DNA by PCR and subsequent phylogenetic analysis ( FINS). A phylogenetic tree using the cytochrome oxidase subunit I (COI) was constructed and the bootstrap values calculated. The mentioned technique allows the genetic identification of more than 50 flatfish species in fresh, frozen, and precooked products. This analytical system was validated and subsequently applied to 30 commercial samples, obtaining 13 that were incorrectly labeled (43%). Four of the mislabeled samples were whole fish (31%), and nine were fillets (69%). The species with the higher rate of incorrect labeling were Pleuronectes platessa (17%) and Solea solea (10%). Other species incorrectly labeled were Hipoglossus hipoglossus (7%), Reinharditus hippoglossoides, Limanda ferruginea, and Microstomus kitt (3% each species). Therefore, this molecular tool is appropriate to clarify questions related with the correct labeling of commercial products, the traceability of raw materials, and the control of imported flatfish, and also can be applied to questions linked to the control of fisheries.

  1. Mutation hot spots in mammalian mitochondrial DNA.

    PubMed

    Galtier, Nicolas; Enard, David; Radondy, Yoan; Bazin, Eric; Belkhir, Khalid

    2006-02-01

    Animal mitochondrial DNA is characterized by a remarkably high level of within-species homoplasy, that is, phylogenetic incongruence between sites of the molecule. Several investigators have invoked recombination to explain it, challenging the dogma of maternal, clonal mitochondrial inheritance in animals. Alternatively, a high level of homoplasy could be explained by the existence of mutation hot spots. By using an exhaustive mammalian data set, we test the hot spot hypothesis by comparing patterns of site-specific polymorphism and divergence in several groups of closely related species, including hominids. We detect significant co-occurrence of synonymous polymorphisms among closely related species in various mammalian groups, and a correlation between the site-specific levels of variability within humans (on one hand) and between Hominoidea species (on the other hand), indicating that mutation hot spots actually exist in mammalian mitochondrial coding regions. The whole data, however, cannot be explained by a simple mutation hot spots model. Rather, we show that the site-specific mutation rate quickly varies in time, so that the same sites are not hypermutable in distinct lineages. This study provides a plausible mutation model that potentially accounts for the peculiar distribution of mitochondrial sequence variation in mammals without the need for invoking recombination. It also gives hints about the proximal causes of mitochondrial site-specific hypermutability in humans.

  2. Phylogenetic relationships and historical biogeography of neotropical parrots (Psittaciformes: Psittacidae: Arini) inferred from mitochondrial and nuclear DNA sequences.

    PubMed

    Tavares, Erika Sendra; Baker, Allan J; Pereira, Sérgio Luiz; Miyaki, Cristina Yumi

    2006-06-01

    Previous hypotheses of phylogenetic relationships among Neotropical parrots were based on limited taxon sampling and lacked support for most internal nodes. In this study we increased the number of taxa (29 species belonging to 25 of the 30 genera) and gene sequences (6388 base pairs of RAG-1, cyt b, NADH2, ATPase 6, ATPase 8, COIII, 12S rDNA, and 16S rDNA) to obtain a stronger molecular phylogenetic hypothesis for this group of birds. Analyses of the combined gene sequences using maximum likelihood and Bayesian methods resulted in a well-supported phylogeny and indicated that amazons and allies are a sister clade to macaws, conures, and relatives, and these two clades are in turn a sister group to parrotlets. Key morphological and behavioral characters used in previous classifications were mapped on the molecular tree and were phylogenetically uninformative. We estimated divergence times of taxa using the molecular tree and Bayesian and penalized likelihood methods that allow for rate variation in DNA substitutions among sites and taxa. Our estimates suggest that the Neotropical parrots shared a common ancestor with Australian parrots 59 Mya (million of years ago; 95% credibility interval (CrI) 66, 51 Mya), well before Australia separated from Antarctica and South America, implying that ancestral parrots were widespread in Gondwanaland. Thus, the divergence of Australian and Neotropical parrots could be attributed to vicariance. The three major clades of Neotropical parrots originated about 50 Mya (95% CrI 57, 41 Mya), coinciding with periods of higher sea level when both Antarctica and South America were fragmented with transcontinental seaways, and likely isolated the ancestors of modern Neotropical parrots in different regions in these continents. The correspondence between major paleoenvironmental changes in South America and the diversification of genera in the clade of amazons and allies between 46 and 16 Mya suggests they diversified exclusively in South

  3. Mitochondrial DNA Damage and its Consequences for Mitochondrial Gene Expression

    PubMed Central

    Cline, Susan D.

    2012-01-01

    How mitochondria process DNA damage and whether a change in the steady-state level of mitochondrial DNA damage (mtDNA) contributes to mitochondrial dysfunction are questions that fuel burgeoning areas of research into aging and disease pathogenesis. Over the past decade, researchers have identified and measured various forms of endogenous and environmental mtDNA damage and have elucidated mtDNA repair pathways. Interestingly, mitochondria do not appear to contain the full range of DNA repair mechanisms that operate in the nucleus, although mtDNA contains types of damage that are targets of each nuclear DNA repair pathway. The reduced repair capacity may, in part, explain the high mutation frequency of the mitochondrial chromosome. Since mtDNA replication is dependent on transcription, mtDNA damage may alter mitochondrial gene expression at three levels: by causing DNA polymerase γ nucleotide incorporation errors leading to mutations, by interfering with the priming of mtDNA replication by the mitochondrial RNA polymerase, or by inducing transcriptional mutagenesis or premature transcript termination. This review summarizes our current knowledge of mtDNA damage, its repair, and its effects on mtDNA integrity and gene expression. PMID:22728831

  4. Automated DNA Sequencing System

    SciTech Connect

    Armstrong, G.A.; Ekkebus, C.P.; Hauser, L.J.; Kress, R.L.; Mural, R.J.

    1999-04-25

    Oak Ridge National Laboratory (ORNL) is developing a core DNA sequencing facility to support biological research endeavors at ORNL and to conduct basic sequencing automation research. This facility is novel because its development is based on existing standard biology laboratory equipment; thus, the development process is of interest to the many small laboratories trying to use automation to control costs and increase throughput. Before automation, biology Laboratory personnel purified DNA, completed cycle sequencing, and prepared 96-well sample plates with commercially available hardware designed specifically for each step in the process. Following purification and thermal cycling, an automated sequencing machine was used for the sequencing. A technician handled all movement of the 96-well sample plates between machines. To automate the process, ORNL is adding a CRS Robotics A- 465 arm, ABI 377 sequencing machine, automated centrifuge, automated refrigerator, and possibly an automated SpeedVac. The entire system will be integrated with one central controller that will direct each machine and the robot. The goal of this system is to completely automate the sequencing procedure from bacterial cell samples through ready-to-be-sequenced DNA and ultimately to completed sequence. The system will be flexible and will accommodate different chemistries than existing automated sequencing lines. The system will be expanded in the future to include colony picking and/or actual sequencing. This discrete event, DNA sequencing system will demonstrate that smaller sequencing labs can achieve cost-effective the laboratory grow.

  5. Molecular systematics and evolution of the "Apollo" butterflies of the genus Parnassius (Lepidoptera: Papilionidae) based on mitochondrial DNA sequence data.

    PubMed

    Omoto, Keiichi; Katoh, Toru; Chichvarkhin, Anton; Yagi, Takashi

    2004-02-04

    Sequences of 777 bp of mtDNA-ND5 locus were determined in order to shed light on the molecular systematics and evolution of the "Apollo" butterflies. Examined were nearly all of about 50 species of the genus Parnassius, together with seven species of the allied genera in the subfamily Parnassiinae (Papilionidae). The NJ and the MP phylogenetic trees show that the "Apollos" constitute a monophyletic group, comprising a number of cluster groups probably reflecting a relatively rapid radiation in evolution. The clusters of species-groups denoted I-VIII correspond to those species-groups recognized on the basis of morphological characters. Our findings will also help understand the biological relationships among several species or subspecies on which the classical taxonomy is in dispute. The unexpected finding is that among the samples of allied genera compared, Hypermnestra helios appears to be the most closely related to the "Apollos", despite morphological and behavioral dissimilarity. Furthermore, in contrast to the previous higher taxonomy, Archon apollinus which is classified in the tribe Parnassiini was found genetically closer to the tribe Zerynthiini, raising a taxonomic controversy.

  6. Mitochondrial genome sequence of the Tibetan wild ass (Equus kiang).

    PubMed

    Luo, Yongjun; Chen, Yu; Liu, Fuyu; Jiang, Chunhua; Gao, Yuqi

    2011-02-01

    The Tibetan wild ass, or kiang (Equus kiang) is endemic to the cold and hypoxic (4000-7000 m above sea level) climates of the montane and alpine grasslands of the Tibetan Plateau. We report here the complete nucleotide sequence of the E. kiang mitochondrial genome. Our results show that E. kiang mitochondrial DNA is 16,634 bp long, and predicted to encode all the 37 genes that are typical for vertebrates.

  7. Recombination sequences in plant mitochondrial genomes: diversity and homologies to known mitochondrial genes.

    PubMed Central

    Stern, D B; Palmer, J D

    1984-01-01

    Several plant mitochondrial genomes contain repeated sequences that are postulated to be sites of homologous intragenomic recombination (1-3). In this report, we have used filter hybridizations to investigate sequence relationships between the cloned mitochondrial DNA (mtDNA) recombination repeats from turnip, spinach and maize and total mtDNA isolated from thirteen species of angiosperms. We find that strong sequence homologies exist between the spinach and turnip recombination repeats and essentially all other mitochondrial genomes tested, whereas a major maize recombination repeat does not hybridize to any other mtDNA. The sequences homologous to the turnip repeat do not appear to function in recombination in any other genome, whereas the spinach repeat hybridizes to reiterated sequences within the mitochondrial genomes of wheat and two species of pokeweed that do appear to be sites of recombination. Thus, although intragenomic recombination is a widespread phenomenon in plant mitochondria, it appears that different sequences either serve as substrates for this function in different species, or else surround a relatively short common recombination site which does not cross-hybridize under our experimental conditions. Identified gene sequences from maize mtDNA were used in heterologous hybridizations to show that the repeated sequences implicated in recombination in turnip and spinach/pokeweed/wheat mitochondria include, or are closely linked to genes for subunit II of cytochrome c oxidase and 26S rRNA, respectively. Together with previous studies indicating that the 18S rRNA gene in wheat mtDNA is contained within a recombination repeat (3), these results imply an unexpectedly frequent association between recombination repeats and plant mitochondrial genes. Images PMID:6473104

  8. Evolutionary Relationship between Two Firefly Species, Curtos costipennis and C. okinawanus (Coleoptera, Lampyridae), in the Ryukyu Islands of Japan Revealed by the Mitochondrial and Nuclear DNA Sequences

    PubMed Central

    Muraji, Masahiko; Arakaki, Norio; Tanizaki, Shigeo

    2012-01-01

    The phylogenetic relationship, biogeography, and evolutionary history of closely related two firefly species, Curtos costipennis and C. okinawanus, distributed in the Ryukyu Islands of Japan were examined based on nucleotide sequences of mitochondrial (2.2 kb long) and nuclear (1.1-1.2 kb long) DNAs. In these analyses, individuals were divided among three genetically distinct local groups, C. costipennis in the Amami region, C. okinawanus in the Okinawa region, and C. costipennis in the Sakishima region. Their mtDNA sequences suggested that ancestral C. costipennis population was first separated between the Central and Southern Ryukyu areas, and the northern half was then subdivided between C. costipennis in the Amami and C. okinawanus in the Okinawa. The application of the molecular evolutionary clocks of coleopteran insects indicated that their vicariance occurred 1.0–1.4 million years ago, suggesting the influence of submergence and subdivision of a paleopeninsula extending between the Ryukyu Islands and continental China through Taiwan in the early Pleistocene. PMID:22629179

  9. Evolutionary relationship between two firefly species, Curtos costipennis and C. okinawanus (Coleoptera, Lampyridae), in the Ryukyu Islands of Japan revealed by the mitochondrial and nuclear DNA sequences.

    PubMed

    Muraji, Masahiko; Arakaki, Norio; Tanizaki, Shigeo

    2012-01-01

    The phylogenetic relationship, biogeography, and evolutionary history of closely related two firefly species, Curtos costipennis and C. okinawanus, distributed in the Ryukyu Islands of Japan were examined based on nucleotide sequences of mitochondrial (2.2 kb long) and nuclear (1.1-1.2 kb long) DNAs. In these analyses, individuals were divided among three genetically distinct local groups, C. costipennis in the Amami region, C. okinawanus in the Okinawa region, and C. costipennis in the Sakishima region. Their mtDNA sequences suggested that ancestral C. costipennis population was first separated between the Central and Southern Ryukyu areas, and the northern half was then subdivided between C. costipennis in the Amami and C. okinawanus in the Okinawa. The application of the molecular evolutionary clocks of coleopteran insects indicated that their vicariance occurred 1.0-1.4 million years ago, suggesting the influence of submergence and subdivision of a paleopeninsula extending between the Ryukyu Islands and continental China through Taiwan in the early Pleistocene.

  10. Mitochondrial and nuclear DNA matching shapes metabolism and healthy ageing.

    PubMed

    Latorre-Pellicer, Ana; Moreno-Loshuertos, Raquel; Lechuga-Vieco, Ana Victoria; Sánchez-Cabo, Fátima; Torroja, Carlos; Acín-Pérez, Rebeca; Calvo, Enrique; Aix, Esther; González-Guerra, Andrés; Logan, Angela; Bernad-Miana, María Luisa; Romanos, Eduardo; Cruz, Raquel; Cogliati, Sara; Sobrino, Beatriz; Carracedo, Ángel; Pérez-Martos, Acisclo; Fernández-Silva, Patricio; Ruíz-Cabello, Jesús; Murphy, Michael P; Flores, Ignacio; Vázquez, Jesús; Enríquez, José Antonio

    2016-07-28

    Human mitochondrial DNA (mtDNA) shows extensive within population sequence variability. Many studies suggest that mtDNA variants may be associated with ageing or diseases, although mechanistic evidence at the molecular level is lacking. Mitochondrial replacement has the potential to prevent transmission of disease-causing oocyte mtDNA. However, extension of this technology requires a comprehensive understanding of the physiological relevance of mtDNA sequence variability and its match with the nuclear-encoded mitochondrial genes. Studies in conplastic animals allow comparison of individuals with the same nuclear genome but different mtDNA variants, and have provided both supporting and refuting evidence that mtDNA variation influences organismal physiology. However, most of these studies did not confirm the conplastic status, focused on younger animals, and did not investigate the full range of physiological and phenotypic variability likely to be influenced by mitochondria. Here we systematically characterized conplastic mice throughout their lifespan using transcriptomic, proteomic,metabolomic, biochemical, physiological and phenotyping studies. We show that mtDNA haplotype profoundly influences mitochondrial proteostasis and reactive oxygen species generation,insulin signalling, obesity, and ageing parameters including telomere shortening and mitochondrial dysfunction, resulting in profound differences in health longevity between conplastic strains.

  11. DNA Sequencing apparatus

    DOEpatents

    Tabor, Stanley; Richardson, Charles C.

    1992-01-01

    An automated DNA sequencing apparatus having a reactor for providing at least two series of DNA products formed from a single primer and a DNA strand, each DNA product of a series differing in molecular weight and having a chain terminating agent at one end; separating means for separating the DNA products to form a series bands, the intensity of substantially all nearby bands in a different series being different, band reading means for determining the position an This invention was made with government support including a grant from the U.S. Public Health Service, contract number AI-06045. The U.S. government has certain rights in the invention.

  12. Mitochondrial Genome Sequences Effectively Reveal the Phylogeny of Hylobates Gibbons

    PubMed Central

    Chan, Yi-Chiao; Roos, Christian; Inoue-Murayama, Miho; Inoue, Eiji; Shih, Chih-Chin; Pei, Kurtis Jai-Chyi; Vigilant, Linda

    2010-01-01

    Background Uniquely among hominoids, gibbons exist as multiple geographically contiguous taxa exhibiting distinctive behavioral, morphological, and karyotypic characteristics. However, our understanding of the evolutionary relationships of the various gibbons, especially among Hylobates species, is still limited because previous studies used limited taxon sampling or short mitochondrial DNA (mtDNA) sequences. Here we use mtDNA genome sequences to reconstruct gibbon phylogenetic relationships and reveal the pattern and timing of divergence events in gibbon evolutionary history. Methodology/Principal Findings We sequenced the mitochondrial genomes of 51 individuals representing 11 species belonging to three genera (Hylobates, Nomascus and Symphalangus) using the high-throughput 454 sequencing system with the parallel tagged sequencing approach. Three phylogenetic analyses (maximum likelihood, Bayesian analysis and neighbor-joining) depicted the gibbon phylogenetic relationships congruently and with strong support values. Most notably, we recover a well-supported phylogeny of the Hylobates gibbons. The estimation of divergence times using Bayesian analysis with relaxed clock model suggests a much more rapid speciation process in Hylobates than in Nomascus. Conclusions/Significance Use of more than 15 kb sequences of the mitochondrial genome provided more informative and robust data than previous studies of short mitochondrial segments (e.g., control region or cytochrome b) as shown by the reliable reconstruction of divergence patterns among Hylobates gibbons. Moreover, molecular dating of the mitogenomic divergence times implied that biogeographic change during the last five million years may be a factor promoting the speciation of Sundaland animals, including Hylobates species. PMID:21203450

  13. Simple sequence repeats in bryophyte mitochondrial genomes.

    PubMed

    Zhao, Chao-Xian; Zhu, Rui-Liang; Liu, Yang

    2016-01-01

    Simple sequence repeats (SSRs) are thought to be common in plant mitochondrial (mt) genomes, but have yet to be fully described for bryophytes. We screened the mt genomes of two liverworts (Marchantia polymorpha and Pleurozia purpurea), two mosses (Physcomitrella patens and Anomodon rugelii) and two hornworts (Phaeoceros laevis and Nothoceros aenigmaticus), and detected 475 SSRs. Some SSRs are found conserved during the evolution, among which except one exists in both liverworts and mosses, all others are shared only by the two liverworts, mosses or hornworts. SSRs are known as DNA tracts having high mutation rates; however, according to our observations, they still can evolve slowly. The conservativeness of these SSRs suggests that they are under strong selection and could play critical roles in maintaining the gene functions.

  14. Strong Purifying Selection in Transmission of Mammalian Mitochondrial DNA

    PubMed Central

    Stewart, James Bruce; Freyer, Christoph; Elson, Joanna L; Wredenberg, Anna; Cansu, Zekiye; Trifunovic, Aleksandra; Larsson, Nils-Göran

    2008-01-01

    There is an intense debate concerning whether selection or demographics has been most important in shaping the sequence variation observed in modern human mitochondrial DNA (mtDNA). Purifying selection is thought to be important in shaping mtDNA sequence evolution, but the strength of this selection has been debated, mainly due to the threshold effect of pathogenic mtDNA mutations and an observed excess of new mtDNA mutations in human population data. We experimentally addressed this issue by studying the maternal transmission of random mtDNA mutations in mtDNA mutator mice expressing a proofreading-deficient mitochondrial DNA polymerase. We report a rapid and strong elimination of nonsynonymous changes in protein-coding genes; the hallmark of purifying selection. There are striking similarities between the mutational patterns in our experimental mouse system and human mtDNA polymorphisms. These data show strong purifying selection against mutations within mtDNA protein-coding genes. To our knowledge, our study presents the first direct experimental observations of the fate of random mtDNA mutations in the mammalian germ line and demonstrates the importance of purifying selection in shaping mitochondrial sequence diversity. PMID:18232733

  15. A complete Neandertal mitochondrial genome sequence determined by high-throughput sequencing

    PubMed Central

    Green, Richard E.; Malaspinas, Anna-Sapfo; Krause, Johannes; Briggs, Adrian W.; Johnson, Philip L. F.; Uhler, Caroline; Meyer, Matthias; Good, Jeffrey M.; Maricic, Tomislav; Stenzel, Udo; Prüfer, Kay; Siebauer, Michael; Burbano, Hernán A.; Ronan, Michael; Rothberg, Jonathan M.; Egholm, Michael; Rudan, Pavao; Brajković, Dejana; Kućan, Željko; Gušić, Ivan; Wikström, Mårten; Laakkonen, Liisa; Kelso, Janet; Slatkin, Montgomery; Pääbo, Svante

    2008-01-01

    Summary A complete mitochondrial (mt) genome sequence was reconstructed from a 38,000-year-old Neandertal individual using 8,341 mtDNA sequences identified among 4.8 Gb of DNA generated from ~0.3 grams of bone. Analysis of the assembled sequence unequivocally establishes that the Neandertal mtDNA falls outside the variation of extant human mtDNAs and allows an estimate of the divergence date between the two mtDNA lineages of 660,000±140,000 years. Of the 13 proteins encoded in the mtDNA, subunit 2 of cytochrome c oxidase of the mitochondrial electron transport chain has experienced the largest number of amino acid substitutions in human ancestors since the separation from Neandertals. There is evidence that purifying selection in the Neandertal mtDNA was reduced compared to other primate lineages suggesting that the effective population size of Neandertals was small. PMID:18692465

  16. The mitochondrial genome sequence of the Tasmanian tiger (Thylacinus cynocephalus)

    PubMed Central

    Miller, Webb; Drautz, Daniela I.; Janecka, Jan E.; Lesk, Arthur M.; Ratan, Aakrosh; Tomsho, Lynn P.; Packard, Mike; Zhang, Yeting; McClellan, Lindsay R.; Qi, Ji; Zhao, Fangqing; Gilbert, M. Thomas P.; Dalén, Love; Arsuaga, Juan Luis; Ericson, Per G.P.; Huson, Daniel H.; Helgen, Kristofer M.; Murphy, William J.; Götherström, Anders; Schuster, Stephan C.

    2009-01-01

    We report the first two complete mitochondrial genome sequences of the thylacine (Thylacinus cynocephalus), or so-called Tasmanian tiger, extinct since 1936. The thylacine's phylogenetic position within australidelphian marsupials has long been debated, and here we provide strong support for the thylacine's basal position in Dasyuromorphia, aided by mitochondrial genome sequence that we generated from the extant numbat (Myrmecobius fasciatus). Surprisingly, both of our thylacine sequences differ by 11%–15% from putative thylacine mitochondrial genes in GenBank, with one of our samples originating from a direct offspring of the previously sequenced individual. Our data sample each mitochondrial nucleotide an average of 50 times, thereby providing the first high-fidelity reference sequence for thylacine population genetics. Our two sequences differ in only five nucleotides out of 15,452, hinting at a very low genetic diversity shortly before extinction. Despite the samples’ heavy contamination with bacterial and human DNA and their temperate storage history, we estimate that as much as one-third of the total DNA in each sample is from the thylacine. The microbial content of the two thylacine samples was subjected to metagenomic analysis, and showed striking differences between a wild-captured individual and a born-in-captivity one. This study therefore adds to the growing evidence that extensive sequencing of museum collections is both feasible and desirable, and can yield complete genomes. PMID:19139089

  17. Experimental strategies towards treating mitochondrial DNA disorders.

    PubMed

    Gardner, Julie L; Craven, Lyndsey; Turnbull, Douglass M; Taylor, Robert W

    2007-06-01

    An extensive range of molecular defects have been identified in the human mitochondrial genome (mtDNA), causing a range of clinical phenotypes characterized by mitochondrial respiratory chain dysfunction. Sadly, given the complexities of mitochondrial genetics, there are no available cures for mtDNA disorders. In this review, we consider experimental, genetic-based strategies that have been or are being explored towards developing treatments, focussing on two specific areas which we are actively pursuing--assessing the benefit of exercise training for patients with mtDNA defects, and the prevention of mtDNA disease transmission.

  18. A molecular phylogeny of the marine mussel genus Perna (Bivalvia: Mytilidae) based on nuclear (ITS1&2) and mitochondrial (COI) DNA sequences.

    PubMed

    Wood, Ann R; Apte, Smita; MacAvoy, Elizabeth S; Gardner, Jonathan P A

    2007-08-01

    A molecular phylogeny is presented for marine mussels of the genus Perna, based on nuclear (ITS1,ITS2) and mitochondrial (COI) DNA sequence data. The three generally recognised species (Perna viridis, Perna perna and Perna canaliculus) and one putative species (Perna picta) were each sampled from several locations within their known geographic distributions. A range of phylogenetic analyses was used to investigate the current taxonomic assignments, evolutionary relationships and the biogeographical history of the genus. The different analyses produced similar, well supported topologies and verified the monophyly of the genus with respect to five mytilid outgroup species. P. perna (Atlantic), P. viridis (Indo-West Pacific), and P. canaliculus (New Zealand) each formed distinct clades, confirming their specific status. Putative P. picta from North Africa clustered within the P. perna clade and is not regarded as a separate species. P. perna and P. canaliculus were the most closely related of the three species. Possible biogeographic explanations for the present species distributions are evaluated.

  19. Molecular phylogenetic position of endangered Wilfredomys within Sigmodontinae (Cricetidae) based on mitochondrial and nuclear DNA sequences and comments on Wiedomyini.

    PubMed

    Machado, Leonardo Ferreira; Passaia, Milena Henrique; Rodrigues, Fernando Pacheco; Peters, Felipe Bortolotto; Sponchiado, Jonas; Valiati, Victor Hugo; Christoff, Alexandre Uarth

    2015-07-20

    Wilfredomys, a monotypic genus of endangered sigmodontine rats, was historically related to the tribe Thomasomyini or considered "incertae sedis". Given no molecular data is available for Wilfredomys, the phylogenetic position of this taxon is uncertain in relation to modern, molecular hypotheses of sigmodontine relationships. We investigate the phylogeny of Wilfredomys to provide a hypothesis of its position within Sigmodontinae based on nuclear and mitochondrial DNA sequences. Bayesian and maximum likelihood phylogenetic analyses recovered Wilfredomys oenax as sister to Wiedomys pyrrhorhinos, and Wie. cerradensis fell out sister to this clade. At the genus level, Phaenomys is sister to Wilfredomys + Wiedomys, forming a novel and well-supported sigmodontine clade. Our results suggest that tribe Wiedomyini should encompass Wilfredomys in addition to Wiedomys and Cholomys, thus the hypothesis that Wiedomys is paraphyletic should be investigated further. Another plausible classification scheme consistent with our results would be to expand Wiedomyini to encompass the clade composed of Phaenomys + Wilfredomys + Wiedomys. Last, our recovery of an "Atlantic clade" composed of lineages restricted to eastern South America supports the idea that this region has likely played an important role in sigmodontine diversification.

  20. The phylogeny of cobras inferred from mitochondrial DNA sequences: evolution of venom spitting and the phylogeography of the African spitting cobras (Serpentes: Elapidae: Naja nigricollis complex).

    PubMed

    Wüster, Wolfgang; Crookes, Steven; Ineich, Ivan; Mané, Youssouph; Pook, Catharine E; Trape, Jean-François; Broadley, Donald G

    2007-11-01

    We use phylogenetic analysis of 1333 bp of mitochondrial DNA sequence to investigate the phylogeny and historical biogeography of the cobra-like elapid snakes, with special reference to the evolution of spitting and the phylogeography of the African spitting cobras, a radiation widespread in open vegetational formations throughout sub-Saharan Africa. Our results suggest that spitting adaptations appear to have evolved three times in cobras, but alternative scenarios cannot be rejected. The Asiatic Naja are monophyletic and originate from a single colonization of Asia from Africa. The radiation of the African spitting Naja appears to date back to the early Miocene and many speciation events in the group predate the Pliocene expansion of grasslands and the radiation of large grazing mammals in Africa. The cladogenic events in this complex appear to have been triggered by both ecological changes and tectonic events associated with the formation and expansion of the African Rift Valley. Taxonomically, our data confirm the inclusion of Boulengerina and Paranaja within Naja, and reveal a clade of African rainforest cobras including N. melanoleuca, Paranaja multifasciata and Boulengerina that constitutes the sister clade of the African open-formation non-spitting cobras. Naja nigricollis is polyphyletic, and we therefore recognize N. nigricincta as a separate species, more closely related to N. ashei and N. mossambica than to N. nigricollis.

  1. Nonneutral mitochondrial DNA variation in humans and chimpanzees

    SciTech Connect

    Nachman, M.W.; Aquadro, C.F.; Brown, W.M.

    1996-03-01

    We sequenced the NADH dehydrogenase subunit 3 (ND3) gene from a sample of 61 humans, five common chimpanzees, and one gorilla to test whether patterns of mitochondrial DNA (mtDNA) variation are consistent with a neutral model of molecular evolution. Within humans and within chimpanzees, the ratio of replacement to silent nucleotide substitutions was higher than observed in comparisons between species, contrary to neutral expectations. To test the generality of this result, we reanalyzed published human RFLP data from the entire mitochondrial genome. Gains of restriction sites relative to a known human mtDNA sequence were used to infer unambiguous nucleotide substitutions. We also compared the complete mtDNA sequences of three humans. Both the RFLP data and the sequence data reveal a higher ratio of replacement to silent nucleotide substitutions within humans than is seen between species. This pattern is observed at most or all human mitochondrial genes and is inconsistent with a strictly neutral model. These data suggest that many mitochondrial protein polymorphisms are slightly deleterious, consistent with studies of human mitochondrial diseases. 59 refs., 2 figs., 8 tabs.

  2. Nuclear gadgets in mitochondrial DNA replication and transcription.

    PubMed

    Clayton, D A

    1991-03-01

    In mammalian mitochondrial DNA, activation of the light-strand promoter mediates both priming of leading-strand replication and initiation of light-strand transcription. Accurate and efficient transcription requires at least two proteins: mitochondrial RNA polymerase and a separable transcription factor that can function across species boundaries. Subsequently, primer RNAs are cleaved by a site-specific ribonucleoprotein endoribonuclease that recognizes short, highly conserved sequence elements in the RNA substrate.

  3. Mutations in mitochondrial DNA causing tubulointerstitial kidney disease

    PubMed Central

    Mallett, Andrew; Posse, Viktor; Moreno, Pablo; Sciacovelli, Marco; Duff, Jennifer; Wiesener, Michael S.; Hudson, Gavin; Gustafsson, Claes M.; Chinnery, Patrick F.; Maxwell, Patrick H.

    2017-01-01

    Tubulointerstitial kidney disease is an important cause of progressive renal failure whose aetiology is incompletely understood. We analysed a large pedigree with maternally inherited tubulointerstitial kidney disease and identified a homoplasmic substitution in the control region of the mitochondrial genome (m.547A>T). While mutations in mtDNA coding sequence are a well recognised cause of disease affecting multiple organs, mutations in the control region have never been shown to cause disease. Strikingly, our patients did not have classical features of mitochondrial disease. Patient fibroblasts showed reduced levels of mitochondrial tRNAPhe, tRNALeu1 and reduced mitochondrial protein translation and respiration. Mitochondrial transfer demonstrated mitochondrial transmission of the defect and in vitro assays showed reduced activity of the heavy strand promoter. We also identified further kindreds with the same phenotype carrying a homoplasmic mutation in mitochondrial tRNAPhe (m.616T>C). Thus mutations in mitochondrial DNA can cause maternally inherited renal disease, likely mediated through reduced function of mitochondrial tRNAPhe. PMID:28267784

  4. Southeast Asian mouth-brooding Betta fighting fish (Teleostei: Perciformes) species and their phylogenetic relationships based on mitochondrial COI and nuclear ITS1 DNA sequences and analyses

    PubMed Central

    Panijpan, Bhinyo; Kowasupat, Chanon; Laosinchai, Parames; Ruenwongsa, Pintip; Phongdara, Amornrat; Senapin, Saengchan; Wanna, Warapond; Phiwsaiya, Kornsunee; Kühne, Jens; Fasquel, Frédéric

    2014-01-01

    Fighting fish species in the genus Betta are found in several Southeast Asian countries. Depending on the mode of paternal care for fertilized eggs and hatchlings, various species of the betta fish are classified as mouth brooders or nest builders whose members in turn have been grouped according to their similarities mainly in morphology. The mouth brooders as well as some nest builders involved in the present study include fishes discovered and identified subsequent to previous reports on species groupings and their positions on phylogenetic trees based on DNA sequences that differ from those used by us in this study. From the mitochondrial COI gene and nuclear ITS1 gene sequences and more accurate analyses we conclude that the following members of the mouth-brooding pairs, named differently previously, are virtually identical, viz the Betta prima–Betta pallida pair and Betta ferox–Betta apollon pair. The Betta simplex, hitherto believed to be one species, could possibly be genetically split into 2 distinct species. In addition, several other established type-locality fishes could harbor cryptic species as judged by genetic differences. Assignments of fish species to groups reported earlier may have to be altered somewhat by the present genetic findings. We propose here a new Betta fish phylogenetic tree which, albeit being similar to the previous ones, is clearly different from them. Our gene-based evidence also leads to assignments of some fishes to new species groups and alters the positions of some species on the new phylogenetic tree, thus implying different ancestral relationships. PMID:25606468

  5. Mitochondrial DNA, restoring Beethovens music.

    PubMed

    Merheb, Maxime; Vaiedelich, Stéphane; Maniguet, Thiérry; Hänni, Catherine

    2016-01-01

    Great ancient composers have endured many obstacles and constraints which are very difficult to understand unless we perform the restoration process of ancient music. Species identification in leather used during manufacturing is the key step to start such a restoration process in order to produce a facsimile of a museum piano. Our study reveals the species identification in the leather covering the hammer head in a piano created by Erard in 1802. This is the last existing piano similar to the piano that Beethoven used with its leather preserved in its original state. The leather sample was not present in a homogeneous piece, yet combined with glue. Using a DNA extraction method that avoids PCR inhibitors; we discovered that sheep and cattle are the origin of the combination. To identify the species in the leather, we focused on the amounts of mitochondrial DNA in both leather and glue and results have led us to the conclusion that the leather used to cover the hammer head in this piano was made of cattle hide.

