Science.gov

Sample records for chloroplast microsatellites reveal

  1. Chloroplast microsatellites reveal colonization and metapopulation dynamics in the Canary Island pine

    PubMed Central

    Navascués, Miguel; Vaxevanidou, Zafeiro; González-Martínez, Santiago C; Climent, José; Gil, Luis; Emerson, Brent C

    2006-01-01

    Chloroplast microsatellites are becoming increasingly popular markers for population genetic studies in plants, but there has been little focus on their potential for demographic inference. In this work the utility of chloroplast microsatellites for the study of population expansions was explored. First, we investigated the power of mismatch distribution analysis and the FS test with coalescent simulations of different demographic scenarios. We then applied those methods to empirical data obtained for the Canary Island pine (Pinus canariensis). The results of the simulations showed that chloroplast microsatellites are sensitive to sudden population growth. The power of the FS test and accuracy of demographic parameter estimates, such as the time of expansion, were reduced proportionally to the level of homoplasy within the data. The analysis of Canary Island pine chloroplast microsatellite data indicated population expansions for almost all sample localities. Demographic expansions at the island level can be explained by the colonisation of the archipelago by the pine, while population expansions of different ages in different localities within an island appear to be the result of local extinctions and recolonisation dynamics. Comparable mitochondrial DNA sequence data from a parasite of P. canariensis, the weevil Brachyderes rugatus, supports this scenario, suggesting a key role for volcanism in the evolution of pine forest communities in the Canary Islands. PMID:16911194

  2. Genepool Variation in Genus Glycine Subgenus Soja Revealed by Polymorphic Nuclear and Chloroplast Microsatellites

    PubMed Central

    Powell, W.; Morgante, M.; Doyle, J. J.; McNicol, J. W.; Tingey, S. V.; Rafalski, A. J.

    1996-01-01

    A combination of nuclear and chloroplast simple sequence repeats (SSRs) have been used to investigate the levels and pattern of variability detected in Glycine max and G. soja genotypes. Based on the analysis of 700 soybean genotypes with 115 restriction fragment length polymorphism (RFLP) probes, 12 accessions were identified that represent 92% of the allelic variability detected in this genepool. These 12 core genotypes together with a sample of G. max and G. soja accessions were evaluated with 11 nuclear SSRs that detected 129 alleles. Compared with the other G. max and G. soja genotypes sampled, the core genotypes represent 40% of the allelic variability detected with SSRs. Despite the multi-allelic nature of soybean SSRs, dendrograms representing phenetic relationships between accessions clustered according to their subspecies origin. In addition to biparentally inherited nuclear SSRs, two uniparentally (maternally) transmitted chloroplast SSRs were also studied. A total of seven haplotypes were identified, and diversity indices of 0.405 +/- 0.088 and 0.159 +/- 0.071 were obtained for the two chloroplast SSRs. The availability of polymorphic SSR loci in the chloroplast genome provides new opportunities to investigate cytonuclear interactions in plants. PMID:8889540

  3. Chloroplast microsatellite markers for Artocarpus (Moraceae) developed from transcriptome sequences

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Premise of the study: Chloroplast microsatellite loci were characterized from transcriptomes of Artocarpus (A.) altilis (breadfruit) and A. camansi (breadnut). They were tested in A. odoratissimus (terap) and A. altilis and evaluated in silico for two congeners. Methods and Results: 15 simple seque...

  4. Chloroplast and nuclear microsatellite analysis of Aegilops cylindrica.

    PubMed

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

    2005-08-01

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

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

    PubMed

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

    2007-12-01

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

  6. The use of chloroplast microsatellite markers for assessing cytoplasmic variation in a watermelon germplasm collection.

    PubMed

    Hu, J-B; Li, J-W; Li, Q; Ma, S-W; Wang, J-M

    2011-11-01

    Fifteen chloroplast microsatellite (cpSSR) markers were tested to analyze cytoplasmic variation in a set of watermelon accessions containing 67 Chinese watermelon germplasms (CWGs) and 19 non-Chinese watermelon germplasms (NCGs), and 11 were polymorphic. These polymorphic cpSSR markers detected 2-4 alleles (mean = 2.8) in all the accessions, with diversity values ranging from 0.047 to 0.427 (mean = 0.252). Based on the polymorphic cpSSR loci, 17 distinct haplotypes were identified, of which six were from CWGs, seven were from NCGs, and four were shared by both of them. Most haplotypes from CWGs were nearly identical at the 11 cpSSR loci, but those from NCGs revealed higher variations. Of the haplotypes from CWGs, a predominant haplotype was found in 76.1% of CWGs, indicating that CWGs suffered a cytoplasmic bottleneck in domestication process and lost most of their cytoplasmic variability. To analyze the relationships among these 17 haplotypes, a dendrogram was constructed based on the cpSSR data using the unweighted pair-group method with arithmetic average (UPGMA). Three distinct groups were generated, revealing a genetic divergence between CWGs and NCGs. From this analysis, we obtained five rare haplotypes which had quite low genetic similarity to the others and would be useful for watermelon breeding in China. The results enriched the knowledge in genetic diversity of CWGs and could be informative for broadening the genetic base of watermelon. PMID:21327542

  7. Chloroplast microsatellite markers for Artocarpus (Moraceae) developed from transcriptome sequences1

    PubMed Central

    Gardner, Elliot M.; Laricchia, Kristen M.; Murphy, Matthew; Ragone, Diane; Scheffler, Brian E.; Simpson, Sheron; Williams, Evelyn W.; Zerega, Nyree J. C.

    2015-01-01

    Premise of the study: Chloroplast microsatellite loci were characterized from transcriptomes of Artocarpus altilis (breadfruit) and A. camansi (breadnut). They were tested in A. odoratissimus (terap) and A. altilis and evaluated in silico for two congeners. Methods and Results: Fifteen simple sequence repeats (SSRs) were identified in chloroplast sequences from four Artocarpus transcriptome assemblies. The markers were evaluated using capillary electrophoresis in A. odoratissimus (105 accessions) and A. altilis (73). They were also evaluated in silico in A. altilis (10), A. camansi (6), and A. altilis × A. mariannensis (7) transcriptomes. All loci were polymorphic in at least one species, with all 15 polymorphic in A. camansi. Per species, average alleles per locus ranged between 2.2 and 2.5. Three loci had evidence of fragment-length homoplasy. Conclusions: These markers will complement existing nuclear markers by enabling confident identification of maternal and clone lines, which are often important in vegetatively propagated crops such as breadfruit. PMID:26421253

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

    PubMed

    Ryzhova, N N; Kochieva, E Z

    2004-08-01

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

  9. Development of chloroplast microsatellite markers for the endangered Maianthemum bicolor (Asparagaceae s.l.)1

    PubMed Central

    Park, Hana; Kim, Changkyun; Lee, You-Mi; Kim, Joo-Hwan

    2016-01-01

    Premise of the study: Ten polymorphic chloroplast microsatellite (cpSSR) markers were developed and characterized in an endemic and endangered herb, Maianthemum bicolor (Asparagaceae s.l.), for use in conservation genetics. Methods and Results: Primer sets flanking each of the 10 cpSSR loci in noncoding regions of the chloroplast genome of M. bicolor were designed. These cpSSR markers were tested on a total of 33 adult individuals from three natural populations in South Korea. The number of alleles per locus ranged from two to three. The unbiased haplotype diversity per locus ranged from 0.061 to 0.682. All markers were successfully transferred to the congeneric species M. japonicum, M. bifolium, and M. dilatatum with polymorphisms among the species. Conclusions: The developed cpSSR markers will be useful in assessing the genetic diversity and population structure of M. bicolor and will help to infer its molecular identification, thereby providing a basis for conservation. PMID:27610276

  10. Genetic structure based on nuclear and chloroplast microsatellite loci of Solanum lycocarpum A. St. Hil. (Solanaceae) in Central Brazil.

    PubMed

    Martins, K; Chaves, L J; Vencovsky, R; Kageyama, P Y

    2011-01-01

    Solanum lycocarpum (Solanaceae) is a woody species found in the Brazilian Cerrado. The flowers are pollinated by Xylocopa spp bees, and seeds are dispersed by mammals with distinct home range sizes. As a consequence, relative contributions of pollen and seeds to overall gene flow can vary according to different spatial scales. We studied the genetic structure of four natural populations of S. lycocarpum separated by 19 to 128 km, including individuals located along dirt roads that interlink three of the populations. A total of 294 individuals were genotyped with five nuclear and six chloroplast microsatellite markers. Significant spatial genetic structure was found in the total set of individuals; the Sp statistic was 0.0086. Population differentiation based on the six chloroplast microsatellite markers (θ(pC) = 0.042) was small and similar to that based on the five nuclear microsatellite markers (θ(p) = 0.054). For this set of populations, pollen and seed flow did not differ significantly from one another (pollen-to-seed flow ratio = 1.22). Capability for long distance seed dispersion and colonization of anthropogenic sites contributes to the ability of S. lycocarpum to maintain genetic diversity. Seed dispersion along dirt roads may be critical in preserving S. lycocarpum genetic diversity in fragmented landscapes. PMID:21523656

  11. Development of Chloroplast Microsatellite Markers and Analysis of Chloroplast Diversity in Chinese Jujube (Ziziphus jujuba Mill.) and Wild Jujube (Ziziphus acidojujuba Mill.).

    PubMed

    Huang, Jian; Yang, Xiaoting; Zhang, Chunmei; Yin, Xiao; Liu, Shipeng; Li, Xingang

    2015-01-01

    Ziziphus is an important genus within the family Rhamnaceae. This genus includes several important fruit tree species that are widely planted in China and India, such as the Chinese jujube (Ziziphus jujuba Mill.), the wild jujube (Z. acidojujuba), and the Indian jujube (Z. mauritiana). However, information about their domestication based on the chlorotype diversity of Chinese jujube population is lacking. In this study, chloroplast microsatellite (cpSSR) markers were developed and used to investigate the genetic relationships between and domestication of jujube cultivars and wild jujube populations. Primer sets flanking each of the 46 cpSSR loci in non-coding regions of the chloroplast genome sequence of Z. jujuba Mill. cv. 'Junzao' were designed. In total, 10 markers showed polymorphisms from 15 samples (9 jujube cultivars and 6 wild jujube individuals), of which 8 loci were due to variations in the number of mononucleotide (A/T) repeats and 2 were due to indels. Six cpSSR markers were used in further analyses of 81 additional samples (63 jujube cultivars, 17 wild jujube samples, and 1 Indian jujube). Using these cpSSR markers, the number of alleles per locus ranged from two to four. In general, the Shannon Index (I) for each cpSSR ranged from 0.159 to 0.1747, and the diversity indices (h) and uh were 0.061 to 0.435 and 0.062 to 0.439, respectively. Seven chlorotypes were found; the Indian jujube showed distinct chlorotypes, and both the Chinese and wild jujube had four chlorotypes and shared two chlorotypes. A dominant chlorotype (G) accounted for 53 of 72 jujube cultivars and 13 of 23 wild jujube individuals. All chlorotypes were highly localized along the Yellow River, from the mid- to the lower reaches, suggesting a wide origin of jujube. These cpSSR markers can be applied to population and evolution studies of Chinese jujube and wild jujube. PMID:26406601

  12. Development of Chloroplast Microsatellite Markers and Analysis of Chloroplast Diversity in Chinese Jujube (Ziziphus jujuba Mill.) and Wild Jujube (Ziziphus acidojujuba Mill.)