  6. Lack of paternal inheritance of muscle mitochondrial DNA in sporadic mitochondrial myopathies.

    PubMed

    Filosto, Massimiliano; Mancuso, Michelangelo; Vives-Bauza, Cristofol; Vilà, Maya R; Shanske, Sara; Hirano, Michio; Andreu, Antoni L; DiMauro, Salvatore

    2003-10-01

    In 2002, paternal inheritance of muscle mitochondrial DNA (mtDNA) was reported in a patient with exercise intolerance and a mitochondrial DNA (mtDNA) mutation restricted to skeletal muscle. To evaluate whether paternal inheritance is a common phenomenon, we studied 10 sporadic patients with skeletal muscle-restricted mtDNA mutations: five harbored mtDNA point mutations in protein-coding genes and five had single mtDNA deletions. We performed haplotype analysis and direct sequencing of the hypervariable regions 1 and 2 of the D-loop in muscle and blood from the patients and, when available, in blood from their parents. We did not observe paternal inheritance in any of our patients.

  7. A comprehensive characterization of rare mitochondrial DNA variants in neuroblastoma

    PubMed Central

    Pignataro, Piero; Lasorsa, Vito Alessandro; Hogarty, Michael D.; Castellano, Aurora; Conte, Massimo; Tonini, Gian Paolo; Iolascon, Achille; Gasparre, Giuseppe; Capasso, Mario

    2016-01-01

    Background Neuroblastoma, a tumor of the developing sympathetic nervous system, is a common childhood neoplasm that is often lethal. Mitochondrial DNA (mtDNA) mutations have been found in most tumors including neuroblastoma. We extracted mtDNA data from a cohort of neuroblastoma samples that had undergone Whole Exome Sequencing (WES) and also used snap-frozen samples in which mtDNA was entirely sequenced by Sanger technology. We next undertook the challenge of determining those mutations that are relevant to, or arisen during tumor development. The bioinformatics pipeline used to extract mitochondrial variants from matched tumor/blood samples was enriched by a set of filters inclusive of heteroplasmic fraction, nucleotide variability, and in silico prediction of pathogenicity. Results Our in silico multistep workflow applied both on WES and Sanger-sequenced neuroblastoma samples, allowed us to identify a limited burden of somatic and germline mitochondrial mutations with a potential pathogenic impact. Conclusions The few singleton germline and somatic mitochondrial mutations emerged, according to our in silico analysis, do not appear to impact on the development of neuroblastoma. Our findings are consistent with the hypothesis that most mitochondrial somatic mutations can be considered as ‘passengers’ and consequently have no discernible effect in this type of cancer. PMID:27351283

  8. Evolutionary Relationships of the Triatoma matogrossensis Subcomplex, the Endemic Triatoma in Central-Western Brazil, Based on Mitochondrial DNA Sequences

    PubMed Central

    Gardim, Sueli; Rocha, Cláudia S.; Almeida, Carlos E.; Takiya, Daniela M.; da Silva, Marco T. A.; Ambrósio, Daniela L.; Cicarelli, Regina M. B.; da Rosa, João A.

    2013-01-01

    The phylogenetic relationships among species of Triatoma matogrossensis subcomplex ( T. baratai, T. guazu, T. matogrossensis, T. sordida, T. vandae, and T. williami) was addressed by using fragments of cytochrome oxidase I (COI), 16S rDNA (16S), and cytochrome b (Cytb) through Bayesian and parsimony analyses. We did not recover a monophyletic T. matogrossensis subcomplex, and their members were found clustered in three strongly supported clades, as follows: i) T. jurbergi + T. matogrossensis + T. vandae + T. garciabesi + T. sordida; ii) with T. guasayana as the sister group of clade (i); and iii) T. williami + T. guazu, however not closely related to the clade formed by the previously mentioned species. The other two endemic species from Central-Western Brazil, T. baratai and T. costalimai, were not recovered with strong clade support as related to other members of this subcomplex. Results call for a further revision in the classification of the subcomplexes within the genus Triatoma. PMID:24002487

  9. Transposon facilitated DNA sequencing

    SciTech Connect

    Berg, D.E.; Berg, C.M.; Huang, H.V.

    1990-01-01

    The purpose of this research is to investigate and develop methods that exploit the power of bacterial transposable elements for large scale DNA sequencing: Our premise is that the use of transposons to put primer binding sites randomly in target DNAs should provide access to all portions of large DNA fragments, without the inefficiencies of methods involving random subcloning and attendant repetitive sequencing, or of sequential synthesis of many oligonucleotide primers that are used to match systematically along a DNA molecule. Two unrelated bacterial transposons, Tn5 and {gamma}{delta}, are being used because they have both proven useful for molecular analyses, and because they differ sufficiently in mechanism and specificity of transposition to merit parallel development.

  10. Complete mitochondrial sequences from Mesolithic Sardinia

    PubMed Central

    Modi, Alessandra; Tassi, Francesca; Susca, Roberta Rosa; Vai, Stefania; Rizzi, Ermanno; Bellis, Gianluca De; Lugliè, Carlo; Gonzalez Fortes, Gloria; Lari, Martina; Barbujani, Guido; Caramelli, David; Ghirotto, Silvia

    2017-01-01

    Little is known about the genetic prehistory of Sardinia because of the scarcity of pre-Neolithic human remains. From a genetic perspective, modern Sardinians are known as genetic outliers in Europe, showing unusually high levels of internal diversity and a close relationship to early European Neolithic farmers. However, how far this peculiar genetic structure extends and how it originated was to date impossible to test. Here we present the first and oldest complete mitochondrial sequences from Sardinia, dated back to 10,000 yBP. These two individuals, while confirming a Mesolithic occupation of the island, belong to rare mtDNA lineages, which have never been found before in Mesolithic samples and that are currently present at low frequencies not only in Sardinia, but in the whole Europe. Preliminary Approximate Bayesian Computations, restricted by biased reference samples for Mesolithic Sardinia (the two typed samples) and Neolithic Europe (limited to central and north European sequences), suggest that the first inhabitants of the island have had a small or negligible contribution to the present-day Sardinian population, which mainly derives its genetic diversity from continental migration into the island by Neolithic times. PMID:28256601

  11. Complete mitochondrial sequences from Mesolithic Sardinia.

    PubMed

    Modi, Alessandra; Tassi, Francesca; Susca, Roberta Rosa; Vai, Stefania; Rizzi, Ermanno; Bellis, Gianluca De; Lugliè, Carlo; Gonzalez Fortes, Gloria; Lari, Martina; Barbujani, Guido; Caramelli, David; Ghirotto, Silvia

    2017-03-03

    Little is known about the genetic prehistory of Sardinia because of the scarcity of pre-Neolithic human remains. From a genetic perspective, modern Sardinians are known as genetic outliers in Europe, showing unusually high levels of internal diversity and a close relationship to early European Neolithic farmers. However, how far this peculiar genetic structure extends and how it originated was to date impossible to test. Here we present the first and oldest complete mitochondrial sequences from Sardinia, dated back to 10,000 yBP. These two individuals, while confirming a Mesolithic occupation of the island, belong to rare mtDNA lineages, which have never been found before in Mesolithic samples and that are currently present at low frequencies not only in Sardinia, but in the whole Europe. Preliminary Approximate Bayesian Computations, restricted by biased reference samples for Mesolithic Sardinia (the two typed samples) and Neolithic Europe (limited to central and north European sequences), suggest that the first inhabitants of the island have had a small or negligible contribution to the present-day Sardinian population, which mainly derives its genetic diversity from continental migration into the island by Neolithic times.

  12. Mitochondrial DNA heterogeneity in Tunisian Berbers.

    PubMed

    Fadhlaoui-Zid, K; Plaza, S; Calafell, F; Ben Amor, M; Comas, D; Bennamar El gaaied, A

    2004-05-01

    Berbers live in groups scattered across North Africa whose origins and genetic relationships with their neighbours are not well established. The first hypervariable segment of the mitochondrial DNA (mtDNA) control region was sequenced in a total of 155 individuals from three Tunisian Berber groups and compared to other North Africans. The mtDNA lineages found belong to a common set of mtDNA haplogroups already described in North Africa. Besides the autochthonous North African U6 haplogroup, a group of L3 lineages characterized by the transition at position 16041 seems to be restricted to North Africans, suggesting that an expansion of this group of lineages took place around 10500 years ago in North Africa, and spread to neighbouring populations. Principal components and the coordinate analyses show that some Berber groups (the Tuareg, the Mozabite, and the Chenini-Douiret) are outliers within the North African genetic landscape. This outlier position is consistent with an isolation process followed by genetic drift in haplotype frequencies, and with the high heterogeneity displayed by Berbers compared to Arab samples as shown in the AMOVA. Despite this Berber heterogeneity, no significant differences were found between Berber and Arab samples, suggesting that the Arabization was mainly a cultural process rather than a demographic replacement.

  13. Mitochondrial swinger replication: DNA replication systematically exchanging nucleotides and short 16S ribosomal DNA swinger inserts.

    PubMed

    Seligmann, Hervé

    2014-11-01

    Assuming systematic exchanges between nucleotides (swinger RNAs) resolves genomic 'parenthood' of some orphan mitochondrial transcripts. Twenty-three different systematic nucleotide exchanges (bijective transformations) exist. Similarities between transcription and replication suggest occurrence of swinger DNA. GenBank searches for swinger DNA matching the 23 swinger versions of human and mouse mitogenomes detect only vertebrate mitochondrial swinger DNA for swinger type AT+CG (from five different studies, 149 sequences) matching three human and mouse mitochondrial genes: 12S and 16S ribosomal RNAs, and cytochrome oxidase subunit I. Exchange A<->T+C<->G conserves self-hybridization properties, putatively explaining swinger biases for rDNA, against protein coding genes. Twenty percent of the regular human mitochondrial 16S rDNA consists of short swinger repeats (from 13 exchanges). Swinger repeats could originate from recombinations between regular and swinger DNA: duplicated mitochondrial genes of the parthenogenetic gecko Heteronotia binoei include fewer short A<->T+C<->G swinger repeats than non-duplicated mitochondrial genomes of that species. Presumably, rare recombinations between female and male mitochondrial genes (and in parthenogenetic situations between duplicated genes), favors reverse-mutations of swinger repeat insertions, probably because most inserts affect negatively ribosomal function. Results show that swinger DNA exists, and indicate that swinger polymerization contributes to the genesis of genetic material and polymorphism.

  14. Adult-onset Mitochondrial Myopathy, Encephalopathy, Lactic Acidosis, and Stroke (MELAS)-like Encephalopathy Diagnosed Based on the Complete Sequencing of Mitochondrial DNA Extracted from Biopsied Muscle without any Myopathic Changes

    PubMed Central

    Mukai, Masako; Nagata, Eiichiro; Mizuma, Atsushi; Yamano, Mitsuhiko; Sugaya, Keizo; Nishino, Ichizo; Goto, Yu-ichi; Takizawa, Shunya

    2017-01-01

    The clinical features of mitochondrial myopathy, encephalopathy, lactic acidosis, and stroke-like episodes (MELAS) are not uniform. We herein report a male patient with unusual MELAS-like encephalopathy who had been experiencing isolated recurrent stroke-like episodes since he was 33 years old without any particular family history. Despite an extensive investigation, he had no other signs suggestive of MELAS. Although the muscle pathology showed a normal appearance, a mitochondrial genome sequence analysis of the biopsied muscle revealed a heteroplasmic m.10158T>C mutation in the mitochondrial complex I subunit gene, MT-ND3. To prevented further deterioration of the higher brain function, the early diagnosis and treatment of mitochondrial stroke-like episodes is important. PMID:28050007

  15. Adult-onset Mitochondrial Myopathy, Encephalopathy, Lactic Acidosis, and Stroke (MELAS)-like Encephalopathy Diagnosed Based on the Complete Sequencing of Mitochondrial DNA Extracted from Biopsied Muscle without any Myopathic Changes.

    PubMed

    Mukai, Masako; Nagata, Eiichiro; Mizuma, Atsushi; Yamano, Mitsuhiko; Sugaya, Keizo; Nishino, Ichizo; Goto, Yu-Ichi; Takizawa, Shunya

    The clinical features of mitochondrial myopathy, encephalopathy, lactic acidosis, and stroke-like episodes (MELAS) are not uniform. We herein report a male patient with unusual MELAS-like encephalopathy who had been experiencing isolated recurrent stroke-like episodes since he was 33 years old without any particular family history. Despite an extensive investigation, he had no other signs suggestive of MELAS. Although the muscle pathology showed a normal appearance, a mitochondrial genome sequence analysis of the biopsied muscle revealed a heteroplasmic m.10158T>C mutation in the mitochondrial complex I subunit gene, MT-ND3. To prevented further deterioration of the higher brain function, the early diagnosis and treatment of mitochondrial stroke-like episodes is important.

  16. Fecal source tracking in water using a mitochondrial DNA microarray.

    PubMed

    Vuong, Nguyet-Minh; Villemur, Richard; Payment, Pierre; Brousseau, Roland; Topp, Edward; Masson, Luke

    2013-01-01

    A mitochondrial-based microarray (mitoArray) was developed for rapid identification of the presence of 28 animals and one family (cervidae) potentially implicated in fecal pollution in mixed activity watersheds. Oligonucleotide probes for genus or subfamily-level identification were targeted within the 12S rRNA - Val tRNA - 16S rRNA region in the mitochondrial genome. This region, called MI-50, was selected based on three criteria: 1) the ability to be amplified by universal primers 2) these universal primer sequences are present in most commercial and domestic animals of interest in source tracking, and 3) that sufficient sequence variation exists within this region to meet the minimal requirements for microarray probe discrimination. To quantify the overall level of mitochondrial DNA (mtDNA) in samples, a quantitative-PCR (Q-PCR) universal primer pair was also developed. Probe validation was performed using DNA extracted from animal tissues and, for many cases, animal-specific fecal samples. To reduce the amplification of potentially interfering fish mtDNA sequences during the MI-50 enrichment step, a clamping PCR method was designed using a fish-specific peptide nucleic acid. DNA extracted from 19 water samples were subjected to both array and independent PCR analyses. Our results confirm that the mitochondrial microarray approach method could accurately detect the dominant animals present in water samples emphasizing the potential for this methodology in the parallel scanning of a large variety of animals normally monitored in fecal source tracking.

  17. (Somatic mutations in nuclear and mitochondrial DNA)

    SciTech Connect

    Not Available

    1992-01-01

    The study is concerned the design of new assays that may detect rare somatic mutations in nuclear and mitochondrial DNA, which may increase upon exposure to mutagens, and thus become a marker of human exposure to such mutagens. Two assays for somatic mutation were presented, one for mitochondrial DNA deletions which was developed by the author, and one for deletions of the ADA gene which resides in the nucleus.

  18. Next-generation sequencing of mixed genomic DNA allows efficient assembly of rearranged mitochondrial genomes in Amolops chunganensis and Quasipaa boulengeri.

    PubMed

    Yuan, Siqi; Xia, Yun; Zheng, Yuchi; Zeng, Xiaomao

    2016-01-01

    Recent improvements in next-generation sequencing (NGS) technologies can facilitate the obtainment of mitochondrial genomes. However, it is not clear whether NGS could be effectively used to reconstruct the mitogenome with high gene rearrangement. These high rearrangements would cause amplification failure, and/or assembly and alignment errors. Here, we choose two frogs with rearranged gene order, Amolops chunganensis and Quasipaa boulengeri, to test whether gene rearrangements affect the mitogenome assembly and alignment by using NGS. The mitogenomes with gene rearrangements are sequenced through Illumina MiSeq genomic sequencing and assembled effectively by Trinity v2.1.0 and SOAPdenovo2. Gene order and contents in the mitogenome of A. chunganensis and Q. boulengeri are typical neobatrachian pattern except for rearrangements at the position of "WANCY" tRNA genes cluster. Further, the mitogenome of Q. boulengeri is characterized with a tandem duplication of trnM. Moreover, we utilize 13 protein-coding genes of A. chunganensis, Q. boulengeri and other neobatrachians to reconstruct the phylogenetic tree for evaluating mitochondrial sequence authenticity of A. chunganensis and Q. boulengeri. In this work, we provide nearly complete mitochondrial genomes of A. chunganensis and Q. boulengeri.

  19. Next-generation sequencing of mixed genomic DNA allows efficient assembly of rearranged mitochondrial genomes in Amolops chunganensis and Quasipaa boulengeri

    PubMed Central

    Yuan, Siqi; Zheng, Yuchi; Zeng, Xiaomao

    2016-01-01

    Recent improvements in next-generation sequencing (NGS) technologies can facilitate the obtainment of mitochondrial genomes. However, it is not clear whether NGS could be effectively used to reconstruct the mitogenome with high gene rearrangement. These high rearrangements would cause amplification failure, and/or assembly and alignment errors. Here, we choose two frogs with rearranged gene order, Amolops chunganensis and Quasipaa boulengeri, to test whether gene rearrangements affect the mitogenome assembly and alignment by using NGS. The mitogenomes with gene rearrangements are sequenced through Illumina MiSeq genomic sequencing and assembled effectively by Trinity v2.1.0 and SOAPdenovo2. Gene order and contents in the mitogenome of A. chunganensis and Q. boulengeri are typical neobatrachian pattern except for rearrangements at the position of “WANCY” tRNA genes cluster. Further, the mitogenome of Q. boulengeri is characterized with a tandem duplication of trnM. Moreover, we utilize 13 protein-coding genes of A. chunganensis, Q. boulengeri and other neobatrachians to reconstruct the phylogenetic tree for evaluating mitochondrial sequence authenticity of A. chunganensis and Q. boulengeri. In this work, we provide nearly complete mitochondrial genomes of A. chunganensis and Q. boulengeri. PMID:27994980

  20. Cryptic Species in the Anopheles (Nyssorhynchus) albitarsis (Diptera: Culicidae) Complex: Incongruence Between Random Amplified Polymorphic DNA-Polymerase Chain Reaction Identification and Analysis of Mitochondrial DNA COI Gene Sequences

    PubMed Central

    LEHR, M. A.; KILPATRICK, C. W.; WILKERSON, R. C.; CONN, J. E.

    2006-01-01

    Random amplified polymorphic DNA (RAPD) diagnostic bands are one tool used to differentiate cryptic mosquito species in the Anopheles albitarsis Complex. Monophyly of four species (A. albitarsis Lynch-Arribálzaga, A. albitarsis B, A. deaneorum Rosa-Freitas, and A. marajoara Galvão & Damasceno) currently identified with the RAPD technique was assessed using sequences of the cytochrome oxidase I (COI) mitochondrial DNA (mtDNA) gene. Maximum parsimony, maximum likelihood, and Bayesian analyses support monophyly for A. albitarsis s.s., A. albitarsis B, and A. deaneorum. Anopheles marajoara, as identified by RAPD banding patterns, was either polyphyletic or paraphyletic in all phylogenetic analyses. The phylogenetic pattern and within-species genetic distances observed in A. marajoara suggest the existence of a previously unidentified species (species E) in northern Brazil and Venezuela. Diagnostic RAPD bands were unable to distinguish between A. marajoara and species E, probably because of the low number of correlated bands used to identify species and weaknesses of the RAPD technique, in particular, violations of the untested assumption of homology of comigrating bands. A. marajoara (even without species E) is paraphyletic with respect to A. deaneorum; if A. deaneorum is a separate species from A. marajoara, then A. marajoara may consist of two or more species in Amazonian Brazil. Based on mtDNA COI sequences, there are at least four phylogenetic species within the Albitarsis Complex: A. albitarsis s.s., A. albitarsis B, A. marajoara, and species E; the species status of A. deaneorum is ambiguous. PMID:17082822

  1. Borrowing Nuclear DNA Helicases to Protect Mitochondrial DNA

    PubMed Central

    Ding, Lin; Liu, Yilun

    2015-01-01

    In normal cells, mitochondria are the primary organelles that generate energy, which is critical for cellular metabolism. Mitochondrial dysfunction, caused by mitochondrial DNA (mtDNA) mutations or an abnormal mtDNA copy number, is linked to a range of human diseases, including Alzheimer’s disease, premature aging‎ and cancer. mtDNA resides in the mitochondrial lumen, and its duplication requires the mtDNA replicative helicase, Twinkle. In addition to Twinkle, many DNA helicases, which are encoded by the nuclear genome and are crucial for nuclear genome integrity, are transported into the mitochondrion to also function in mtDNA replication and repair. To date, these helicases include RecQ-like helicase 4 (RECQ4), petite integration frequency 1 (PIF1), DNA replication helicase/nuclease 2 (DNA2) and suppressor of var1 3-like protein 1 (SUV3). Although the nuclear functions of some of these DNA helicases have been extensively studied, the regulation of their mitochondrial transport and the mechanisms by which they contribute to mtDNA synthesis and maintenance remain largely unknown. In this review, we attempt to summarize recent research progress on the role of mammalian DNA helicases in mitochondrial genome maintenance and the effects on mitochondria-associated diseases. PMID:25984607

  2. Borrowing nuclear DNA helicases to protect mitochondrial DNA.

    PubMed

    Ding, Lin; Liu, Yilun

    2015-05-13

    In normal cells, mitochondria are the primary organelles that generate energy, which is critical for cellular metabolism. Mitochondrial dysfunction, caused by mitochondrial DNA (mtDNA) mutations or an abnormal mtDNA copy number, is linked to a range of human diseases, including Alzheimer's disease, premature aging‎ and cancer. mtDNA resides in the mitochondrial lumen, and its duplication requires the mtDNA replicative helicase, Twinkle. In addition to Twinkle, many DNA helicases, which are encoded by the nuclear genome and are crucial for nuclear genome integrity, are transported into the mitochondrion to also function in mtDNA replication and repair. To date, these helicases include RecQ-like helicase 4 (RECQ4), petite integration frequency 1 (PIF1), DNA replication helicase/nuclease 2 (DNA2) and suppressor of var1 3-like protein 1 (SUV3). Although the nuclear functions of some of these DNA helicases have been extensively studied, the regulation of their mitochondrial transport and the mechanisms by which they contribute to mtDNA synthesis and maintenance remain largely unknown. In this review, we attempt to summarize recent research progress on the role of mammalian DNA helicases in mitochondrial genome maintenance and the effects on mitochondria-associated diseases.

  3. Next-generation sequencing for mitochondrial disorders

    PubMed Central

    Carroll, C J; Brilhante, V; Suomalainen, A

    2014-01-01

    A great deal of our understanding of mitochondrial function has come from studies of inherited mitochondrial diseases, but still majority of the patients lack molecular diagnosis. Furthermore, effective treatments for mitochondrial disorders do not exist. Development of therapies has been complicated by the fact that the diseases are extremely heterogeneous, and collecting large enough cohorts of similarly affected individuals to assess new therapies properly has been difficult. Next-generation sequencing technologies have in the last few years been shown to be an effective method for the genetic diagnosis of inherited mitochondrial diseases. Here we review the strategies and findings from studies applying next-generation sequencing methods for the genetic diagnosis of mitochondrial disorders. Detailed knowledge of molecular causes also enables collection of homogenous cohorts of patients for therapy trials, and therefore boosts development of intervention. Linked Articles This article is part of a themed issue on Mitochondrial Pharmacology: Energy, Injury & Beyond. To view the other articles in this issue visit http://dx.doi.org/10.1111/bph.2014.171.issue-8 PMID:24138576

  4. Mitochondrial DNA insertions in the nuclear Capra hircus genome.

    PubMed

    Ning, F Y; Fu, J; Du, Z H

    2017-01-23

    Nuclear mitochondrial pseudogenes (numts), originating from mtDNA insertions into the nuclear genome, have been detected in many species. However, the distribution of numts in the newly published nuclear genome of domestic goat (Capra hircus) has not yet been explored. We used the entire goat mtDNA sequence and nuclear genome, to identify 118 numts using BLAST. Of these, 79 were able to map sequences to the genome. Further analysis showed that the size of the numts ranged from 318 to 9608 bp, and the homologous identity between numts and their respective corresponding mtDNA fragments varied between 65 and 99%. The identified Yunnan black goat numts covered nearly all the mitochondrial genes including mtDNA control region, and were distributed over all chromosomes with the exception of chromosomes 18, 21, and 25. The Y chromosome was excluded from our analysis, as sequence data are currently not available. Among the discovered 79 numts that we were able to map to the genome, 26 relatively complete mitochondrial genes were detected. Our results constitute valuable information for subsequent studies related to mitochondrial genes and goat evolution.

  5. Frequent somatic transfer of mitochondrial DNA into the nuclear genome of human cancer cells.

    PubMed

    Ju, Young Seok; Tubio, Jose M C; Mifsud, William; Fu, Beiyuan; Davies, Helen R; Ramakrishna, Manasa; Li, Yilong; Yates, Lucy; Gundem, Gunes; Tarpey, Patrick S; Behjati, Sam; Papaemmanuil, Elli; Martin, Sancha; Fullam, Anthony; Gerstung, Moritz; Nangalia, Jyoti; Green, Anthony R; Caldas, Carlos; Borg, Åke; Tutt, Andrew; Lee, Ming Ta Michael; van't Veer, Laura J; Tan, Benita K T; Aparicio, Samuel; Span, Paul N; Martens, John W M; Knappskog, Stian; Vincent-Salomon, Anne; Børresen-Dale, Anne-Lise; Eyfjörd, Jórunn Erla; Myklebost, Ola; Flanagan, Adrienne M; Foster, Christopher; Neal, David E; Cooper, Colin; Eeles, Rosalind; Bova, Steven G; Lakhani, Sunil R; Desmedt, Christine; Thomas, Gilles; Richardson, Andrea L; Purdie, Colin A; Thompson, Alastair M; McDermott, Ultan; Yang, Fengtang; Nik-Zainal, Serena; Campbell, Peter J; Stratton, Michael R

    2015-06-01

    Mitochondrial genomes are separated from the nuclear genome for most of the cell cycle by the nuclear double membrane, intervening cytoplasm, and the mitochondrial double membrane. Despite these physical barriers, we show that somatically acquired mitochondrial-nuclear genome fusion sequences are present in cancer cells. Most occur in conjunction with intranuclear genomic rearrangements, and the features of the fusion fragments indicate that nonhomologous end joining and/or replication-dependent DNA double-strand break repair are the dominant mechanisms involved. Remarkably, mitochondrial-nuclear genome fusions occur at a similar rate per base pair of DNA as interchromosomal nuclear rearrangements, indicating the presence of a high frequency of contact between mitochondrial and nuclear DNA in some somatic cells. Transmission of mitochondrial DNA to the nuclear genome occurs in neoplastically transformed cells, but we do not exclude the possibility that some mitochondrial-nuclear DNA fusions observed in cancer occurred years earlier in normal somatic cells.

  6. DNA methyltransferase 1 mutations and mitochondrial pathology: is mtDNA methylated?

    PubMed Central

    Maresca, Alessandra; Zaffagnini, Mirko; Caporali, Leonardo; Carelli, Valerio; Zanna, Claudia

    2015-01-01

    Autosomal dominant cerebellar ataxia-deafness and narcolepsy (ADCA-DN) and Hereditary sensory neuropathy with dementia and hearing loss (HSN1E) are two rare, overlapping neurodegenerative syndromes that have been recently linked to allelic dominant pathogenic mutations in the DNMT1 gene, coding for DNA (cytosine-5)-methyltransferase 1 (DNMT1). DNMT1 is the enzyme responsible for maintaining the nuclear genome methylation patterns during the DNA replication and repair, thus regulating gene expression. The mutations responsible for ADCA-DN and HSN1E affect the replication foci targeting sequence domain, which regulates DNMT1 binding to chromatin. DNMT1 dysfunction is anticipated to lead to a global alteration of the DNA methylation pattern with predictable downstream consequences on gene expression. Interestingly, ADCA-DN and HSN1E phenotypes share some clinical features typical of mitochondrial diseases, such as optic atrophy, peripheral neuropathy, and deafness, and some biochemical evidence of mitochondrial dysfunction. The recent discovery of a mitochondrial isoform of DNMT1 and its proposed role in methylating mitochondrial DNA (mtDNA) suggests that DNMT1 mutations may directly affect mtDNA and mitochondrial physiology. On the basis of this latter finding the link between DNMT1 abnormal activity and mitochondrial dysfunction in ADCA-DN and HSN1E appears intuitive, however, mtDNA methylation remains highly debated. In the last years several groups demonstrated the presence of 5-methylcytosine in mtDNA by different approaches, but, on the other end, the opposite evidence that mtDNA is not methylated has also been published. Since over 1500 mitochondrial proteins are encoded by the nuclear genome, the altered methylation of these genes may well have a critical role in leading to the mitochondrial impairment observed in ADCA-DN and HSN1E. Thus, many open questions still remain unanswered, such as why mtDNA should be methylated, and how this process is regulated and

  7. Methods for Efficient Elimination of Mitochondrial DNA from Cultured Cells

    PubMed Central

    Spadafora, Domenico; Kozhukhar, Nataliya; Chouljenko, Vladimir N.; Kousoulas, Konstantin G.; Alexeyev, Mikhail F.

    2016-01-01

    Here, we document that persistent mitochondria DNA (mtDNA) damage due to mitochondrial overexpression of the Y147A mutant uracil-N-glycosylase as well as mitochondrial overexpression of bacterial Exonuclease III or Herpes Simplex Virus protein UL12.5M185 can induce a complete loss of mtDNA (ρ0 phenotype) without compromising the viability of cells cultured in media supplemented with uridine and pyruvate. Furthermore, we use these observations to develop rapid, sequence-independent methods for the elimination of mtDNA, and demonstrate utility of these methods for generating ρ0 cells of human, mouse and rat origin. We also demonstrate that ρ0 cells generated by each of these three methods can serve as recipients of mtDNA in fusions with enucleated cells. PMID:27136098

  8. Molecular characterization of parthenogenic Fasciola sp. in Korea on the basis of DNA sequences of ribosomal ITS1 and mitochondrial NDI gene.

    PubMed

    Itagaki, Tadashi; Kikawa, Masayuki; Terasaki, Kunio; Shibahara, Toshiyuki; Fukuda, Koichi

    2005-11-01

    Nucleotide sequences of ribosomal internal transcribed spacer (ITS1) and mitochondrial NADH dehydrogenase I (NDI) gene were analyzed to genetically characterize aspermic Fasciola forms in Korea. From the difference in ITS1 sequences, Korean flukes were divided into 3 haplotypes represented by Kor1, Kor2 and Kor1/2, which had nucleotides identical to F. hepatica, F. gigantica and those overlapped between the two species, respectively. NDI sequences also showed that Korean flukes could be classified into 3 distinct haplotypes (Kor1: F. hepatica-type, Kor2a and Kor2b: F. gigantica-type). The sequences of Kor1 and Kor2a were 100% identical to those of the haplotypes Fsp1and Fsp2, respectively, which are major Fasciola forms in Japan. These findings strongly suggest that aspermic Fasciola forms in Korea and Japan originated from same ancestors and have recently spread throughout both countries.

  9. Improving upon nature's somatic mitochondrial DNA therapies.

    PubMed

    Dani, M A; Dani, S U

    2010-06-01

    Mitochondrial DNA (mtDNA) directs key metabolic functions in eukaryotic cells. While a number of mtDNA mutations are known causes of human diseases and age-related dysfunctions, some mtDNA haplotypes are associated with extreme longevity. Despite the mutagenic mitochondrial environment naturally enhancing somatic mtDNA mutation rates, mtDNA remains grossly stable along generations of plant and animal species including man. This relative stability can be accounted for by the purging of deleterious mutations by natural selection operating on growing cells, tissues, organisms and populations, as observed in gametogenesis, embryogenesis, oncogenesis and cladogenesis. In the adult multicellular organism, however, mtDNA mutations accumulate in slowly dividing cells, and, to a much higher degree, in postmitotic cells and tissues. Dynamic mitochondrial fusion and fission, by redistributing polymorphic mtDNA molecules; mitophagy, by clearing defective mitochondria and mutated mtDNA; compensatory mutations and mtDNA repair can compensate for the accumulation of mtDNA mutations only to a certain extent, thereby creating a dysfunctional threshold. Here we hypothesize that this threshold is naturally up-regulated by both vertical and horizontal transfers of mtDNA from stem cells or cell types which retain the capacity of purging deleterious mtDNA through cell division and natural selection in the adult organism. When these natural cell and tissue mtDNA reserves are exhausted, artificial mtDNA therapy may provide for additional threshold up-regulation. Replacement of mtDNA has been already successfully accomplished in early stage embryos and stem cells in a number of species including primates. It is thus simply a matter of refinement of technique that somatic mtDNA therapy, i.e., therapy of pathological conditions based on the transfer of mtDNA to somatic eukaryotic cells and tissues, becomes a medical reality.