    PubMed Central

    Huang, Jian; Yang, Xiaoting; Zhang, Chunmei; Yin, Xiao; Liu, Shipeng; Li, Xingang

    2015-01-01

    Ziziphus is an important genus within the family Rhamnaceae. This genus includes several important fruit tree species that are widely planted in China and India, such as the Chinese jujube (Ziziphus jujuba Mill.), the wild jujube (Z. acidojujuba), and the Indian jujube (Z. mauritiana). However, information about their domestication based on the chlorotype diversity of Chinese jujube population is lacking. In this study, chloroplast microsatellite (cpSSR) markers were developed and used to investigate the genetic relationships between and domestication of jujube cultivars and wild jujube populations. Primer sets flanking each of the 46 cpSSR loci in non-coding regions of the chloroplast genome sequence of Z. jujuba Mill. cv. ‘Junzao’ were designed. In total, 10 markers showed polymorphisms from 15 samples (9 jujube cultivars and 6 wild jujube individuals), of which 8 loci were due to variations in the number of mononucleotide (A/T) repeats and 2 were due to indels. Six cpSSR markers were used in further analyses of 81 additional samples (63 jujube cultivars, 17 wild jujube samples, and 1 Indian jujube). Using these cpSSR markers, the number of alleles per locus ranged from two to four. In general, the Shannon Index (I) for each cpSSR ranged from 0.159 to 0.1747, and the diversity indices (h) and uh were 0.061 to 0.435 and 0.062 to 0.439, respectively. Seven chlorotypes were found; the Indian jujube showed distinct chlorotypes, and both the Chinese and wild jujube had four chlorotypes and shared two chlorotypes. A dominant chlorotype (G) accounted for 53 of 72 jujube cultivars and 13 of 23 wild jujube individuals. All chlorotypes were highly localized along the Yellow River, from the mid- to the lower reaches, suggesting a wide origin of jujube. These cpSSR markers can be applied to population and evolution studies of Chinese jujube and wild jujube. PMID:26406601

  13. Population Structure in Naegleria fowleri as Revealed by Microsatellite Markers

    PubMed Central

    Coupat-Goutaland, Bénédicte; Régoudis, Estelle; Besseyrias, Matthieu; Mularoni, Angélique; Binet, Marie; Herbelin, Pascaline; Pélandakis, Michel

    2016-01-01

    Naegleria sp. is a free living amoeba belonging to the Heterolobosea class. Over 40 species of Naegleria were identified and recovered worldwide in different habitats such as swimming pools, freshwater lakes, soil or dust. Among them, N. fowleri, is a human pathogen responsible for primary amoeboic meningoencephalitis (PAM). Around 300 cases were reported in 40 years worldwide but PAM is a fatal disease of the central nervous system with only 5% survival of infected patients. Since both pathogenic and non pathogenic species were encountered in the environment, detection and dispersal mode are crucial points in the fight against this pathogenic agent. Previous studies on identification and genotyping of N. fowleri strains were focused on RAPD analysis and on ITS sequencing and identified 5 variants: euro-american, south pacific, widespread, cattenom and chooz. Microsatellites are powerful markers in population genetics with broad spectrum of applications (such as paternity test, fingerprinting, genetic mapping or genetic structure analysis). They are characterized by a high degree of length polymorphism. The aim of this study was to genotype N. fowleri strains using microsatellites markers in order to track this population and to better understand its evolution. Six microsatellite loci and 47 strains from different geographical origins were used for this analysis. The microsatellite markers revealed a level of discrimination higher than any other marker used until now, enabling the identification of seven genetic groups, included in the five main genetic groups based on the previous RAPD and ITS analyses. This analysis also allowed us to go further in identifying private alleles highlighting intra-group variability. A better identification of the N. fowleri isolates could be done with this type of analysis and could allow a better tracking of the clinical and environmental N. fowleri strains. PMID:27035434

  14. Population Structure in Naegleria fowleri as Revealed by Microsatellite Markers.

    PubMed

    Coupat-Goutaland, Bénédicte; Régoudis, Estelle; Besseyrias, Matthieu; Mularoni, Angélique; Binet, Marie; Herbelin, Pascaline; Pélandakis, Michel

    2016-01-01

    Naegleria sp. is a free living amoeba belonging to the Heterolobosea class. Over 40 species of Naegleria were identified and recovered worldwide in different habitats such as swimming pools, freshwater lakes, soil or dust. Among them, N. fowleri, is a human pathogen responsible for primary amoeboic meningoencephalitis (PAM). Around 300 cases were reported in 40 years worldwide but PAM is a fatal disease of the central nervous system with only 5% survival of infected patients. Since both pathogenic and non pathogenic species were encountered in the environment, detection and dispersal mode are crucial points in the fight against this pathogenic agent. Previous studies on identification and genotyping of N. fowleri strains were focused on RAPD analysis and on ITS sequencing and identified 5 variants: euro-american, south pacific, widespread, cattenom and chooz. Microsatellites are powerful markers in population genetics with broad spectrum of applications (such as paternity test, fingerprinting, genetic mapping or genetic structure analysis). They are characterized by a high degree of length polymorphism. The aim of this study was to genotype N. fowleri strains using microsatellites markers in order to track this population and to better understand its evolution. Six microsatellite loci and 47 strains from different geographical origins were used for this analysis. The microsatellite markers revealed a level of discrimination higher than any other marker used until now, enabling the identification of seven genetic groups, included in the five main genetic groups based on the previous RAPD and ITS analyses. This analysis also allowed us to go further in identifying private alleles highlighting intra-group variability. A better identification of the N. fowleri isolates could be done with this type of analysis and could allow a better tracking of the clinical and environmental N. fowleri strains. PMID:27035434

  15. Small effect of fragmentation on the genetic diversity of Dalbergia monticola, an endangered tree species of the eastern forest of Madagascar, detected by chloroplast and nuclear microsatellites

    PubMed Central

    Andrianoelina, O.; Favreau, B.; Ramamonjisoa, L.; Bouvet, J.-M.

    2009-01-01

    Background and Aims The oriental forest ecosystem in Madagascar has been seriously impacted by fragmentation. The pattern of genetic diversity was analysed on a tree species, Dalbergia monticola, which plays an important economic role in Madagascar and is one of the many endangered tree species in the eastern forest. Methods Leaves from 546 individuals belonging to 18 small populations affected by different levels of fragmentation were genotyped using eight nuclear (nuc) and three chloroplast (cp) microsatellite markers. Key Results For nuclear microsatellites, allelic richness (R) and heterozygosity (He,nuc) differed between types of forest: R = 7·36 and R = 9·55, He,nuc = 0·64 and He,nuc = 0·80 in fragmented and non-fragmented forest, respectively, but the differences were not significant. Only the mean number of alleles (Na,nuc) and the fixation index FIS differed significantly: Na,nuc = 9·41 and Na,nuc = 13·18, FIS = 0·06 and FIS = 0·15 in fragmented and non-fragmented forests, respectively. For chloroplast microsatellites, estimated genetic diversity was higher in non-fragmented forest, but the difference was not significant. No recent bottleneck effect was detected for either population. Overall differentiation was low for nuclear microsatellites (FST,nuc = 0·08) and moderate for chloroplast microsatellites (FST,cp = 0·49). A clear relationship was observed between genetic and geographic distance (r = 0·42 P < 0·01 and r = 0·42 P = 0·03 for nuclear and chloroplast microsatellites, respectively), suggesting a pattern of isolation by distance. Analysis of population structure using the neighbor-joining method or Bayesian models separated southern populations from central and northern populations with nuclear microsatellites, and grouped the population according to regions with chloroplast microsatellites, but did not separate the fragmented populations. Conclusions Residual diversity and genetic structure of populations of D. monticola in

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

    PubMed

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

    2011-04-01

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

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

    PubMed Central

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

    2011-01-01

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

  18. Genetic variation and phylogeography of Stauracanthus (Fabaceae, Genisteae) from the Iberian Peninsula and northern Morocco assessed by chloroplast microsatellite (cpSSR) markers.

    PubMed

    Pardo, Cristina; Cubas, Paloma; Tahiri, Hikmat

    2008-01-01

    The tribe Genisteae includes genera of great ecological importance in Mediterranean countries because they are dominant elements of many plant communities. Genetic variation and diversification patterns in Stauracanthus (Genisteae) provide information relevant for the study of the processes of diversification in relation to the environmental history of the western Mediterranean. Nineteen populations of S. boivinii and S. genistoides were assessed by 11 chloroplast microsatellite markers, revealing 44 haplotypes. Both species had different haplotypes and contrasting patterns of karyological, morphological, and genetic variation. In the minimum spanning tree of the haplotypes, AMOVA analysis, and nested clade analysis, S. boivinii had high levels of differentiation and restricted gene flow among populations. Allopatric differentiation occurred between the Moroccan and Iberian populations of S. genistoides, although S. genistoides subsp. spectabilis and subsp. vicentinus had high levels of differentiation among populations (F(ST)), whereas S. genistoides subsp. genistoides had a low F(ST). Genetic patterns are discussed in relation to the Messinian salinity crisis (MSC): hard conditions drove plants to refuge habitats along the Atlantic coast and higher altitude areas in the Moroccan mountains (S. genistoides subsp. spectabilis and S. boivinii). After the MSC, S. boivinii underwent polyploidization and expansion, whereas S. genistoides expanded and continued diversifying into S. genistoides subspp. genistoides and vicentinus. PMID:21632320

  19. Repression of Essential Chloroplast Genes Reveals New Signaling Pathways and Regulatory Feedback Loops in Chlamydomonas[W

    PubMed Central

    Ramundo, Silvia; Rahire, Michèle; Schaad, Olivier; Rochaix, Jean-David

    2013-01-01

    Although reverse genetics has been used to elucidate the function of numerous chloroplast proteins, the characterization of essential plastid genes and their role in chloroplast biogenesis and cell survival has not yet been achieved. Therefore, we developed a robust repressible chloroplast gene expression system in the unicellular alga Chlamydomonas reinhardtii based mainly on a vitamin-repressible riboswitch, and we used this system to study the role of two essential chloroplast genes: ribosomal protein S12 (rps12), encoding a plastid ribosomal protein, and rpoA, encoding the α-subunit of chloroplast bacterial-like RNA polymerase. Repression of either of these two genes leads to the arrest of cell growth, and it induces a response that involves changes in expression of nuclear genes implicated in chloroplast biogenesis, protein turnover, and stress. This response also leads to the overaccumulation of several plastid transcripts and reveals the existence of multiple negative regulatory feedback loops in the chloroplast gene circuitry. PMID:23292734

  20. Native architecture of the Chlamydomonas chloroplast revealed by in situ cryo-electron tomography

    PubMed Central

    Engel, Benjamin D; Schaffer, Miroslava; Kuhn Cuellar, Luis; Villa, Elizabeth; Plitzko, Jürgen M; Baumeister, Wolfgang

    2015-01-01

    Chloroplast function is orchestrated by the organelle's intricate architecture. By combining cryo-focused ion beam milling of vitreous Chlamydomonas cells with cryo-electron tomography, we acquired three-dimensional structures of the chloroplast in its native state within the cell. Chloroplast envelope inner membrane invaginations were frequently found in close association with thylakoid tips, and the tips of multiple thylakoid stacks converged at dynamic sites on the chloroplast envelope, implicating lipid transport in thylakoid biogenesis. Subtomogram averaging and nearest neighbor analysis revealed that RuBisCO complexes were hexagonally packed within the pyrenoid, with ∼15 nm between their centers. Thylakoid stacks and the pyrenoid were connected by cylindrical pyrenoid tubules, physically bridging the sites of light-dependent photosynthesis and light-independent carbon fixation. Multiple parallel minitubules were bundled within each pyrenoid tubule, possibly serving as conduits for the targeted one-dimensional diffusion of small molecules such as ATP and sugars between the chloroplast stroma and the pyrenoid matrix. DOI: http://dx.doi.org/10.7554/eLife.04889.001 PMID:25584625

  1. Phaseolin expression in tobacco chloroplast reveals an autoregulatory mechanism in heterologous protein translation.

    PubMed

    De Marchis, Francesca; Bellucci, Michele; Pompa, Andrea

    2016-02-01

    Plastid DNA engineering is a well-established research area of plant biotechnology, and plastid transgenes often give high expression levels. However, it is still almost impossible to predict the accumulation rate of heterologous protein in transplastomic plants, and there are many cases of unsuccessful transgene expression. Chloroplasts regulate their proteome at the post-transcriptional level, mainly through translation control. One of the mechanisms to modulate the translation has been described in plant chloroplasts for the chloroplast-encoded subunits of multiprotein complexes, and the autoregulation of the translation initiation of these subunits depends on the availability of their assembly partners [control by epistasy of synthesis (CES)]. In Chlamydomonas reinhardtii, autoregulation of endogenous proteins recruited in the assembly of functional complexes has also been reported. In this study, we revealed a self-regulation mechanism triggered by the accumulation of a soluble recombinant protein, phaseolin, in the stroma of chloroplast-transformed tobacco plants. Immunoblotting experiments showed that phaseolin could avoid this self-regulation mechanism when targeted to the thylakoids in transplastomic plants. To inhibit the thylakoid-targeted phaseolin translation as well, this protein was expressed in the presence of a nuclear version of the phaseolin gene with a transit peptide. Pulse-chase and polysome analysis revealed that phaseolin mRNA translation on plastid ribosomes was repressed due to the accumulation in the stroma of the same soluble polypeptide imported from the cytosol. We suggest that translation autoregulation in chloroplast is not limited to heteromeric protein subunits but also involves at least some of the foreign soluble recombinant proteins, leading to the inhibition of plastome-encoded transgene expression in chloroplast. PMID:26031839

  2. Comparison of Transcriptional Changes to Chloroplast and Mitochondrial Perturbations Reveals Common and Specific Responses in Arabidopsis

    PubMed Central

    Van Aken, Olivier; Whelan, James

    2012-01-01

    Throughout the life of a plant, the biogenesis and fine-tuning of energy organelles is essential both under normal growth and stress conditions. Communication from organelle to nucleus is essential to adapt gene regulation and protein synthesis specifically to the current needs of the plant. This organelle-to-nuclear communication is termed retrograde signaling and has been studied extensively over the last decades. In this study we have used large-scale gene expression data sets relating to perturbations of chloroplast and mitochondrial function to gain further insights into plant retrograde signaling and how mitochondrial and chloroplast retrograde pathways interact and differ. Twenty seven studies were included that assess transcript profiles in response to chemical inhibition as well as genetic mutations of organellar proteins. The results show a highly significant overlap between gene expression changes triggered by chloroplast and mitochondrial perturbations. These overlapping gene expression changes appear to be common with general abiotic, biotic, and nutrient stresses. However, retrograde signaling pathways are capable of distinguishing the source of the perturbation as indicated by a statistical overrepresentation of changes in genes encoding proteins of the affected organelle. Organelle-specific overrepresented functional categories among others relate to energy metabolism and protein synthesis. Our analysis also suggests that WRKY transcription factors play a coordinating role on the interface of both organellar signaling pathways. Global comparison of the expression profiles for each experiment revealed that the recently identified chloroplast retrograde pathway using phospho-adenosine phosphate is possibly more related to mitochondrial than chloroplast perturbations. Furthermore, new marker genes have been identified that respond specifically to mitochondrial and/or chloroplast dysfunction. PMID:23269925

  3. Recent similarity in distribution ranges does not mean a similar postglacial history: a phylogeographical study of the boreal tree species Alnus incana based on microsatellite and chloroplast DNA variation.

    PubMed

    Mandák, Bohumil; Havrdová, Alena; Krak, Karol; Hadincová, Věroslava; Vít, Petr; Zákravský, Petr; Douda, Jan

    2016-06-01

    We reconstructed the historical pattern of postglacial biogeographic range expansion of the boreal tree species Alnus incana in Europe. To assess population genetic structure and diversity, we performed a combined analysis of nuclear microsatellite loci and chloroplast DNA sequences (65 populations, 1004 individuals). Analysis of haplotype and microsatellite diversity revealed that southeastern refugial populations situated in the Carpathians and the Balkan Peninsula did not spread north and cannot be considered as important source populations for postglacial recolonization of Europe; populations in Eastern Europe did not establish Fennoscandian populations; populations in Fennoscandia and Eastern Europe have no unique genetic cluster, but represent a mix with a predominant cluster typical for Central Europe; and that colonization of Fennoscandia and Eastern Europe took place from Central Europe. Our findings highlight the importance of an effective refugium in Central Europe located outside classical southern refugia confirming the existence of northern refugia for boreal trees in Europe. The postglacial range expansion of A. incana did not follow the model established for Picea abies. Fennoscandian populations are not derived from Eastern European ones, but from Central European ones. PMID:26831816

  4. The Historical Demography and Genetic Variation of the Endangered Cycas multipinnata (Cycadaceae) in the Red River Region, Examined by Chloroplast DNA Sequences and Microsatellite Markers

    PubMed Central

    Gong, Yi-Qing; Zhan, Qing-Qing; Nguyen, Khang Sinh; Nguyen, Hiep Tien; Wang, Yue-Hua; Gong, Xun

    2015-01-01

    Cycas multipinnata C.J. Chen & S.Y. Yang is a cycad endemic to the Red River drainage region that occurs under evergreen forest on steep limestone slopes in Southwest China and northern Vietnam. It is listed as endangered due to habitat loss and over-collecting for the ornamental plant trade, and only several populations remain. In this study, we assess the genetic variation, population structure, and phylogeography of C. multipinnata populations to help develop strategies for the conservation of the species. 60 individuals from six populations were used for chloroplast DNA (cpDNA) sequencing and 100 individuals from five populations were genotyped using 17 nuclear microsatellites. High genetic differentiation among populations was detected, suggesting that pollen or seed dispersal was restricted within populations. Two main genetic clusters were observed in both the cpDNA and microsatellite loci, corresponding to Yunnan China and northern Vietnam. These clusters indicated low levels of gene flow between the regions since their divergence in the late Pleistocene, which was inferred from both Bayesian and coalescent analysis. In addition, the result of a Bayesian skyline plot based on cpDNA portrayed a long history of constant population size followed by a decline in the last 50,000 years of C. multipinnata that was perhaps affected by the Quaternary glaciations, a finding that was also supported by the Garza-Williamson index calculated from the microsatellite data. The genetic consequences produced by climatic oscillations and anthropogenic disturbances are considered key pressures on C. multipinnata. To establish a conservation management plan, each population of C. multipinnata should be recognized as a Management Unit (MU). In situ and ex situ actions, such as controlling overexploitation and creating a germplasm bank with high genetic diversity, should be urgently implemented to preserve this species. PMID:25689828

  5. The historical demography and genetic variation of the endangered Cycas multipinnata (Cycadaceae) in the red river region, examined by chloroplast DNA sequences and microsatellite markers.

    PubMed

    Gong, Yi-Qing; Zhan, Qing-Qing; Nguyen, Khang Sinh; Nguyen, Hiep Tien; Wang, Yue-Hua; Gong, Xun

    2015-01-01

    Cycas multipinnata C.J. Chen & S.Y. Yang is a cycad endemic to the Red River drainage region that occurs under evergreen forest on steep limestone slopes in Southwest China and northern Vietnam. It is listed as endangered due to habitat loss and over-collecting for the ornamental plant trade, and only several populations remain. In this study, we assess the genetic variation, population structure, and phylogeography of C. multipinnata populations to help develop strategies for the conservation of the species. 60 individuals from six populations were used for chloroplast DNA (cpDNA) sequencing and 100 individuals from five populations were genotyped using 17 nuclear microsatellites. High genetic differentiation among populations was detected, suggesting that pollen or seed dispersal was restricted within populations. Two main genetic clusters were observed in both the cpDNA and microsatellite loci, corresponding to Yunnan China and northern Vietnam. These clusters indicated low levels of gene flow between the regions since their divergence in the late Pleistocene, which was inferred from both Bayesian and coalescent analysis. In addition, the result of a Bayesian skyline plot based on cpDNA portrayed a long history of constant population size followed by a decline in the last 50,000 years of C. multipinnata that was perhaps affected by the Quaternary glaciations, a finding that was also supported by the Garza-Williamson index calculated from the microsatellite data. The genetic consequences produced by climatic oscillations and anthropogenic disturbances are considered key pressures on C. multipinnata. To establish a conservation management plan, each population of C. multipinnata should be recognized as a Management Unit (MU). In situ and ex situ actions, such as controlling overexploitation and creating a germplasm bank with high genetic diversity, should be urgently implemented to preserve this species. PMID:25689828

  6. Population analysis of microsatellite genotypes reveals a signature associated with ovarian cancer.

    PubMed

    Fonville, Natalie C; Vaksman, Zalman; McIver, Lauren J; Garner, Harold R

    2015-05-10

    Ovarian cancer (OV) ranks fifth in cancer deaths among women, yet there remain few informative biomarkers for this disease. Microsatellites are repetitive genomic regions which we hypothesize could be a source of novel biomarkers for OV and have traditionally been under-appreciated relative to Single Nucleotide Polymorphisms (SNPs). In this study, we explore microsatellite variation as a potential novel source of genomic variation associated with OV. Exomes from 305 OV patient germline samples and 54 tumors, sequenced as part of The Cancer Genome Atlas, were analyzed for microsatellite variation and compared to healthy females sequenced as part of the 1,000 Genomes Project. We identified a subset of 60 microsatellite loci with genotypes that varied significantly between the OV and healthy female populations. Using these loci as a signature set, we classified germline genomes as 'at risk' for OV with a sensitivity of 90.1% and a specificity of 87.6%. Cross-analysis with a similar set of breast cancer associated loci identified individuals 'at risk' for both diseases. This study revealed a genotype-based microsatellite signature present in the germlines of individuals diagnosed with OV, and provides the basis for a potential novel risk assessment diagnostic for OV and new personal genomics targets in tumors. PMID:25779658

  7. Crystallization of the c14-rotor of the chloroplast ATP synthase reveals that it contains pigments

    PubMed Central

    Varco-Merth, Benjamin; Fromme, Raimund; Wang, Meitian; Fromme, Petra

    2012-01-01

    The ATP synthase is one of the most important enzymes on earth as it couples the transmembrane electrochemical potential of protons to the synthesis of ATP from ADP and inorganic phosphate, providing the main ATP source of almost all higher life on earth. During ATP synthesis, stepwise protonation of a conserved carboxylate on each protein subunit of an oligomeric ring of 10–15 c-subunits is commonly thought to drive rotation of the rotor moiety (c10–14γε) relative to stator moiety (α3β3δab2). Here we report the isolation and crystallization of the c14-ring of subunit c from the spinach chloroplast enzyme diffracting as far as 2.8 Å. Though ATP synthase was not previously known to contain any pigments, the crystals of the c-subunit possessed a strong yellow color. The pigment analysis revealed that they contain 1 chlorophyll and 2 carotenoids, thereby showing for the first time that the chloroplast ATP synthase contains cofactors, leading to the question of the possible roles of the functions of the pigments in the chloroplast ATP synthase. PMID:18515064

  8. The Genetic Relationship between Leishmania aethiopica and Leishmania tropica Revealed by Comparing Microsatellite Profiles

    PubMed Central

    Krayter, Lena; Schnur, Lionel F.; Schönian, Gabriele

    2015-01-01

    Background Leishmania (Leishmania) aethiopica and L. (L.) tropica cause cutaneous leishmaniases and appear to be related. L. aethiopica is geographically restricted to Ethiopia and Kenya; L. tropica is widely dispersed from the Eastern Mediterranean, through the Middle East into eastern India and in north, east and south Africa. Their phylogenetic inter-relationship is only partially revealed. Some studies indicate a close relationship. Here, eight strains of L. aethiopica were characterized genetically and compared with 156 strains of L. tropica from most of the latter species' geographical range to discern the closeness. Methodology/Principal Findings Twelve unlinked microsatellite markers previously used to genotype strains of L. tropica were successfully applied to the eight strains of L. aethiopica and their microsatellite profiles were compared to those of 156 strains of L. tropica from various geographical locations that were isolated from human cases of cutaneous and visceral leishmaniasis, hyraxes and sand fly vectors. All the microsatellite profiles were subjected to various analytical algorithms: Bayesian statistics, distance-based and factorial correspondence analysis, revealing: (i) the species L. aethiopica, though geographically restricted, is genetically very heterogeneous; (ii) the strains of L. aethiopica formed a distinct genetic cluster; and (iii) strains of L. aethiopica are closely related to strains of L. tropica and more so to the African ones, although, by factorial correspondence analysis, clearly separate from them. Conclusions/Significance The successful application of the 12 microsatellite markers, originally considered species-specific for the species L. tropica, to strains of L. aethiopica confirmed the close relationship between these two species. The Bayesian and distance-based methods clustered the strains of L. aethiopica among African strains of L. tropica, while the factorial correspondence analysis indicated a clear separation