  10. Enhanced tumorigenicity by mitochondrial DNA mild mutations.

    PubMed

    Cruz-Bermúdez, Alberto; Vallejo, Carmen G; Vicente-Blanco, Ramiro J; Gallardo, María Esther; Fernández-Moreno, Miguel Ángel; Quintanilla, Miguel; Garesse, Rafael

    2015-05-30

    To understand how mitochondria are involved in malignant transformation we have generated a collection of transmitochondrial cybrid cell lines on the same nuclear background (143B) but with mutant mitochondrial DNA (mtDNA) variants with different degrees of pathogenicity. These include the severe mutation in the tRNALys gene, m.8363G>A, and the three milder yet prevalent Leber's hereditary optic neuropathy (LHON) mutations in the MT-ND1 (m.3460G>A), MT-ND4 (m.11778G>A) and MT-ND6 (m.14484T>C) mitochondrial genes. We found that 143B ρ0 cells devoid of mtDNA and cybrids harboring wild type mtDNA or that causing severe mitochondrial dysfunction do not produce tumors when injected in nude mice. By contrast cybrids containing mild mutant mtDNAs exhibit different tumorigenic capacities, depending on OXPHOS dysfunction.The differences in tumorigenicity correlate with an enhanced resistance to apoptosis and high levels of NOX expression. However, the final capacity of the different cybrid cell lines to generate tumors is most likely a consequence of a complex array of pro-oncogenic and anti-oncogenic factors associated with mitochondrial dysfunction.Our results demonstrate the essential role of mtDNA in tumorigenesis and explain the numerous and varied mtDNA mutations found in human tumors, most of which give rise to mild mitochondrial dysfunction.

  11. DNA sequences encoding osteoinductive products

    SciTech Connect

    Wang, E.A.; Wozney, J.M.; Rosen, V.

    1991-05-07

    This patent describes an isolated DNA sequence encoding an osteoinductive protein the DNA sequence comprising a coding sequence. It comprises: nucleotide No.1 through nucleotide No.387, nucleotide No.356 through nucleotide No.1543, nucleotide $402 through nucleotide No.1626, naturally occurring allelic sequences and equivalent degenerative codon sequences and sequences which hybridize to any of sequences under stringent hybridization conditions; and encode a protein characterized by the ability to induce the formation of bone and/or cartilage.

  12. Evidence for Recombination of Mitochondrial DNA in Triploid Crucian Carp

    PubMed Central

    Guo, Xinhong; Liu, Shaojun; Liu, Yun

    2006-01-01

    In this study, we report the complete mitochondrial DNA (mtDNA) sequences of the allotetraploid and triploid crucian carp and compare the complete mtDNA sequences between the triploid crucian carp and its female parent Japanese crucian carp and between the triploid crucian carp and its male parent allotetraploid. Our results indicate that the complete mtDNA nucleotide identity (98%) between the triploid crucian carp and its male parent allotetraploid was higher than that (93%) between the triploid crucian carp and its female parent Japanese crucian carp. Moreover, the presence of a pattern of identity and difference at synonymous sites of mitochondrial genomes between the triploid crucian carp and its parents provides direct evidence that triploid crucian carp possessed the recombination mtDNA fragment (12,759 bp) derived from the paternal fish. These results suggest that mtDNA recombination was derived from the fusion of the maternal and paternal mtDNAs. Compared with the haploid egg with one set of genome from the Japanese crucian carp, the diploid sperm with two sets of genomes from the allotetraploid could more easily make its mtDNA fuse with the mtDNA of the haploid egg. In addition, the triple hybrid nature of the triploid crucian carp probably allowed its better mtDNA recombination. In summary, our results provide the first evidence of mtDNA combination in polyploid fish. PMID:16322508

  13. The complete mitochondrial DNA sequence of the green alga Pseudendoclonium akinetum (Ulvophyceae) highlights distinctive evolutionary trends in the chlorophyta and suggests a sister-group relationship between the Ulvophyceae and Chlorophyceae.

    PubMed

    Pombert, Jean-François; Otis, Christian; Lemieux, Claude; Turmel, Monique

    2004-05-01

    The mitochondrial genome has undergone radical changes in both the Chlorophyta and Streptophyta, yet little is known about the dynamics of mtDNA evolution in either of these lineages. In the Chlorophyta, which comprises four of the five recognized classes of green algae (Prasinophyceae, Trebouxiophyceae, Ulvophyceae, and Chlorophyceae), the mitochondrial genome varies from 16 to 55 kb. This genome has retained a compact gene organization and a relatively complex gene repertoire ("ancestral" pattern) in the basal lineages represented by the Trebouxiophyceae and Prasinophyceae, whereas it has been reduced in size and gene complement and tends to evolve much more rapidly at the sequence level ("reduced-derived" pattern of evolution) in the Chlorophyceae and the lineage leading to the enigmatic chlorophyte Pedinomonas. To gain information about the evolutionary trends of mtDNA in the Ulvophyceae and also to gain insights into the phylogenetic relationships between ulvophytes and other chlorophytes, we have determined the mtDNA sequence of Pseudendoclonium akinetum. At 95,880 bp, Pseudendoclonium mtDNA is the largest green-algal mitochondrial genome sequenced to date and has the lowest gene density. These derived features are reminiscent of the "expanded" pattern exhibited by embryophyte mtDNAs, indicating that convergent evolution towards genome expansion has occurred independently in the Chlorophyta and Streptophyta. With 57 conserved genes, the gene repertoire of Pseudendoclonium mtDNA is slightly smaller than those of the prasinophyte Nephroselmis olivacea and the trebouxiophyte Prototheca wickerhamii. This ulvophyte mtDNA contains seven group I introns, four of which have homologs in green-algal mtDNAs displaying an "ancestral" or a "reduced-derived" pattern of evolution. Like its counterpart in the chlorophycean green alga Scenedesmus obliquus, it features numerous small, dispersed repeats in intergenic regions and introns. Its overall rate of sequence evolution

  14. Fractal analysis of DNA sequence data

    SciTech Connect

    Berthelsen, C.L.

    1993-01-01

    DNA sequence databases are growing at an almost exponential rate. New analysis methods are needed to extract knowledge about the organization of nucleotides from this vast amount of data. Fractal analysis is a new scientific paradigm that has been used successfully in many domains including the biological and physical sciences. Biological growth is a nonlinear dynamic process and some have suggested that to consider fractal geometry as a biological design principle may be most productive. This research is an exploratory study of the application of fractal analysis to DNA sequence data. A simple random fractal, the random walk, is used to represent DNA sequences. The fractal dimension of these walks is then estimated using the [open quote]sandbox method[close quote]. Analysis of 164 human DNA sequences compared to three types of control sequences (random, base-content matched, and dimer-content matched) reveals that long-range correlations are present in DNA that are not explained by base or dimer frequencies. The study also revealed that the fractal dimension of coding sequences was significantly lower than sequences that were primarily noncoding, indicating the presence of longer-range correlations in functional sequences. The multifractal spectrum is used to analyze fractals that are heterogeneous and have a different fractal dimension for subsets with different scalings. The multifractal spectrum of the random walks of twelve mitochondrial genome sequences was estimated. Eight vertebrate mtDNA sequences had uniformly lower spectra values than did four invertebrate mtDNA sequences. Thus, vertebrate mitochondria show significantly longer-range correlations than to invertebrate mitochondria. The higher multifractal spectra values for invertebrate mitochondria suggest a more random organization of the sequences. This research also includes considerable theoretical work on the effects of finite size, embedding dimension, and scaling ranges.

  15. Phylogeny of the genus Hegeter (Tenebrionidae, Coleoptera) and its colonization of the Canary Islands deduced from Cytochrome Oxidase I mitochondrial DNA sequences.

    PubMed

    Juan, C; Oromi, P; Hewitt, G M

    1996-04-01

    The genus Hegeter comprises 23 species of darkling beetles (Tenebrionidae) endemic to the Macaronesian archipelagos, with 21 of them exclusive to the Canary Islands. We have sequenced 438 bp of the mitochondrial Cytochrome Oxidase I gene in 17 species (24 taxa) of Canarian Hegeter. Estimates of nucleotide composition, transition/transversion ratios and nucleotide change frequencies are very similar to those found in another tenebrionid Canarian genus Pimelia, indicating that similar molecular mechanisms are driving the sequence evolution. The sequence variation found allows phylogenetic analyses of the genus and the deduction of colonization patterns. These involve sequential island invasion with more rapid establishment and radiation than found in the related beetles of the genus Pimelia.

  16. Molecular characterization of Hysterothylacium fabri (Nematoda: Anisakidae) from Zeus faber (Pisces: Zeidae) caught off the Mediterranean coasts of Turkey based on nuclear ribosomal and mitochondrial DNA sequences.

    PubMed

    Pekmezci, Gokmen Zafer; Yardimci, Banu; Onuk, Ertan Emek; Umur, Sinasi

    2014-02-01

    In the present study, Hysterothylacium fabri was found in the coasts of the Mediterranean Sea, Turkey and characterized by sequencing of nuclear (internal transcribed spacer, ITS) and mitochondrial (cytochrome c oxidase subunit 2, cox2) markers. Pairwise comparison between the entire ITS fragment including ITS-1, 5.8S, ITS-2 sequences of the H. fabri isolates from the Mediterranean Sea (Turkey, KC852206) and other H. fabri isolates from the South China Sea (JQ520158), the South Korea waters (JX974558) showed differences ranged from 0.1 and 1.1%. With the present study, H. fabri from the Mediterranean Sea was characterized for the first time by sequencing of the cox2 gene.

  17. Very Short Mitochondrial DNA Fragments and Heteroplasmy in Human Plasma

    PubMed Central

    Zhang, Ruoyu; Nakahira, Kiichi; Guo, Xiaoxian; Choi, Augustine M.K.; Gu, Zhenglong

    2016-01-01

    Cell free DNA (cfDNA) has received increasing attention and has been studied in a broad range of clinical conditions. However, few studies have focused on mitochondrial DNA (mtDNA) in the cell free form. We optimized DNA isolation and sequencing library preparation protocols to better retain short DNA fragments from plasma, and applied these optimized methods to plasma samples from patients with sepsis. Our methods can retain substantially shorter DNA, resulting in an average of 11.5 fold increase in short DNA fragments yield (DNA <100bp). We report that cf-mtDNA in plasma is highly enriched in short-size cfDNA (30~60 bp). Motivated by this unique size distribution, we size-selected short cfDNA, which further increased the mtDNA recovery rate by an average of 10.4 fold. We then detected mtDNA heteroplasmy in plasma from 3 patients. In one patient who previously received bone marrow transplantation, different minor allele frequencies were observed between plasma and leukocytes at heteroplasmic sites, consistent with mixed-tissue origin for cfDNA. For the other two patients, the heteroplasmy pattern is also different between plasma and leukocyte. Our study shed new lights into the architecture of the cfDNA, and mtDNA heteroplasmy identified in plasma provides new potential for biomarker discovery. PMID:27811968

  18. Sequencing strategy for the whole mitochondrial genome resulting in high quality sequences

    PubMed Central

    Fendt, Liane; Zimmermann, Bettina; Daniaux, Martin; Parson, Walther

    2009-01-01

    Background It has been demonstrated that a reliable and fail-safe sequencing strategy is mandatory for high-quality analysis of mitochondrial (mt) DNA, as the sequencing and base-calling process is prone to error. Here, we present a high quality, reliable and easy handling manual procedure for the sequencing of full mt genomes that is also appropriate for laboratories where fully automated processes are not available. Results We amplified whole mitochondrial genomes as two overlapping PCR-fragments comprising each about 8500 bases in length. We developed a set of 96 primers that can be applied to a (manual) 96 well-based technology, which resulted in at least double strand sequence coverage of the entire coding region (codR). Conclusion This elaborated sequencing strategy is straightforward and allows for an unambiguous sequence analysis and interpretation including sometimes challenging phenomena such as point and length heteroplasmy that are relevant for the investigation of forensic and clinical samples. PMID:19331681

  19. Mitochondrial DNA mutations in single human blood cells.

    PubMed

    Yao, Yong-Gang; Kajigaya, Sachiko; Young, Neal S

    2015-09-01

    Determination mitochondrial DNA (mtDNA) sequences from extremely small amounts of DNA extracted from tissue of limited amounts and/or degraded samples is frequently employed in medical, forensic, and anthropologic studies. Polymerase chain reaction (PCR) amplification followed by DNA cloning is a routine method, especially to examine heteroplasmy of mtDNA mutations. In this review, we compare the mtDNA mutation patterns detected by three different sequencing strategies. Cloning and sequencing methods that are based on PCR amplification of DNA extracted from either single cells or pooled cells yield a high frequency of mutations, partly due to the artifacts introduced by PCR and/or the DNA cloning process. Direct sequencing of PCR product which has been amplified from DNA in individual cells is able to detect the low levels of mtDNA mutations present within a cell. We further summarize the findings in our recent studies that utilized this single cell method to assay mtDNA mutation patterns in different human blood cells. Our data show that many somatic mutations observed in the end-stage differentiated cells are found in hematopoietic stem cells (HSCs) and progenitors within the CD34(+) cell compartment. Accumulation of mtDNA variations in the individual CD34+ cells is affected by both aging and family genetic background. Granulocytes harbor higher numbers of mutations compared with the other cells, such as CD34(+) cells and lymphocytes. Serial assessment of mtDNA mutations in a population of single CD34(+) cells obtained from the same donor over time suggests stability of some somatic mutations. CD34(+) cell clones from a donor marked by specific mtDNA somatic mutations can be found in the recipient after transplantation. The significance of these findings is discussed in terms of the lineage tracing of HSCs, aging effect on accumulation of mtDNA mutations and the usage of mtDNA sequence in forensic identification.

  20. The complete mitochondrial genome sequence of Pampus argenteus (Perciformes: Stromateidae).

    PubMed

    Sun, Dandan; Cheng, Qiqun; Qiao, Huiying; Chen, Ying

    2016-01-01

    In this study, we sequenced and annotated the complete mitochondrial genome of Pampus argenteus (Perciformes: Stromateidae). The mitogenome is 17,098 bp in length, which contains 13 protein-coding genes, 2 rRNA genes, 23 tRNA genes and 2 non-coding regions: origin of light-strand replication (OL) and control region (D-loop). The overall nucleotide base composition of P. argenteus mtDNA is A 30.35%, C 25.55%, G 15.28% and T 28.82%, with an A + T content of 59.17%. Except for ND6 gene and eight tRNA genes, all other mitochondrial genes were encoded on the heavy strand. The mitochondrial genome of P. argenteus may be helpful to the studies on conservation genetics and stock evaluation of P. argenteus resource, as well as molecular phylogeny and species identification of Stromateidae.

  1. [Molecular identification and detection of moon jellyfish (Aurelia sp.) based on partial sequencing of mitochondrial 16S rDNA and COI].

    PubMed

    Wang, Jian-Yan; Zhen, Yu; Wang, Guo-shan; Mi, Tie-Zhu; Yu, Zhi-gang

    2013-03-01

    Taking the moon jellyfish Aurelia sp. commonly found in our coastal sea areas as test object, its genome DNA was extracted, the partial sequences of mt-16S rDNA (650 bp) and mt-COI (709 bp) were PCR-amplified, and, after purification, cloning, and sequencing, the sequences obtained were BLASTn-analyzed. The sequences of greater difference with those of the other jellyfish were chosen, and eight specific primers for the mt-16S rDNA and mt-COI of Aurelia sp. were designed, respectively. The specificity test indicated that the primer AS3 for the mt-16S rDNA and the primer AC3 for the mt-COI were excellent in rapidly detecting the target jellyfish from Rhopilema esculentum, Nemopilema nomurai, Cyanea nozakii, Acromitus sp., and Aurelia sp., and thus, the techniques for the molecular identification and detection of moon jellyfish were preliminarily established, which could get rid of the limitations in classical morphological identification of Aurelia sp. , being able to find the Aurelia sp. in the samples more quickly and accurately.

  2. A comprehensive characterization of mitochondrial DNA mutations in glioblastoma multiforme.

    PubMed

    Vidone, Michele; Clima, Rosanna; Santorsola, Mariangela; Calabrese, Claudia; Girolimetti, Giulia; Kurelac, Ivana; Amato, Laura Benedetta; Iommarini, Luisa; Trevisan, Elisa; Leone, Marco; Soffietti, Riccardo; Morra, Isabella; Faccani, Giuliano; Attimonelli, Marcella; Porcelli, Anna Maria; Gasparre, Giuseppe

    2015-06-01

    Glioblastoma multiforme (GBM) is the most malignant brain cancer in adults, with a poor prognosis, whose molecular stratification still represents a challenge in pathology and clinics. On the other hand, mitochondrial DNA (mtDNA) mutations have been found in most tumors as modifiers of the bioenergetics state, albeit in GBM a characterization of the mtDNA status is lacking to date. Here, a characterization of the burden of mtDNA mutations in GBM samples was performed. First, investigation of tumor-specific vs. non tumor-specific mutations was carried out with the MToolBox bioinformatics pipeline by analyzing 45 matched tumor/blood samples, from whole genome or whole exome sequencing datasets obtained from The Cancer Genome Atlas (TCGA) consortium. Additionally, the entire mtDNA sequence was obtained in a dataset of 104 fresh-frozen GBM samples. Mitochondrial mutations with potential pathogenic interest were prioritized based on heteroplasmic fraction, nucleotide variability, and in silico prediction of pathogenicity. A preliminary biochemical analysis of the activity of mitochondrial respiratory complexes was also performed on fresh-frozen GBM samples. Although a high number of mutations was detected, we report that the large majority of them does not pass the prioritization filters. Therefore, a relatively limited burden of pathogenic mutations is indeed carried by GBM, which did not appear to determine a general impairment of the respiratory chain. This article is part of a Directed Issue entitled: Energy Metabolism Disorders and Therapies.

  3. Mitochondrial DNA Phylogeography of the Norway Rat

    PubMed Central

    Song, Ying; Lan, Zhenjiang; Kohn, Michael H.

    2014-01-01

    Central Eastern Asia, foremost the area bordering northern China and Mongolia, has been thought to be the geographic region where Norway rats (Rattus norvegicus) have originated. However recent fossil analyses pointed to their origin in southern China. Moreover, whereas analyses of fossils dated the species' origin as ∼1.2–1.6 million years ago (Mya), molecular analyses yielded ∼0.5–2.9 Mya. Here, to study the geographic origin of the Norway rat and its spread across the globe we analyzed new and all published mitochondrial DNA cytochrome-b (cyt-b; N = 156) and D-loop (N = 212) sequences representing wild rats from four continents and select inbred strains. Our results are consistent with an origin of the Norway rat in southern China ∼1.3 Mya, subsequent prehistoric differentiation and spread in China and Asia from an initially weakly structured ancestral population, followed by further spread and differentiation across the globe during historic times. The recent spreading occurred mostly from derived European populations rather than from archaic Asian populations. We trace laboratory strains to wild lineages from Europe and North America and these represent a subset of the diversity of the rat; leaving Asian lineages largely untapped as a resource for biomedical models. By studying rats from Europe we made the observation that mtDNA diversity cannot be interpreted without consideration of pest control and, possibly, the evolution of rodenticide resistance. However, demographic models explored by forward-time simulations cannot fully explain the low mtDNA diversity of European rats and lack of haplotype sharing with their source from Asia. Comprehensive nuclear marker analyses of a larger sample of Norway rats representing the world are needed to better resolve the evolutionary history of wild rats and of laboratory rats, as well as to better understand the evolution of anticoagulant resistance. PMID:24586325

  4. Mitochondrial DNA phylogeography of the Norway rat.

    PubMed

    Song, Ying; Lan, Zhenjiang; Kohn, Michael H

    2014-01-01

    Central Eastern Asia, foremost the area bordering northern China and Mongolia, has been thought to be the geographic region where Norway rats (Rattus norvegicus) have originated. However recent fossil analyses pointed to their origin in southern China. Moreover, whereas analyses of fossils dated the species' origin as ∼ 1.2-1.6 million years ago (Mya), molecular analyses yielded ∼ 0.5-2.9 Mya. Here, to study the geographic origin of the Norway rat and its spread across the globe we analyzed new and all published mitochondrial DNA cytochrome-b (cyt-b; N = 156) and D-loop (N = 212) sequences representing wild rats from four continents and select inbred strains. Our results are consistent with an origin of the Norway rat in southern China ∼ 1.3 Mya, subsequent prehistoric differentiation and spread in China and Asia from an initially weakly structured ancestral population, followed by further spread and differentiation across the globe during historic times. The recent spreading occurred mostly from derived European populations rather than from archaic Asian populations. We trace laboratory strains to wild lineages from Europe and North America and these represent a subset of the diversity of the rat; leaving Asian lineages largely untapped as a resource for biomedical models. By studying rats from Europe we made the observation that mtDNA diversity cannot be interpreted without consideration of pest control and, possibly, the evolution of rodenticide resistance. However, demographic models explored by forward-time simulations cannot fully explain the low mtDNA diversity of European rats and lack of haplotype sharing with their source from Asia. Comprehensive nuclear marker analyses of a larger sample of Norway rats representing the world are needed to better resolve the evolutionary history of wild rats and of laboratory rats, as well as to better understand the evolution of anticoagulant resistance.

  5. Sephardic signature in haplogroup T mitochondrial DNA.

    PubMed

    Bedford, Felice L

    2012-04-01

    A rare combination of mutations within mitochondrial DNA subhaplogroup T2e is identified as affiliated with Sephardic Jews, a group that has received relatively little attention. Four investigations were pursued: Search of the motif in 250 000 control region records across 8 databases, comparison of frequencies of T subhaplogroups (T1, T2b, T2c, T2e, T4, T(*)) across 11 diverse populations, creation of a phylogenic median-joining network from public T2e control region entries, and analysis of one Sephardic mitochondrial full genomic sequence with the motif. It was found that the rare motif belonged only to Sephardic descendents (Turkey, Bulgaria), to inhabitants of North American regions known for secret Spanish-Jewish colonization, or were consistent with Sephardic ancestry. The incidence of subhaplogroup T2e decreased from the Western Arabian Peninsula to Italy to Spain and into Western Europe. The ratio of sister subhaplogroups T2e to T2b was found to vary 40-fold across populations from a low in the British Isles to a high in Saudi Arabia with the ratio in Sephardim more similar to Saudi Arabia, Egypt, and Italy than to hosts Spain and Portugal. Coding region mutations of 2308G and 14499T may locate the Sephardic signature within T2e, but additional samples and reworking of current T2e phylogenetic branch structure is needed. The Sephardic Turkish community has a less pronounced founder effect than some Ashkenazi groups considered singly (eg, Polish), but other comparisons of interest await comparable averaging. Registries of signatures will benefit the study of populations with a large number of smaller-size founders.

  6. The complete mitochondrial genome sequence of Coreoperca whiteheadi (Perciformes: Serranidae).

    PubMed

    Lv, Liyuan; Tian, Changxu; Liang, Xufang; Yuan, Yongchao; Zhao, Cheng; Song, Yi

    2016-01-01

    In this paper, the complete mitochondrial DNA (mtDNA) sequence of Coreoperca whiteheadi was determined. The complete mtDNA genome sequence of C. whiteheadi is 16,483 bp in length. It consists of 13 protein-coding genes, 22 transfer RNA genes, 2 rRNA genes and 2 non-coding regions. Overall base composition of mitogenome is estimated to be 28.30% for A, 29.33% for C, 16.06% for G and 26.32% for T, respectively, with a high A + T content (54.62%). The complete mitogenome of the C. whiteheadi could contribute to basic researches on population history, molecular systematics and phylogeography. It is also helpful to the reasonable utilization and development of rational management strategies for C. whiteheadi resource.

  7. mitoSAVE: mitochondrial sequence analysis of variants in Excel.

    PubMed

    King, Jonathan L; Sajantila, Antti; Budowle, Bruce

    2014-09-01

    The mitochondrial genome (mtGenome) contains genetic information amenable to numerous applications such as medical research, population and evolutionary studies, and human identity testing. However, inconsistent nomenclature assignment makes haplotype comparison difficult and can lead to false exclusion of potentially useful profiles. Massively Parallel Sequencing (MPS) is a platform for sequencing large datasets and potentially whole populations with relative ease. However, the data generated are not easily parsed and interpreted. With this in mind, mitoSAVE has been developed to enable fast conversion of Variant Call Format (VCF) files. mitoSAVE is an Excel-based workbook that converts data within the VCF into mtDNA haplotypes using phylogenetically-established nomenclature as well as rule-based alignments consistent with current forensic standards. mitoSAVE is formatted for human mitochondrial genome; however, it can easily be adapted to support other reasonably small genomes.

  8. Characterization of mitochondrial DNA in primary cardiomyopathies.

    PubMed

    Bobba, A; Giannattasio, S; Pucci, A; Lippolis, R; Camaschella, C; Marra, E

    1995-12-29

    With the aim of studying the involvement of the mitochondrial genome in the impairment of heart function, mitochondrial DNA was analyzed by modified primer shift-polymerase chain reaction in a panel of young patients affected by primary cardiomyopathies. Mitochondrial DNA molecules harboring the 7436 bp deletion were specifically found in cardiomyopathic patients as compared with a panel of control subjects. The 4977 bp deletion was commonly detected among the subjects analyzed whereas none of the specific tRNA gene point mutations generally associated with the cardiomyopathic trait were detected. The presence of the 7436 bp deletion as a consequence of a premature aging of the heart muscle, secondary to heart dysfunction, is discussed.

  9. The Dynamics of DNA Sequencing.

    ERIC Educational Resources Information Center

    Morvillo, Nancy

    1997-01-01

    Describes a paper-and-pencil activity that helps students understand DNA sequencing and expands student understanding of DNA structure, replication, and gel electrophoresis. Appropriate for advanced biology students who are familiar with the Sanger method. (DDR)

  10. Characterization of Nucleotide Misincorporation Patterns in the Iceman's Mitochondrial DNA

    PubMed Central

    Olivieri, Cristina; Ermini, Luca; Rizzi, Ermanno; Corti, Giorgio; Bonnal, Raoul; Luciani, Stefania; Marota, Isolina; De Bellis, Gianluca; Rollo, Franco

    2010-01-01

    Background The degradation of DNA represents one of the main issues in the genetic analysis of archeological specimens. In the recent years, a particular kind of post-mortem DNA modification giving rise to nucleotide misincorporation (“miscoding lesions”) has been the object of extensive investigations. Methodology/Principal Findings To improve our knowledge regarding the nature and incidence of ancient DNA nucleotide misincorporations, we have utilized 6,859 (629,975 bp) mitochondrial (mt) DNA sequences obtained from the 5,350–5,100-years-old, freeze-desiccated human mummy popularly known as the Tyrolean Iceman or Ötzi. To generate the sequences, we have applied a mixed PCR/pyrosequencing procedure allowing one to obtain a particularly high sequence coverage. As a control, we have produced further 8,982 (805,155 bp) mtDNA sequences from a contemporary specimen using the same system and starting from the same template copy number of the ancient sample. From the analysis of the nucleotide misincorporation rate in ancient, modern, and putative contaminant sequences, we observed that the rate of misincorporation is significantly lower in modern and putative contaminant sequence datasets than in ancient sequences. In contrast, type 2 transitions represent the vast majority (85%) of the observed nucleotide misincorporations in ancient sequences. Conclusions/Significance This study provides a further contribution to the knowledge of nucleotide misincorporation patterns in DNA sequences obtained from freeze-preserved archeological specimens. In the Iceman system, ancient sequences can be clearly distinguished from contaminants on the basis of nucleotide misincorporation rates. This observation confirms a previous identification of the ancient mummy sequences made on a purely phylogenetical basis. The present investigation provides further indication that the majority of ancient DNA damage is reflected by type 2 (cytosine→thymine/guanine→adenine) transitions and

  11. Biosensors for DNA sequence detection

    NASA Technical Reports Server (NTRS)

    Vercoutere, Wenonah; Akeson, Mark

    2002-01-01

    DNA biosensors are being developed as alternatives to conventional DNA microarrays. These devices couple signal transduction directly to sequence recognition. Some of the most sensitive and functional technologies use fibre optics or electrochemical sensors in combination with DNA hybridization. In a shift from sequence recognition by hybridization, two emerging single-molecule techniques read sequence composition using zero-mode waveguides or electrical impedance in nanoscale pores.

  12. Mitochondrial DNA hypomethylation in chrome plating workers.

    PubMed

    Yang, Linqing; Xia, Bo; Yang, Xueqin; Ding, Hong; Wu, Desheng; Zhang, Huimin; Jiang, Gaofeng; Liu, Jianjun; Zhuang, Zhixiong

    2016-01-22

    A matched case-control study was conducted to examine the relationship between chromium (Cr) exposure and variation in mitochondrial (mt) DNA methylation. We enrolled 29 pairs of subjects in this study; Cr exposure was confirmed in the cases by detecting blood Cr and other metal ion concentrations. DNA damage caused by Cr exposure was determined in terms of binucleated micronucleus frequency (BNMN) and mtDNA copy number. Finally, a Sequenom MassARRAY platform was applied to inspect the DNA methylation levels of mitochondrially encoded tRNA phenylalanine (MT-TF), mitochondrially encoded 12S RNA (MT-RNR1), and long interspersed nucleotide element-1 (LINE-1) genes. The blood Cr ion concentration and micronucleus frequency of the Cr-exposed group were higher than those of the control group, whereas the mtDNA copy number remained unchanged. The methylation levels of MT-TF and MT-RNR1 but not LINE-1 were significantly lower in Cr-exposed workers. Pearson correlation analysis showed that workers with higher blood Cr ion concentrations exhibited lower MT-TF and MT-RNR1 gene methylation, and multiple linear regression analysis indicated that CpG sites 1 and 2 in MT-TF and CpG site 6 in MT-RNR1 were affected. These results suggested that methylation level of mtDNA has the possibility of acting as an alternative effect biomarker for Cr exposure.

  13. Graphene nanodevices for DNA sequencing

    NASA Astrophysics Data System (ADS)

    Heerema, Stephanie J.; Dekker, Cees

    2016-02-01

    Fast, cheap, and reliable DNA sequencing could be one of the most disruptive innovations of this decade, as it will pave the way for personalized medicine. In pursuit of such technology, a variety of nanotechnology-based approaches have been explored and established, including sequencing with nanopores. Owing to its unique structure and properties, graphene provides interesting opportunities for the development of a new sequencing technology. In recent years, a wide range of creative ideas for graphene sequencers have been theoretically proposed and the first experimental demonstrations have begun to appear. Here, we review the different approaches to using graphene nanodevices for DNA sequencing, which involve DNA passing through graphene nanopores, nanogaps, and nanoribbons, and the physisorption of DNA on graphene nanostructures. We discuss the advantages and problems of each of these key techniques, and provide a perspective on the use of graphene in future DNA sequencing technology.

  14. Geographic patterns of genetic variation in a broadly distributed marine vertebrate: new insights into loggerhead turtle stock structure from expanded mitochondrial DNA sequences.

    PubMed

    Shamblin, Brian M; Bolten, Alan B; Abreu-Grobois, F Alberto; Bjorndal, Karen A; Cardona, Luis; Carreras, Carlos; Clusa, Marcel; Monzón-Argüello, Catalina; Nairn, Campbell J; Nielsen, Janne T; Nel, Ronel; Soares, Luciano S; Stewart, Kelly R; Vilaça, Sibelle T; Türkozan, Oguz; Yilmaz, Can; Dutton, Peter H

    2014-01-01

    Previous genetic studies have demonstrated that natal homing shapes the stock structure of marine turtle nesting populations. However, widespread sharing of common haplotypes based on short segments of the mitochondrial control region often limits resolution of the demographic connectivity of populations. Recent studies employing longer control region sequences to resolve haplotype sharing have focused on regional assessments of genetic structure and phylogeography. Here we synthesize available control region sequences for loggerhead turtles from the Mediterranean Sea, Atlantic, and western Indian Ocean basins. These data represent six of the nine globally significant regional management units (RMUs) for the species and include novel sequence data from Brazil, Cape Verde, South Africa and Oman. Genetic tests of differentiation among 42 rookeries represented by short sequences (380 bp haplotypes from 3,486 samples) and 40 rookeries represented by long sequences (∼800 bp haplotypes from 3,434 samples) supported the distinction of the six RMUs analyzed as well as recognition of at least 18 demographically independent management units (MUs) with respect to female natal homing. A total of 59 haplotypes were resolved. These haplotypes belonged to two highly divergent global lineages, with haplogroup I represented primarily by CC-A1, CC-A4, and CC-A11 variants and haplogroup II represented by CC-A2 and derived variants. Geographic distribution patterns of haplogroup II haplotypes and the nested position of CC-A11.6 from Oman among the Atlantic haplotypes invoke recent colonization of the Indian Ocean from the Atlantic for both global lineages. The haplotypes we confirmed for western Indian Ocean RMUs allow reinterpretation of previous mixed stock analysis and further suggest that contemporary migratory connectivity between the Indian and Atlantic Oceans occurs on a broader scale than previously hypothesized. This study represents a valuable model for conducting

  15. Geographic Patterns of Genetic Variation in a Broadly Distributed Marine Vertebrate: New Insights into Loggerhead Turtle Stock Structure from Expanded Mitochondrial DNA Sequences

    PubMed Central

    Shamblin, Brian M.; Bolten, Alan B.; Abreu-Grobois, F. Alberto; Bjorndal, Karen A.; Cardona, Luis; Carreras, Carlos; Clusa, Marcel; Monzón-Argüello, Catalina; Nairn, Campbell J.; Nielsen, Janne T.; Nel, Ronel; Soares, Luciano S.; Stewart, Kelly R.; Vilaça, Sibelle T.; Türkozan, Oguz; Yilmaz, Can; Dutton, Peter H.