  9. Nuclear microsatellite variation in Malagasy baobabs (Adansonia, Bombacoideae, Malvaceae) reveals past hybridization and introgression

    PubMed Central

    Leong Pock Tsy, Jean-Michel; Lumaret, Roselyne; Flaven-Noguier, Elodie; Sauve, Mathieu; Dubois, Marie-Pierre; Danthu, Pascal

    2013-01-01

    Background and Aims Adansonia comprises nine species, six of which are endemic to Madagascar. Genetic relationships between the Malagasy species remain unresolved due to conflicting results between nuclear and plastid DNA variation. Morphologically intermediate individuals between distinct species have been identified, indicative of interspecific hybridization. In this paper, microsatellite data are used to identify potential cases of hybridization and to provide insights into the evolutionary history of the genus on Madagascar. Methods Eleven microsatellites amplified with new primers developed for Adansonia rubrostipa were used to analyse 672 individuals collected at 27 sites for the six Malagasy species and morphologically intermediate individuals. Rates of individual admixture were examined using three Bayesian clustering programs, STRUCTURE, BAPS and NewHybrids, with no a priori species assignment. Key Results Population differentiation was coherent, with recognized species boundaries. In the four Malagasy species of section Longitubae, 8·0, 9·0 and 9·5 % of individuals with mixed genotypes were identified by BAPS, NewHybrids and STRUCTURE, respectively. At sites with sympatric populations of A. rubrostipa and A. za, NewHybrids indicated these individuals to be F2 and, predominantly, backcrosses with both parental species. In northern Madagascar, two populations of trees combining A. za and A. perrieri morphology and microsatellite alleles were identified in the current absence of the parental species. Conclusions The clear genetic differentiation observed between the six species may reflect their adaptation to different assortments of climate regimes and habitats during the colonization of the island. Microsatellite variation reveals that hybridization probably occurred in secondary contact between species of section Longitubae. This type of hybridization may also have been involved in the differentiation of a local new stabilized entity showing specific

  10. Chloroplast phylogenomic analyses reveal the deepest-branching lineage of the Chlorophyta, Palmophyllophyceae class. nov.

    PubMed Central

    Leliaert, Frederik; Tronholm, Ana; Lemieux, Claude; Turmel, Monique; DePriest, Michael S.; Bhattacharya, Debashish; Karol, Kenneth G.; Fredericq, Suzanne; Zechman, Frederick W.; Lopez-Bautista, Juan M.

    2016-01-01

    The green plants (Viridiplantae) are an ancient group of eukaryotes comprising two main clades: the Chlorophyta, which includes a wide diversity of green algae, and the Streptophyta, which consists of freshwater green algae and the land plants. The early-diverging lineages of the Viridiplantae comprise unicellular algae, and multicellularity has evolved independently in the two clades. Recent molecular data have revealed an unrecognized early-diverging lineage of green plants, the Palmophyllales, with a unique form of multicellularity, and typically found in deep water. The phylogenetic position of this enigmatic group, however, remained uncertain. Here we elucidate the evolutionary affinity of the Palmophyllales using chloroplast genomic, and nuclear rDNA data. Phylogenetic analyses firmly place the palmophyllalean Verdigellas peltata along with species of Prasinococcales (prasinophyte clade VI) in the deepest-branching clade of the Chlorophyta. The small, compact and intronless chloroplast genome (cpDNA) of V. peltata shows striking similarities in gene content and organization with the cpDNAs of Prasinococcales and the streptophyte Mesostigma viride, indicating that cpDNA architecture has been extremely well conserved in these deep-branching lineages of green plants. The phylogenetic distinctness of the Palmophyllales-Prasinococcales clade, characterized by unique ultrastructural features, warrants recognition of a new class of green plants, Palmophyllophyceae class. nov. PMID:27157793

  11. Chloroplast remodeling during state transitions in Chlamydomonas reinhardtii as revealed by noninvasive techniques in vivo

    PubMed Central

    Nagy, Gergely; Ünnep, Renáta; Zsiros, Ottó; Tokutsu, Ryutaro; Takizawa, Kenji; Porcar, Lionel; Moyet, Lucas; Petroutsos, Dimitris; Garab, Győző; Finazzi, Giovanni; Minagawa, Jun

    2014-01-01

    Plants respond to changes in light quality by regulating the absorption capacity of their photosystems. These short-term adaptations use redox-controlled, reversible phosphorylation of the light-harvesting complexes (LHCIIs) to regulate the relative absorption cross-section of the two photosystems (PSs), commonly referred to as state transitions. It is acknowledged that state transitions induce substantial reorganizations of the PSs. However, their consequences on the chloroplast structure are more controversial. Here, we investigate how state transitions affect the chloroplast structure and function using complementary approaches for the living cells of Chlamydomonas reinhardtii. Using small-angle neutron scattering, we found a strong periodicity of the thylakoids in state 1, with characteristic repeat distances of ∼200 Å, which was almost completely lost in state 2. As revealed by circular dichroism, changes in the thylakoid periodicity were paralleled by modifications in the long-range order arrangement of the photosynthetic complexes, which was reduced by ∼20% in state 2 compared with state 1, but was not abolished. Furthermore, absorption spectroscopy reveals that the enhancement of PSI antenna size during state 1 to state 2 transition (∼20%) is not commensurate to the decrease in PSII antenna size (∼70%), leading to the possibility that a large part of the phosphorylated LHCIIs do not bind to PSI, but instead form energetically quenched complexes, which were shown to be either associated with PSII supercomplexes or in a free form. Altogether these noninvasive in vivo approaches allow us to present a more likely scenario for state transitions that explains their molecular mechanism and physiological consequences. PMID:24639515

  12. The complete chloroplast DNA sequence of the green alga Oltmannsiellopsis viridis reveals a distinctive quadripartite architecture in the chloroplast genome of early diverging ulvophytes

    PubMed Central

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

    2006-01-01

    Background The phylum Chlorophyta contains the majority of the green algae and is divided into four classes. The basal position of the Prasinophyceae has been well documented, but the divergence order of the Ulvophyceae, Trebouxiophyceae and Chlorophyceae is currently debated. The four complete chloroplast DNA (cpDNA) sequences presently available for representatives of these classes have revealed extensive variability in overall structure, gene content, intron composition and gene order. The chloroplast genome of Pseudendoclonium (Ulvophyceae), in particular, is characterized by an atypical quadripartite architecture that deviates from the ancestral type by a large inverted repeat (IR) featuring an inverted rRNA operon and a small single-copy (SSC) region containing 14 genes normally found in the large single-copy (LSC) region. To gain insights into the nature of the events that led to the reorganization of the chloroplast genome in the Ulvophyceae, we have determined the complete cpDNA sequence of Oltmannsiellopsis viridis, a representative of a distinct, early diverging lineage. Results The 151,933 bp IR-containing genome of Oltmannsiellopsis differs considerably from Pseudendoclonium and other chlorophyte cpDNAs in intron content and gene order, but shares close similarities with its ulvophyte homologue at the levels of quadripartite architecture, gene content and gene density. Oltmannsiellopsis cpDNA encodes 105 genes, contains five group I introns, and features many short dispersed repeats. As in Pseudendoclonium cpDNA, the rRNA genes in the IR are transcribed toward the single copy region featuring the genes typically found in the ancestral LSC region, and the opposite single copy region harbours genes characteristic of both the ancestral SSC and LSC regions. The 52 genes that were transferred from the ancestral LSC to SSC region include 12 of those observed in Pseudendoclonium cpDNA. Surprisingly, the overall gene organization of Oltmannsiellopsis cp

  13. Comparative Chloroplast Genomics Reveals the Evolution of Pinaceae Genera and Subfamilies

    PubMed Central

    Lin, Ching-Ping; Huang, Jen-Pan; Wu, Chung-Shien; Hsu, Chih-Yao; Chaw, Shu-Miaw

    2010-01-01

    As the largest and the basal-most family of conifers, Pinaceae provides key insights into the evolutionary history of conifers. We present comparative chloroplast genomics and analysis of concatenated 49 chloroplast protein-coding genes common to 19 gymnosperms, including 15 species from 8 Pinaceous genera, to address the long-standing controversy about Pinaceae phylogeny. The complete cpDNAs of Cathaya argyrophylla and Cedrus deodara (Abitoideae) and draft cpDNAs of Larix decidua, Picea morrisonicola, and Pseudotsuga wilsoniana are reported. We found 21- and 42-kb inversions in congeneric species and different populations of Pinaceous species, which indicates that structural polymorphics may be common and ancient in Pinaceae. Our phylogenetic analyses reveal that Cedrus is clustered with Abies–Keteleeria rather than the basal-most genus of Pinaceae and that Cathaya is closer to Pinus than to Picea or Larix–Pseudotsuga. Topology and structural change tests and indel-distribution comparisons lend further evidence to our phylogenetic finding. Our molecular datings suggest that Pinaceae first evolved during Early Jurassic, and diversification of Pinaceous subfamilies and genera took place during Mid-Jurassic and Lower Cretaceous, respectively. Using different maximum-likelihood divergences as thresholds, we conclude that 2 (Abietoideae and Larix–Pseudotsuga–Piceae–Cathaya–Pinus), 4 (Cedrus, non-Cedrus Abietoideae, Larix–Pseudotsuga, and Piceae–Cathaya–Pinus), or 5 (Cedrus, non-Cedrus Abietoideae, Larix–Pseudotsuga, Picea, and Cathaya–Pinus) groups/subfamilies are more reasonable delimitations for Pinaceae. Specifically, our views on subfamilial classifications differ from previous studies in terms of the rank of Cedrus and with recognition of more than two subfamilies. PMID:20651328

  14. A chloroplast genealogy of myrmecophytic Macaranga species (Euphorbiaceae) in Southeast Asia reveals hybridization, vicariance and long-distance dispersals.

    PubMed

    Bänfer, Gudrun; Moog, Ute; Fiala, Brigitte; Mohamed, Maryati; Weising, Kurt; Blattner, Frank R

    2006-12-01

    Macaranga (Euphorbiaceae) includes about 280 species with a palaeotropic distribution. The genus not only comprises some of the most prominent pioneer tree species in Southeast Asian lowland dipterocarp forests, it also exhibits a substantial radiation of ant-plants (myrmecophytes). Obligate ant-plant mutualisms are formed by about 30 Macaranga species and 13 ant species of the genera Crematogaster or Camponotus. To improve our understanding of the co-evolution of the ants and their host plants, we aim at reconstructing comparative organellar phylogeographies of both partners across their distributional range. Preliminary evidence indicated that chloroplast DNA introgression among closely related Macaranga species might occur. We therefore constructed a comprehensive chloroplast genealogy based on DNA sequence data from the noncoding ccmp2, ccmp6, and atpB-rbcL regions for 144 individuals from 41 Macaranga species, covering all major evolutionary lineages within the three sections that contain myrmecophytes. A total of 88 chloroplast haplotypes were identified, and grouped into a statistical parsimony network that clearly distinguished sections and well-defined subsectional groups. Within these groups, the arrangement of haplotypes followed geographical rather than taxonomical criteria. Thus, up to six chloroplast haplotypes were found within single species, and up to seven species shared a single haplotype. The spatial distribution of the chloroplast types revealed several dispersals between the Malay Peninsula and Borneo, and a deep split between Sabah and the remainder of Borneo. Our large-scale chloroplast genealogy highlights the complex history of migration, hybridization, and speciation in the myrmecophytes of the genus Macaranga. It will serve as a guideline for adequate sampling and data interpretation in phylogeographic studies of individual Macaranga species and species groups. PMID:17107473

  15. Covariations in the nuclear chloroplast transcriptome reveal a regulatory master-switch

    PubMed Central

    Richly, Erik; Dietzmann, Angela; Biehl, Alexander; Kurth, Joachim; Laloi, Christophe; Apel, Klaus; Salamini, Francesco; Leister, Dario

    2003-01-01

    The evolution of the endosymbiotic progenitor into the chloroplast organelle was associated with the transfer of numerous chloroplast genes into the nucleus. Hence, inter-organellar signalling, and the co-ordinated expression of sets of nuclear genes, was set up to control the metabolic and developmental status of the chloroplast. Here, we show by the differential-expression analysis of 3,292 genes, that most of the 35 environmental and genetic conditions tested, including plastid signalling mutations, elicit only three main classes of response from the nuclear chloroplast transcriptome. Two classes, probably involving GUN (genomes uncoupled)-type plastid signalling, are characterized by alterations, in opposite directions, in the expression of largely overlapping sets of genes. PMID:12776738

  16. POLYMORPHIC CHLOROPLAST MICROSATELLITE MARKERS IN THE OCTOPLOID LEPIDIUM MEYENII (BRASSICACEAE) AND CROSS-SPECIES AMPLIFICATION IN LEPIDIUM

    PubMed Central

    Hasan, Nabeeh A.; Mummenhoff, Klaus; Quiros, Carlos F.; Tay, C. David; Bailey, C. Donovan

    2013-01-01

    Premise of the study As a crop and medicinal plant, the octoploid Andean endemic Lepidium meyenii suffers from taxonomic uncertainty. Few molecular markers are available to genotype individuals or track gene flow in wild and cultivated material. Methods and Results Using available sequence data, eight cpSSR primer pairs were developed for L. meyenii. Levels of polymorphism checked in 56 individual L. meyenii, including cultivated and wild material, revealed that the number of alleles per locus ranged from three to five, and intrapopulation allele frequencies ranged from 0.071 to 1.0. Polymerase-chain-reaction screens using our cpSSR primers in 27 other Lepidium species and three Coronopus species suggested a high degree of interspecific amplification. Conclusions These polymorphic cpSSR markers should prove useful in characterizing genetic variation among cultivated and wild L. meyenii. Additionally, interspecific amplifications suggest that these markers will be useful for the study of related taxa. PMID:21616787

  17. Microsatellite development for the genus Guibourtia (Fabaceae, Caesalpinioideae) reveals diploid and polyploid species1

    PubMed Central

    Tosso, Felicien; Doucet, Jean-Louis; Kaymak, Esra; Daïnou, Kasso; Duminil, Jérôme; Hardy, Olivier J.

    2016-01-01

    Premise of the study: Nuclear microsatellites (nSSRs) were designed for Guibourtia tessmannii (Fabaceae, Caesalpinioideae), a highly exploited African timber tree, to study population genetic structure and gene flow. Methods and Results: We developed 16 polymorphic nSSRs from a genomic library tested in three populations of G. tessmannii and two populations of G. coleosperma. These nSSRs display three to 14 alleles per locus (mean 8.94) in G. tessmannii. Cross-amplification tests in nine congeneric species demonstrated that the genus Guibourtia contains diploid and polyploid species. Flow cytometry results combined with nSSR profiles suggest that G. tessmannii is octoploid. Conclusions: nSSRs revealed that African Guibourtia species include both diploid and polyploid species. These markers will provide information on the mating system, patterns of gene flow, and genetic structure of African Guibourtia species. PMID:27437170

  18. Proteomic comparison reveals the contribution of chloroplast to salt tolerance of a wheat introgression line.

    PubMed

    Xu, Wenjing; Lv, Hongjun; Zhao, Mingming; Li, Yongchao; Qi, Yueying; Peng, Zhenying; Xia, Guangmin; Wang, Mengcheng

    2016-01-01

    We previously bred a salt tolerant wheat cv. SR3 with bread wheat cv. JN177 as the parent via asymmetric somatic hybridization, and found that the tolerance is partially attributed to the superior photosynthesis capacity. Here, we compared the proteomes of two cultivars to unravel the basis of superior photosynthesis capacity. In the maps of two dimensional difference gel electrophoresis (2D-DIGE), there were 26 differentially expressed proteins (DEPs), including 18 cultivar-based and 8 stress-responsive ones. 21 of 26 DEPs were identified and classified into four categories, including photosynthesis, photosynthesis system stability, linolenic acid metabolism, and protein synthesis in chloroplast. The chloroplast localization of some DEPs confirmed that the identified DEPs function in the chloroplast. The overexpression of a DEP enhanced salt tolerance in Arabidopsis thaliana. In line with these data, it is concluded that the contribution of chloroplast to high salinity tolerance of wheat cv. SR3 appears to include higher photosynthesis efficiency by promoting system protection and ROS clearance, stronger production of phytohormone JA by enhancing metabolism activity, and modulating the in chloroplast synthesis of proteins. PMID:27562633

  19. Proteomic comparison reveals the contribution of chloroplast to salt tolerance of a wheat introgression line

    PubMed Central

    Xu, Wenjing; Lv, Hongjun; Zhao, Mingming; Li, Yongchao; Qi, Yueying; Peng, Zhenying; Xia, Guangmin; Wang, Mengcheng

    2016-01-01

    We previously bred a salt tolerant wheat cv. SR3 with bread wheat cv. JN177 as the parent via asymmetric somatic hybridization, and found that the tolerance is partially attributed to the superior photosynthesis capacity. Here, we compared the proteomes of two cultivars to unravel the basis of superior photosynthesis capacity. In the maps of two dimensional difference gel electrophoresis (2D-DIGE), there were 26 differentially expressed proteins (DEPs), including 18 cultivar-based and 8 stress-responsive ones. 21 of 26 DEPs were identified and classified into four categories, including photosynthesis, photosynthesis system stability, linolenic acid metabolism, and protein synthesis in chloroplast. The chloroplast localization of some DEPs confirmed that the identified DEPs function in the chloroplast. The overexpression of a DEP enhanced salt tolerance in Arabidopsis thaliana. In line with these data, it is concluded that the contribution of chloroplast to high salinity tolerance of wheat cv. SR3 appears to include higher photosynthesis efficiency by promoting system protection and ROS clearance, stronger production of phytohormone JA by enhancing metabolism activity, and modulating the in chloroplast synthesis of proteins. PMID:27562633

  20. The complete chloroplast genome of Ginkgo biloba reveals the mechanism of inverted repeat contraction.

    PubMed

    Lin, Ching-Ping; Wu, Chung-Shien; Huang, Ya-Yi; Chaw, Shu-Miaw

    2012-01-01

    We determined the complete chloroplast genome (cpDNA) of Ginkgo biloba (common name: ginkgo), the only relict of ginkgophytes from the Triassic Period. The cpDNA molecule of ginkgo is quadripartite and circular, with a length of 156,945 bp, which is 6,458 bp shorter than that of Cycas taitungensis. In ginkgo cpDNA, rpl23 becomes pseudo, only one copy of ycf2 is retained, and there are at least five editing sites. We propose that the retained ycf2 is a duplicate of the ancestral ycf2, and the ancestral one has been lost from the inverted repeat A (IR(A)). This loss event should have occurred and led to the contraction of IRs after ginkgos diverged from other gymnosperms. A novel cluster of three transfer RNA (tRNA) genes, trnY-AUA, trnC-ACA, and trnSeC-UCA, was predicted to be located between trnC-GCA and rpoB of the large single-copy region. Our phylogenetic analysis strongly suggests that the three predicted tRNA genes are duplicates of trnC-GCA. Interestingly, in ginkgo cpDNA, the loss of one ycf2 copy does not significantly elevate the synonymous rate (Ks) of the retained copy, which disagrees with the view of Perry and Wolfe (2002) that one of the two-copy genes is subjected to elevated Ks when its counterpart has been lost. We hypothesize that the loss of one ycf2 is likely recent, and therefore, the acquired Ks of the retained copy is low. Our data reveal that ginkgo possesses several unique features that contribute to our understanding of the cpDNA evolution in seed plants. PMID:22403032

  1. Phylogenetic affinities of the grasses to other monocots as revealed by molecular analysis of chloroplast DNA.

    PubMed

    Katayama, H; Ogihara, Y

    1996-05-01

    The distribution of structural alterations of the chloroplast genome found in grass chloroplast (cp) DNA in comparison with that of tobacco was systematically surveyed in the cpDNAs of monocots. Southern hybridization and/or PCR analyses for the detection of (1) three inversions in the large single-copy region, (2) loss of an intron in the rpoC1 gene, (3) an extra-sequence insertion in the rpoC2 gene, (4) the deletion of ORF2280, (5) rearrangements of the accD (ORF512) gene, and (6) non-reciprocal translocation of the rpl23 gene, were carried out on cpDNAs isolated from 58 species, 22 families, and 11 orders, which covered almost all families of monocots. These structural alterations of cpDNA mostly occurred at the family level. However, only part of the Restionaceae possessed the inversion that characterizes the lineage of grass differentiation. The order of mutational events made it possible to reconstruct grass phylogeny in monocots. Since no variations in structural alterations of the cpDNA were found among the Poaceae, grass plants were inferred to have originated from an ancestor harboring these structural alterations of the chloroplast genome. These phylogenetic relationships were supported by the sequence data of rbcL. PMID:8662197

  2. Microsatellite markers reveal genetic divergence among wild and cultured populations of Chinese sucker Myxocyprinus asiaticus.

    PubMed

    Cheng, W W; Wang, D Q; Wang, C Y; Du, H; Wei, Q W

    2016-01-01

    Studies of genetic diversity and genetic population structure are critical for the conservation and management of endangered species. The Chinese sucker Myxocyprinus asiaticus is a vulnerable monotypic species in China, which is at a risk of decline owing to fluctuations in effective population size and other demographic and environmental factors. We screened 11 microsatellite loci in 214 individuals to assess genetic differentiation in both wild and cultured populations. The single extant wild population had a higher number of alleles (13) than the cultured populations (average 7.3). High levels of genetic diversity, expressed as observed and expected heterozygosity (HO = 0.771, HE = 0.748, respectively), were found in both wild and cultured populations. We also report significant differentiation among wild and cultured populations (global FST = 0.023, P < 0.001). Both STRUCTURE analysis and neighbor-joining tree revealed three moderately divergent primary genetic clusters: the wild Yangtze population and the Sichuan population were each identified as an individual cluster, with the remaining populations clustered together. Twenty-two samples collected from the Yangtze River were assigned to the cultured population, demonstrating the efficacy of artificial propagation to avoid drastic reduction in the population size of M. asiaticus. These genetic data support the endangered status of the M. asiaticus and have implications for conservation management planning. PMID:27173283

  3. Comparative Proteomics of Chloroplasts Envelopes from Bundle Sheath and Mesophyll Chloroplasts Reveals Novel Membrane Proteins with a Possible Role in C4-Related Metabolite Fluxes and Development

    PubMed Central

    Manandhar-Shrestha, K.; Tamot, B.; Pratt, E. P. S.; Saitie, S.; Bräutigam, A.; Weber, A. P. M.; Hoffmann-Benning, Susanne

    2013-01-01

    As the world population grows, our need for food increases drastically. Limited amounts of arable land lead to a competition between food and fuel crops, while changes in the global climate may impact future crop yields. Thus, a second “green revolution” will need a better understanding of the processes essential for plant growth and development. One approach toward the solution of this problem is to better understand regulatory and transport processes in C4 plants. C4 plants display an up to 10-fold higher apparent CO2 assimilation and higher yields while maintaining high water use efficiency. This requires differential regulation of mesophyll (M) and bundle sheath (BS) chloroplast development as well as higher metabolic fluxes of photosynthetic intermediates between cells and particularly across chloroplast envelopes. While previous analyses of overall chloroplast membranes have yielded significant insight, our comparative proteomics approach using enriched BS and M chloroplast envelopes of Zea mays allowed us to identify 37 proteins of unknown function that have not been seen in these earlier studies. We identified 280 proteins, 84% of which are known/predicted to be present in chloroplasts. Seventy-four percent have a known or predicted membrane association. Twenty-one membrane proteins were 2–15 times more abundant in BS cells, while 36 of the proteins were more abundant in M chloroplast envelopes. These proteins could represent additional candidates of proteins essential for development or metabolite transport processes in C4 plants. RT-PCR confirmed differential expression of 13 candidate genes. Chloroplast association for seven proteins was confirmed using YFP/GFP labeling. Gene expression of four putative transporters was examined throughout the leaf and during the greening of leaves. Genes for a PIC-like protein and an ER-AP-like protein show an early transient increase in gene expression during the transition to light. In addition, PIC gene