    2014-01-01

    Previous genetic studies have demonstrated that natal homing shapes the stock structure of marine turtle nesting populations. However, widespread sharing of common haplotypes based on short segments of the mitochondrial control region often limits resolution of the demographic connectivity of populations. Recent studies employing longer control region sequences to resolve haplotype sharing have focused on regional assessments of genetic structure and phylogeography. Here we synthesize available control region sequences for loggerhead turtles from the Mediterranean Sea, Atlantic, and western Indian Ocean basins. These data represent six of the nine globally significant regional management units (RMUs) for the species and include novel sequence data from Brazil, Cape Verde, South Africa and Oman. Genetic tests of differentiation among 42 rookeries represented by short sequences (380 bp haplotypes from 3,486 samples) and 40 rookeries represented by long sequences (∼800 bp haplotypes from 3,434 samples) supported the distinction of the six RMUs analyzed as well as recognition of at least 18 demographically independent management units (MUs) with respect to female natal homing. A total of 59 haplotypes were resolved. These haplotypes belonged to two highly divergent global lineages, with haplogroup I represented primarily by CC-A1, CC-A4, and CC-A11 variants and haplogroup II represented by CC-A2 and derived variants. Geographic distribution patterns of haplogroup II haplotypes and the nested position of CC-A11.6 from Oman among the Atlantic haplotypes invoke recent colonization of the Indian Ocean from the Atlantic for both global lineages. The haplotypes we confirmed for western Indian Ocean RMUs allow reinterpretation of previous mixed stock analysis and further suggest that contemporary migratory connectivity between the Indian and Atlantic Oceans occurs on a broader scale than previously hypothesized. This study represents a valuable model for conducting

  16. Application of 2-D graphical representation of DNA sequence

    NASA Astrophysics Data System (ADS)

    Liao, Bo; Tan, Mingshu; Ding, Kequan

    2005-10-01

    Recently, we proposed a 2-D graphical representation of DNA sequence [Bo Liao, A 2-D graphical representation of DNA sequence, Chem. Phys. Lett. 401 (2005) 196-199]. Based on this representation, we consider properties of mutations and compute the similarities among 11 mitochondrial sequences belonging to different species. The elements of the similarity matrix are used to construct phylogenic tree. Unlike most existing phylogeny construction methods, the proposed method does not require multiple alignment.

  17. Mitochondrial sequence variation suggests an African influence in Portuguese cattle.

    PubMed Central

    Cymbron, T; Loftus, R T; Malheiro, M I; Bradley, D G

    1999-01-01

    A total of 49 samples from indigenous Portuguese cattle breeds were analysed for sequence variation in the hypervariable region of the mitochondrial DNA D-loop. Sequence comparison and phylogenetic analyses revealed that haplotypes fell into two distinct groups. These corresponded with two separate haplotype clusters into which, respectively, all African, or alternatively all sequences of European origin, have previously been shown to fall. Here, the majority of sequences of African type were encountered in three southern, as compared to three northern breeds. This pattern of African influence may reflect an intercontinental admixture in the initial origins of Iberian breeds, or it is perhaps an introgression dating from the long and influential Moorish occupation of the south of the Iberian peninsula. PMID:10212450

  18. Mitochondrial DNA polymorphism in a maternal lineage of Holstein cows.

    PubMed Central

    Hauswirth, W W; Laipis, P J

    1982-01-01

    Two mitochondrial genotypes are shown to exist within one Holstein cow maternal lineage. They were detected by the appearance of an extra Hae III recognition site in one genotype. The nucleotide sequence of this region has been determined and the genotypes are distinguished by an adenine/guanine base transition which creates the new Hae III site. This point mutation occurs within an open reading frame at the third position of a glycine codon and therefore does not alter the amino acid sequence. The present pattern of genotypes within the lineage demands that multiple shifts between genotypes must have occurred within the past 20 years with the most rapid shift taking place in no more than 4 years and indicates that mitochondrial DNA polymorphism can occur between maternally related mammals. The process that gave rise to different genotypes in one lineage is clearly of fundamental importance in understanding intraspecific mitochondrial polymorphism and evolution in mammals. Several potential mechanisms for rapid mitochondrial DNA variation are discussed in light of these results. Images PMID:6289312

  19. Complete mitochondrial genome sequence of Nectogale elegans.

    PubMed

    Huang, Ting; Yan, Chaochao; Tan, Zheng; Tu, Feiyun; Yue, Bisong; Zhang, Xiuyue

    2014-08-01

    The elegant water shrew (Nectogale elegans) belongs to the family Soricidae, and distributes in northern South Asia, central and southern China and northern Southeast Asia. In this study, the complete mitochondrial genome of N. elegans was sequenced. It was determined to be 17,460 bases, and included 13 protein-coding genes (PCGs), 22 tRNA genes, 2 ribosomal RNA genes and one non-coding region, which is similar to other mammalian mitochondrial genomes. Bayesian inference and maximum likelihood methods were used to construct phylogenetic trees based on 12 heavy-strand concatenated PCGs. Phylogenetic analyses further confirmed that Crocidurinae diverged prior to Soricinae, and Sorex unguiculatus differentiated earlier than N. elegans.

  20. Molecular phylogeny of isolates of Ctenocephalides felis and related species based on analysis of ITS1, ITS2 and mitochondrial 16S rDNA sequences and random binding primers.

    PubMed

    Vobis, M; D'Haese, J; Mehlhorn, H; Mencke, N; Blagburn, B L; Bond, R; Denholm, I; Dryden, M W; Payne, P; Rust, M K; Schroeder, I; Vaughn, M B; Bledsoe, D

    2004-10-01

    The phylogenetic relationships among 31 different flea isolates representing seven different species were studied by nucleotide sequence comparison of the internal transcribed spacer 1 (ITS1), internal transcribed spacer 2 (ITS2) and/or mitochondrial 16S ribosomal RNA gene (mt16S-rDNA) to examine the patterns of variation. Results show that all regions are useful in discriminating among flea species. In Ctenocephalides felis and Tunga penetrans, some differences in these gene regions occurred among different isolates within the same species. In the latter case, the differences are in the mt16S-rDNA region, with one isolate showing 48% divergence in nucleotide sequence. The taxonomic implications of this result are unclear at present. The gene regions revealed differences between C. felis isolates only after DNA sequencing the PCR products. Further differentiation among C. felis isolates was obtained using four different random binding primers (decamers) and primers for mammalian aldolase to amplify narrow differences in the genome. Using these primers we were able to discriminate between different C. felis isolates and determine that some of the genetic variation coincided with minor differences in response to the control agent imidacloprid. However, overall findings do not support the existence of subspecies of C. felis.

  1. Restoration of normal embryogenesis by mitochondrial supplementation in pig oocytes exhibiting mitochondrial DNA deficiency

    PubMed Central

    Cagnone, Gael L. M.; Tsai, Te-Sha; Makanji, Yogeshwar; Matthews, Pamela; Gould, Jodee; Bonkowski, Michael S.; Elgass, Kirstin D.; Wong, Ashley S. A.; Wu, Lindsay E.; McKenzie, Matthew; Sinclair, David A.; John, Justin C. St.

    2016-01-01

    An increasing number of women fail to achieve pregnancy due to either failed fertilization or embryo arrest during preimplantation development. This often results from decreased oocyte quality. Indeed, reduced mitochondrial DNA copy number (mitochondrial DNA deficiency) may disrupt oocyte quality in some women. To overcome mitochondrial DNA deficiency, whilst maintaining genetic identity, we supplemented pig oocytes selected for mitochondrial DNA deficiency, reduced cytoplasmic maturation and lower developmental competence, with autologous populations of mitochondrial isolate at fertilization. Supplementation increased development to blastocyst, the final stage of preimplantation development, and promoted mitochondrial DNA replication prior to embryonic genome activation in mitochondrial DNA deficient oocytes but not in oocytes with normal levels of mitochondrial DNA. Blastocysts exhibited transcriptome profiles more closely resembling those of blastocysts from developmentally competent oocytes. Furthermore, mitochondrial supplementation reduced gene expression patterns associated with metabolic disorders that were identified in blastocysts from mitochondrial DNA deficient oocytes. These results demonstrate the importance of the oocyte’s mitochondrial DNA investment in fertilization outcome and subsequent embryo development to mitochondrial DNA deficient oocytes. PMID:26987907

  2. Preferential recombination between GC clusters in yeast mitochondrial DNA.

    PubMed Central

    Dieckmann, C L; Gandy, B

    1987-01-01

    Yeast mitochondrial DNA molecules have long, AT-rich intergenic spacers punctuated by short GC clusters. GC-rich elements have previously been characterized by others as preferred sites for intramolecular recombination leading to the formation of subgenomic petite molecules. In the present study we show that GC clusters are favored sites for intermolecular recombination between a petite and the wild-type grande genome. The petite studied retains 6.5 kb of mitochondrial DNA reiterated tandemly to form molecules consisting of repeated units. Genetic selection for integration of tandem 6.5 kb repeats of the petite into the grande genome yielded a novel recombination event. One of two crossovers in a double exchange event occurred as expected in the 6.5 kb of matching sequence between the genomes, whereas the second exchange involved a 44 bp GC cluster in the petite and another 44 bp GC cluster in the grande genome 700 bp proximal to the region of homology. Creation of a mitochondrial DNA molecule with a repetitive region led to secondary recombination events that generated a family of molecules with zero to several petite units. The finding that 44 bp GC clusters are preferred as sites for intermolecular exchange adds to the data on petite excision implicating these elements as recombinational hotspots in the yeast mitochondrial genome. Images Fig. 3. Fig. 4. Fig. 5. PMID:3327690

  3. DNA double-strand breaks activate ATM independent of mitochondrial dysfunction in A549 cells.

    PubMed

    Kalifa, Lidza; Gewandter, Jennifer S; Staversky, Rhonda J; Sia, Elaine A; Brookes, Paul S; O'Reilly, Michael A

    2014-10-01

    Excessive nuclear or mitochondrial DNA damage can lead to mitochondrial dysfunction, decreased energy production, and increased generation of reactive oxygen species (ROS). Although numerous cell signaling pathways are activated when cells are injured, the ataxia telangiectasia mutant (ATM) protein has emerged as a major regulator of the response to both mitochondrial dysfunction and nuclear DNA double-strand breaks (DSBs). Because mitochondrial dysfunction is often a response to excessive DNA damage, it has been difficult to determine whether nuclear and/or mitochondrial DNA DSBs activate ATM independent of mitochondrial dysfunction. In this study, mitochondrial and nuclear DNA DSBs were generated in the A549 human lung adenocarcinoma cell line by infecting with retroviruses expressing the restriction endonuclease PstI fused to a mitochondrial targeting sequence (MTS) or nuclear localization sequence (NLS) and a hemagglutinin antigen epitope tag (HA). Expression of MTS-PstI-HA or NLS-PstI-HA activated the DNA damage response defined by phosphorylation of ATM, the tumor suppressor protein p53 (TP53), KRAB-associated protein (KAP)-1, and structural maintenance of chromosomes (SMC)-1. Phosphorylated ATM and SMC1 were detected in nuclear fractions, whereas phosphorylated TP53 and KAP1 were detected in both mitochondrial and nuclear fractions. PstI also enhanced expression of the cyclin-dependent kinase inhibitor p21 and inhibited cell growth. This response to DNA damage occurred in the absence of detectable mitochondrial dysfunction and excess production of ROS. These findings reveal that DNA DSBs are sufficient to activate ATM independent of mitochondrial dysfunction and suggest that the activated form of ATM and some of its substrates are restricted to the nuclear compartment, regardless of the site of DNA damage.

  4. Complete mitochondrial DNA sequence of the endangered frog Odorrana ishikawae (family Ranidae) and unexpected diversity of mt gene arrangements in ranids.

    PubMed

    Kurabayashi, Atsushi; Yoshikawa, Natsuhiko; Sato, Naoki; Hayashi, Yoko; Oumi, Shohei; Fujii, Tamotsu; Sumida, Masayuki

    2010-08-01

    We determined the complete nucleotide sequence of the mitochondrial (mt) genome of an endangered Japanese frog, Odorrana ishikawae (family Ranidae). We also sequenced partial mt genomes of three other Odorrana and six ranid species to survey the diversity of genomic organizations and elucidate the phylogenetic problems remaining in this frog family. The O. ishikawae mt genome contained the 37 mt genes and single control region (CR) typically found in vertebrate mtDNAs, but the region of Light-strand replication origin (OL) was triplicated in this species. Four protein-encoding genes (atp6, nd2, nd3, and nd5) were found to have high sequence divergence and to be usable for population genetics studies on this endangered species. Among the surveyed ranids, only two species (Rana and Lithobates) manifested the typical neobatrachian-type mt gene arrangement. In contrast, relatively large gene rearrangements were found in Amolops, Babina, and Staurois species; and translocations of single tRNA genes (trns) were observed in Glandirana and Odorrana species. Though the inter-generic and interspecific relationships of ranid taxa remain to be elucidated based on 12S and 16S rrn sequence data, some of the derived mt gene orders were found to have synapomorphic features useful for solving problematic ranid phylogenies. The tandem duplication and random loss (TDRL) model, the traditional model for mt gene rearrangement, failed to easily explain several of the mt gene rearrangements observed here. Indeed, the recent recombination-based gene rearrangement models seemed to be more suitable for this purpose. The high frequency of gene translocations involving a specific trn block (trnH-trnS1) and several single tRNA genes suggest that there may be a retrotranslocation in ranid mt genomes.

  5. PCR-based analysis of mitochondrial DNA copy number, mitochondrial DNA damage, and nuclear DNA damage

    PubMed Central

    Gonzalez-Hunt, Claudia P.; Rooney, John P.; Ryde, Ian T.; Anbalagan, Charumathi; Joglekar, Rashmi

    2016-01-01

    Because of the role DNA damage and depletion play in human disease, it is important to develop and improve tools to assess these endpoints. This unit describes PCR-based methods to measure nuclear and mitochondrial DNA damage and copy number. Long amplicon quantitative polymerase chain reaction (LA-QPCR) is used to detect DNA damage by measuring the number of polymerase-inhibiting lesions present based on the amount of PCR amplification; real-time PCR (RT-PCR) is used to calculate genome content. In this unit we provide step-by-step instructions to perform these assays in Homo sapiens, Mus musculus, Rattus norvegicus, Caenorhabditis elegans, Drosophila melanogaster, Danio rerio, Oryzias latipes, Fundulus grandis, and Fundulus heteroclitus, and discuss the advantages and disadvantages of these assays. PMID:26828332

  6. Sequence independent amplification of DNA

    DOEpatents

    Bohlander, Stefan K.

    1998-01-01

    The present invention is a rapid sequence-independent amplification procedure (SIA). Even minute amounts of DNA from various sources can be amplified independent of any sequence requirements of the DNA or any a priori knowledge of any sequence characteristics of the DNA to be amplified. This method allows, for example the sequence independent amplification of microdissected chromosomal material and the reliable construction of high quality fluorescent in situ hybridization (FISH) probes from YACs or from other sources. These probes can be used to localize YACs on metaphase chromosomes but also--with high efficiency--in interphase nuclei.

  7. Sequence independent amplification of DNA

    DOEpatents

    Bohlander, S.K.

    1998-03-24

    The present invention is a rapid sequence-independent amplification procedure (SIA). Even minute amounts of DNA from various sources can be amplified independent of any sequence requirements of the DNA or any a priori knowledge of any sequence characteristics of the DNA to be amplified. This method allows, for example, the sequence independent amplification of microdissected chromosomal material and the reliable construction of high quality fluorescent in situ hybridization (FISH) probes from YACs or from other sources. These probes can be used to localize YACs on metaphase chromosomes but also--with high efficiency--in interphase nuclei. 25 figs.

  8. Mitochondrial DNA disease: new options for prevention.

    PubMed

    Craven, Lyndsey; Elson, Joanna L; Irving, Laura; Tuppen, Helen A; Lister, Lisa M; Greggains, Gareth D; Byerley, Samantha; Murdoch, Alison P; Herbert, Mary; Turnbull, Doug

    2011-10-15

    Very recently, two papers have presented intriguing data suggesting that prevention of transmission of human mitochondrial DNA (mtDNA) disease is possible. [Craven, L., Tuppen, H.A., Greggains, G.D., Harbottle, S.J., Murphy, J.L., Cree, L.M., Murdoch, A.P., Chinnery, P.F., Taylor, R.W., Lightowlers, R.N. et al. (2010) Pronuclear transfer in human embryos to prevent transmission of mitochondrial DNA disease. Nature, 465, 82-85. Tachibana, M., Sparman, M., Sritanaudomchai, H., Ma, H., Clepper, L., Woodward, J., Li, Y., Ramsey, C., Kolotushkina, O. and Mitalipov, S. (2009) Mitochondrial gene replacement in primate offspring and embryonic stem cells. Nature, 461, 367-372.] These recent advances raise hopes for families with mtDNA disease; however, the successful translational of these techniques to clinical practice will require further research to test for safety and to maximize efficacy. Furthermore, in the UK, amendment to the current legislation will be required. Here, we discuss the clinical and scientific background, studies we believe are important to establish safety and efficacy of the techniques and some of the potential concerns about the use of these approaches.

  9. The inheritance of pathogenic mitochondrial DNA mutations.

    PubMed

    Cree, L M; Samuels, D C; Chinnery, P F

    2009-12-01

    Mitochondrial DNA mutations cause disease in >1 in 5000 of the population, and approximately 1 in 200 of the population are asymptomatic carriers of a pathogenic mtDNA mutation. Many patients with these pathogenic mtDNA mutations present with a progressive, disabling neurological syndrome that leads to major disability and premature death. There is currently no effective treatment for mitochondrial disorders, placing great emphasis on preventing the transmission of these diseases. An empiric approach can be used to guide genetic counseling for common mtDNA mutations, but many families transmit rare or unique molecular defects. There is therefore a pressing need to develop techniques to prevent transmission based on a solid understanding of the biological mechanisms. Several recent studies have cast new light on the genetics and cell biology of mtDNA inheritance, but these studies have also raised new controversies. Here we compare and contrast these findings and discuss their relevance for the transmission of human mtDNA diseases.

  10. Complete mtDNA sequences of two millipedes suggest a new model for mitochondrial gene rearrangements: Duplication and non-random loss

    SciTech Connect

    Lavrov, Dennis V.; Boore, Jeffrey L.; Brown, Wesley M.

    2001-11-08

    We determined the complete mtDNA sequences of the millipedes Narceus annularus and Thyropygus sp. (Arthropoda: Diplopoda) and identified in both genomes all 37 genes typical for metazoan mtDNA. The arrangement of these genes is identical in the two millipedes, but differs from that inferred to be ancestral for arthropods by the location of four genes/gene clusters. This novel gene arrangement is unusual for animal mtDNA, in that genes with opposite transcriptional polarities are clustered in the genome and the two clusters are separated by two non-coding regions. The only exception to this pattern is the gene for cysteine tRNA, which is located in the part of the genome that otherwise contains all genes with the opposite transcriptional polarity. We suggest that a mechanism involving complete mtDNA duplication followed by the loss of genes, predetermined by their transcriptional polarity and location in the genome, could generate this gene arrangement from the one ancestral for arthropods. The proposed mechanism has important implications for phylogenetic inferences that are drawn on the basis of gene arrangement comparisons.

  11. Chromosome specific repetitive DNA sequences

    DOEpatents

    Moyzis, Robert K.; Meyne, Julianne

    1991-01-01

    A method is provided for determining specific nucleotide sequences useful in forming a probe which can identify specific chromosomes, preferably through in situ hybridization within the cell itself. In one embodiment, chromosome preferential nucleotide sequences are first determined from a library of recombinant DNA clones having families of repetitive sequences. Library clones are identified with a low homology with a sequence of repetitive DNA families to which the first clones respectively belong and variant sequences are then identified by selecting clones having a pattern of hybridization with genomic DNA dissimilar to the hybridization pattern shown by the respective families. In another embodiment, variant sequences are selected from a sequence of a known repetitive DNA family. The selected variant sequence is classified as chromosome specific, chromosome preferential, or chromosome nonspecific. Sequences which are classified as chromosome preferential are further sequenced and regions are identified having a low homology with other regions of the chromosome preferential sequence or with known sequences of other family me This invention is the result of a contract with the Department of Energy (Contract No. W-7405-ENG-36).

  12. Biparental inheritance of organelles in Pelargonium: evidence for intergenomic recombination of mitochondrial DNA.

    PubMed

    Apitz, Janina; Weihe, Andreas; Pohlheim, Frank; Börner, Thomas

    2013-02-01

    While uniparental transmission of mtDNA is widespread and dominating in eukaryotes leaving mutation as the major source of genotypic diversity, recently, biparental inheritance of mitochondrial genes has been demonstrated in reciprocal crosses of Pelargonium zonale and P. inquinans. The thereby arising heteroplasmy carries the potential for recombination between mtDNAs of different descent, i.e. between the parental mitochondrial genomes. We have analyzed these Pelargonium hybrids for mitochondrial intergenomic recombination events by examining differences in DNA blot hybridization patterns of the mitochondrial genes atp1 and cob. Further investigation of these genes and their flanking regions using nucleotide sequence polymorphisms and PCR revealed DNA segments in the progeny, which contained both P. zonale and P. inquinans sequences suggesting an intergenomic recombination in hybrids of Pelargonium. This turns Pelargonium into an interesting subject for studies of recombination and evolutionary dynamics of mitochondrial genomes.

  13. Mitochondrial genome sequences of Nematocera (lower Diptera): evidence of rearrangement following a complete genome duplication in a winter crane fly.

    PubMed

    Beckenbach, Andrew T

    2012-01-01

    The complete mitochondrial DNA sequences of eight representatives of lower Diptera, suborder Nematocera, along with nearly complete sequences from two other species, are presented. These taxa represent eight families not previously represented by complete mitochondrial DNA sequences. Most of the sequences retain the ancestral dipteran mitochondrial gene arrangement, while one sequence, that of the midge Arachnocampa flava (family Keroplatidae), has an inversion of the trnE gene. The most unusual result is the extensive rearrangement of the mitochondrial genome of a winter crane fly, Paracladura trichoptera (family Trichocera). The pattern of rearrangement indicates that the mechanism of rearrangement involved a tandem duplication of the entire mitochondrial genome, followed by random and nonrandom loss of one copy of each gene. Another winter crane fly retains the ancestral diperan gene arrangement. A preliminary mitochondrial phylogeny of the Diptera is also presented.

  14. Sequencing of complete mitochondrial genome of brown algal Saccharina sp. ye-F.

    PubMed

    Fan, Xiao; Wang, Shuai; Xu, Dong; Zhang, Xiaowen; Xu, Le; Miao, Yu; Ye, Naihao

    2016-09-01

    The complete sequence (37 657 bp) of the mitochondrial DNA (mtDNA) of the Saccharina sp. ye-F was determined using Illumina sequencing data (Illumina Inc., San Diego, CA). The genome contains 38 protein-coding genes (PCG), three ribosomal RNA (rRNA), and 25 transfer RNA (tRNA) genes that are typical of Saccharina mtDNA. A phylogenetic analysis based on the mitochondrial genomes of brown algae indicated that Saccharina sp. ye-F and Saccharina longissima, Saccharina japonica are the most closely related species, which strongly supports their close phylogenetic affinity.

  15. Sequencing of complete mitochondrial genome of brown algal Saccharina sp. ye-W.

    PubMed

    Wang, Shuai; Fan, Xiao; Xu, Dong; Zhang, Xiaowen; Miao, Yu; Xu, Le; Ye, Naihao

    2016-07-01

    The complete sequence (37 657 bp) of the mitochondrial DNA (mtDNA) of the Saccharina sp. ye-W was determined using Illumina sequencing data. The genome contains 38 protein-coding genes (PCG), three ribosomal RNA (rRNA), 25 transfer RNA (tRNA) genes that are typical of Saccharina mtDNA. Phylogenetic analysis based on the mitochondrial genomes of brown algae indicated that Saccharina sp. ye-W and Saccharina longissima, Saccharina japonica are the most closely related species, which strongly supports their close phylogenetic affinity.

  16. Sequencing of complete mitochondrial genome of brown algal Saccharina sp. ye-G.

    PubMed

    Guan, Zheng; Fan, Xiao; Wang, Shuai; Xu, Dong; Zhang, Xiaowen; Wang, Dongsheng; Miao, Yu; Ye, Naihao

    2016-05-01

    The complete sequence (37,673 bp) of the mitochondrial DNA (mtDNA) of the Saccharina sp. ye-G was determined using Illumina sequencing data. The genome contains 38 protein-coding genes (PCG), 3 ribosomal RNA (rRNA), 25 transfer RNA (tRNA) genes that are typical of Saccharina mtDNA. A phylogenetic analysis based on the mitochondrial genomes of brown algae indicated that Saccharina sp. ye-G and Saccharina longissima, Saccharina japonica are the most closely related species, which strongly supports their close phylogenetic affinity.

  17. Mitochondrial DNA data reveal cryptic species within Taenia krabbei.

    PubMed

    Lavikainen, Antti; Haukisalmi, Voitto; Lehtinen, Markus J; Laaksonen, Sauli; Holmström, Sauli; Isomursu, Marja; Oksanen, Antti; Meri, Seppo

    2010-06-01

    Cysticerci of Taenia sp. from two elks (Alces alces) in Finland were characterized using morphological criteria and sequences of two mitochondrial DNA regions. The host species, size, structure and location of the cysticerci indicated that they might belong to Taenia krabbei, a circumpolar species occurring in a sylvatic life cycle in wild canids and cervids. Based on the number, length and shape of the rostellar hooks, the specimens could not be unambiguously defined as belonging to T. krabbei, T. cervi, T. ovis or T. solium. In the phylogenetic analysis, based on mitochondrial nucleotide sequence data, Taenia sp. was placed as a sister species of T. solium, distant from T. krabbei isolates previously characterized from Svalbard. This indicates that the Finnish and the Svalbard isolates, resembling T. krabbei, cannot represent a single species. The results suggest that careful morphological and genetic analyses of further isolates from intermediate and definitive hosts are required to define the taxonomic status of these two cryptic species.

  18. Mitochondrial DNA analysis in Parkinson's disease.

    PubMed

    Schapira, A H; Holt, I J; Sweeney, M; Harding, A E; Jenner, P; Marsden, C D

    1990-01-01

    The reduced form of nicotinamide adenine dinucleotide coenzyme Q reductase (complex I) activity has recently been shown to be deficient in the substantia nigra of patients dying with Parkinson's disease. This biochemical defect is identical to that produced by the neurotoxin 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine (MPTP), which also produces parkinsonism in humans. Complex I comprises 25 polypeptides, seven of which are encoded by mitochondrial DNA. Restriction fragment analysis of substantia nigra DNA from six patients with Parkinson's disease did not show any major deletion. In two cases, there were different novel polymorphisms that were not observed in control brain (n = 6) or blood (n = 34) samples.

  19. Clonal expansion of early to mid-life mitochondrial DNA point mutations drives mitochondrial dysfunction during human ageing.

    PubMed

    Greaves, Laura C; Nooteboom, Marco; Elson, Joanna L; Tuppen, Helen A L; Taylor, Geoffrey A; Commane, Daniel M; Arasaradnam, Ramesh P; Khrapko, Konstantin; Taylor, Robert W; Kirkwood, Thomas B L; Mathers, John C; Turnbull, Douglass M

    2014-09-01

    Age-related decline in the integrity of mitochondria is an important contributor to the human ageing process. In a number of ageing stem cell populations, this decline in mitochondrial function is due to clonal expansion of individual mitochondrial DNA (mtDNA) point mutations within single cells. However the dynamics of this process and when these mtDNA mutations occur initially are poorly understood. Using human colorectal epithelium as an exemplar tissue with a well-defined stem cell population, we analysed samples from 207 healthy participants aged 17-78 years using a combination of techniques (Random Mutation Capture, Next Generation Sequencing and mitochondrial enzyme histochemistry), and show that: 1) non-pathogenic mtDNA mutations are present from early embryogenesis or may be transmitted through the germline, whereas pathogenic mtDNA mutations are detected in the somatic cells, providing evidence for purifying selection in humans, 2) pathogenic mtDNA mutations are present from early adulthood (<20 years of age), at both low levels and as clonal expansions, 3) low level mtDNA mutation frequency does not change significantly with age, suggesting that mtDNA mutation rate does not increase significantly with age, and 4) clonally expanded mtDNA mutations increase dramatically with age. These data confirm that clonal expansion of mtDNA mutations, some of which are generated very early in life, is the major driving force behind the mitochondrial dysfunction associated with ageing of the human colorectal epithelium.

  20. Triangulating the provenance of African elephants using mitochondrial DNA

    PubMed Central

    Ishida, Yasuko; Georgiadis, Nicholas J; Hondo, Tomoko; Roca, Alfred L

    2013-01-01

    African elephant mitochondrial (mt) DNA follows a distinctive evolutionary trajectory. As females do not migrate between elephant herds, mtDNA exhibits low geographic dispersal. We therefore examined the effectiveness of mtDNA for assigning the provenance of African elephants (or their ivory). For 653 savanna and forest elephants from 22 localities in 13 countries, 4258 bp of mtDNA was sequenced. We detected eight mtDNA subclades, of which seven had regionally restricted distributions. Among 108 unique haplotypes identified, 72% were found at only one locality and 84% were country specific, while 44% of individuals carried a haplotype detected only at their sampling locality. We combined 316 bp of our control region sequences with those generated by previous trans-national surveys of African elephants. Among 101 unique control region haplotypes detected in African elephants across 81 locations in 22 countries, 62% were present in only a single country. Applying our mtDNA results to a previous microsatellite-based assignment study would improve estimates of the provenance of elephants in 115 of 122 mis-assigned cases. Nuclear partitioning followed species boundaries and not mtDNA subclade boundaries. For taxa such as elephants in which nuclear and mtDNA markers differ in phylogeography, combining the two markers can triangulate the origins of confiscated wildlife products. PMID:23798975

  1. Higher plant mitochondrial DNA: Genomes, genes, mutants, transcription, translation

    SciTech Connect

    Not Available

    1986-01-01

    This volume contains brief summaries of 63 presentations given at the International Workshop on Higher Plant Mitochondrial DNA. The presentations are organized into topical discussions addressing plant genomes, mitochondrial genes, cytoplasmic male sterility, transcription, translation, plasmids and tissue culture. (DT)

  2. Gene trees reveal repeated instances of mitochondrial DNA introgression in orangethroat darters (percidae: etheostoma).

    PubMed

    Bossu, Christen M; Near, Thomas J

    2009-02-01

    Phylogenies of closely related animal species are often inferred using mitochondrial DNA (mtDNA) gene sequences. The accuracy of mtDNA gene trees is compromised through hybridization that leads to introgression of mitochondrial genomes. Using DNA sequences from 6 single-copy nuclear genes and 2 regions of the mitochondrial genome, we investigated the temporal and geographic signature of mitochondrial and nuclear introgression in the Etheostoma spectabile darter clade. Phylogenetic analyses of the nuclear genes result in the monophyly of the E. spectabile clade; however, with respect to sampled specimens of 5 species (Etheostoma fragi, Etheostoma uniporum, Etheostoma pulchellum, Etheostoma burri, and E. spectabile), the mitochondrial phylogeny is inconsistent with E. spectabile clade monophyly. Etheostoma uniporum and E. fragi are both fixed for heterospecific mitochondrial genomes. Limited nuclear introgression is restricted to E. uniporum. Our analyses show that the pattern of introgression is consistently asymmetric, with movement of heterospecific mitochondrial haplotypes and nuclear alleles into E. spectabile clade species; introgressive hybridization spans broad temporal scales; and introgression is restricted to species and populations in the Ozarks. The introgressed mitochondrial genome observed in E. fragi has an obscure phylogenetic placement among darters, an ancient age, and is possibly a mitochondrial fossil from an Etheostoma species that has subsequently gone extinct. These results indicate that introgression, both ancient and more contemporaneous, characterizes the history of diversification in the E. spectabile species clade and may be relatively common among clades comprising the species-rich North American freshwater fauna.

  3. Ancient DNA sequences point to a large loss of mitochondrial genetic diversity in the saiga antelope (Saiga tatarica) since the Pleistocene.