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

    PubMed

    Amos, William

    2010-09-01

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

  5. Genetic diversity and structure in Leishmania infantum populations from southeastern Europe revealed by microsatellite analysis

    PubMed Central

    2013-01-01

    Background The dynamic re-emergence of visceral leishmaniasis (VL) in south Europe and the northward shift to Leishmania-free European countries are well-documented. However, the epidemiology of VL due to Leishmania infantum in southeastern (SE) Europe and the Balkans is inadequately examined. Herein, we aim to re-evaluate and compare the population structure of L. infantum in SE and southwestern (SW) Europe. Methods Leishmania strains collected from humans and canines in Turkey, Cyprus, Bulgaria, Greece, Albania and Croatia, were characterized by the K26-PCR assay and multilocus enzyme electrophoresis (MLEE). Genetic diversity was assessed by multilocus microsatellite typing (MLMT) and MLM Types were analyzed by model- and distance- based algorithms to infer the population structure of 128 L. infantum strains. Results L. infantum MON-1 was found predominant in SE Europe, whilst 16.8% of strains were MON-98. Distinct genetic populations revealed clear differentiation between SE and SW European strains. Interestingly, Cypriot canine isolates were genetically isolated and formed a monophyletic group, suggesting the constitution of a clonal MON-1 population circulating among dogs. In contrast, two highly heterogeneous populations enclosed all MON-1 and MON-98 strains from the other SE European countries. Structure sub-clustering, phylogenetic and Splitstree analysis also revealed two distinct Croatian subpopulations. A mosaic of evolutionary effects resulted in consecutive sub-structuring, which indicated substantial differentiation and gene flow among strains of both zymodemes. Conclusions This is the first population genetic study of L. infantum in SE Europe and the Balkans. Our findings demonstrate the differentiation between SE and SW European strains; revealing the partition of Croatian strains between these populations and the genetic isolation of Cypriot strains. This mirrors the geographic position of Croatia located in central Europe and the natural

  6. Empirical evaluation reveals best fit of a logistic mutation model for human Y-chromosomal microsatellites.

    PubMed

    Jochens, Arne; Caliebe, Amke; Rösler, Uwe; Krawczak, Michael

    2011-12-01

    The rate of microsatellite mutation is dependent upon both the allele length and the repeat motif, but the exact nature of this relationship is still unknown. We analyzed data on the inheritance of human Y-chromosomal microsatellites in father-son duos, taken from 24 published reports and comprising 15,285 directly observable meioses. At the six microsatellites analyzed (DYS19, DYS389I, DYS390, DYS391, DYS392, and DYS393), a total of 162 mutations were observed. For each locus, we employed a maximum-likelihood approach to evaluate one of several single-step mutation models on the basis of the data. For five of the six loci considered, a novel logistic mutation model was found to provide the best fit according to Akaike's information criterion. This implies that the mutation probability at the loci increases (nonlinearly) with allele length at a rate that differs between upward and downward mutations. For DYS392, the best fit was provided by a linear model in which upward and downward mutation probabilities increase equally with allele length. This is the first study to empirically compare different microsatellite mutation models in a locus-specific fashion. PMID:21968190

  7. Empirical Evaluation Reveals Best Fit of a Logistic Mutation Model for Human Y-Chromosomal Microsatellites

    PubMed Central

    Jochens, Arne; Caliebe, Amke; Rösler, Uwe; Krawczak, Michael

    2011-01-01

    The rate of microsatellite mutation is dependent upon both the allele length and the repeat motif, but the exact nature of this relationship is still unknown. We analyzed data on the inheritance of human Y-chromosomal microsatellites in father–son duos, taken from 24 published reports and comprising 15,285 directly observable meioses. At the six microsatellites analyzed (DYS19, DYS389I, DYS390, DYS391, DYS392, and DYS393), a total of 162 mutations were observed. For each locus, we employed a maximum-likelihood approach to evaluate one of several single-step mutation models on the basis of the data. For five of the six loci considered, a novel logistic mutation model was found to provide the best fit according to Akaike’s information criterion. This implies that the mutation probability at the loci increases (nonlinearly) with allele length at a rate that differs between upward and downward mutations. For DYS392, the best fit was provided by a linear model in which upward and downward mutation probabilities increase equally with allele length. This is the first study to empirically compare different microsatellite mutation models in a locus-specific fashion. PMID:21968190

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

    PubMed

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

    2015-06-01

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

  9. What phylogeny and gene genealogy analyses reveal about homoplasy in citrus microsatellite alleles

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Sixty-five microsatellite alleles from three Simple Sequence Repeat (SSR) loci (cAGG9, CCT01 and GT03) of various Citrus, Fortunella or Poncirus accessions were cloned and sequenced to determine their mode of evolution. This data was used to assess sequence variation by calculating the average numb...

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

    PubMed

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

    2011-01-01

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

  11. Microsatellites reveal substantial among-population genetic differentiation and strong inbreeding in the relict fern Dryopteris aemula

    PubMed Central

    Jiménez, Ares; Holderegger, Rolf; Csencsics, Daniela; Quintanilla, Luis G.

    2010-01-01

    Background and Aims A previous study detected no allozyme diversity in Iberian populations of the buckler-fern Dryopteris aemula. The use of a more sensitive marker, such as microsatellites, was thus needed to reveal the genetic diversity, breeding system and spatial genetic structure of this species in natural populations. Methods Eight microsatellite loci for D. aemula were developed and their cross-amplification with other ferns was tested. Five polymorphic loci were used to characterize the amount and distribution of genetic diversity of D. aemula in three populations from the Iberian Peninsula and one population from the Azores. Key Results Most microsatellite markers developed were transferable to taxa close to D. aemula. Overall genetic variation was low (HT = 0·447), but was higher in the Azorean population than in the Iberian populations of this species. Among-population genetic differentiation was high (FST = 0·520). All loci strongly departed from Hardy–Weinberg equilibrium. In the population where genetic structure was studied, no spatial autocorrelation was found in any distance class. Conclusions The higher genetic diversity observed in the Azorean population studied suggested a possible refugium in this region from which mainland Europe has been recolonized after the Pleistocene glaciations. High among-population genetic differentiation indicated restricted gene flow (i.e. lack of spore exchange) across the highly fragmented area occupied by D. aemula. The deviations from Hardy–Weinberg equilibrium reflected strong inbreeding in D. aemula, a trait rarely observed in homosporous ferns. The absence of spatial genetic structure indicated effective spore dispersal over short distances. Additionally, the cross-amplification of some D. aemula microsatellites makes them suitable for use in other Dryopteris taxa. PMID:20495199

  12. A microsatellite linkage map of striped bass (Morone saxatilis) reveals conserved synteny with the three-spined stickleback (Gasterosteus aculeatus).

    PubMed

    Liu, Sixin; Rexroad, Caird E; Couch, Charlene R; Cordes, Jan F; Reece, Kimberly S; Sullivan, Craig V

    2012-04-01

    The striped bass (Morone saxatilis) and its relatives (genus Morone) are of great importance to fisheries and aquaculture in North America. As part of a collaborative effort to employ molecular genetics technologies in striped bass breeding programs, we previously developed nearly 500 microsatellite markers. The objectives of this study were to construct a microsatellite linkage map of striped bass and to examine conserved synteny between striped bass and three-spined stickleback (Gasterosteus aculeatus). Of 480 microsatellite markers screened for polymorphism, 289 informative markers were identified and used to genotype two half-sib mapping families. Twenty-six linkage groups were assembled, and only two markers remain unlinked. The sex-averaged map spans 1,623.8 cM with an average marker density of 5.78 cM per marker. Among 287 striped bass microsatellite markers assigned to linkage groups, 169 (58.9%) showed homology to sequences on stickleback chromosomes or scaffolds. Comparison between the stickleback genome and the striped bass linkage map revealed conserved synteny between these two species. This is the first linkage map for any of the Morone species. This map will be useful for molecular mapping and marker-assisted selection of genes of interest in striped bass breeding programs. The conserved synteny between striped bass and stickleback will facilitate fine mapping of genome regions of interest and will serve as a new resource for comparative mapping with other Perciform fishes such as European sea bass (Dicentrarchus labrax), gilthead sea bream (Sparus aurata), and tilapia (Oreochromis ssp.). PMID:21968826

  13. Genetic interactions reveal that specific defects of chloroplast translation are associated with the suppression of var2-mediated leaf variegation.

    PubMed

    Liu, Xiayan; Zheng, Mengdi; Wang, Rui; Wang, Ruijuan; An, Lijun; Rodermel, Steve R; Yu, Fei

    2013-10-01

    Arabidopsis thaliana L. yellow variegated (var2) mutant is defective in a chloroplast FtsH family metalloprotease, AtFtsH2/VAR2, and displays an intriguing green and white leaf variegation. This unique var2-mediated leaf variegation offers a simple yet powerful tool for dissecting the genetic regulation of chloroplast development. Here, we report the isolation and characterization of a new var2 suppressor gene, SUPPRESSOR OF VARIEGATION8 (SVR8), which encodes a putative chloroplast ribosomal large subunit protein, L24. Mutations in SVR8 suppress var2 leaf variegation at ambient temperature and partially suppress the cold-induced chlorosis phenotype of var2. Loss of SVR8 causes unique chloroplast rRNA processing defects, particularly the 23S-4.5S dicistronic precursor. The recovery of the major abnormal processing site in svr8 23S-4.5S precursor indicate that it does not lie in the same position where SVR8/L24 binds on the ribosome. Surprisingly, we found that the loss of a chloroplast ribosomal small subunit protein, S21, results in aberrant chloroplast rRNA processing but not suppression of var2 variegation. These findings suggest that the disruption of specific aspects of chloroplast translation, rather than a general impairment in chloroplast translation, suppress var2 variegation and the existence of complex genetic interactions in chloroplast development. PMID:23721655

  14. Novel Polymorphic Microsatellite Markers Reveal Genetic Differentiation between Two Sympatric Types of Galaxea fascicularis

    PubMed Central

    Nakajima, Yuichi; Shinzato, Chuya; Satoh, Noriyuki; Mitarai, Satoshi

    2015-01-01

    The reef-building, scleractinian coral, Galaxea fascicularis, is classified into soft and hard types, based on nematocyst morphology. This character is correlated with the length of the mitochondrial non-coding region (mt-Long: soft colony type, and nematocysts with wide capsules and long shafts; mt-Short: hard colony type, and nematocysts with thin capsules and short shafts). We isolated and characterized novel polymorphic microsatellite markers for G. fascicularis using next-generation sequencing. Based upon the mitochondrial non-coding region, 53 of the 97 colonies collected were mt-Long (mt-L) and 44 were mt-Short (mt-S). Among the 53 mt-L colonies, 27 loci were identified as amplifiable, polymorphic microsatellite loci, devoid of somatic mutations and free of scoring errors. Eleven of those 27 loci were also amplifiable and polymorphic in the 44 mt-S colonies; these 11 are cross-type microsatellite loci. The other 16 loci were considered useful only for mt-L colonies. These 27 loci identified 10 multilocus lineages (MLLs) among the 53 mt-L colonies (NMLL/N = 0.189), and the 11 cross-type loci identified 7 MLLs in 44 mt-S colonies (NMLL/N = 0.159). Significant genetic differentiation between the two types was detected based on the genetic differentiation index (FST = 0.080, P = 0.001). Bayesian clustering also indicated that these two types are genetically isolated. While nuclear microsatellite genotypes also showed genetic differentiation between mitochondrial types, the mechanism of divergence is not yet clear. These markers will be useful to estimate genetic diversity, differentiation, and connectivity among populations, and to understand evolutionary processes, including divergence of types in G. fascicularis. PMID:26147677

  15. Unique haplotypes of cacao trees as revealed by trnH-psbA chloroplast DNA

    PubMed Central

    Gutiérrez-López, Nidia; Ovando-Medina, Isidro; Salvador-Figueroa, Miguel; Molina-Freaner, Francisco; Avendaño-Arrazate, Carlos H.

    2016-01-01

    Cacao trees have been cultivated in Mesoamerica for at least 4,000 years. In this study, we analyzed sequence variation in the chloroplast DNA trnH-psbA intergenic spacer from 28 cacao trees from different farms in the Soconusco region in southern Mexico. Genetic relationships were established by two analysis approaches based on geographic origin (five populations) and genetic origin (based on a previous study). We identified six polymorphic sites, including five insertion/deletion (indels) types and one transversion. The overall nucleotide diversity was low for both approaches (geographic = 0.0032 and genetic = 0.0038). Conversely, we obtained moderate to high haplotype diversity (0.66 and 0.80) with 10 and 12 haplotypes, respectively. The common haplotype (H1) for both networks included cacao trees from all geographic locations (geographic approach) and four genetic groups (genetic approach). This common haplotype (ancient) derived a set of intermediate haplotypes and singletons interconnected by one or two mutational steps, which suggested directional selection and event purification from the expansion of narrow populations. Cacao trees from Soconusco region were grouped into one cluster without any evidence of subclustering based on AMOVA (FST = 0) and SAMOVA (FST = 0.04393) results. One population (Mazatán) showed a high haplotype frequency; thus, this population could be considered an important reservoir of genetic material. The indels located in the trnH-psbA intergenic spacer of cacao trees could be useful as markers for the development of DNA barcoding. PMID:27076998

  16. Chloroplast DNA phylogeography reveals colonization history of a Neotropical tree, Cedrela odorata L., in Mesoamerica.

    PubMed

    Cavers, S; Navarro, C; Lowe, A J

    2003-06-01

    Spanish Cedar (Cedrela odorata L.) is a globally important timber species which has been severely exploited in Mesoamerica for over 200 years. Using polymerase chain reaction-restriction fragment length polymorphisms, its chloroplast (cp) DNA phylogeography was studied in Mesoamerica with samples from 29 populations in six countries. Five haplotypes were characterized, phylogenetically grouped into three lineages (Northern, Central and Southern). Spatial analysis of ordered genetic distance confirmed deviation from a pattern of isolation by distance. The geographically proximate Northern and Central cpDNA lineages were genetically the most differentiated, with the Southern lineage appearing between them on a minimum spanning tree. However, populations possessing Southern lineage haplotypes occupy distinct moist habitats, in contrast to populations possessing Northern and Central lineage haplotypes which occupy drier and more seasonal habitats. Given the known colonization of the proto-Mesoamerican peninsula by South American flora and fauna prior to the formation of the Isthmus of Panama, it seems most likely that the observed population structure in C. odorata results from repeated colonization of Mesoamerica from South American source populations. Such a model would imply an ancient, pre-Isthmian colonization of a dry-adapted type (possessing the Northern lineage or a prototype thereof), with a secondary colonization via the land bridge. Following this, a more recent (possibly post-Pleistocene) expansion of moist-adapted types possessing the Southern lineage from the south fits the known vegetation history of the region. PMID:12755874

  17. Microsatellite marker based genetic linkage maps of Oreochromis aureus and O. niloticus (Cichlidae): extensive linkage group segment homologies revealed.

    PubMed

    McConnell, S K; Beynon, C; Leamon, J; Skibinski, D O

    2000-06-01

    Partial genetic linkage maps, based on microsatellite markers, were constructed for two tilapia species, Oreochromis aureus and Oreochromis niloticus using an interspecific backcross population. The linkage map for O. aureus comprised 28 markers on 10 linkage groups and covered 212.8 CM. Nine markers were mapped to four linkage groups on an O. niloticus female linkage map covering 40.6 CM. Results revealed a high degree of conservation of synteny between the linkage groups defined in O. aureus and the previously published genetic linkage map of O. niloticus. PMID:10895314

  18. Unique haplotypes of cacao trees as revealed by trnH-psbA chloroplast DNA.

    PubMed

    Gutiérrez-López, Nidia; Ovando-Medina, Isidro; Salvador-Figueroa, Miguel; Molina-Freaner, Francisco; Avendaño-Arrazate, Carlos H; Vázquez-Ovando, Alfredo

    2016-01-01

    Cacao trees have been cultivated in Mesoamerica for at least 4,000 years. In this study, we analyzed sequence variation in the chloroplast DNA trnH-psbA intergenic spacer from 28 cacao trees from different farms in the Soconusco region in southern Mexico. Genetic relationships were established by two analysis approaches based on geographic origin (five populations) and genetic origin (based on a previous study). We identified six polymorphic sites, including five insertion/deletion (indels) types and one transversion. The overall nucleotide diversity was low for both approaches (geographic = 0.0032 and genetic = 0.0038). Conversely, we obtained moderate to high haplotype diversity (0.66 and 0.80) with 10 and 12 haplotypes, respectively. The common haplotype (H1) for both networks included cacao trees from all geographic locations (geographic approach) and four genetic groups (genetic approach). This common haplotype (ancient) derived a set of intermediate haplotypes and singletons interconnected by one or two mutational steps, which suggested directional selection and event purification from the expansion of narrow populations. Cacao trees from Soconusco region were grouped into one cluster without any evidence of subclustering based on AMOVA (F ST = 0) and SAMOVA (F ST = 0.04393) results. One population (Mazatán) showed a high haplotype frequency; thus, this population could be considered an important reservoir of genetic material. The indels located in the trnH-psbA intergenic spacer of cacao trees could be useful as markers for the development of DNA barcoding. PMID:27076998

  19. Microsatellite analysis reveals genetically distinct populations of red pine (Pinus resinosa, Pinaceae).

    PubMed

    Boys, Jacquelyn; Cherry, Marilyn; Dayanandan, Selvadurai

    2005-05-01

    Red pine (Pinus resinosa Ait.) is an ecologically and economically important forest tree species of northeastern North America and is considered one of the most genetically depauperate conifer species in the region. We have isolated and characterized 13 nuclear microsatellite loci by screening a partial genomic library with di-, tri-, and tetranucleotide repeat oligonucleotide probes. In an analysis of over 500 individuals representing 17 red pine populations from Manitoba through Newfoundland, five polymorphic microsatellite loci with an average of nine alleles per locus were identified. The mean expected and observed heterozygosity values were 0.508 and 0.185, respectively. Significant departures from Hardy-Weinberg equilibrium with excess homozygosity indicating high levels of inbreeding were evident in all populations studied. The population differentiation was high with 28-35% of genetic variation partitioned among populations. The genetic distance analysis showed that three northeastern (two Newfoundland and one New Brunswick) populations are genetically distinct from the remaining populations. The coalescence-based analysis suggests that "northeastern" and "main" populations likely became isolated during the most recent Pleistocene glacial period, and severe population bottlenecks may have led to the evolution of a highly selfing mating system in red pine. PMID:21652464

  20. Moroccan Leishmania infantum: Genetic Diversity and Population Structure as Revealed by Multi-Locus Microsatellite Typing

    PubMed Central

    Lemrani, Meryem; Mouna, Idrissi; Mohammed, Hida; Mostafa, Sabri; Rhajaoui, Mohamed; Hamarsheh, Omar; Schönian, Gabriele

    2013-01-01

    Leishmania infantum causes Visceral and cutaneous leishmaniasis in northern Morocco. It predominantly affects children under 5 years with incidence of 150 cases/year. Genetic variability and population structure have been investigated for 33 strains isolated from infected dogs and humans in Morocco. A multilocus microsatellite typing (MLMT) approach was used in which a MLMtype based on size variation in 14 independent microsatellite markers was compiled for each strain. MLMT profiles of 10 Tunisian, 10 Algerian and 21 European strains which belonged to zymodeme MON-1 and non-MON-1 according to multilocus enzyme electrophoresis (MLEE) were included for comparison. A Bayesian model-based approach and phylogenetic analysis inferred two L.infantum sub-populations; Sub-population A consists of 13 Moroccan strains grouped with all European strains of MON-1 type; and sub-population B consists of 15 Moroccan strains grouped with the Tunisian and Algerian MON-1 strains. Theses sub-populations were significantly different from each other and from the Tunisian, Algerian and European non MON-1 strains which constructed one separate population. The presence of these two sub-populations co-existing in Moroccan endemics suggests multiple introduction of L. infantum from/to Morocco; (1) Introduction from/to the neighboring North African countries, (2) Introduction from/to the Europe. These scenarios are supported by the presence of sub-population B and sub-population A respectively. Gene flow was noticed between sub-populations A and B. Five strains showed mixed A/B genotypes indicating possible recombination between the two populations. MLMT has proven to be a powerful tool for eco-epidemiological and population genetic investigations of Leishmania. PMID:24147078

  1. An Arabidopsis soluble chloroplast proteomic analysis reveals the participation of the Executer pathway in response to increased light conditions

    PubMed Central

    Uberegui, Estefanía; Hall, Michael; Lorenzo, Óscar; Schröder, Wolfgang P.; Balsera, Mónica

    2015-01-01

    The Executer1 and Executer2 proteins have a fundamental role in the signalling pathway mediated by singlet oxygen in chloroplast; nonetheless, not much is known yet about their specific activity and features. Herein, we have followed a differential-expression proteomics approach to analyse the impact of Executer on the soluble chloroplast protein abundance in Arabidopsis. Because singlet oxygen plays a significant role in signalling the oxidative response of plants to light, our analysis also included the soluble chloroplast proteome of plants exposed to a moderate light intensity in the time frame of hours. A number of light- and genotype-responsive proteins were detected, and mass-spectrometry identification showed changes in abundance of several photosynthesis- and carbon metabolism-related proteins as well as proteins involved in plastid mRNA processing. Our results support the participation of the Executer proteins in signalling and control of chloroplast metabolism, and in the regulation of plant response to environmental changes. PMID:25740923

  2. Microsatellite markers reveal the potential for kin selection on black grouse leks

    PubMed Central

    glund, J. H; Alatalo, R. V.; Lundberg, A.; ki, P. T. Rintam; Lindell, J.

    1999-01-01

    The evolution of social behaviour has puzzled biologists since Darwin. Since Hamilton's theoretical work in the 1960s it has been realized that social behaviour may evolve through the effects of kinship. By helping relatives, an individual may pass on its genes despite negative effects on its own reproduction. Leks are groups of males that females visit primarily to mate. The selective advantage for males to join such social groups has been given much recent attention, but no clear picture has yet emerged. Here we show, using microsatellite analysis, that males but not females of a lekking bird (the black grouse, Tetrao tetrix) are genetically structured at the lek level. We interpret this structuring to be the effects of strong natal philopatry in males. This has the consequence that males on any specific lek should be more related than expected by chance as indicated by our genetic data. Our results thus suggest that kin selection is a factor that needs to be considered in the evolution and maintenance of the lek mating system in black grouse and sheds new light on models of lek evolution.

  3. Gene flow of Acanthaster planci (L.) in relation to ocean currents revealed by microsatellite analysis.

    PubMed

    Yasuda, Nina; Nagai, Satoshi; Hamaguchi, Masami; Okaji, Ken; Gérard, Karin; Nadaoka, Kazuo

    2009-04-01

    Population outbreaks of the coral-eating starfish, Acanthaster planci, are hypothesized to spread to many localities in the Indo-Pacific Ocean through dispersal of planktonic larvae. To elucidate the gene flow of A. planci across the Indo-Pacific in relation to ocean currents and to test the larval dispersal hypothesis, the genetic structure among 23 samples over the Indo-Pacific was analysed using seven highly polymorphic microsatellite loci. The F-statistics and genetic admixture analysis detected genetically distinct groups in accordance with ocean current systems, that is, the Southeast African group (Kenya and Mayotte), the Northwestern Pacific group (the Philippines and Japan), Palau, the North Central Pacific group (Majuro and Pohnpei), the Great Barrier Reef, Fiji, and French Polynesia, with a large genetic break between the Indian and Pacific Oceans. A pattern of significant isolation by distance was observed among all samples (P = 0.001, r = 0.88, n = 253, Mantel test), indicating restricted gene flow among the samples in accordance with geographical distances. The data also indicated strong gene flow within the Southeast African, Northwestern Pacific, and Great Barrier Reef groups. These results suggest that the western boundary currents have strong influence on gene flow of this species and may trigger secondary outbreaks. PMID:19302361

  4. Microsatellites loci reveal heterozygosis and population structure in vampire bats (Desmodus rotundus) (Chiroptera: Phyllostomidae) of Mexico.