    PubMed

    Campos, Paula F; Kristensen, Tommy; Orlando, Ludovic; Sher, Andrei; Kholodova, Marina V; Götherström, Anders; Hofreiter, Michael; Drucker, Dorothée G; Kosintsev, Pavel; Tikhonov, Alexei; Baryshnikov, Gennady F; Willerslev, Eske; Gilbert, M Thomas P

    2010-11-01

    Prior to the Holocene, the range of the saiga antelope (Saiga tatarica) spanned from France to the Northwest Territories of Canada. Although its distribution subsequently contracted to the steppes of Central Asia, historical records indicate that it remained extremely abundant until the end of the Soviet Union, after which its populations were reduced by over 95%. We have analysed the mitochondrial control region sequence variation of 27 ancient and 38 modern specimens, to assay how the species' genetic diversity has changed since the Pleistocene. Phylogenetic analyses reveal the existence of two well-supported, and clearly distinct, clades of saiga. The first, spanning a time range from >49,500 (14) C ybp to the present, comprises all the modern specimens and ancient samples from the Northern Urals, Middle Urals and Northeast Yakutia. The second clade is exclusive to the Northern Urals and includes samples dating from between 40,400 to 10,250 (14) C ybp. Current genetic diversity is much lower than that present during the Pleistocene, an observation that data modelling using serial coalescent indicates cannot be explained by genetic drift in a population of constant size. Approximate Bayesian Computation analyses show the observed data is more compatible with a drastic population size reduction (c. 66-77%) following either a demographic bottleneck in the course of the Holocene or late Pleistocene, or a geographic fragmentation (followed by local extinction of one subpopulation) at the Holocene/Pleistocene transition.

  4. Cryptic variation in an ecological indicator organism: mitochondrial and nuclear DNA sequence data confirm distinct lineages of Baetis harrisoni Barnard (Ephemeroptera: Baetidae) in southern Africa

    PubMed Central

    2012-01-01

    Background Baetis harrisoni Barnard is a mayfly frequently encountered in river studies across Africa, but the external morphological features used for identifying nymphs have been observed to vary subtly between different geographic locations. It has been associated with a wide range of ecological conditions, including pH extremes of pH 2.9–10.0 in polluted waters. We present a molecular study of the genetic variation within B. harrisoni across 21 rivers in its distribution range in southern Africa. Results Four gene regions were examined, two mitochondrial (cytochrome c oxidase subunit I [COI] and small subunit ribosomal 16S rDNA [16S]) and two nuclear (elongation factor 1 alpha [EF1α] and phosphoenolpyruvate carboxykinase [PEPCK]). Bayesian and parsimony approaches to phylogeny reconstruction resulted in five well-supported major lineages, which were confirmed using a general mixed Yule-coalescent (GMYC) model. Results from the EF1α gene were significantly incongruent with both mitochondrial and nuclear (PEPCK) results, possibly due to incomplete lineage sorting of the EF1α gene. Mean between-clade distance estimated using the COI and PEPCK data was found to be an order of magnitude greater than the within-clade distance and comparable to that previously reported for other recognised Baetis species. Analysis of the Isolation by Distance (IBD) between all samples showed a small but significant effect of IBD. Within each lineage the contribution of IBD was minimal. Tentative dating analyses using an uncorrelated log-normal relaxed clock and two published estimates of COI mutation rates suggest that diversification within the group occurred throughout the Pliocene and mid-Miocene (~2.4–11.5 mya). Conclusions The distinct lineages of B. harrisoni correspond to categorical environmental variation, with two lineages comprising samples from streams that flow through acidic Table Mountain Sandstone and three lineages with samples from neutral-to-alkaline streams

  5. Distribution of mitochondrial DNA fragments in the nuclear genome of the honeybee.

    PubMed

    Du, W X; Qin, Y C

    2015-10-27

    Nuclear mitochondrial pseudogenes (numts), which originated from mitochondrial DNA (mtDNA) insertions in the nuclear genome, have been detected in many species. The distribution of numts in the honeybee nuclear genome has not yet been fully reported. By referring to the whole honeybee mtDNA sequence and to the recent version of the honeybee nuclear genome, 236 reference sequences were identified by BLAST, with 90 unmapped. The size of the numts ranged from 219 to 3788 bp, and the homologous identity between numts and their corresponding mtDNA fragments varied from 71 to 93%. Furthermore, identified honeybee numts covered nearly all mitochondrial genes and were distributed over all chromosomes. This study provides useful information for further research related to mitochondrial genes and the evolution of the honeybee.

  6. Mitochondrial Genome Sequencing and Development of Genetic Markers for the Detection of DNA of Invasive Bighead and Silver Carp (Hypophthalmichthys nobilis and H. molitrix) in Environmental Water Samples from the United States

    PubMed Central

    Farrington, Heather L.; Edwards, Christine E.; Guan, Xin; Carr, Matthew R.; Baerwaldt, Kelly; Lance, Richard F.

    2015-01-01

    Invasive Asian bighead and silver carp (Hypophthalmichthys nobilis and H. molitrix) pose a substantial threat to North American aquatic ecosystems. Recently, environmental DNA (eDNA), genetic material shed by organisms into their environment that can be detected by non-invasive sampling strategies and genetic assays, has gained recognition as a tool for tracking the invasion front of these species toward the Great Lakes. The goal of this study was to develop new species-specific conventional PCR (cPCR) and quantitative (qPCR) markers for detection of these species in North American surface waters. We first generated complete mitochondrial genome sequences from 33 bighead and 29 silver carp individuals collected throughout their introduced range. These sequences were aligned with those from other common and closely related fish species from the Illinois River watershed to identify and design new species-specific markers for the detection of bighead and silver carp DNA in environmental water samples. We then tested these genetic markers in the laboratory for species-specificity and sensitivity. Newly developed markers performed well in field trials, did not have any false positive detections, and many markers had much higher detection rates and sensitivity compared to the markers currently used in eDNA surveillance programs. We also explored the use of multiple genetic markers to determine whether it would improve detection rates, results of which showed that using multiple highly sensitive markers should maximize detection rates in environmental samples. The new markers developed in this study greatly expand the number of species-specific genetic markers available to track the invasion front of bighead and silver carp and will improve the resolution of these assays. Additionally, the use of the qPCR markers developed in this study may reduce sample processing time and cost of eDNA monitoring for these species. PMID:25706532

  7. Mitochondrial genome sequencing and development of genetic markers for the detection of DNA of invasive bighead and silver carp (Hypophthalmichthys nobilis and H. molitrix) in environmental water samples from the United States.

    PubMed

    Farrington, Heather L; Edwards, Christine E; Guan, Xin; Carr, Matthew R; Baerwaldt, Kelly; Lance, Richard F

    2015-01-01

    Invasive Asian bighead and silver carp (Hypophthalmichthys nobilis and H. molitrix) pose a substantial threat to North American aquatic ecosystems. Recently, environmental DNA (eDNA), genetic material shed by organisms into their environment that can be detected by non-invasive sampling strategies and genetic assays, has gained recognition as a tool for tracking the invasion front of these species toward the Great Lakes. The goal of this study was to develop new species-specific conventional PCR (cPCR) and quantitative (qPCR) markers for detection of these species in North American surface waters. We first generated complete mitochondrial genome sequences from 33 bighead and 29 silver carp individuals collected throughout their introduced range. These sequences were aligned with those from other common and closely related fish species from the Illinois River watershed to identify and design new species-specific markers for the detection of bighead and silver carp DNA in environmental water samples. We then tested these genetic markers in the laboratory for species-specificity and sensitivity. Newly developed markers performed well in field trials, did not have any false positive detections, and many markers had much higher detection rates and sensitivity compared to the markers currently used in eDNA surveillance programs. We also explored the use of multiple genetic markers to determine whether it would improve detection rates, results of which showed that using multiple highly sensitive markers should maximize detection rates in environmental samples. The new markers developed in this study greatly expand the number of species-specific genetic markers available to track the invasion front of bighead and silver carp and will improve the resolution of these assays. Additionally, the use of the qPCR markers developed in this study may reduce sample processing time and cost of eDNA monitoring for these species.

  8. The complete mitochondrial genome sequence of the liverwort Pleurozia purpurea reveals extremely conservative mitochondrial genome evolution in liverworts.

    PubMed

    Wang, Bin; Xue, Jiayu; Li, Libo; Liu, Yang; Qiu, Yin-Long

    2009-12-01

    Plant mitochondrial genomes have been known to be highly unusual in their large sizes, frequent intra-genomic rearrangement, and generally conservative sequence evolution. Recent studies show that in early land plants the mitochondrial genomes exhibit a mixed mode of conservative yet dynamic evolution. Here, we report the completely sequenced mitochondrial genome from the liverwort Pleurozia purpurea. The circular genome has a size of 168,526 base pairs, containing 43 protein-coding genes, 3 rRNA genes, 25 tRNA genes, and 31 group I or II introns. It differs from the Marchantia polymorpha mitochondrial genome, the only other liverwort chondriome that has been sequenced, in lacking two genes (trnRucg and trnTggu) and one intron (rrn18i1065gII). The two genomes have identical gene orders and highly similar sequences in exons, introns, and intergenic spacers. Finally, a comparative analysis of duplicated trnRucu and other trnR genes from the two liverworts and several other organisms identified the recent lateral origin of trnRucg in Marchantia mtDNA through modification of a duplicated trnRucu. This study shows that the mitochondrial genomes evolve extremely slowly in liverworts, the earliest-diverging lineage of extant land plants, in stark contrast to what is known of highly dynamic evolution of mitochondrial genomes in seed plants.

  9. Biotools: Patenting DNA sequences

    SciTech Connect

    Yablonsky, M.D.; Hone, W.J.

    1995-07-01

    The decision, known as In re Deuel{sup 2}, rejects the PTO`s interpretation of a previous decision of the Federal Circuit and makes it more possible that a {open_quotes}nucleic acid of a particular sequence{close_quotes} - commonly known as a gene sequence - may be patentable. 15 refs.

  10. A mitochondrial retroplasmid integrates into mitochondrial DNA by a novel mechanism involving the synthesis of a hybrid cDNA and homologous recombination.

    PubMed Central

    Chiang, C C; Kennell, J C; Wanner, L A; Lambowitz, A M

    1994-01-01

    The Mauriceville and Varkud mitochondrial plasmids of Neurospora spp. are closely related, small circular DNAs that propagate via an RNA intermediate and reverse transcription. Although the plasmids ordinarily replicate autonomously, they can also integrate into mitochondrial DNA (mtDNA), yielding defective mtDNAs that in some cases cause senescence. To investigate the integration mechanism, we analyzed four cases in which the Varkud plasmid integrated into the mitochondrial small rRNA gene, three in wild-type subcultures and one in a senescent mutant. Our analysis suggests that the integrations occurred by the plasmid reverse transcriptase template switching between the plasmid transcript and internal sequences in the mitochondrial small rRNA to yield hybrid cDNAs that circularized and recombined homologously with the mtDNA. The integrated plasmid sequences are transcribed, presumably from the mitochondrial small rRNA promoters, resulting in hybrid RNAs containing the 5' segment of the mitochondrial small rRNA linked head-to-tail to the full-length plasmid transcript. Analysis of additional senescent mutants revealed three cases in which the plasmid used the same mechanism to integrate at other locations in the mtDNA. In these cases, circular variant plasmids that had incorporated a mitochondrial tRNA or tRNA-like sequence by template switching integrated by homologous recombination at the site of the corresponding tRNA or tRNA-like sequence in mtDNA. This simple integration mechanism involving template switching to generate a hybrid cDNA that integrates homologously could have been used by primitive retroelements prior to the acquisition of a specialized integration machinery. Images PMID:7523850

  11. Selective Enrichment and Sequencing of Whole Mitochondrial Genomes in the Presence of Nuclear Encoded Mitochondrial Pseudogenes (Numts)

    PubMed Central

    Wolff, Jonci N.; Shearman, Deborah C. A.; Brooks, Rob C.; Ballard, John W. O.

    2012-01-01

    Numts are an integral component of many eukaryote genomes offering a snapshot of the evolutionary process that led from the incorporation of an α-proteobacterium into a larger eukaryotic cell some 1.8 billion years ago. Although numt sequence can be harnessed as molecular marker, these sequences often remain unidentified and are mistaken for genuine mtDNA leading to erroneous interpretation of mtDNA data sets. It is therefore indispensable that during the process of amplifying and sequencing mitochondrial genes, preventive measures are taken to ensure the exclusion of numts to guarantee the recovery of genuine mtDNA. This applies to mtDNA analyses in general but especially to studies where mtDNAs are sequenced de novo as the launch pad for subsequent mtDNA-based research. By using a combination of dilution series and nested rolling circle amplification (RCA), we present a novel strategy to selectively amplify mtDNA and exclude the amplification of numt sequence. We have successfully applied this strategy to de novo sequence the mtDNA of the Black Field Cricket Teleogryllus commodus, a species known to contain numts. Aligning our assembled sequence to the reference genome of Teleogryllus emma (GenBank EU557269.1) led to the identification of a numt sequence in the reference sequence. This unexpected result further highlights the need of a reliable and accessible strategy to eliminate this source of error. PMID:22606342

  12. Inter- and intraspecific mitochondrial DNA variation in North American bears (Ursus)

    USGS Publications Warehouse

    Cronin, M.A.; Amstrup, S.; Garner, G.; Vyse, Ernest R.

    1991-01-01

    We assessed mitochondrial DNA variation in North American black bears (Ursus americanus), brown bears (Ursus arctos), and polar bears (Ursus maritimus). Divergent mitochondrial DNA haplotypes (0.05 base substitutions per nucleotide) were identified in populations of black bears from Montana and Oregon. In contrast, very similar haplotypes occur in black bears across North America. This discordance of haplotype phylogeny and geographic distribution indicates that there has been maintenance of polymorphism and considerable gene flow throughout the history of the species. Intraspecific mitochondrial DNA sequence divergence in brown bears and polar bears is lower than in black bears. The two morphological forms of U. arctos, grizzly and coastal brown bears, are not in distinct mtDNA lineages. Interspecific comparisons indicate that brown bears and polar bears share similar mitochondrial DNA (0.023 base substitutions per nucleotide) which is quite divergent (0.078 base substitutions per nucleotide) from that of black bears. High mitochondrial DNA divergence within black bears and paraphyletic relationships of brown and polar bear mitochondrial DNA indicate that intraspecific variation across species' ranges should be considered in phylogenetic analyses of mitochondrial DNA.

  13. Number matters: control of mammalian mitochondrial DNA copy number.

    PubMed

    Clay Montier, Laura L; Deng, Janice J; Bai, Yidong

    2009-03-01

    Regulation of mitochondrial biogenesis is essential for proper cellular functioning. Mitochondrial DNA (mtDNA) depletion and the resulting mitochondrial malfunction have been implicated in cancer, neurodegeneration, diabetes, aging, and many other human diseases. Although it is known that the dynamics of the mammalian mitochondrial genome are not linked with that of the nuclear genome, very little is known about the mechanism of mtDNA propagation. Nevertheless, our understanding of the mode of mtDNA replication has advanced in recent years, though not without some controversies. This review summarizes our current knowledge of mtDNA copy number control in mammalian cells, while focusing on both mtDNA replication and turnover. Although mtDNA copy number is seemingly in excess, we reason that mtDNA copy number control is an important aspect of mitochondrial genetics and biogenesis and is essential for normal cellular function.

  14. Isolation and analysis of high quality nuclear DNA with reduced organellar DNA for plant genome sequencing and resequencing

    PubMed Central

    2011-01-01

    Background High throughput sequencing (HTS) technologies have revolutionized the field of genomics by drastically reducing the cost of sequencing, making it feasible for individual labs to sequence or resequence plant genomes. Obtaining high quality, high molecular weight DNA from plants poses significant challenges due to the high copy number of chloroplast and mitochondrial DNA, as well as high levels of phenolic compounds and polysaccharides. Multiple methods have been used to isolate DNA from plants; the CTAB method is commonly used to isolate total cellular DNA from plants that contain nuclear DNA, as well as chloroplast and mitochondrial DNA. Alternatively, DNA can be isolated from nuclei to minimize chloroplast and mitochondrial DNA contamination. Results We describe optimized protocols for isolation of nuclear DNA from eight different plant species encompassing both monocot and eudicot species. These protocols use nuclei isolation to minimize chloroplast and mitochondrial DNA contamination. We also developed a protocol to determine the number of chloroplast and mitochondrial DNA copies relative to the nuclear DNA using quantitative real time PCR (qPCR). We compared DNA isolated from nuclei to total cellular DNA isolated with the CTAB method. As expected, DNA isolated from nuclei consistently yielded nuclear DNA with fewer chloroplast and mitochondrial DNA copies, as compared to the total cellular DNA prepared with the CTAB method. This protocol will allow for analysis of the quality and quantity of nuclear DNA before starting a plant whole genome sequencing or resequencing experiment. Conclusions Extracting high quality, high molecular weight nuclear DNA in plants has the potential to be a bottleneck in the era of whole genome sequencing and resequencing. The methods that are described here provide a framework for researchers to extract and quantify nuclear DNA in multiple types of plants. PMID:21599914

  15. Complete mitochondrial genome sequence of a Hungarian red deer (Cervus elaphus hippelaphus) from high-throughput sequencing data and its phylogenetic position within the family Cervidae.

    PubMed

    Frank, Krisztián; Barta, Endre; Bana, Nóra Á; Nagy, János; Horn, Péter; Orosz, László; Stéger, Viktor

    2016-06-01

    Recently, there has been considerable interest in genetic differentiation in the Cervidae family. A common tool used to determine genetic variation in different species, breeds and populations is mitochondrial DNA analysis, which can be used to estimate phylogenetic relationships among animal taxa and for molecular phylogenetic evolution analysis. With the development of sequencing technology, more and more mitochondrial sequences have been made available in public databases, including whole mitochondrial DNA sequences. These data have been used for phylogenetic analysis of animal species, and for studies of evolutionary processes. We determined the complete mitochondrial genome of a Central European red deer, Cervus elaphus hippelaphus, from Hungary by a next generation sequencing technology. The mitochondrial genome is 16 354 bp in length and contains 13 protein-coding genes, two rRNA genes, 22 tRNA genes and a control region, all of which are arranged similar as in other vertebrates. We made phylogenetic analyses with the new sequence and 76 available mitochondrial sequences of Cervidae, using Bos taurus mitochondrial sequence as outgroup. We used 'neighbor joining' and 'maximum likelihood' methods on whole mitochondrial genome sequences; the consensus phylogenetic trees supported monophyly of the family Cervidae; it was divided into two subfamilies, Cervinae and Capreolinae, and five tribes, Cervini, Muntiacini, Alceini, Odocoileini, and Capreolini. The evolutionary structure of the family Cervidae can be reconstructed by phylogenetic analysis based on whole mitochondrial genomes; which method could be used broadly in phylogenetic evolutionary analysis of animal taxa.

  16. Historical relationships among Neotropical lowland forest areas of endemism as determined by mitochondrial DNA sequence variation within the Wedge-billed Woodcreeper (Aves: Dendrocolaptidae: Glyphorynchus spirurus).

    PubMed

    Marks, Ben D; Hackett, Shannon J; Capparella, Angelo P

    2002-07-01

    Studies of the distribution of South American taxa have identified several areas of endemism that may have contributed to the historical diversification of the region. We constructed a phylogeny of Glyphorynchus spirurus (Aves: Dendrocolaptidae) populations using mtDNA sequence data from portions of cytochrome b, NADH dehydrogenase subunit II (ND2), and complete NADH dehydrogenase subunit III (ND3). Using this phylogeny we evaluate five previous hypotheses of area-relationships, two based on phylogenetic studies of morphological characters in birds and three based on parsimony analysis of endemism in birds and primates. Maximum likelihood and maximum parsimony analyses recovered two phylogenetic hypotheses that differed in the placement of one of the areas. Within each of the areas of endemism, the two analyses support the same clades. Neither of the phylogenetic hypotheses for Glyphorynchus exactly matches any of the five previous hypotheses of area-relationships, although ambiguous support exists for one of them. Five areas-Central America, Inambari, Napo, Pará, and Rondônia-are supported as composites with component taxa having phylogenetic affinities with more than one area. Data reported here also indicate high levels of sequence divergence within Glyphorynchus. Genetic breaks within Glyphorynchus are only partially congruent with subspecific taxonomy. The regional sampling design used makes this study the largest scale genetic assay of a widespread Neotropical avian taxon published to date.

  17. The complete mitochondrial genome sequence of Eimeria magna (Apicomplexa: Coccidia).

    PubMed

    Tian, Si-Qin; Cui, Ping; Fang, Su-Fang; Liu, Guo-Hua; Wang, Chun-Ren; Zhu, Xing-Quan

    2015-01-01

    In the present study, we determined the complete mitochondrial DNA (mtDNA) sequence of Eimeria magna from rabbits for the first time, and compared its gene contents and genome organizations with that of seven Eimeria spp. from domestic chickens. The size of the complete mt genome sequence of E. magna is 6249 bp, which consists of 3 protein-coding genes (cytb, cox1 and cox3), 12 gene fragments for the large subunit (LSU) rRNA, and 7 gene fragments for the small subunit (SSU) rRNA, without transfer RNA genes, in accordance with that of Eimeria spp. from chickens. The putative direction of translation for three genes (cytb, cox1 and cox3) was the same as those of Eimeria species from domestic chickens. The content of A + T is 65.16% for E. magna mt genome (29.73% A, 35.43% T, 17.09 G and 17.75% C). The E. magna mt genome sequence provides novel mtDNA markers for studying the molecular epidemiology and population genetics of Eimeria spp. and has implications for the molecular diagnosis and control of rabbit coccidiosis.

  18. The sequence of sequencers: The history of sequencing DNA.

    PubMed

    Heather, James M; Chain, Benjamin

    2016-01-01

    Determining the order of nucleic acid residues in biological samples is an integral component of a wide variety of research applications. Over the last fifty years large numbers of researchers have applied themselves to the production of techniques and technologies to facilitate this feat, sequencing DNA and RNA molecules. This time-scale has witnessed tremendous changes, moving from sequencing short oligonucleotides to millions of bases, from struggling towards the deduction of the coding sequence of a single gene to rapid and widely available whole genome sequencing. This article traverses those years, iterating through the different generations of sequencing technology, highlighting some of the key discoveries, researchers, and sequences along the way.

  19. Image analysis for DNA sequencing

    NASA Astrophysics Data System (ADS)

    Palaniappan, Kannappan; Huang, Thomas S.

    1991-07-01

    There is a great deal of interest in automating the process of DNA (deoxyribonucleic acid) sequencing to support the analysis of genomic DNA such as the Human and Mouse Genome projects. In one class of gel-based sequencing protocols autoradiograph images are generated in the final step and usually require manual interpretation to reconstruct the DNA sequence represented by the image. The need to handle a large volume of sequence information necessitates automation of the manual autoradiograph reading step through image analysis in order to reduce the length of time required to obtain sequence data and reduce transcription errors. Various adaptive image enhancement, segmentation and alignment methods were applied to autoradiograph images. The methods are adaptive to the local characteristics of the image such as noise, background signal, or presence of edges. Once the two-dimensional data is converted to a set of aligned one-dimensional profiles waveform analysis is used to determine the location of each band which represents one nucleotide in the sequence. Different classification strategies including a rule-based approach are investigated to map the profile signals, augmented with the original two-dimensional image data as necessary, to textual DNA sequence information.

  20. Saami mitochondrial DNA reveals deep maternal lineage clusters.

    PubMed

    Delghandi, M; Utsi, E; Krauss, S

    1998-01-01

    The mitochondrial DNA of 62 Saami from the north of Norway was analyzed in the D loop hypervariable region I and II and sequences were compared to other gene pools. Two major (lineage 1 and 2) and two minor (lineage 3 and 4) maternal lineage clusters were found. Lineage 1 (56.9% of all hitherto analyzed Saami samples) contains a substantial number of branching haplotypes which are unknown in European gene pools. Lineage 2 (31.5%) and lineage 4 (3.6%) have few branching points and are present at a low rate throughout European gene pools. Lineage 3 (4.7%) has polymorphisms characteristic of circumpolar lineages.

  1. Mitochondrial DNA content, an inaccurate biomarker of mitochondrial alteration in human immunodeficiency virus-related lipodystrophy.

    PubMed

    Kim, Min Ji; Jardel, Claude; Barthélémy, Cyrille; Jan, Véronique; Bastard, Jean Philippe; Fillaut-Chapin, Sandrine; Houry, Sydney; Capeau, Jacqueline; Lombès, Anne

    2008-05-01

    Lipoatrophy is a prevalent side effect of antiretroviral treatment of human immunodeficiency virus (HIV) infection. Its mechanisms are still disputed but include mitochondrial toxicity and, in particular, mitochondrial DNA (mtDNA) depletion induced by nucleoside reverse transcriptase inhibitors. To obtain an integrated evaluation of the mitochondrial alteration in lipoatrophy, we investigated the DNA, RNA, and protein levels in 15 samples of abdominal subcutaneous adipose tissue from HIV-infected patients with peripheral lipoatrophy and compared the results with those for 15 samples from age- and body mass index-matched controls. The DNA and RNA analyses used PCR-based techniques, while proteins were quantified with enzyme-linked immunosorbent assay and measurement of activities with spectrophotometric assays. Depletion of mtDNA and mtDNA-encoded MT-CO2 mRNA was present, but normal levels of mtDNA-dependent activity (cytochrome c oxidase) and protein (MT-CO2p) showed that it was compensated for. An increase in nuclear-DNA-dependent mitochondrial activities (citrate synthase and malate dehydrogenase) and protein (COX4I1p), as well as transcriptional up-regulation of nuclear-DNA-encoded mitochondrial genes (COX4I1 and UCP2), demonstrated increased mitochondrial biogenesis. However, the expression of the known transcription factors of mitochondrial biogenesis (TFAM, NRF1, GABPA, PPARGC1A, PPARGC1B, and PPRC1) was normal or decreased. Increased amounts of activated caspase 3 and of DDIT3 mRNA showed the induction of apoptosis and oxidative stress, respectively. The mtDNA content did not correlate with any other mitochondrial parameter. In conclusion, mtDNA content does not appear to be an accurate biomarker of mitochondrial alteration in lipoatrophic adipose tissue. The preservation of mtDNA-dependent mitochondrial functions occurred despite severe mtDNA depletion. The presence of significant oxidative stress and apoptosis did not correlate with the mtDNA content.

  2. Mitochondrial DNA Content, an Inaccurate Biomarker of Mitochondrial Alteration in Human Immunodeficiency Virus-Related Lipodystrophy▿

    PubMed Central

    Kim, Min Ji; Jardel, Claude; Barthélémy, Cyrille; Jan, Véronique; Bastard, Jean Philippe; Fillaut-Chapin, Sandrine; Houry, Sydney; Capeau, Jacqueline; Lombès, Anne

    2008-01-01

    Lipoatrophy is a prevalent side effect of antiretroviral treatment of human immunodeficiency virus (HIV) infection. Its mechanisms are still disputed but include mitochondrial toxicity and, in particular, mitochondrial DNA (mtDNA) depletion induced by nucleoside reverse transcriptase inhibitors. To obtain an integrated evaluation of the mitochondrial alteration in lipoatrophy, we investigated the DNA, RNA, and protein levels in 15 samples of abdominal subcutaneous adipose tissue from HIV-infected patients with peripheral lipoatrophy and compared the results with those for 15 samples from age- and body mass index-matched controls. The DNA and RNA analyses used PCR-based techniques, while proteins were quantified with enzyme-linked immunosorbent assay and measurement of activities with spectrophotometric assays. Depletion of mtDNA and mtDNA-encoded MT-CO2 mRNA was present, but normal levels of mtDNA-dependent activity (cytochrome c oxidase) and protein (MT-CO2p) showed that it was compensated for. An increase in nuclear-DNA-dependent mitochondrial activities (citrate synthase and malate dehydrogenase) and protein (COX4I1p), as well as transcriptional up-regulation of nuclear-DNA-encoded mitochondrial genes (COX4I1 and UCP2), demonstrated increased mitochondrial biogenesis. However, the expression of the known transcription factors of mitochondrial biogenesis (TFAM, NRF1, GABPA, PPARGC1A, PPARGC1B, and PPRC1) was normal or decreased. Increased amounts of activated caspase 3 and of DDIT3 mRNA showed the induction of apoptosis and oxidative stress, respectively. The mtDNA content did not correlate with any other mitochondrial parameter. In conclusion, mtDNA content does not appear to be an accurate biomarker of mitochondrial alteration in lipoatrophic adipose tissue. The preservation of mtDNA-dependent mitochondrial functions occurred despite severe mtDNA depletion. The presence of significant oxidative stress and apoptosis did not correlate with the mtDNA content. PMID

  3. DNA Sequencing Sensors: An Overview

    PubMed Central

    Garrido-Cardenas, Jose Antonio; Garcia-Maroto, Federico; Alvarez-Bermejo, Jose Antonio; Manzano-Agugliaro, Francisco

    2017-01-01

    The first sequencing of a complete genome was published forty years ago by the double Nobel Prize in Chemistry winner Frederick Sanger. That corresponded to the small sized genome of a bacteriophage, but since then there have been many complex organisms whose DNA have been sequenced. This was possible thanks to continuous advances in the fields of biochemistry and molecular genetics, but also in other areas such as nanotechnology and computing. Nowadays, sequencing sensors based on genetic material have little to do with those used by Sanger. The emergence of mass sequencing sensors, or new generation sequencing (NGS) meant a quantitative leap both in the volume of genetic material that was able to be sequenced in each trial, as well as in the time per run and its cost. One can envisage that incoming technologies, already known as fourth generation sequencing, will continue to cheapen the trials by increasing DNA reading lengths in each run. All of this would be impossible without sensors and detection systems becoming smaller and more precise. This article provides a comprehensive overview on sensors for DNA sequencing developed within the last 40 years. PMID:28335417

  4. Statistical properties of DNA sequences

    NASA Technical Reports Server (NTRS)

    Peng, C. K.; Buldyrev, S. V.; Goldberger, A. L.; Havlin, S.; Mantegna, R. N.; Simons, M.; Stanley, H. E.

    1995-01-01

    We review evidence supporting the idea that the DNA sequence in genes containing non-coding regions is correlated, and that the correlation is remarkably long range--indeed, nucleotides thousands of base pairs distant are correlated. We do not find such a long-range correlation in the coding regions of the gene. We resolve the problem of the "non-stationarity" feature of the sequence of base pairs by applying a new algorithm called detrended fluctuation analysis (DFA). We address the claim of Voss that there is no difference in the statistical properties of coding and non-coding regions of DNA by systematically applying the DFA algorithm, as well as standard FFT analysis, to every DNA sequence (33301 coding and 29453 non-coding) in the entire GenBank database. Finally, we describe briefly some recent work showing that the non-coding sequences have certain statistical features in common with natural and artificial languages. Specifically, we adapt to DNA the Zipf approach to analyzing linguistic texts. These statistical properties of non-coding sequences support the possibility that non-coding regions of DNA may carry biological information.

  5. Neandertal DNA sequences and the origin of modern humans.

    PubMed

    Krings, M; Stone, A; Schmitz, R W; Krainitzki, H; Stoneking, M; Pääbo, S

    1997-07-11

    DNA was extracted from the Neandertal-type specimen found in 1856 in western Germany. By sequencing clones from short overlapping PCR products, a hitherto unknown mitochondrial (mt) DNA sequence was determined. Multiple controls indicate that this sequence is endogenous to the fossil. Sequence comparisons with human mtDNA sequences, as well as phylogenetic analyses, show that the Neandertal sequence falls outside the variation of modern humans. Furthermore, the age of the common ancestor of the Neandertal and modern human mtDNAs is estimated to be four times greater than that of the common ancestor of human mtDNAs. This suggests that Neandertals went extinct without contributing mtDNA to modern humans.

  6. A genome-wide map of mitochondrial DNA recombination in yeast.

    PubMed

    Fritsch, Emilie S; Chabbert, Christophe D; Klaus, Bernd; Steinmetz, Lars M

    2014-10-01

    In eukaryotic cells, the production of cellular energy requires close interplay between nuclear and mitochondrial genomes. The mitochondrial genome is essential in that it encodes several genes involved in oxidative phosphorylation. Each cell contains several mitochondrial genome copies and mitochondrial DNA recombination is a widespread process occurring in plants, fungi, protists, and invertebrates. Saccharomyces cerevisiae has proved to be an excellent model to dissect mitochondrial biology. Several studies have focused on DNA recombination in this organelle, yet mostly relied on reporter genes or artificial systems. However, no complete mitochondrial recombination map has been released for any eukaryote so far. In the present work, we sequenced pools of diploids originating from a cross between two different S. cerevisiae strains to detect recombination events. This strategy allowed us to generate the first genome-wide map of recombination for yeast mitochondrial DNA. We demonstrated that recombination events are enriched in specific hotspots preferentially localized in non-protein-coding regions. Additionally, comparison of the recombination profiles of two different crosses showed that the genetic background affects hotspot localization and recombination rates. Finally, to gain insights into the mechanisms involved in mitochondrial recombination, we assessed the impact of individual depletion of four genes previously associated with this process. Deletion of NTG1 and MGT1 did not substantially influence the recombination landscape, alluding to the potential presence of additional regulatory factors. Our findings also revealed the loss of large mitochondrial DNA regions in the absence of MHR1, suggesting a pivotal role for Mhr1 in mitochondrial genome maintenance during mating. This study provides a comprehensive overview of mitochondrial DNA recombination in yeast and thus paves the way for future mechanistic studies of mitochondrial recombination and genome

  7. Differentiation of mitochondrial DNA and Y chromosomes in Russian populations.

    PubMed

    Malyarchuk, Boris; Derenko, Miroslava; Grzybowski, Tomasz; Lunkina, Arina; Czarny, Jakub; Rychkov, Serge; Morozova, Irina; Denisova, Galina; Miścicka-Sliwka, Danuta

    2004-12-01

    The genetic composition of the Russian population was investigated by analyzing both mitochondrial DNA (mtDNA) and Y-chromosome loci polymorphisms that allow for the different components of a population gene pool to be studied, depending on the mode of DNA marker inheritance. mtDNA sequence variation was examined by using hypervariable segment I (HVSI) sequencing and restriction analysis of the haplogroup-specific sites in 325 individuals representing 5 Russian populations from the European part of Russia. The Y-chromosome variation was investigated in 338 individuals from 8 Russian populations (including 5 populations analyzed for mtDNA variation) using 12 binary markers. For both uniparental systems most of the observed haplogroups fell into major West Eurasian haplogroups (97.9% and 99.7% for mtDNA and Y-chromosome haplogroups, respectively). Multidimensional scaling analysis based on pairwise F(ST) values between mtDNA HVSI sequences in Russians compared to other European populations revealed a considerable heterogeneity of Russian populations; populations from the southern and western parts of Russia are separated from eastern and northern populations. Meanwhile, the multidimensional scaling analysis based on Y-chromosome haplogroup F(ST) values demonstrates that the Russian gene pool is close to central-eastern European populations, with a much higher similarity to the Baltic and Finno-Ugric male pools from northern European Russia. This discrepancy in the depth of penetration of mtDNA and Y-chromosome lineages characteristic for the most southwestern Russian populations into the east and north of eastern Europe appears to indicate that Russian colonization of the northeastern territories might have been accomplished mainly by males rather than by females.

  8. Mitochondrial DNA phylogeography of least cisco Coregonus sardinella in Alaska.

    PubMed

    Padula, V M; Causey, D; López, J A

    2017-03-01

    This study presents the first detailed analysis of the mitochondrial DNA diversity of least cisco Coregonus sardinella in Alaska using a 678 bp segment of the control region (D-loop) of the mitochondrial genome. Findings suggest that the history of C. sardinella in Alaska differs from that of other species of Coregonus present in the state and surrounding regions. The examined populations of C. sardinella are genetically diverse across Alaska. Sixty-eight distinct mitochondrial haplotypes were identified among 305 individuals sampled from nine locations. The haplotype minimum spanning network and phylogeny showed a modest level of geographic segregation among haplotypes, suggesting high levels of on-going or recent connectivity among distant populations. Observed ΦST values and the results of homogeneity and AMOVAs indicate incipient genetic differentiation between aggregations in three broad regional groups. Sites north of the Brooks Range formed one group, sites in the Yukon and Selawik Rivers formed a second group and sites south of the Yukon drainage formed the third group. Overall, the sequence data showed that a large proportion of mtDNA genetic variation in C. sardinella is shared across Alaska, but this variation is not homogeneously distributed across all regions and for all haplotype groups.

  9. Phylogenetic divisions among Collared peccaries (Pecari tajacu) detected using mitochondrial and nuclear sequences.

    PubMed

    Gongora, Jaime; Morales, Socorro; Bernal, Jaime Eduardo; Moran, Chris

    2006-10-01

    The Collared peccary (Pecari tajacu) is one of the three extant recognised species of the family Tayassuidae, living in the Americas. To understand phylogenetic relationships among Collared peccaries, the entire mitochondrial DNA control region and cytochrome b as well as partial nuclear GPIP and PRE-1 P27, PRE-1 P642 and TYR sequences from specimens from Colombia, Argentina, Bolivia, Mexico, United States and Australian zoo animals of unknown origin were analysed. Separate and combined analyses of the mitochondrial sequences provided good resolution of Collared peccary relationships. Nuclear sequences were partially informative when combined sequence analyses were performed. Maximum Likelihood analyses of mitochondrial sequences showed that Collared peccaries clustered in two major clades, representing North-Central American and South American specimens. Collared peccaries from Colombia are paraphyletic. Statistical Parsimony analysis of combined nuclear sequences showed a distribution of DNA variants consistent with mitochondrial sequence analyses. However, there is an uncoupling of nuclear and mitochondrial sequence variation in two specimens from Colombia. The present study suggests the recent contact of isolated populations within Colombia and possible mitochondrial introgression between the North/Central clade and the South clade. Pairwise genetic distances comparison of mitochondrial sequences show that divergence between the two major clades of the Collared peccary was higher and comparable respectively with that within and between the other two recognised peccary species. Divergence between the two major clades of the Collared peccary was also higher than that observed within and even between recognised species of the Suidae family. The divergence within the major clades of the Collared peccary showed comparable values with those observed within the other two species of Tayassuidae and within six species of Suidae. The results show that the geographically

  10. Acceptance of Domestic Cat Mitochondrial DNA in a Criminal Proceeding

    PubMed Central

    Lyons, Leslie A.; Grahn, Robert A.; Kun, Teri J.; Netzel, Linda R.; Wictum, Elizabeth E.; Halverson, Joy L.

    2014-01-01

    Shed hair from domestic animals readily adheres to clothing and other contact items, providing a source of transfer evidence for criminal investigations. Mitochondrial DNA is often the only option for DNA analysis of shed hair. Human mitochondrial DNA analysis has been accepted in the US court system since 1996. The murder trial of the State of Missouri versus Henry L. Polk, Jr. represents the first legal proceeding where cat mitochondrial DNA analysis was introduced into evidence. The mitochondrial DNA evidence was initially considered inadmissible due to concerns about the cat dataset and the scientific acceptance of the marker. Those concerns were subsequently addressed, and the evidence was deemed admissible. This report reviews the case in regards to the cat biological evidence and its ultimate admission as generally accepted and reliable. Expansion and saturation analysis of the cat mitochondrial DNA control region dataset supported the initial interpretation of the evidence. PMID:25086413

  11. Acceptance of domestic cat mitochondrial DNA in a criminal proceeding.

    PubMed

    Lyons, Leslie A; Grahn, Robert A; Kun, Teri J; Netzel, Linda R; Wictum, Elizabeth E; Halverson, Joy L

    2014-11-01

    Shed hair from domestic animals readily adheres to clothing and other contact items, providing a source of transfer evidence for criminal investigations. Mitochondrial DNA is often the only option for DNA analysis of shed hair. Human mitochondrial DNA analysis has been accepted in the US court system since 1996. The murder trial of the State of Missouri versus Henry L. Polk, Jr. represents the first legal proceeding where cat mitochondrial DNA analysis was introduced into evidence. The mitochondrial DNA evidence was initially considered inadmissible due to concerns about the cat dataset and the scientific acceptance of the marker. Those concerns were subsequently addressed, and the evidence was deemed admissible. This report reviews the case in regards to the cat biological evidence and its ultimate admission as generally accepted and reliable. Expansion and saturation analysis of the cat mitochondrial DNA control region dataset supported the initial interpretation of the evidence.

  12. Irc3 is a mitochondrial DNA branch migration enzyme

    PubMed Central

    Gaidutšik, Ilja; Sedman, Tiina; Sillamaa, Sirelin; Sedman, Juhan

    2016-01-01

    Integrity of mitochondrial DNA (mtDNA) is essential for cellular energy metabolism. In the budding yeast Saccharomyces cerevisiae, a large number of nuclear genes influence the stability of mitochondrial genome; however, most corresponding gene products act indirectly and the actual molecular mechanisms of mtDNA inheritance remain poorly characterized. Recently, we found that a Superfamily II helicase Irc3 is required for the maintenance of mitochondrial genome integrity. Here we show that Irc3 is a mitochondrial DNA branch migration enzyme. Irc3 modulates mtDNA metabolic intermediates by preferential binding and unwinding Holliday junctions and replication fork structures. Furthermore, we demonstrate that the loss of Irc3 can be complemented with mitochondrially targeted RecG of Escherichia coli. We suggest that Irc3 could support the stability of mtDNA by stimulating fork regression and branch migration or by inhibiting the formation of irregular branched molecules. PMID:27194389

  13. Impaired mitochondrial respiration and decreased fatigue resistance followed by severe muscle weakness in skeletal muscle of mitochondrial DNA mutator mice.

    PubMed

    Yamada, Takashi; Ivarsson, Niklas; Hernández, Andrés; Fahlström, Andreas; Cheng, Arthur J; Zhang, Shi-Jin; Bruton, Joseph D; Ulfhake, Brun; Westerblad, Håkan

    2012-12-01

    Mitochondrial dysfunction can drastically impair muscle function, with weakness and exercise intolerance as key symptoms. Here we examine the time course of development of muscle dysfunction in a mouse model of premature ageing induced by defective proofreading function of mitochondrial DNA (mtDNA) polymerase (mtDNA mutator mouse). Isolated fast-twitch muscles and single muscle fibres from young (3-5 months) and end-stage (11 months) mtDNA mutator mice were compared to age-matched control mice. Force and free myoplasmic [Ca(2+)] ([Ca(2+)](i)) were measured under resting conditions and during fatigue induced by repeated tetani. Muscles of young mtDNA mutator mice displayed no weakness in the rested state, but had lower force and [Ca(2+)](i) than control mice during induction of fatigue. Muscles of young mtDNA mutator mice showed decreased activities of citrate synthase and β-hydroxyacyl-coenzyme A dehydrogenase, reduced expression of cytochrome c oxidase, and decreased expression of triggers of mitochondrial biogenesis (PGC-1α, PPARα, AMPK). Muscles from end-stage mtDNA mutator mice showed weakness under resting conditions with markedly decreased tetanic [Ca(2+)](i), force per cross-sectional area and protein expression of the sarcoplasmic reticulum Ca(2+) pump (SERCA1). In conclusion, fast-twitch muscles of prematurely ageing mtDNA mutator mice display a sequence of deleterious mitochondrial-to-nucleus signalling with an initial decrease in oxidative capacity, which was not counteracted by activation of signalling to increase mitochondrial biogenesis. This was followed by severe muscle weakness in the end stage. These results have implication for normal ageing and suggest that decreased mitochondrial oxidative capacity due to a sedentary lifestyle may predispose towards muscle weakness developing later in life.

  14. Urinary mitochondrial DNA is a biomarker of mitochondrial disruption and renal dysfunction in acute kidney injury

    PubMed Central

    Whitaker, Ryan M.; Stallons, L. Jay; Kneff, Joshua E.; Alge, Joseph L.; Harmon, Jennifer L.; Rahn, Jennifer J.; Arthur, John M.; Beeson, Craig C.; Chan, Sherine L.; Schnellmann, Rick G.

    2015-01-01

    Recent studies show the importance of mitochondrial dysfunction in the initiation and progression of acute kidney injury (AKI). However, no biomarkers exist linking renal injury to mitochondrial function and integrity. To this end, we evaluated urinary mitochondrial DNA (UmtDNA) as a biomarker of renal injury and function in humans with AKI following cardiac surgery. mtDNA was isolated from the urine of patients following cardiac surgery and quantified by qPCR. Patients were stratified into no AKI, stable AKI and progressive AKI groups based on Acute Kidney Injury Network (AKIN) staging. UmtDNA was elevated in progressive AKI patients, and was associated with progression of patients with AKI at collection to higher AKIN stages. To evaluate the relationship of UmtDNA to measures of renal mitochondrial integrity in AKI, mice were subjected to sham surgery or varying degrees of ischemia followed by 24 hours of reperfusion. UmtDNA increased in mice after 10-15 minutes of ischemia and positively correlated with ischemia time. Furthermore, UmtDNA was predictive of AKI in the mouse model. Finally, UmtDNA levels were negatively correlated with renal cortical mtDNA and mitochondrial gene expression. These translational studies demonstrate that UmtDNA is associated with recovery from AKI following cardiac surgery by serving as an indicator of mitochondrial integrity. Thus, UmtDNA may serve as valuable biomarker for the development of mitochondrial targeted therapies in AKI. PMID:26287315

  15. Genetics Home Reference: MPV17-related hepatocerebral mitochondrial DNA depletion syndrome

    MedlinePlus

    ... mitochondrial DNA depletion syndrome MPV17-related hepatocerebral mitochondrial DNA depletion syndrome Enable Javascript to view the expand/ ... All Close All Description MPV17 -related hepatocerebral mitochondrial DNA depletion syndrome is an inherited disorder that can ...

  16. Mitochondrial DNA polymorphisms associated with longevity in the Turkish population.

    PubMed

    Guney, Ozgur; Ak, Handan; Atay, Sevcan; Ozkaya, Ali Burak; Aydin, Hikmet Hakan

    2014-07-01

    The accumulation of mutations in mitochondrial DNA is a widely recognized mechanism for aging and age related diseases. However, studies indicate that some mutations could be beneficial to longevity by slowing down the function of the electron transport chain, reducing free radical production. In this study, we re-sequenced the entire mitochondrial DNA from 50 individuals and examined aging-related variations in the Turkish population. We evaluated sequence data by comparing whole SNP frequencies, individual SNP frequencies, the effect of SNPs, SNP accumulation in certain mtDNA regions and haplotype profiles between elderly and control groups. The frequency of total mitochondrial SNPs was significantly higher in nonagenarians than controls (p=0.0094). Furthermore, non-coding, synonymous and tRNA mutations were more prevalent in the 90+ group compared to controls (p=0.0001, p<0.001, p=0.0096, respectively). A73G and C152T polymorphisms were significantly associated with longevity in the Turkish population (p=0.0086 and p=0.004, respectively). Additionally, C150T was specific to the 90+ group, but the difference failed to reach statistical significance (p=0.053). We also detected a novel transversion in the ATPase6 gene (C8899A) that was negatively associated with longevity (p=0.0016). Examining the distribution of SNPs among genes and functionally associated gene regions revealed a significant accumulation of mutations in the D-loop region and genes encoding Complex I subunits (ND1-6) (p<0.0001, p=0.0302, respectively). Moreover, there was an increase in the non-synonymous mutation frequency of Complex I genes in aged subjects (p<0.0001). Haplotype H was also significantly increased in the control group (p=0.0405). Overall, our findings support a role for mitochondrial genome variations and the functionality of oxidative phosphorylation in longevity. In this report, we sequenced the whole mtDNA of the Turkish population for the first time.

  17. Mitochondrial DNA: impacting central and peripheral nervous systems

    PubMed Central

    Carelli, Valerio

    2014-01-01

    Because of their high-energy metabolism, neurons are highly dependent on mitochondria, which generate cellular ATP through oxidative phosphorylation. The mitochondrial genome encodes for critical components of the oxidative phosphorylation pathway machinery, and therefore mutations in mitochondrial DNA (mtDNA) cause energy production defects that frequently have severe neurological manifestations. Here, we review the principles of mitochondrial genetics and focus on prototypical mitochondrial diseases to illustrate how primary defects in mtDNA or secondary defects in mtDNA due to nuclear genome mutations can cause prominent neurological and multisystem features. In addition, we discuss the pathophysiological mechanisms underlying mitochondrial diseases, the cellular mechanisms that protect mitochondrial integrity, and the prospects for therapy. PMID:25521375

  18. The little big genome: the organization of mitochondrial DNA

    PubMed Central

    Garcia, Iraselia; Jones, Edith; Ramos, Manuel; Innis-Whitehouse, Wendy; Gilkerson, Robert

    2017-01-01

    The small (16,569 base pair) human mitochondrial genome plays a significant role in cell metabolism and homeostasis. Mitochondrial DNA (mtDNA) contributes to the generation of complexes which are essential to oxidative phosphorylation (OXPHOS). As such, mtDNA is directly integrated into mitochondrial biogenesis and signaling and regulates mitochondrial metabolism in concert with nuclear-encoded mitochondrial factors. Mitochondria are a highly dynamic, pleiomorphic network that undergoes fission and fusion events. Within this network, mtDNAs are packaged into structures called nucleoids which are actively distributed in discrete foci within the network. This sensitive organelle is frequently disrupted by insults such as oxidants and inflammatory cytokines, and undergoes genomic damage with double- and single-strand breaks that impair its function. Collectively, mtDNA is emerging as a highly sensitive indicator of cellular stress, which is directly integrated into the mitochondrial network as a contributor of a wide range of critical signaling pathways. PMID:27814641

  19. Commentary: Mitochondrial DNA damage and loss in diabetes

    PubMed Central

    Gilkerson, Robert

    2017-01-01

    This commentary discusses damage and loss of mitochondrial DNA (mtDNA) in type 2 diabetes mellitus from both the clinical and experimental perspectives. Increasingly, an array of studies in experimental models and patients suggests that the cellular stresses of insulin resistance in type 2 diabetes damage mtDNA, leading to loss of mitochondrial genetic content. As such, mtDNA is emerging as both a valuable monitoring tool and translational preventive target for metabolic disease. PMID:27253402

  20. Mitochondrial DNA affinity of several Jewish communities.

    PubMed

    Ritte, U; Neufeld, E; Prager, E M; Gross, M; Hakim, I; Khatib, A; Bonné-Tamir, B

    1993-06-01

    The mitochondrial DNA (mtDNA) of 332 individuals from Israel, including 270 Jews (originating from 7 communities) and 62 Arabs, was analyzed. Each mtDNA haplotype was determined by the fragment patterns of restriction enzymes HpaI, BamHI, HaeII, MspI (HpaII), and AvaII. The variability of the total sample and of each community was high. Of 40 different haplotypes, 20 were found more than once. Most haplotypes are typical of Caucasians, but African types were found among Ethiopian Jews and to a lesser extent among Arabs. The communities differed in their haplotypes: Chi-square tests among six communities showed significant differences for most pairwise comparisons and nonsignificant differences involving mainly the Moroccan Jews. In a genetic distance analysis only the Ethiopian Jews appeared to be distinguished from the other communities. According to a GST analysis, approximately 30% of the variation among the mtDNA restriction maps is attributable to differences between communities.

  1. The past, present and future of mitochondrial genomics: have we sequenced enough mtDNAs?

    PubMed Central

    2016-01-01

    The year 2014 saw more than a thousand new mitochondrial genome sequences deposited in GenBank—an almost 15% increase from the previous year. Hundreds of peer-reviewed articles accompanied these genomes, making mitochondrial DNAs (mtDNAs) the most sequenced and reported type of eukaryotic chromosome. These mtDNA data have advanced a wide range of scientific fields, from forensics to anthropology to medicine to molecular evolution. But for many biological lineages, mtDNAs are so well sampled that newly published genomes are arguably no longer contributing significantly to the progression of science, and in some cases they are tying up valuable resources, particularly journal editors and referees. Is it time to acknowledge that as a research community we have published enough mitochondrial genome papers? Here, I address this question, exploring the history, milestones and impacts of mitochondrial genomics, the benefits and drawbacks of continuing to publish mtDNAs at a high rate and what the future may hold for such an important and popular genetic marker. I highlight groups for which mtDNAs are still poorly sampled, thus meriting further investigation, and recommend that more energy be spent characterizing aspects of mitochondrial genomes apart from the DNA sequence, such as their chromosomal and transcriptional architectures. Ultimately, one should be mindful before writing a mitochondrial genome paper. Consider perhaps sending the sequence directly to GenBank instead, and be sure to annotate it correctly before submission. PMID:26117139

  2. Structural Complexity of DNA Sequence

    PubMed Central

    Liou, Cheng-Yuan; Cheng, Wei-Chen; Tsai, Huai-Ying

    2013-01-01

    In modern bioinformatics, finding an efficient way to allocate sequence fragments with biological functions is an important issue. This paper presents a structural approach based on context-free grammars extracted from original DNA or protein sequences. This approach is radically different from all those statistical methods. Furthermore, this approach is compared with a topological entropy-based method for consistency and difference of the complexity results. PMID:23662161

  3. Natural radioactivity and human mitochondrial DNA mutations

    PubMed Central

    Forster, Lucy; Forster, Peter; Lutz-Bonengel, Sabine; Willkomm, Horst; Brinkmann, Bernd

    2002-01-01

    Radioactivity is known to induce tumors, chromosome lesions, and minisatellite length mutations, but its effects on the DNA sequence have not previously been studied. A coastal peninsula in Kerala (India) contains the world's highest level of natural radioactivity in a densely populated area, offering an opportunity to characterize radiation-associated DNA mutations. We sampled 248 pedigrees (988 individuals) in the high-radiation peninsula and in nearby low-radiation islands as a control population. We sequenced their mtDNA, and found that the pedigrees living in the high-radiation area have significantly (P < 0.01) increased germ-line point mutations between mothers and their offspring. In each mutation case, we confirmed maternity by autosomal profiling. Strikingly, the radioactive conditions accelerate mutations at nucleotide positions that have been evolutionary hot spots for at least 60,000 years. PMID:12370437

  4. The potential role for use of mitochondrial DNA copy number as predictive biomarker in presbycusis

    PubMed Central

    Falah, Masoumeh; Houshmand, Massoud; Najafi, Mohammad; Balali, Maryam; Mahmoudian, Saeid; Asghari, Alimohamad; Emamdjomeh, Hessamaldin; Farhadi, Mohammad

    2016-01-01

    Objectives Age-related hearing impairment, or presbycusis, is the most common communication disorder and neurodegenerative disease in the elderly. Its prevalence is expected to increase, due to the trend of growth of the elderly population. The current diagnostic test for detection of presbycusis is implemented after there has been a change in hearing sensitivity. Identification of a pre-diagnostic biomarker would raise the possibility of preserving hearing sensitivity before damage occurs. Mitochondrial dysfunction, including the production of reactive oxygen species and induction of expression of apoptotic genes, participates in the progression of presbycusis. Mitochondrial DNA sequence variation has a critical role in presbycusis. However, the nature of the relationship between mitochondrial DNA copy number, an important biomarker in many other diseases, and presbycusis is undetermined. Methods Fifty-four subjects with presbycusis and 29 healthy controls were selected after ear, nose, throat examination and pure-tone audiometry. DNA was extracted from peripheral blood samples. The copy number of mitochondrial DNA relative to the nuclear genome was measured by quantitative real-time polymerase chain reaction. Results Subjects with presbycusis had a lower median mitochondrial DNA copy number than healthy subjects and the difference was statistically significant (P=0.007). Mitochondrial DNA copy number was also significantly associated with degree of hearing impairment (P=0.025) and audiogram configuration (P=0.022). Conclusion The findings of this study suggest that lower mitochondrial DNA copy number is responsible for presbycusis through alteration of mitochondrial function. Moreover, the significant association of mitochondrial DNA copy number in peripheral blood samples with the degree of hearing impairment and audiogram configuration has potential for use as a standard test for presbycusis, providing the possibility of the development of an easy

  5. The complete sequence of the mitochondrial genome of the African Penguin (Spheniscus demersus).

    PubMed

    Labuschagne, Christiaan; Kotzé, Antoinette; Grobler, J Paul; Dalton, Desiré L

    2014-01-15

    The complete mitochondrial genome of the African Penguin (Spheniscus demersus) was sequenced. The molecule was sequenced via next generation sequencing and primer walking. The size of the genome is 17,346 bp in length. Comparison with the mitochondrial DNA of two other penguin genomes that have so far been reported was conducted namely; Little blue penguin (Eudyptula minor) and the Rockhopper penguin (Eudyptes chrysocome). This analysis made it possible to identify common penguin mitochondrial DNA characteristics. The S. demersus mtDNA genome is very similar, both in composition and length to both the E. chrysocome and E. minor genomes. The gene content of the African penguin mitochondrial genome is typical of vertebrates and all three penguin species have the standard gene order originally identified in the chicken. The control region for S. demersus is located between tRNA-Glu and tRNA-Phe and all three species of penguins contain two sets of similar repeats with varying copy numbers towards the 3' end of the control region, accounting for the size variance. This is the first report of the complete nucleotide sequence for the mitochondrial genome of the African penguin, S. demersus. These results can be subsequently used to provide information for penguin phylogenetic studies and insights into the evolution of genomes.

  6. The Mitochondrial DNA Polymerase in Health and Disease

    PubMed Central

    Copeland, William C.

    2014-01-01

    Since mutations in mitochondrial DNA (MtDNA) have been shown to be a cause of many mitochondrial diseases as well as aging, it is important to understand the origin of these mutations and how replication proteins modulate this process. DNA polymerase γ (pol γ) is the polymease that is responsible for replication and repair of mtDNA. Pol γ has three main roles in mtDNA maintanence and mutagenesis. As the only known DNA polymerase in mitochondria, pol γ is required for all replication and repair functions and is the main source of errors produced in our mtDNA. Pol γ is also sensitive to a host of antiviral nucleoside analogs used to treat HIV-1 infections, which can cause an induced mitochondrial toxicity. Finally, the gene for pol γ, POLG, is a genetic locus for several mitochondrial disease with over 150 genetic mutations currently identified. PMID:20012584

  7. Mitochondrial DNA of ancient Cumanians: culturally Asian steppe nomadic immigrants with substantially more western Eurasian mitochondrial DNA lineages.

    PubMed

    Bogácsi-Szabó, Erika; Kalmár, Tibor; Csányi, Bernadett; Tömöry, Gyöngyvér; Czibula, Agnes; Priskin, Katalin; Horváth, Ferenc; Downes, Christopher Stephen; Raskó, István

    2005-10-01

    The Cumanians were originally Asian pastoral nomads who in the 13th century migrated to Hungary. We have examined mitochondrial DNA from members of the earliest Cumanian population in Hungary from two archeologically well-documented excavations and from 74 modern Hungarians from different rural locations in Hungary. Haplogroups were defined based on HVS I sequences and examinations of haplogroup-associated polymorphic sites of the protein coding region and of HVS II. To exclude contamination, some ancient DNA samples were cloned. A database was created from previously published mtDNA HVS I sequences (representing 2,615 individuals from different Asian and European populations) and 74 modem Hungarian sequences from the present study. This database was used to determine the relationships between the ancient Cumanians, modern Hungarians, and Eurasian populations and to estimate the genetic distances between these populations. We attempted to deduce the genetic trace of the migration of Cumanians. This study is the first ancient DNA characterization of an eastern pastoral nomad population that migrated into Europe. The results indicate that, while still possessing a Central Asian steppe culture, the Cumanians received a large admixture of maternal genes from more westerly populations before arriving in Hungary. A similar dilution of genetic, but not cultural, factors may have accompanied the settlement of other Asian nomads in Europe.

  8. Mitochondrial DNA variation of domestic sheep (Ovis aries) in Kenya.

    PubMed

    Resende, Adriana; Gonçalves, Joana; Muigai, Anne W T; Pereira, Filipe

    2016-06-01

    The history of domestic sheep (Ovis aries) in Africa remains largely unknown. After being first introduced from the Near East, sheep gradually spread through the African continent with pastoral societies. The eastern part of Africa was important either for the first diffusion of sheep southward or for putative secondary introductions from the Arabian Peninsula or southern Asia. We analysed mitochondrial DNA control region sequences of 91 domestic sheep from Kenya and found a high diversity of matrilines from the widespread haplogroup B, whereas only a single individual from haplogroup A was detected. Our phylogeography analyses of more than 500 available mitochondrial DNA sequences also identified ancestral haplotypes that were probably first introduced in Africa and are now widely distributed. Moreover, we found no evidence of an admixture between East and West African sheep. The presence of shared haplotypes in eastern and ancient southern African sheep suggests the possible southward movement of sheep along the eastern part of Africa. Finally, we found no evidence of an extensive introduction of sheep from southern Asia into Africa via the Indian Ocean trade. The overall findings on the phylogeography of East African domestic sheep set the grounds for understanding the origin and subsequent movements of sheep in Africa. The richness of maternal lineages in Kenyan breeds is of prime importance for future conservation and breeding programmes.

  9. Base composition at mtDNA boundaries suggests a DNA triple helix model for human mitochondrial DNA large-scale rearrangements.

    PubMed

    Rocher, Christophe; Letellier, Thierry; Copeland, William C; Lestienne, Patrick

    2002-06-01

    Different mechanisms have been proposed to account for mitochondrial DNA (mtDNA) instability based on the presence of short homologous sequences (direct repeats, DR) at the potential boundaries of mtDNA rearrangements. Among them, slippage-mispairing of the replication complex during the asymmetric replication cycle of the mammalian mitochondrial DNA has been proposed to account for the preferential localization of deletions. This mechanism involves a transfer of the replication complex from the first neo-synthesized heavy (H) strand of the DR1, to the DR2, thus bypassing the intervening sequence and producing a deleted molecule. Nevertheless, the nature of the bonds between the DNA strands remains unknown as the forward sequence of DR2, beyond the replication complex, stays double-stranded. Here, we have analyzed the base composition of the DR at the boundaries of mtDNA deletions and duplications and found a skewed pyrimidine content of about 75% in the light-strand DNA template. This suggests the possible building of a DNA triple helix between the G-rich neo-synthesized DR1 and the base-paired homologous G.C-rich DR2. In vitro experiments with the purified human DNA polymerase gamma subunits enabled us to show that the third DNA strand may be used as a primer for DNA replication, using a template with the direct repeat forming a hairpin, with which the primer could initiate DNA replication. These data suggest a novel molecular basis for mitochondrial DNA rearrangements through the distributive nature of the DNA polymerase gamma, at the level of the direct repeats. A general model accounting for large-scale mitochondrial DNA deletion and duplication is proposed. These experiments extend to a DNA polymerase from an eucaryote source the use of a DNA triple helix strand as a primer, like other DNA polymerases from phage and bacterial origins.

  10. Ancient mtDNA sequences from the First Australians revisited

    PubMed Central

    Subramanian, Sankar; Wright, Joanne L.; Endicott, Phillip; Westaway, Michael Carrington; Huynen, Leon; Parson, Walther; Millar, Craig D.; Willerslev, Eske; Lambert, David M.

    2016-01-01

    The publication in 2001 by Adcock et al. [Adcock GJ, et al. (2001) Proc Natl Acad Sci USA 98(2):537–542] in PNAS reported the recovery of short mtDNA sequences from ancient Australians, including the 42,000-y-old Mungo Man [Willandra Lakes Hominid (WLH3)]. This landmark study in human ancient DNA suggested that an early modern human mitochondrial lineage emerged in Asia and that the theory of modern human origins could no longer be considered solely through the lens of the “Out of Africa” model. To evaluate these claims, we used second generation DNA sequencing and capture methods as well as PCR-based and single-primer extension (SPEX) approaches to reexamine the same four Willandra Lakes and Kow Swamp 8 (KS8) remains studied in the work by Adcock et al. Two of the remains sampled contained no identifiable human DNA (WLH15 and WLH55), whereas the Mungo Man (WLH3) sample contained no Aboriginal Australian DNA. KS8 reveals human mitochondrial sequences that differ from the previously inferred sequence. Instead, we recover a total of five modern European contaminants from Mungo Man (WLH3). We show that the remaining sample (WLH4) contains ∼1.4% human DNA, from which we assembled two complete mitochondrial genomes. One of these was a previously unidentified Aboriginal Australian haplotype belonging to haplogroup S2 that we sequenced to a high coverage. The other was a contaminating modern European mitochondrial haplotype. Although none of the sequences that we recovered matched those reported by Adcock et al., except a contaminant, these findings show the feasibility of obtaining important information from ancient Aboriginal Australian remains. PMID:27274055

  11. Ancient mtDNA sequences from the First Australians revisited.

    PubMed

    Heupink, Tim H; Subramanian, Sankar; Wright, Joanne L; Endicott, Phillip; Westaway, Michael Carrington; Huynen, Leon; Parson, Walther; Millar, Craig D; Willerslev, Eske; Lambert, David M

    2016-06-21

    The publication in 2001 by Adcock et al. [Adcock GJ, et al. (2001) Proc Natl Acad Sci USA 98(2):537-542] in PNAS reported the recovery of short mtDNA sequences from ancient Australians, including the 42,000-y-old Mungo Man [Willandra Lakes Hominid (WLH3)]. This landmark study in human ancient DNA suggested that an early modern human mitochondrial lineage emerged in Asia and that the theory of modern human origins could no longer be considered solely through the lens of the "Out of Africa" model. To evaluate these claims, we used second generation DNA sequencing and capture methods as well as PCR-based and single-primer extension (SPEX) approaches to reexamine the same four Willandra Lakes and Kow Swamp 8 (KS8) remains studied in the work by Adcock et al. Two of the remains sampled contained no identifiable human DNA (WLH15 and WLH55), whereas the Mungo Man (WLH3) sample contained no Aboriginal Australian DNA. KS8 reveals human mitochondrial sequences that differ from the previously inferred sequence. Instead, we recover a total of five modern European contaminants from Mungo Man (WLH3). We show that the remaining sample (WLH4) contains ∼1.4% human DNA, from which we assembled two complete mitochondrial genomes. One of these was a previously unidentified Aboriginal Australian haplotype belonging to haplogroup S2 that we sequenced to a high coverage. The other was a contaminating modern European mitochondrial haplotype. Although none of the sequences that we recovered matched those reported by Adcock et al., except a contaminant, these findings show the feasibility of obtaining important information from ancient Aboriginal Australian remains.

  12. Apparatus for improved DNA sequencing

    DOEpatents

    Douthart, Richard J.; Crowell, Shannon L.

    1996-01-01

    This invention is a means for the rapid sequencing of DNA samples. More specifically, it consists of a new design direct blotting electrophoresis unit. The DNA sequence is deposited on a membrane attached to a rotating drum. Initial data compaction is facilitated by the use of a machined multi-channeled plate called a ribbon channel plate. Each channel is an isolated mini gel system much like a gel filled capillary. The system as a whole, however, is in a slab gel like format with the advantages of uniformity and easy reusability. The system can be used in different embodiments. The drum system is unique in that after deposition the drum rotates the deposited DNA into a large non-buffer open space where processing and detection can occur. The drum can also be removed in toto to special workstations for downstream processing, multiplexing and detection.

  13. Apparatus for improved DNA sequencing

    DOEpatents

    Douthart, R.J.; Crowell, S.L.

    1996-05-07

    This invention is a means for the rapid sequencing of DNA samples. More specifically, it consists of a new design direct blotting electrophoresis unit. The DNA sequence is deposited on a membrane attached to a rotating drum. Initial data compaction is facilitated by the use of a machined multi-channeled plate called a ribbon channel plate. Each channel is an isolated mini gel system much like a gel filled capillary. The system as a whole, however, is in a slab gel like format with the advantages of uniformity and easy reusability. The system can be used in different embodiments. The drum system is unique in that after deposition the drum rotates the deposited DNA into a large non-buffer open space where processing and detection can occur. The drum can also be removed in toto to special workstations for downstream processing, multiplexing and detection. 18 figs.

  14. SCID mice containing muscle with human mitochondrial DNA mutations. An animal model for mitochondrial DNA defects.

    PubMed Central

    Clark, K M; Watt, D J; Lightowlers, R N; Johnson, M A; Relvas, J B; Taanman, J W; Turnbull, D M

    1998-01-01

    Defects of the mitochondrial genome are important causes of disease. Despite major advances in our investigation of patients, there is no effective therapy. Progress in this area is limited by the absence of any animal models in which we can evaluate treatment. To develop such a model we have injected human myoblasts into the tibialis anterior of SCID mice after inducing necrosis. After injection of normal human myoblasts, regenerating fibers expressed human beta-spectrin, confirming they were derived from fusion of human myoblasts. The stability of the muscle fibers was inferred by demonstrating the formation of motor end plates on the regenerating fibers. In addition, we show the presence of human cytochrome c oxidase subunit II, which is encoded by the mitochondrial genome, in the regenerated fibers. After injection of human myoblasts containing either the A8344G or the T8993C heteroplasmic mitochondrial DNA mutations, human beta-spectrin positive fibers were found to contain the mutation at a similar level to the injected myoblasts. These studies highlight the potential value of this model for the study of mitochondrial DNA defects. PMID:9854044

  15. Application of mitochondrial DNA polymorphism to meloidogyne molecular population biology.

    PubMed

    Hyman, B C; Whipple, L E

    1996-09-01

    Recent advances in molecular biology have enabled the genotyping of individual nematodes, facilitating the analysis of genetic variability within and among plant-pathogenic nematode isolates. This review first describes representative examples of how RFLP, RAPD, AFLP, and DNA sequence analysis have been employed to describe populations of several phytonematodes, including the pinewood, burrowing, root-knot, and cyst nematodes. The second portion of this paper evaluates the utility of a size-variable mitochondrial DNA locus to examine the genetic structure of Meloidogyne isolates using two alternate methodologies, variable number tandem repeat (VNTR) and repeat associated poiymorphism (RAP) analysis. VNTR analysis has revealed genetic variation among individual nematodes, whereas RAP may provide useful markers for species and population differentiation.

  16. Complete Mitochondrial Genome Sequence of the Pezizomycete Pyronema confluens

    PubMed Central

    2016-01-01

    The complete mitochondrial genome of the ascomycete Pyronema confluens has been sequenced. The circular genome has a size of 191 kb and contains 48 protein-coding genes, 26 tRNA genes, and two rRNA genes. Of the protein-coding genes, 14 encode conserved mitochondrial proteins, and 31 encode predicted homing endonuclease genes. PMID:27174271

  17. Mitochondrial Genome Sequence of the Glass Sponge Oopsacas minuta

    PubMed Central

    Santini, Sébastien; Rocher, Caroline; Le Bivic, André

    2015-01-01

    We report the complete mitochondrial genome sequence of the Mediterranean glass sponge Oopsacas minuta. This 19-kb mitochondrial genome has 24 noncoding genes (22 tRNAs and 2 rRNAs) and 14 protein-encoding genes coding for 11 subunits of respiratory chain complexes and 3 ATP synthase subunits. PMID:26227597

  18. Staphylococcus aureus Sepsis Induces Early Renal Mitochondrial DNA Repair and Mitochondrial Biogenesis in Mice

    PubMed Central

    Bartz, Raquel R.; Fu, Ping; Suliman, Hagir B.; Crowley, Stephen D.; MacGarvey, Nancy Chou; Welty-Wolf, Karen; Piantadosi, Claude A.

    2014-01-01

    Acute kidney injury (AKI) contributes to the high morbidity and mortality of multi-system organ failure in sepsis. However, recovery of renal function after sepsis-induced AKI suggests active repair of energy-producing pathways. Here, we tested the hypothesis in mice that Staphyloccocus aureus sepsis damages mitochondrial DNA (mtDNA) in the kidney and activates mtDNA repair and mitochondrial biogenesis. Sepsis was induced in wild-type C57Bl/6J and Cox-8 Gfp-tagged mitochondrial-reporter mice via intraperitoneal fibrin clots embedded with S. aureus. Kidneys from surviving mice were harvested at time zero (control), 24, or 48 hours after infection and evaluated for renal inflammation, oxidative stress markers, mtDNA content, and mitochondrial biogenesis markers, and OGG1 and UDG mitochondrial DNA repair enzymes. We examined the kidneys of the mitochondrial reporter mice for changes in staining density and distribution. S. aureus sepsis induced sharp amplification of renal Tnf, Il-10, and Ngal mRNAs with decreased renal mtDNA content and increased tubular and glomerular cell death and accumulation of protein carbonyls and 8-OHdG. Subsequently, mtDNA repair and mitochondrial biogenesis was evidenced by elevated OGG1 levels and significant increases in NRF-1, NRF-2, and mtTFA expression. Overall, renal mitochondrial mass, tracked by citrate synthase mRNA and protein, increased in parallel with changes in mitochondrial GFP-fluorescence especially in proximal tubules in the renal cortex and medulla. Sub-lethal S. aureus sepsis thus induces widespread renal mitochondrial damage that triggers the induction of the renal mtDNA repair protein, OGG1, and mitochondrial biogenesis as a conspicuous resolution mechanism after systemic bacterial infection. PMID:24988481

  19. Reduction of nuclear encoded enzymes of mitochondrial energy metabolism in cells devoid of mitochondrial DNA.

    PubMed

    Mueller, Edith E; Mayr, Johannes A; Zimmermann, Franz A; Feichtinger, René G; Stanger, Olaf; Sperl, Wolfgang; Kofler, Barbara

    2012-01-20

    Mitochondrial DNA (mtDNA) depletion syndromes are generally associated with reduced activities of oxidative phosphorylation (OXPHOS) enzymes that contain subunits encoded by mtDNA. Conversely, entirely nuclear encoded mitochondrial enzymes in these syndromes, such as the tricarboxylic acid cycle enzyme citrate synthase (CS) and OXPHOS complex II, usually exhibit normal or compensatory enhanced activities. Here we report that a human cell line devoid of mtDNA (HEK293 ρ(0) cells) has diminished activities of both complex II and CS. This finding indicates the existence of a feedback mechanism in ρ(0) cells that downregulates the expression of entirely nuclear encoded components of mitochondrial energy metabolism.

  20. The sequence of sequencers: The history of sequencing DNA

    PubMed Central

    Heather, James M.; Chain, Benjamin

    2016-01-01

    Determining the order of nucleic acid residues in biological samples is an integral component of a wide variety of research applications. Over the last fifty years large numbers of researchers have applied themselves to the production of techniques and technologies to facilitate this feat, sequencing DNA and RNA molecules. This time-scale has witnessed tremendous changes, moving from sequencing short oligonucleotides to millions of bases, from struggling towards the deduction of the coding sequence of a single gene to rapid and widely available whole genome sequencing. This article traverses those years, iterating through the different generations of sequencing technology, highlighting some of the key discoveries, researchers, and sequences along the way. PMID:26554401

  1. Mitochondrial genome of the moon jelly Aurelia aurita (Cnidaria, Scyphozoa): A linear DNA molecule encoding a putative DNA-dependent DNA polymerase.

    PubMed

    Shao, Zhiyong; Graf, Shannon; Chaga, Oleg Y; Lavrov, Dennis V

    2006-10-15

    The 16,937-nuceotide sequence of the linear mitochondrial DNA (mt-DNA) molecule of the moon jelly Aurelia aurita (Cnidaria, Scyphozoa) - the first mtDNA sequence from the class Scypozoa and the first sequence of a linear mtDNA from Metazoa - has been determined. This sequence contains genes for 13 energy pathway proteins, small and large subunit rRNAs, and methionine and tryptophan tRNAs. In addition, two open reading frames of 324 and 969 base pairs in length have been found. The deduced amino-acid sequence of one of them, ORF969, displays extensive sequence similarity with the polymerase [but not the exonuclease] domain of family B DNA polymerases, and this ORF has been tentatively identified as dnab. This is the first report of dnab in animal mtDNA. The genes in A. aurita mtDNA are arranged in two clusters with opposite transcriptional polarities; transcription proceeding toward the ends of the molecule. The determined sequences at the ends of the molecule are nearly identical but inverted and lack any obvious potential secondary structures or telomere-like repeat elements. The acquisition of mitochondrial genomic data for the second class of Cnidaria allows us to reconstruct characteristic features of mitochondrial evolution in this animal phylum.

  2. Extent of heterogeneity in mitochondrial DNA of European populations.

    PubMed

    Melton, T; Wilson, M; Batzer, M; Stoneking, M

    1997-05-01

    Variation in the mitochondrial DNA (mtDNA) control region as detected by sequence-specific oligonucleotide (SSO) probes is described for 595 individuals from six European or European-derived populations. Estimates of diversity for mtDNA types exceed 0.91 in all populations, while 50% of the 158 types which were observed occur only once. Of 68 shared types, most occur rarely (< 3% of the total population); only one type occurs at a frequency greater than 10%, and it is present at comparable frequencies in all six populations (18-29%). An analysis of molecular variance (AMOVA) incorporating genetic distances between types shows that 100% of the variation present in the total sample is attributable to within-population diversity, while there are essentially no between-population differences. Another AMOVA was performed for the first hypervariable region SSO sites only, which included this sample plus an additional 537 SSO types from mine more European populations that were inferred from published mtDNA control region sequence data. Similar results were obtained, with over 99% of the variation overall attributable to within-population differences, and less than 1% of the variation attributable to between-population differences. The Saami were the most different from other populations, which had been observed in an earlier study of nucleotide sequence data. Overall, there is no statistically significant heterogeneity for European populations (p > 0.001), and these groups are virtually indistinguishable with respect to mtDNA SSO types. These results demonstrate the utility of mtDNA typing for forensic investigations.

  3. Mitochondrial DNA variation in the Viking age population of Norway.

    PubMed

    Krzewińska, Maja; Bjørnstad, Gro; Skoglund, Pontus; Olason, Pall Isolfur; Bill, Jan; Götherström, Anders; Hagelberg, Erika

    2015-01-19

    The medieval Norsemen or Vikings had an important biological and cultural impact on many parts of Europe through raids, colonization and trade, from about AD 793 to 1066. To help understand the genetic affinities of the ancient Norsemen, and their genetic contribution to the gene pool of other Europeans, we analysed DNA markers in Late Iron Age skeletal remains from Norway. DNA was extracted from 80 individuals, and mitochondrial DNA polymorphisms were detected by next-generation sequencing. The sequences of 45 ancient Norwegians were verified as genuine through the identification of damage patterns characteristic of ancient DNA. The ancient Norwegians were genetically similar to previously analysed ancient Icelanders, and to present-day Shetland and Orkney Islanders, Norwegians, Swedes, Scots, English, German and French. The Viking Age population had higher frequencies of K*, U*, V* and I* haplogroups than their modern counterparts, but a lower proportion of T* and H* haplogroups. Three individuals carried haplotypes that are rare in Norway today (U5b1b1, Hg A* and an uncommon variant of H*). Our combined analyses indicate that Norse women were important agents in the overseas expansion and settlement of the Vikings, and that women from the Orkneys and Western Isles contributed to the colonization of Iceland.

  4. Mitochondrial DNA variation in the Viking age population of Norway

    PubMed Central

    Krzewińska, Maja; Bjørnstad, Gro; Skoglund, Pontus; Olason, Pall Isolfur; Bill, Jan; Götherström, Anders; Hagelberg, Erika

    2015-01-01

    The medieval Norsemen or Vikings had an important biological and cultural impact on many parts of Europe through raids, colonization and trade, from about AD 793 to 1066. To help understand the genetic affinities of the ancient Norsemen, and their genetic contribution to the gene pool of other Europeans, we analysed DNA markers in Late Iron Age skeletal remains from Norway. DNA was extracted from 80 individuals, and mitochondrial DNA polymorphisms were detected by next-generation sequencing. The sequences of 45 ancient Norwegians were verified as genuine through the identification of damage patterns characteristic of ancient DNA. The ancient Norwegians were genetically similar to previously analysed ancient Icelanders, and to present-day Shetland and Orkney Islanders, Norwegians, Swedes, Scots, English, German and French. The Viking Age population had higher frequencies of K*, U*, V* and I* haplogroups than their modern counterparts, but a lower proportion of T* and H* haplogroups. Three individuals carried haplotypes that are rare in Norway today (U5b1b1, Hg A* and an uncommon variant of H*). Our combined analyses indicate that Norse women were important agents in the overseas expansion and settlement of the Vikings, and that women from the Orkneys and Western Isles contributed to the colonization of Iceland. PMID:25487335

  5. Mathematical modeling of the role of mitochondrial fusion and fission in mitochondrial DNA maintenance.

    PubMed

    Tam, Zhi Yang; Gruber, Jan; Halliwell, Barry; Gunawan, Rudiyanto

    2013-01-01

    Accumulation of mitochondrial DNA (mtDNA) mutations has been implicated in a wide range of human pathologies, including neurodegenerative diseases, sarcopenia, and the aging process itself. In cells, mtDNA molecules are constantly turned over (i.e. replicated and degraded) and are also exchanged among mitochondria during the fusion and fission of these organelles. While the expansion of a mutant mtDNA population is believed to occur by random segregation of these molecules during turnover, the role of mitochondrial fusion-fission in this context is currently not well understood. In this study, an in silico modeling approach is taken to investigate the effects of mitochondrial fusion and fission dynamics on mutant mtDNA accumulation. Here we report model simulations suggesting that when mitochondrial fusion-fission rate is low, the slow mtDNA mixing can lead to an uneven distribution of mutant mtDNA among mitochondria in between two mitochondrial autophagic events leading to more stochasticity in the outcomes from a single random autophagic event. Consequently, slower mitochondrial fusion-fission results in higher variability in the mtDNA mutation burden among cells in a tissue over time, and mtDNA mutations have a higher propensity to clonally expand due to the increased stochasticity. When these mutations affect cellular energetics, nuclear retrograde signalling can upregulate mtDNA replication, which is expected to slow clonal expansion of these mutant mtDNA. However, our simulations suggest that the protective ability of retrograde signalling depends on the efficiency of fusion-fission process. Our results thus shed light on the interplay between mitochondrial fusion-fission and mtDNA turnover and may explain the mechanism underlying the experimentally observed increase in the accumulation of mtDNA mutations when either mitochondrial fusion or fission is inhibited.

  6. Maternal inheritance of mitochondrial DNA by diverse mechanisms to eliminate paternal mitochondrial DNA.

    PubMed

    Sato, Miyuki; Sato, Ken

    2013-08-01

    The mitochondrion is an organelle that has its own DNA (mtDNA). Mitochondria play essential roles in energy production and in various cellular processes such as metabolism and signal transduction. In most animals, including humans, although the sperm-derived paternal mitochondria enter the oocyte cytoplasm after fertilization, their mtDNA is never transmitted to the offspring. This pattern of mtDNA inheritance is well known as "maternal inheritance." However, how the paternal mitochondria and mtDNA are eliminated from the cytoplasm of gametes or zygotes remains an enigma. Recently, a variety of mechanisms, including specific nuclease-dependent systems, ubiquitin-proteasome system, and autophagy have been shown to degrade the paternal mtDNA or the paternal mitochondria themselves in order to prevent paternal mtDNA transmission. In this review, we will address the current state of knowledge of the molecular mechanisms underlying the elimination of paternal mtDNA or mitochondrial structures for ensuring the maternal transmission of mtDNA.

  7. Mitochondrial genome acquisition restores respiratory function and tumorigenic potential of cancer cells without mitochondrial DNA.

    PubMed

    Tan, An S; Baty, James W; Dong, Lan-Feng; Bezawork-Geleta, Ayenachew; Endaya, Berwini; Goodwin, Jacob; Bajzikova, Martina; Kovarova, Jaromira; Peterka, Martin; Yan, Bing; Pesdar, Elham Alizadeh; Sobol, Margarita; Filimonenko, Anatolyj; Stuart, Shani; Vondrusova, Magdalena; Kluckova, Katarina; Sachaphibulkij, Karishma; Rohlena, Jakub; Hozak, Pavel; Truksa, Jaroslav; Eccles, David; Haupt, Larisa M; Griffiths, Lyn R; Neuzil, Jiri; Berridge, Michael V

    2015-01-06

    We report that tumor cells without mitochondrial DNA (mtDNA) show delayed tumor growth, and that tumor formation is associated with acquisition of mtDNA from host cells. This leads to partial recovery of mitochondrial function in cells derived from primary tumors grown from cells without mtDNA and a shorter lag in tumor growth. Cell lines from circulating tumor cells showed further recovery of mitochondrial respiration and an intermediate lag to tumor growth, while cells from lung metastases exhibited full restoration of respiratory function and no lag in tumor growth. Stepwise assembly of mitochondrial respiratory (super)complexes was correlated with acquisition of respiratory function. Our findings indicate horizontal transfer of mtDNA from host cells in the tumor microenvironment to tumor cells with compromised respiratory function to re-establish respiration and tumor-initiating efficacy. These results suggest pathophysiological processes for overcoming mtDNA damage and support the notion of high plasticity of malignant cells.

  8. Linear Plasmids and the Rate of Sequence Evolution in Plant Mitochondrial Genomes

    PubMed Central

    Warren, Jessica M.; Simmons, Mark P.; Wu, Zhiqiang; Sloan, Daniel B.

    2016-01-01

    The mitochondrial genomes of flowering plants experience frequent insertions of foreign sequences, including linear plasmids that also exist in standalone forms within mitochondria, but the history and phylogenetic distribution of plasmid insertions is not well known. Taking advantage of the increased availability of plant mitochondrial genome sequences, we performed phylogenetic analyses to reconstruct the evolutionary history of these plasmids and plasmid-derived insertions. Mitochondrial genomes from multiple land plant lineages (including liverworts, lycophytes, ferns, and gymnosperms) include fragmented remnants from ancient plasmid insertions. Such insertions are much more recent and widespread in angiosperms, in which approximately 75% of sequenced mitochondrial genomes contain identifiable plasmid insertions. Although conflicts between plasmid and angiosperm phylogenies provide clear evidence of repeated horizontal transfers, we were still able to detect significant phylogenetic concordance, indicating that mitochondrial plasmids have also experienced sustained periods of (effectively) vertical transmission in angiosperms. The observed levels of sequence divergence in plasmid-derived genes suggest that nucleotide substitution rates in these plasmids, which often encode their own viral-like DNA polymerases, are orders of magnitude higher than in mitochondrial chromosomes. Based on these results, we hypothesize that the periodic incorporation of mitochondrial genes into plasmids contributes to the remarkable heterogeneity in substitution rates among genes that has recently been discovered in some angiosperm mitochondrial genomes. In support of this hypothesis, we show that the recently acquired ψtrnP-trnW gene region in a maize linear plasmid is evolving significantly faster than homologous sequences that have been retained in the mitochondrial chromosome in closely related grasses. PMID:26759362

  9. Differentiating between monozygotic twins through next-generation mitochondrial genome sequencing.

    PubMed

    Wang, Zheng; Zhu, Ruxin; Zhang, Suhua; Bian, Yinnan; Lu, Daru; Li, Chengtao

    2015-12-01

    Monozygotic (MZ) twins, considered to be genetically identical, cannot be distinguished from one another by standard forensic DNA testing. A recent study employed whole genome sequencing to identify extremely rare mutations and reported that mutation analysis could be used to differentiate between MZ twins. Compared with nuclear DNA, mitochondrial DNA (mtDNA) has higher mutation rates; therefore, minor differences theoretically exist in MZ twins' mitochondrial genome (mtGenome). However, conventional Sanger-type sequencing (STS) is neither amenable to, nor feasible for, the detection of low-level sequence variants. The recent introduction of massively parallel sequencing (MPS) has the capability to sequence many targeted regions of multiple samples simultaneously with desirable depth of coverage. Thus, the aim of this study was to assess whether full mtGenome sequencing analysis can be used to differentiate between MZ twins. Ten sets of MZ twins provided blood samples that underwent extraction, quantification, mtDNA enrichment, library preparation, and ultra-deep sequencing. Point heteroplasmies were observed in eight sets of MZ twins, and a single nucleotide variant (nt15301) was detected in five sets of MZ twins. Thus, this study demonstrates that ultra-deep mtGenome sequencing could be used to differentiate between MZ twins.

  10. Sequence analysis of the complete mitochondrial genome of Youxian sheldrake.

    PubMed

    He, Shao-Ping; Liu, Li-Li; Yu, Qi-Fang; Li, Si; He, Jian-Hua

    2016-01-01

    Youxian sheldrake is excellent native breeds in Hunan province in China. The complete mitochondrial (mt) genome sequence plays an important role in the accurate determination of phylogenetic relationships among metazoans. This is the first study to determine the complete mitochondrial genome sequence of Youxian sheldrake using PCR-based amplification and Sanger sequencing. The characteristic of the entire mitochondrial genome was analyzed in detail, the total length of the mitogenome is 16,605 bp, with the base composition of 29.21% A, 22.18% T, 32.84% C, 15.77% G in the Youxian sheldrake. It contained 2 ribosomal RNA genes, 13 protein-coding genes, 22 transfer RNA genes and a major non-coding control region (D-loop region). The complete mitochondrial genome sequence of Youxian sheldrake provided an important data for further study of the phylogenetics of poultry, and available data for the genetics and breeding.

  11. Extensive polymorphism in the mitochondrial DNA of apes.

    PubMed Central

    Ferris, S D; Brown, W M; Davidson, W S; Wilson, A C

    1981-01-01

    Ape species are 2-10 times more variable than the human species with respect to the nucleotide sequence of mtDNA, even though ape populations have been smaller than the human population for at least 10,000 years. This finding was made by comparing purified mtDNAs from 27 individuals with the aid of 25 restriction endonucleases; for an additional 59 individuals, comparisons were made with fewer enzymes by using the blot hybridization method. The amount of intraspecific sequence divergence was greatest between orangutans of Borneo and Sumatra. Among common chimpanzees, a large component of the variation is due to two highly distinct forms of mtDNA that may reflect a major geographic subdivision. The least amount of sequence variation occurred among lowland gorillas, which exhibit only twice as much sequence variation as humans. The large intraspecific differences among apes, together with the geological and protein evidence, leads us to propose that each ape species is the remnant of an ancient and widespread population that became subdivided geographically and reduced in size and range, perhaps by hominid competition. The low variation among human mtDNAs is consistent with geological evidence that the human species is young. The distribution of site changes within the mitochondrial genome was also examined. Comparison of closely related mtDNAs shows that the ribosomal RNA genes have diverged more slowly than the rest of the genome. PMID:6273863

  12. Mitochondrial bioenergetics and drug-induced toxicity in a panel of mouse embryonic fibroblasts with mitochondrial DNA single nucleotide polymorphisms

    SciTech Connect

    Pereira, Claudia V.; Oliveira, Paulo J.; Will, Yvonne; Nadanaciva, Sashi

    2012-10-15

    Mitochondrial DNA (mtDNA) variations including single nucleotide polymorphisms (SNPs) have been proposed to be involved in idiosyncratic drug reactions. However, current in vitro and in vivo models lack the genetic diversity seen in the human population. Our hypothesis is that different cell strains with distinct mtDNA SNPs may have different mitochondrial bioenergetic profiles and may therefore vary in their response to drug-induced toxicity. Therefore, we used an in vitro system composed of four strains of mouse embryonic fibroblasts (MEFs) with mtDNA polymorphisms. We sequenced mtDNA from embryonic fibroblasts isolated from four mouse strains, C57BL/6J, MOLF/EiJ, CZECHII/EiJ and PERA/EiJ, with the latter two being sequenced for the first time. The bioenergetic profile of the four strains of MEFs was investigated at both passages 3 and 10. Our results showed that there were clear differences among the four strains of MEFs at both passages, with CZECHII/EiJ having a lower mitochondrial robustness when compared to C57BL/6J, followed by MOLF/EiJ and PERA/EiJ. Seven drugs known to impair mitochondrial function were tested for their effect on the ATP content of the four strains of MEFs in both glucose- and galactose-containing media. Our results showed that there were strain-dependent differences in the response to some of the drugs. We propose that this model is a useful starting point to study compounds that may cause mitochondrial off-target toxicity in early stages of drug development, thus decreasing the number of experimental animals used. -- Highlights: ► mtDNA SNPs may be linked to individual predisposition to drug-induced toxicity. ► CZECHII/EiJ and PERA/EiJ mtDNA was sequenced for the first time in this study. ► Strain-dependent mitochondrial capacity differences were measured. ► Strain-dependent differences in response to mitochondrial toxicants were observed.

  13. Complete Mitochondrial Genome Sequence of Sunflower (Helianthus annuus L.)

    PubMed Central

    Ebert, Daniel P.; Kane, Nolan C.; Rieseberg, Loren H.

    2016-01-01

    This is the first complete mitochondrial genome sequence for sunflower and the first complete mitochondrial genome for any member of Asteraceae, the largest plant family, which includes over 23,000 named species. The master circle is 300,945-bp long and includes 27 protein-coding sequences, 18 tRNAs, and the 26S, 5S, and 18S rRNAs. PMID:27635002

  14. Proteomic Dissection of the Mitochondrial DNA Metabolism Apparatus in Arabidopsis

    SciTech Connect

    SAlly A. Mackenzie

    2004-01-06

    This study involves the investigation of nuclear genetic components that regulate mitochondrial genome behavior in higher plants. The approach utilizes the advanced plant model system of Arabidopsis thaliana to identify and functionally characterize multiple components of the mitochondrial DNA replication, recombination and mismatch repair system and their interaction partners. The rationale for the research stems from the central importance of mitochondria to overall cellular metabolism and the essential nature of the mitochondrial genome to mitochondrial function. Relatively little is understood about mitochondrial DNA maintenance and transmission in higher eukaryotes, and the higher plant mitochondrial genome displays unique properties and behavior. This investigation has revealed at least three important properties of plant mitochondrial DNA metabolism components. (1) Many are dual targeted to mitochondrial and chloroplasts by novel mechanisms, suggesting that the mitochondria a nd chloroplast share their genome maintenance apparatus. (2)The MSH1 gene, originating as a component of mismatch repair, has evolved uniquely in plants to participate in differential replication of the mitochondrial genome. (3) This mitochondrial differential replication process, termed substoichiometric shifting and also involving a RecA-related gene, appears to represent an adaptive mechanism to expand plant reproductive capacity and is likely present throughout the plant kingdom.

  15. Mitochondrial DNA of Vitis vinifera and the issue of rampant horizontal gene transfer.

    PubMed

    Goremykin, Vadim V; Salamini, Francesco; Velasco, Riccardo; Viola, Roberto

    2009-01-01

    The mitochondrial genome of grape (Vitis vinifera), the largest organelle genome sequenced so far, is presented. The genome is 773,279 nt long and has the highest coding capacity among known angiosperm mitochondrial DNAs (mtDNAs). The proportion of promiscuous DNA of plastid origin in the genome is also the largest ever reported for an angiosperm mtDNA, both in absolute and relative terms. In all, 42.4% of chloroplast genome of Vitis has been incorporated into its mitochondrial genome. In order to test if horizontal gene transfer (HGT) has also contributed to the gene content of the grape mtDNA, we built phylogenetic trees with the coding sequences of mitochondrial genes of grape and their homologs from plant mitochondrial genomes. Many incongruent gene tree topologies were obtained. However, the extent of incongruence between these gene trees is not significantly greater than that observed among optimal trees for chloroplast genes, the common ancestry of which has never been in doubt. In both cases, we attribute this incongruence to artifacts of tree reconstruction, insufficient numbers of characters, and gene paralogy. This finding leads us to question the recent phylogenetic interpretation of Bergthorsson et al. (2003, 2004) and Richardson and Palmer (2007) that rampant HGT into the mtDNA of Amborella best explains phylogenetic incongruence between mitochondrial gene trees for angiosperms. The only evidence for HGT into the Vitis mtDNA found involves fragments of two coding sequences stemming from two closteroviruses that cause the leaf roll disease of this plant. We also report that analysis of sequences shared by both chloroplast and mitochondrial genomes provides evidence for a previously unknown gene transfer route from the mitochondrion to the chloroplast.

  16. Mitochondrial DNA haplogroup H structure in North Africa

    PubMed Central

    Ennafaa, Hajer; Cabrera, Vicente M; Abu-Amero, Khaled K; González, Ana M; Amor, Mohamed B; Bouhaha, Rym; Dzimiri, Nduna; Elgaaïed, Amel B; Larruga, José M

    2009-01-01

    Background The Strait of Gibraltar separating the Iberian Peninsula from North Africa is thought to be a stronger barrier to gene flow for male than for female lineages. However, the recent subdivision of the haplogroup H at mitochondrial DNA (mtDNA) level has revealed greater genetic differentiation among geographic regions than previously detected. The dissection of the mtDNA haplogroup H in North Africa, and its comparison with the Iberian Peninsula and Near-East profiles would help clarify the relative affinities among these regions. Results Like the Iberian Peninsula, the dominant mtDNA haplogroup H subgroups in North Africa are H1 (42%) and H3 (13%). The similarity between these regions is stronger in the North-West edge affecting mainly Moroccan Arabs, West Saharans and Mauritanians, and decreases eastwards probably due to gene flow from Near East as attested for the higher frequencies of H4, H5, H7, H8 and H11 subgroups. Moroccan Berbers show stronger affinities with Tunisian and Tunisian Berbers than with Moroccan Arabs. Coalescence ages for H1 (11 ± 2 ky) and H3 (11 ± 4 ky) in North Africa point to the possibility of a late Palaeolithic settlement for these lineages similar to those found for other mtDNA haplogroups. Total and partial mtDNA genomic sequencing unveiled stronger mtDNA differentiation among regions than previously found using HVSI mtDNA based analysis. Conclusion The subdivision of the mtDNA haplogroup H in North Africa has confirmed that the genetic differentiation found among Western and Eastern populations is mainly due to geographical rather than cultural barriers. It also shows that the historical Arabian role on the region had more a cultural than a demic effect. Whole mtDNA sequencing of identical H haplotypes based on HVSI and RFLP information has unveiled additional mtDNA differences between North African and Iberian Peninsula lineages, pointing to an older mtDNA genetic flow between regions than previously thought. Based on this

  17. Interspecific Comparison and annotation of two complete mitochondrial genome sequences from the plant pathogenic fungus Mycosphaerella graminicola

    SciTech Connect

    Millenbaugh, Bonnie A; Pangilinan, Jasmyn L.; Torriani, Stefano F.F.; Goodwin, Stephen B.; Kema, Gert H.J.; McDonald, Bruce A.

    2007-12-07

    The mitochondrial genomes of two isolates of the wheat pathogen Mycosphaerella graminicola were sequenced completely and compared to identify polymorphic regions. This organism is of interest because it is phylogenetically distant from other fungi with sequenced mitochondrial genomes and it has shown discordant patterns of nuclear and mitochondrial diversity. The mitochondrial genome of M. graminicola is a circular molecule of approximately 43,960 bp containing the typical genes coding for 14 proteins related to oxidative phosphorylation, one RNA polymerase, two rRNA genes and a set of 27 tRNAs. The mitochondrial DNA of M. graminicola lacks the gene encoding the putative ribosomal protein (rps5-like), commonly found in fungal mitochondrial genomes. Most of the tRNA genes were clustered with a gene order conserved with many other ascomycetes. A sample of thirty-five additional strains representing the known global mt diversity was partially sequenced to measure overall mitochondrial variability within the species. Little variation was found, confirming previous RFLP-based findings of low mitochondrial diversity. The mitochondrial sequence of M. graminicola is the first reported from the family Mycosphaerellaceae or the order Capnodiales. The sequence also provides a tool to better understand the development of fungicide resistance and the conflicting pattern of high nuclear and low mitochondrial diversity in global populations of this fungus.

  18. Structure of mitochondrial DNA control region of Pholis fangi and its phylogenetic implication

    NASA Astrophysics Data System (ADS)

    Li, Lin; Zhang, Hui; Sun, Dianrong; Gao, Tianxiang

    2014-06-01

    In this study, the entire mitochondrial DNA (mtDNA) control region (CR) of Pholis fangi was amplified via polymerase chain reaction followed by direct sequencing. The length of the mtDNA CR consensus sequence of P. fangi was 853 bp in length. In accordance with the recognition sites as were previously reported in fish species, the mtDNA CR sequence of P. fangi can be divided into 3 domains, i.e., the extended terminal associated sequence (ETAS), the central conserved sequence block (CSB), and the CSB domain. In addition, the following structures were identified in the mtDNA CR sequence of P. fangi: 2 ETASs in the ETAS domain (TAS and cTAS), 6 CSBs in the central CSB domain (CSB-F to CSB-A), and 3 CSBs in the CSB domain (CSB-1 to CSB-3). These demonstrated that the structure of the mtDNA CR of P. fangi was substantially different from those of most other fish species. The mtDNA CR sequence of P. fangi contained one conserved region from 656 bp to 815 bp. Similar to most other fish species, P. fangi has no tandem repeat sequences in its mtDNA CR sequence. Phylogenetic analysis based on the complete mtDNA CR sequences showed that there were no genetic differences within P. fangi populations of the same geographical origin and between P. fangi populations of different geographical origins.

  19. Identification of Forensic Samples via Mitochondrial DNA in the Undergraduate Biochemistry Laboratory

    NASA Astrophysics Data System (ADS)

    Millard, Julie T.; Pilon, André M.

    2003-04-01

    A recent forensic approach for identification of unknown biological samples is mitochondrial DNA (mtDNA) sequencing. We describe a laboratory exercise suitable for an undergraduate biochemistry course in which the polymerase chain reaction is used to amplify a 440 base pair hypervariable region of human mtDNA from a variety of "crime scene" samples (e.g., teeth, hair, nails, cigarettes, envelope flaps, toothbrushes, and chewing gum). Amplification is verified via agarose gel electrophoresis and then samples are subjected to cycle sequencing. Sequence alignments are made via the program CLUSTAL W, allowing students to compare samples and solve the "crime."

  20. Human mitochondrial DNA: roles of inherited and somatic mutations

    PubMed Central

    Schon, Eric A.; DiMauro, Salvatore; Hirano, Michio

    2014-01-01

    Mutations in the human mitochondrial genome are known to cause an array of diverse disorders, most of which are maternally inherited, and all of which are associated with defects in oxidative energy metabolism. It is now emerging that somatic mutations in mitochondrial DNA (mtDNA) are also linked to other complex traits, including neurodegenerative diseases, ageing and cancer. Here we discuss insights into the roles of mtDNA mutations in a wide variety of diseases, highlighting the interesting genetic characteristics of the mitochondrial genome and challenges in studying its contribution to pathogenesis. PMID:23154810

  1. A 454 sequencing approach to dipteran mitochondrial genome research.

    PubMed

    Ramakodi, Meganathan P; Singh, Baneshwar; Wells, Jeffrey D; Guerrero, Felix; Ray, David A

    2015-01-01

    The availability of complete mitochondrial genome (mtgenome) data for Diptera, one of the largest metazoan orders, in public databases is limited. The advent of high throughput sequencing technology provides the potential to generate mtgenomes for many species affordably and quickly. However, these technologies need to be validated for dipterans as the members of this clade play important economic and research roles. Illumina and 454 sequencing platforms are widely used in genomic research involving non-model organisms. The Illumina platform has already been utilized for generating mitochondrial genomes without using conventional long range PCR for insects whereas the power of 454 sequencing for generating mitochondrial genome drafts without PCR has not yet been validated for insects. Thus, this study examines the utility of 454 sequencing approach for dipteran mtgenomic research. We generated complete or nearly complete mitochondrial genomes for Cochliomyia hominivorax, Haematobia irritans, Phormia regina and Sarcophaga crassipalpis using a 454 sequencing approach. Comparisons between newly obtained and existing assemblies for C. hominivorax and H. irritans revealed no major discrepancies and verified the utility of 454 sequencing for dipteran mitochondrial genomes. We also report the complete mitochondrial sequences for two forensically important flies, P. regina and S. crassipalpis, which could be used to provide useful information to legal personnel. Comparative analyses revealed that dipterans follow similar codon usage and nucleotide biases that could be due to mutational and selection pressures. This study illustrates the utility of 454 sequencing to obtain complete mitochondrial genomes for dipterans without the aid of conventional molecular techniques such as PCR and cloning and validates this method of mtgenome sequencing in arthropods.

  2. Channel plate for DNA sequencing

    DOEpatents

    Douthart, Richard J.; Crowell, Shannon L.

    1998-01-01

    This invention is a channel plate that facilitates data compaction in DNA sequencing. The channel plate has a length, a width and a thickness, and further has a plurality of channels that are parallel. Each channel has a depth partially through the thickness of the channel plate. Additionally an interface edge permits electrical communication across an interface through a buffer to a deposition membrane surface.

  3. Channel plate for DNA sequencing

    DOEpatents

    Douthart, R.J.; Crowell, S.L.

    1998-01-13

    This invention is a channel plate that facilitates data compaction in DNA sequencing. The channel plate has a length, a width and a thickness, and further has a plurality of channels that are parallel. Each channel has a depth partially through the thickness of the channel plate. Additionally an interface edge permits electrical communication across an interface through a buffer to a deposition membrane surface. 15 figs.

  4. The complete mitochondrial genome sequence of Oceanic whitetip shark, Carcharhinus longimanus (Carcharhiniformes: Carcharhinidae).

    PubMed

    Li, Weiwen; Dai, Xiaojie; Xu, Qianghua; Wu, Feng; Gao, Chunxia; Zhang, Yanbo

    2016-05-01

    The complete mitochondrial DNA sequence of Carcharhinus longimanus was determined and analyzed. The complete mtDNA genome sequence of C. longimanus was 16,706 bp in length. It contained 22 tRNA genes, 2 rRNA genes, 13 protein-coding genes and 2 non-conding regions: control region (D-loop) and origin of light-strand replication (OL). The complete mitogenome sequence information of C. longimanus can provide a useful data for further studies on molecular systematics, stock evaluation, taxonomic status and conservation genetics.

  5. DNA Sequencing Using capillary Electrophoresis

    SciTech Connect

    Dr. Barry Karger

    2011-05-09

    The overall goal of this program was to develop capillary electrophoresis as the tool to be used to sequence for the first time the Human Genome. Our program was part of the Human Genome Project. In this work, we were highly successful and the replaceable polymer we developed, linear polyacrylamide, was used by the DOE sequencing lab in California to sequence a significant portion of the human genome using the MegaBase multiple capillary array electrophoresis instrument. In this final report, we summarize our efforts and success. We began our work by separating by capillary electrophoresis double strand oligonucleotides using cross-linked polyacrylamide gels in fused silica capillaries. This work showed the potential of the methodology. However, preparation of such cross-linked gel capillaries was difficult with poor reproducibility, and even more important, the columns were not very stable. We improved stability by using non-cross linked linear polyacrylamide. Here, the entangled linear chains could move when osmotic pressure (e.g. sample injection) was imposed on the polymer matrix. This relaxation of the polymer dissipated the stress in the column. Our next advance was to use significantly lower concentrations of the linear polyacrylamide that the polymer could be automatically blown out after each run and replaced with fresh linear polymer solution. In this way, a new column was available for each analytical run. Finally, while testing many linear polymers, we selected linear polyacrylamide as the best matrix as it was the most hydrophilic polymer available. Under our DOE program, we demonstrated initially the success of the linear polyacrylamide to separate double strand DNA. We note that the method is used even today to assay purity of double stranded DNA fragments. Our focus, of course, was on the separation of single stranded DNA for sequencing purposes. In one paper, we demonstrated the success of our approach in sequencing up to 500 bases. Other

  6. Chronic Ethanol Consumption Increases Myocardial Mitochondrial DNA Mutations: A Potential Contribution by Mitochondrial Topoisomerases

    PubMed Central

    Laurent, D.; Mathew, J.E.; Mitry, M.; Taft, M.; Force, A.; Edwards, J.G.

    2014-01-01

    Aims: Alcoholic cardiomyopathy (ACM) presents as decreased myocardial contractility, arrhythmias and secondary non-ischemic dilated cardiomyopathy leading to heart failure. Mitochondrial dysfunction is known to have a significant role in the development and complications of ACM. This study investigated if chronic ethanol feeding promoted myocardial mitochondrial topoisomerase dysfunction as one underlying cause of mitochondrial DNA (mtDNA) damage and mitochondrial dysfunction in ACM. Methods: The impact of chronic ethanol exposure on the myocardial mitochondria was examined in both neonatal cardiomyocytes using 50 mM ethanol for 6 days and in rats assigned to control or ethanol feeding groups for 4 months. Results: Chronic ethanol feeding led to significant (P < 0.05) decreases in M-mode Fractional Shortening, ejection fraction, and the cardiac output index as well as increases in Tau. Ethanol feeding promoted mitochondrial dysfunction as evidenced by significantly decreased left ventricle cytochrome oxidase activity and decreases in mitochondrial protein content. Both in rats and in cultured cardiomyocytes, chronic ethanol presentation significantly increased mtDNA damage. Using isolated myocardial mitochondria, both mitochondrial topoisomerase-dependent DNA cleavage and DNA relaxation were significantly altered by ethanol feeding. Conclusion: Chronic ethanol feeding compromised cardiovascular and mitochondrial function as a result of a decline in mtDNA integrity that was in part the consequence of mitochondrial topoisomerase dysfunction. Understanding the regulation of the mitochondrial topoisomerases is critical for protection of mtDNA, not only for the management of alcoholic cardiomyopathy, but also for the many other clinical treatments that targets the topoisomerases in the alcoholic patient. PMID:24852753

  7. Comprehensive scanning of somatic mitochondrial DNA alterations in acute leukemia developing from myelodysplastic syndromes.

    PubMed

    Linnartz, Bjoern; Anglmayer, Roswitha; Zanssen, Stefanie

    2004-03-15

    Myelodysplastic syndromes (MDS) are clonal myeloid disorders characterized by ineffective hematopoiesis resulting in refractory cytopenias. Transformation resulting in acute myeloblastic leukemia is the final stage in the multistep process of MDS evolution. Functional relevant mutations of mitochondrial DNA (mtDNA) have been related to sideroblastic anemia and MDS. To investigate the role of mtDNA in malignant transformation to acute leukemia, we used high-resolution techniques such as single-strand conformational polymorphism and fluorescence sequencing for investigation of the whole mitochondrial genome from blood cells of 10 patients with MDS. Functionally relevant point mutations in mitochondrial RNA and polypeptide-encoding genes were detected in 50% of patients with MDS. Their increasing mutation load connects MDS and the developing acute myeloid leukemias. Several point mutations of mtDNA, including secondary point mutations for Leber's hereditary optic neuropathy, occur in one bone marrow and may synergically affect bone marrow stem cells by an apoptotic pathway.

  8. Mitochondrial DNA exhibits resistance to induced point and deletion mutations

    PubMed Central

    Valente, William J.; Ericson, Nolan G.; Long, Alexandra S.; White, Paul A.; Marchetti, Francesco; Bielas, Jason H.

    2016-01-01

    The accumulation of somatic mitochondrial DNA (mtDNA) mutations contributes to the pathogenesis of human disease. Currently, mitochondrial mutations are largely considered results of inaccurate processing of its heavily damaged genome. However, mainly from a lack of methods to monitor mtDNA mutations with sufficient sensitivity and accuracy, a link between mtDNA damage and mutation has not been established. To test the hypothesis that mtDNA-damaging agents induce mtDNA mutations, we exposed MutaTMMouse mice to benzo[a]pyrene (B[a]P) or N-ethyl-N-nitrosourea (ENU), daily for 28 consecutive days, and quantified mtDNA point and deletion mutations in bone marrow and liver using our newly developed Digital Random Mutation Capture (dRMC) and Digital Deletion Detection (3D) assays. Surprisingly, our results demonstrate mutagen treatment did not increase mitochondrial point or deletion mutation frequencies, despite evidence both compounds increase nuclear DNA mutations and demonstrated B[a]P adduct formation in mtDNA. These findings contradict models of mtDNA mutagenesis that assert the elevated rate of mtDNA mutation stems from damage sensitivity and abridged repair capacity. Rather, our results demonstrate induced mtDNA damage does not readily convert into mutation. These findings suggest robust mitochondrial damage responses repress induced mutations after mutagen exposure. PMID:27550180

  9. Hydrogen Sulfide Maintains Mitochondrial DNA Replication via Demethylation of TFAM

    PubMed Central

    Li, Shuangshuang

    2015-01-01

    Abstract Aims: Hydrogen sulfide (H2S) exerts a wide range of actions in the body, especially in the modulation of mitochondrial functions. The normal replication of mitochondrial DNA (mtDNA) is critical for cellular energy metabolism and mitochondrial biogenesis. The aim of this study was to investigate whether H2S affects mtDNA replication and the underlying mechanisms. We hypothesize that H2S maintains mtDNA copy number via inhibition of Dnmt3a transcription and TFAM promoter methylation. Results: Here, we demonstrated that deficiency of cystathionine gamma-lyase (CSE), a major H2S-producing enzyme, reduces mtDNA copy number and mitochondrial contents, and it inhibits the expressions of mitochondrial transcription factor A (TFAM) and mitochondrial marker genes in both smooth muscle cells and aorta tissues from mice. Supply of exogenous H2S stimulated mtDNA copy number and strengthened the expressions of TFAM and mitochondrial marker genes. TFAM knockdown diminished H2S-enhanced mtDNA copy number. In addition, CSE deficiency induced the expression of DNA methyltransferase 3a (Dnmt3a) and TFAM promoter DNA methylation, and H2S repressed Dnmt3a expression, resulting in TFAM promoter demethylation. We further found that H2S S-sulfhydrates transcription repressor interferon regulatory factor 1 (IRF-1) and enhances the binding of IRF-1 with Dnmt3a promoter after reduced Dnmt3a transcription. H2S had little effects on the expression of Dnmt1 and Dnmt3b as well as on ten-eleven translocation methylcytosine dioxygenase 1, 2, and 3. Innovation: A sufficient level of H2S is able to inhibit TFAM promoter methylation and maintain mtDNA copy number. Conclusion: CSE/H2S system contributes to mtDNA replication and cellular bioenergetics and provides a novel therapeutic avenue for cardiovascular diseases. Antioxid. Redox Signal. 23, 630–642. PMID:25758951

  10. Defeating numts: semi-pure mitochondrial DNA from eggs and simple purification methods for field-collected wildlife tissues.

    PubMed

    Ibarguchi, Gabriela; Friesen, Vicki L; Lougheed, Stephen C

    2006-11-01

    Mitochondrial DNA (mtDNA) continues to play a pivotal role in phylogeographic, phylogenetic, and population genetic studies. PCR amplification with mitochondrial primers often yields ambiguous sequences, in part because of the co-amplification of nuclear copies of mitochondrial genes (numts) and true mitochondrial heteroplasmy arising from mutations, hybridization with paternal leakage, gene duplications, and recombination. Failing to detect numts or to distinguish the origin of such homologous sequences results in the incorrect interpretation of data. However, few studies obtain purified mtDNA to confirm the mitochondrial origin of the first reference sequences for a species. Here, we demonstrate the importance and ease of obtaining semi-pure mtDNA from wildlife tissues, preserved under various typical field conditions, and investigate the success of 3 commercial extraction kits, cesium-chloride gradient mtDNA purification, long-template PCR amplification, cloning, and more species-specific degenerate primers. Using more detailed avian examples, we illustrate that unfertilized or undeveloped eggs provide the purest sources of mtDNA; that kits provide an alternative to cesium-chloride gradient methods; and that long-template PCR, cloning, and degenerate primers cannot be used to produce reliable mitochondrial reference sequences, but can be powerful tools when used in conjunction with purified mtDNA stocks to distinguish numts from true heteroplasmy.

  11. Mechanisms of Uniparental Mitochondrial DNA Inheritance in Cryptococcus neoformans.

    PubMed

    Gyawali, Rachana; Lin, Xiaorong

    2011-12-01

    In contrast to the nuclear genome, the mitochondrial genome does not follow Mendelian laws of inheritance. The nuclear genome of meiotic progeny comes from the recombination of both parental genomes, whereas the meiotic progeny could inherit mitochondria from one, the other, or both parents. In fact, one fascinating phenomenon is that mitochondrial DNA in the majority of eukaryotes is inherited from only one particular parent. Typically, such unidirectional and uniparental inheritance of mitochondrial DNA can be explained by the size of the gametes involved in mating, with the larger gamete contributing towards mitochondrial DNA inheritance. However, in the human fungal pathogen Cryptococcus neoformans, bisexual mating involves the fusion of two isogamous cells of mating type (MAT) a and MATα, yet the mitochondrial DNA is inherited predominantly from the MATa parent. Although the exact mechanism underlying such uniparental mitochondrial inheritance in this fungus is still unclear, various hypotheses have been proposed. Elucidating the mechanism of mitochondrial inheritance in this clinically important and genetically amenable eukaryotic microbe will yield insights into general mechanisms that are likely conserved in higher eukaryotes. In this review, we highlight studies on Cryptococcus mitochondrial inheritance and point out some important questions that need to be addressed in the future.

  12. Highly conserved D-loop-like nuclear mitochondrial sequences (Numts) in tiger (Panthera tigris).

    PubMed

    Zhang, Wenping; Zhang, Zhihe; Shen, Fujun; Hou, Rong; Lv, Xiaoping; Yue, Bisong

    2006-08-01

    Using oligonucleotide primers designed to match hypervariable segments I (HVS-1) of Panthera tigris mitochondrial DNA (mtDNA), we amplified two different PCR products (500 bp and 287 bp) in the tiger (Panthera tigris), but got only one PCR product (287 bp) in the leopard (Panthera pardus). Sequence analyses indicated that the sequence of 287 bp was a D-loop-like nuclear mitochondrial sequence (Numts), indicating a nuclear transfer that occurred approximately 4.8-17 million years ago in the tiger and 4.6-16 million years ago in the leopard. Although the mtDNA D-loop sequence has a rapid rate of evolution, the 287-bp Numts are highly conserved; they are nearly identical in tiger subspecies and only 1.742% different between tiger and leopard. Thus, such sequences represent molecular 'fossils' that can shed light on evolution of the mitochondrial genome and may be the most appropriate outgroup for phylogenetic analysis. This is also proved by comparing the phylogenetic trees reconstructed using the D-loop sequence of snow leopard and the 287-bp Numts as outgroup.

  13. Microhomology-mediated end joining is the principal mediator of double-strand break repair during mitochondrial DNA lesions.

    PubMed

    Tadi, Satish Kumar; Sebastian, Robin; Dahal, Sumedha; Babu, Ravi K; Choudhary, Bibha; Raghavan, Sathees C

    2016-01-15

    Mitochondrial DNA (mtDNA) deletions are associated with various mitochondrial disorders. The deletions identified in humans are flanked by short, directly repeated mitochondrial DNA sequences; however, the mechanism of such DNA rearrangements has yet to be elucidated. In contrast to nuclear DNA (nDNA), mtDNA is more exposed to oxidative damage, which may result in double-strand breaks (DSBs). Although DSB repair in nDNA is well studied, repair mechanisms in mitochondria are not characterized. In the present study, we investigate the mechanisms of DSB repair in mitochondria using in vitro and ex vivo assays. Whereas classical NHEJ (C-NHEJ) is undetectable, microhomology-mediated alternative NHEJ efficiently repairs DSBs in mitochondria. Of interest, robust microhomology-mediated end joining (MMEJ) was observed with DNA substrates bearing 5-, 8-, 10-, 13-, 16-, 19-, and 22-nt microhomology. Furthermore, MMEJ efficiency was enhanced with an increase in the length of homology. Western blotting, immunoprecipitation, and protein inhibition assays suggest the involvement of CtIP, FEN1, MRE11, and PARP1 in mitochondrial MMEJ. Knockdown studies, in conjunction with other experiments, demonstrated that DNA ligase III, but not ligase IV or ligase I, is primarily responsible for the final sealing of DSBs during mitochondrial MMEJ. These observations highlight the central role of MMEJ in maintenance of mammalian mitochondrial genome integrity and is likely relevant for deletions observed in many human mitochondrial disorders.

  14. Revealing latitudinal patterns of mitochondrial DNA diversity in Chileans.

    PubMed

    Gómez-Carballa, Alberto; Moreno, Fabián; Álvarez-Iglesias, Vanesa; Martinón-Torres, Federico; García-Magariños, Manuel; Pantoja-Astudillo, Jaime A; Aguirre-Morales, Eugenia; Bustos, Patricio; Salas, Antonio

    2016-01-01

    The territory of Chile is particularly long and narrow, which combined with its mountainous terrain, makes it a unique scenario for human genetic studies. We obtained 995 control region mitochondrial DNA (mtDNA) sequences from Chileans representing populations living at different latitudes of the country from the North to the southernmost region. The majority of the mtDNA profiles are of Native American origin (∼88%). The remaining haplotypes are mostly of recent European origin (∼11%), and only a minor proportion is of recent African ancestry (∼1%). While these proportions are relatively uniform across the country, more structured patterns of diversity emerge when examining the variation from a phylogeographic perspective. For instance, haplogroup A2 reaches ∼9% in the North, and its frequency decreases gradually to ∼1% in the southernmost populations, while the frequency of haplogroup D (sub-haplogroups D1 and D4) follows the opposite pattern: 36% in the southernmost region, gradually decreasing to 21% in the North. Furthermore, there are remarkable signatures of founder effects in specific sub-clades of Native American (e.g. haplogroups D1j and D4p) and European (e.g. haplogroups T2b3 and K1a4a1a+195) ancestry. We conclude that the magnitude of the latitudinal differences observed in the patterns of mtDNA variation might be relevant in forensic casework.

  15. A restriction map of Xenopus laevis mitochondrial DNA.

    PubMed

    Cordonnier, A M; Vannier, P A; Brun, G M

    1982-08-01

    The mitochondrial DNA from Xenopus laevis is a 17.4 x 10(3)-base-pair circular DNA molecule. The mapping of this DNA, using 19 different restriction endonucleases is reported here. The sites are as follows: 1 for BamHI, PstI, SacI, SalI, BalI; 2 for BglII, SacII, EcoRI, ClaI, 3 for XhoI, 4 for AvaI, XbaI, PvuII, 5 for HindIII, 6 for HhaI, BclI, HpaI, 10 for AvaII and 11 for HincII. The same sites (except for one of the two ClaI sites) are observed in the molecule cloned in pBR322 DNA. The fragments corresponding to 62 cleavage sites have all been ordered and precisely located. They provide suitable conditions for further investigations connected with the study of replication and nucleotide sequence determination of this molecule.

  16. Holes influence the mutation spectrum of human mitochondrial DNA

    NASA Astrophysics Data System (ADS)

    Villagran, Martha; Miller, John

    Mutations drive evolution and disease, showing highly non-random patterns of variant frequency vs. nucleotide position. We use computational DNA hole spectroscopy [M.Y. Suarez-Villagran & J.H. Miller, Sci. Rep. 5, 13571 (2015)] to reveal sites of enhanced hole probability in selected regions of human mitochondrial DNA. A hole is a mobile site of positive charge created when an electron is removed, for example by radiation or contact with a mutagenic agent. The hole spectra are quantum mechanically computed using a two-stranded tight binding model of DNA. We observe significant correlation between spectra of hole probabilities and of genetic variation frequencies from the MITOMAP database. These results suggest that hole-enhanced mutation mechanisms exert a substantial, perhaps dominant, influence on mutation patterns in DNA. One example is where a trapped hole induces a hydrogen bond shift, known as tautomerization, which then triggers a base-pair mismatch during replication. Our results deepen overall understanding of sequence specific mutation rates, encompassing both hotspots and cold spots, which drive molecular evolution.

  17. Mitochondrial DNA Haplogroups and Neurocognitive Impairment During HIV Infection

    PubMed Central

    Hulgan, Todd; Samuels, David C.; Bush, William; Ellis, Ronald J.; Letendre, Scott L.; Heaton, Robert K.; Franklin, Donald R.; Straub, Peter; Murdock, Deborah G.; Clifford, David B.; Collier, Ann C.; Gelman, Benjamin B.; Marra, Christina M.; McArthur, Justin C.; McCutchan, J. Allen; Morgello, Susan; Simpson, David M.; Grant, Igor; Kallianpur, Asha R.

    2015-01-01

    Background. Neurocognitive impairment (NCI) remains an important complication in persons infected with human immunodeficiency virus (HIV). Ancestry-related mitochondrial DNA (mtDNA) haplogroups have been associated with outcomes of HIV infection and combination antiretroviral therapy (CART), and with neurodegenerative diseases. We hypothesize that mtDNA haplogroups are associated with NCI in HIV-infected adults and performed a genetic association study in the CNS HIV Antiretroviral Therapy Effects Research (CHARTER) cohort. Methods. CHARTER is an observational study of ambulatory HIV-infected adults. Haplogroups were assigned using mtDNA sequence, and principal components were derived from ancestry-informative nuclear DNA variants. Outcomes were cross-sectional global deficit score (GDS) as a continuous measure, GDS impairment (GDS ≥ 0.50), and HIV-associated neurocognitive disorder (HAND) using international criteria. Multivariable models were adjusted for comorbidity status (incidental vs contributing), current CART, plasma HIV RNA, reading ability, and CD4 cell nadir. Results. Haplogroups were available from 1027 persons; median age 43 years, median CD4 nadir 178 cells/mm3, 72% on CART, and 46% with HAND. The 102 (9.9%) persons of genetically determined admixed Hispanic ancestry had more impairment by GDS or HAND than persons of European or African ancestry (P < .001 for all). In multivariate models including persons of admixed Hispanic ancestry, those with haplogroup B had lower GDS (β = −0.34; P = .008) and less GDS impairment (odds ratio = 0.16; 95% confidence interval, .04, .63; P = .009) than other haplogroups. There were no significant haplogroup associations among persons of European or African ancestry. Conclusions. In these mostly CART-treated persons, mtDNA haplogroup B was associated with less NCI among persons of genetically determined Hispanic ancestry. mtDNA variation may represent an ancestry-specific factor influencing NCI in HIV

  18. History of plastid DNA insertions reveals weak deletion and at mutation biases in angiosperm mitochondrial genomes.

    PubMed

    Sloan, Daniel B; Wu, Zhiqiang

    2014-11-21

    Angiosperm mitochondrial genomes exhibit many unusual properties, including heterogeneous nucleotide composition and exceptionally large and variable genome sizes. Determining the role of nonadaptive mechanisms such as mutation bias in shaping the molecular evolution of these unique genomes has proven challenging because their dynamic structures generally prevent identification of homologous intergenic sequences for comparative analyses. Here, we report an analysis of angiosperm mitochondrial DNA sequences that are derived from inserted plastid DNA (mtpts). The availability of numerous completely sequenced plastid genomes allows us to infer the evolutionary history of these insertions, including the specific nucleotide substitutions and indels that have occurred because their incorporation into the mitochondrial genome. Our analysis confirmed that many mtpts have a complex history, including frequent gene conversion and multiple examples of horizontal transfer between divergent angiosperm lineages. Nevertheless, it is clear that the majority of extant mtpt sequence in angiosperms is the product of recent transfer (or gene conversion) and is subject to rapid loss/deterioration, suggesting that most mtpts are evolving relatively free from functional constraint. The evolution of mtpt sequences reveals a pattern of biased mutational input in angiosperm mitochondrial genomes, including an excess of small deletions over insertions and a skew toward nucleotide substitutions that increase AT content. However, these mutation biases are far weaker than have been observed in many other cellular genomes, providing insight into some of the notable features of angiosperm mitochondrial architecture, including the retention of large intergenic regions and the relatively neutral GC content found in these regions.

  19. Mitochondrial DNA haplogroups and short-term neurological outcomes of ischemic stroke

    PubMed Central

    Cai, Biyang; Zhang, Zhizhong; Liu, Keting; Fan, Wenping; Zhang, Yumeng; Xie, Xia; Dai, Minhui; Cao, Liping; Bai, Wen; Du, Juan; Dai, Qiliang; Zhou, Shuyu; Zhang, Hao; Zhu, Wusheng; Ma, Minmin; Liu, Wenhua; Liu, Xinfeng; Xu, Gelin

    2015-01-01

    Stroke is one of the leading causes of death and long-term disability worldwide. Mitochondrial DNA (mtDNA) is a potential contributor for the sex differences of ischemic stroke heritability. Although mtDNA haplogroups were associated with stroke onset, their impacts on stroke outcomes remain unclear. This study aimed to evaluate the impacts of mtDNA haplogroups on short-term outcomes of neurological functions in patients with ischemic stroke. A total of 303 patients were included, and their clinical data and mtDNA sequences were analyzed. Based on the changes between baseline and 14-day follow-up stroke severity, our results showed that haplogroup N9 was an independent protective factor against neurological worsening in acute ischemic stroke patients. These findings supported that mtDNA variants play a role in post-stroke neurological recovery, thus providing evidences for future pharmacological intervention in mitochondrial function. PMID:25993529

  20. The Yeast Mitochondrial RNA Polymerase and Transcription Factor Complex Catalyzes Efficient Priming of DNA Synthesis on Single-stranded DNA.

    PubMed

    Ramachandran, Aparna; Nandakumar, Divya; Deshpande, Aishwarya P; Lucas, Thomas P; R-Bhojappa, Ramanagouda; Tang, Guo-Qing; Raney, Kevin; Yin, Y Whitney; Patel, Smita S

    2016-08-05

    Primases use single-stranded (ss) DNAs as templates to synthesize short oligoribonucleotide primers that initiate lagging strand DNA synthesis or reprime DNA synthesis after replication fork collapse, but the origin of this activity in the mitochondria remains unclear. Herein, we show that the Saccharomyces cerevisiae mitochondrial RNA polymerase (Rpo41) and its transcription factor (Mtf1) is an efficient primase that initiates DNA synthesis on ssDNA coated with the yeast mitochondrial ssDNA-binding protein, Rim1. Both Rpo41 and Rpo41-Mtf1 can synthesize short and long RNAs on ssDNA template and prime DNA synthesis by the yeast mitochondrial DNA polymerase Mip1. However, the ssDNA-binding protein Rim1 severely inhibits the RNA synthesis activity of Rpo41, but not the Rpo41-Mtf1 complex, which continues to prime DNA synthesis efficiently in the presence of Rim1. We show that RNAs as short as 10-12 nt serve as primers for DNA synthesis. Characterization of the RNA-DNA products shows that Rpo41 and Rpo41-Mtf1 have slightly different priming specificity. However, both prefer to initiate with ATP from short priming sequences such as 3'-TCC, TTC, and TTT, and the consensus sequence is 3'-Pu(Py)2-3 Based on our studies, we propose that Rpo41-Mtf1 is an attractive candidate for serving as the primase to initiate lagging strand DNA synthesis during normal replication and/or to restart stalled replication from downstream ssDNA.

  1. [Somatic mutations in nuclear and mitochondrial DNA]. Progress report

    SciTech Connect

    Not Available

    1992-09-01

    The study is concerned the design of new assays that may detect rare somatic mutations in nuclear and mitochondrial DNA, which may increase upon exposure to mutagens, and thus become a marker of human exposure to such mutagens. Two assays for somatic mutation were presented, one for mitochondrial DNA deletions which was developed by the author, and one for deletions of the ADA gene which resides in the nucleus.

  2. A molecular phylogeny of Hemiptera inferred from mitochondrial genome sequences.

    PubMed

    Song, Nan; Liang, Ai-Ping; Bu, Cui-Ping

    2012-01-01

    Classically, Hemiptera is comprised of two suborders: Homoptera and Heteroptera. Homoptera includes Cicadomorpha, Fulgoromorpha and Sternorrhyncha. However, according to previous molecular phylogenetic studies based on 18S rDNA, Fulgoromorpha has a closer relationship to Heteroptera than to other hemipterans, leaving Homoptera as paraphyletic. Therefore, the position of Fulgoromorpha is important for studying phylogenetic structure of Hemiptera. We inferred the evolutionary affiliations of twenty-five superfamilies of Hemiptera using mitochondrial protein-coding genes and rRNAs. We sequenced three mitogenomes, from Pyrops candelaria, Lycorma delicatula and Ricania marginalis, representing two additional families in Fulgoromorpha. Pyrops and Lycorma are representatives of an additional major family Fulgoridae in Fulgoromorpha, whereas Ricania is a second representative of the highly derived clade Ricaniidae. The organization and size of these mitogenomes are similar to those of the sequenced fulgoroid species. Our consensus phylogeny of Hemiptera largely supported the relationships (((Fulgoromorpha,Sternorrhyncha),Cicadomorpha),Heteroptera), and thus supported the classic phylogeny of Hemiptera. Selection of optimal evolutionary models (exclusion and inclusion of two rRNA genes or of third codon positions of protein-coding genes) demonstrated that rapidly evolving and saturated sites should be removed from the analyses.

  3. Peripheral blood mitochondrial DNA/nuclear DNA (mtDNA/nDNA) ratio as a marker of mitochondrial toxicities of stavudine containing antiretroviral thera