    PubMed

    Romero-Nava, Claudia; León-Paniagua, Livia; Ortega, Jorge

    2014-06-01

    A limited number of studies have focused on the population genetic structure of vampire bats (Desmous rotundus) in America. This medium-sized bat is distributed in tropical areas of the continent with high prevalence in forested livestock areas. The aim of this work was to characterize the vampire population structure and their genetic differentiation. For this, we followed standard methods by which live vampires (caught by mist-netting) and preserved material from scientific collections, were obtained for a total of 15 different locations, ranging from Chihuahua (North) to Quintana Roo (Southeast). Tissue samples were obtained from both live and collected animals, and the genetic differentiation, within and among localities, was assessed by the use of seven microsatellite loci. Our results showed that all loci were polymorphic and no private alleles were detected. High levels of heterozygosis were detected when the proportion of alleles in each locus were compared. Pairwise (ST) and R(ST) detected significant genetic differentiation among individuals from different localities. Our population structure results indicate the presence of eleven clusters, with a high percentage of assigned individuals to some specific collecting site. PMID:25102648

  5. Microsatellites reveal a lack of structure in Australian populations of the diamondback moth, Plutella xylostella (L.).

    PubMed

    Endersby, N M; McKechnie, S W; Ridland, P M; Weeks, A R

    2006-01-01

    The diamondback moth, Plutella xylostella, is renowned for developing resistance to insecticides and causing significant economic damage to Brassica vegetable crops throughout the world. Yet despite its economic importance, little is known about the population structure and movement patterns of this pest both at local and regional scales. In Australia, the movement patterns and insecticide resistance status of P. xylostella infesting canola, vegetables, forage brassicas and weeds have fundamental implications for the management of this pest. Here we use six polymorphic microsatellite loci to investigate population structure and gene flow in Australian populations of P. xylostella. Samples of P. xylostella from New Zealand, Malaysia, Indonesia and Kenya were also scored at these loci. We found no evidence of population structure within Australia, with most populations having low inbreeding coefficients and in Hardy-Weinberg equilibrium. In addition, a sample from the North Island of New Zealand was indistinguishable from the Australian samples. However, large genetic differences were found between the Australia/New Zealand samples and samples from Kenya, Malaysia and Indonesia. There was no relationship between genetic distance and geographic distance among Australian and New Zealand samples. Two of the loci were found to have null alleles, the frequency of which was increased in the populations outside the Australia/New Zealand region. We discuss these results with reference to insecticide resistance management strategies for P. xylostella in Australia. PMID:16367834

  6. The Complete Sequence of the Acacia ligulata Chloroplast Genome Reveals a Highly Divergent clpP1 Gene

    PubMed Central

    Williams, Anna V.; Boykin, Laura M.; Howell, Katharine A.; Nevill, Paul G.; Small, Ian

    2015-01-01

    Legumes are a highly diverse angiosperm family that include many agriculturally important species. To date, 21 complete chloroplast genomes have been sequenced from legume crops confined to the Papilionoideae subfamily. Here we report the first chloroplast genome from the Mimosoideae, Acacia ligulata, and compare it to the previously sequenced legume genomes. The A. ligulata chloroplast genome is 158,724 bp in size, comprising inverted repeats of 25,925 bp and single-copy regions of 88,576 bp and 18,298 bp. Acacia ligulata lacks the inversion present in many of the Papilionoideae, but is not otherwise significantly different in terms of gene and repeat content. The key feature is its highly divergent clpP1 gene, normally considered essential in chloroplast genomes. In A. ligulata, although transcribed and spliced, it probably encodes a catalytically inactive protein. This study provides a significant resource for further genetic research into Acacia and the Mimosoideae. The divergent clpP1 gene suggests that Acacia will provide an interesting source of information on the evolution and functional diversity of the chloroplast Clp protease complex. PMID:25955637

  7. Genetic Analysis of Arabidopsis Mutants Impaired in Plastid Lipid Import Reveals a Role of Membrane Lipids in Chloroplast Division

    SciTech Connect

    Fan, J.; Xu, C.

    2011-03-01

    The biogenesis of photosynthetic membranes in plants relies largely on lipid import from the endoplasmic reticulum (ER) and this lipid transport process is mediated by TGD proteins in Arabidopsis. Such a dependency of chloroplast biogenesis on ER-to-plastid lipid transport was recently exemplified by analyzing double mutants between tgd1-1 or tgd4-3 and fad6 mutants. The fad6 mutants are defective in the desaturation of membrane lipids in chloroplasts and therefore dependent on import of polyunsaturated lipid precursors from the ER for constructing a competent thylakoid membrane system. In support of a critical role of TGD proteins in ER-to-plastid lipid trafficking, we showed that the introduction of the tgd mutations into fad6 mutant backgrounds led to drastic reductions in relative amounts of thylakoid lipids. Moreover, the tgd1-1 fad6 and tgd4-3 fad6 double mutants were deficient in polyunsaturated fatty acids in chloroplast membrane lipids, and severely compromised in the biogenesis of photosynthetic membrane systems. Here we report that these double mutants are severely impaired in chloroplast division. The possible role of membrane lipids in chloroplast division is discussed.

  8. Microsatellite Markers Reveal Strong Genetic Structure in the Endemic Chilean Dolphin

    PubMed Central

    Pérez-Alvarez, María José; Olavarría, Carlos; Moraga, Rodrigo; Baker, C. Scott; Hamner, Rebecca M.; Poulin, Elie

    2015-01-01

    Understanding genetic differentiation and speciation processes in marine species with high dispersal capabilities is challenging. The Chilean dolphin, Cephalorhynchus eutropia, is the only endemic cetacean of Chile and is found in two different coastal habitats: a northern habitat with exposed coastlines, bays and estuaries from Valparaíso (33°02′S) to Chiloé (42°00′S), and a southern habitat with highly fragmented inshore coastline, channels and fjords between Chiloé and Navarino Island (55°14′S). With the aim of evaluating the potential existence of conservation units for this species, we analyzed the genetic diversity and population structure of the Chilean dolphin along its entire range. We genotyped 21 dinucleotide microsatellites for 53 skin samples collected between 1998 and 2012 (swab: n = 8, biopsy: n = 38, entanglement n = 7). Bayesian clustering and spatial model analyses identified two genetically distinct populations corresponding to the northern and southern habitats. Genetic diversity levels were similar in the two populations (He: 0.42 v/s 0.45 for southern and northern populations, respectively), while effective size population was higher in the southern area (Ne: 101 v/s 39). Genetic differentiation between these two populations was high and significant (FST = 0.15 and RST = 0.19), indicating little or no current gene flow. Because of the absence of evident geographical barriers between the northern and southern populations, we propose that genetic differentiation may reflect ecological adaptation to the different habitat conditions and resource uses. Therefore, the two genetic populations of this endemic and Near Threatened species should be considered as different conservation units with independent management strategies. PMID:25898340

  9. Genotypic diversity and differentiation among populations of two benthic freshwater diatoms as revealed by microsatellites.

    PubMed

    Vanormelingen, Pieter; Evans, Katharine M; Mann, David G; Lance, Stacey; Debeer, Ann-Eline; D'Hondt, Sofie; Verstraete, Tine; De Meester, Luc; Vyverman, Wim

    2015-09-01

    Given their large population sizes and presumed high dispersal capacity, protists are expected to exhibit homogeneous population structure over large spatial scales. On the other hand, the fragmented and short-lived nature of the lentic freshwater habitats that many protists inhabit promotes strong population differentiation. We used microsatellites in two benthic freshwater diatoms, Eunotia bilunaris 'robust' and Sellaphora capitata, sampled from within a pond and connected ponds, through isolated ponds from the same region to western Europe to determine the spatial scale at which differentiation appears. Because periods of low genotypic diversity contribute to population differentiation, we also assessed genotypic diversity. While genotypic diversity was very high to maximal in most samples of both species, some had a markedly lower diversity, with up to half (Eunotia) and over 90% (Sellaphora) of the strains having the same multilocus genotype. Population differentiation showed an isolation-by-distance pattern with very low standardized FST values between samples from the same or connected ponds but high values between isolated ponds, even when situated in the same region. Partial rbcL sequences in Eunotia were consistent with this pattern as isolated ponds in the same region could differ widely in haplotype composition. Populations identified by Structure corresponded to the source ponds, confirming that 'pond' is the main factor structuring these populations. We conclude that freshwater benthic diatom populations are highly fragmented on a regional scale, reflecting either less dispersal than is often assumed or reduced establishment success of immigrants, so that dispersal does not translate into gene flow. PMID:26227512

  10. Microsatellite Marker Analysis Reveals the Complex Phylogeographic History of Rhododendron ferrugineum (Ericaceae) in the Pyrenees

    PubMed Central

    Charrier, Olivia; Dupont, Pierre; Pornon, André; Escaravage, Nathalie

    2014-01-01

    Genetic variation within plant species is determined by a number of factors such as reproductive mode, breeding system, life history traits and climatic events. In alpine regions, plants experience heterogenic abiotic conditions that influence the population's genetic structure. The aim of this study was to investigate the genetic structure and phylogeographic history of the subalpine shrub Rhododendron ferrugineum across the Pyrenees and the links between the populations in the Pyrenees, the Alps and Jura Mountains. We used 27 microsatellite markers to genotype 645 samples from 29 Pyrenean populations, three from the Alps and one from the Jura Mountains. These data were used to estimate population genetics statistics such as allelic richness, observed heterozygosity, expected heterozygosity, fixation index, inbreeding coefficient and number of migrants. Genetic diversity was found to be higher in the Alps than in the Pyrenees suggesting colonization waves from the Alps to the Pyrenees. Two separate genetic lineages were found in both the Alps and Pyrenees, with a substructure of five genetic clusters in the Pyrenees where a loss of genetic diversity was noted. The strong differentiation among clusters is maintained by low gene flow across populations. Moreover, some populations showed higher genetic diversity than others and presented rare alleles that may indicate the presence of alpine refugia. Two lineages of R. ferrugineum have colonized the Pyrenees from the Alps. Then, during glaciation events R. ferrugineum survived in the Pyrenees in different refugia such as lowland refugia at the eastern part of the chain and nunataks at high elevations leading to a clustered genetic pattern. PMID:24667824

  11. Microsatellite-based genotyping of Candida parapsilosis sensu stricto isolates reveals dominance and persistence of a particular epidemiological clone among neonatal intensive care unit patients.

    PubMed

    Romeo, Orazio; Delfino, Demetrio; Cascio, Antonio; Lo Passo, Carla; Amorini, Maria; Romeo, Daniela; Pernice, Ida

    2013-01-01

    In this study, using multilocus microsatellite analysis, we report the genetic characterization of 27 Candida parapsilosis isolates recovered in two different periods of time (2007-2009 and 2011-2012) from infants hospitalized in the neonatal intensive care unit of a hospital in Messina, Italy. The results revealed the persistence and dominance of a particular infectious genotype among NICU patients and highlight the power of the used microsatellite markers in clarifying epidemiologic associations, detect micro-evolutionary variations and facilitating the recognition of outbreaks. PMID:23022715

  12. Microsatellite analysis of Rosa damascena Mill. accessions reveals genetic similarity between genotypes used for rose oil production and old Damask rose varieties.

    PubMed

    Rusanov, K; Kovacheva, N; Vosman, B; Zhang, L; Rajapakse, S; Atanassov, A; Atanassov, I

    2005-08-01

    Damask roses are grown in several European and Asiatic countries for rose oil production. Twenty-six oil-bearing Rosa damascena Mill. accessions and 13 garden Damask roses were assayed by molecular markers. Microsatellite genotyping demonstrated that R. damascena Mill. accessions from Bulgaria, Iran, and India and old European Damask rose varieties possess identical microsatellite profiles, suggesting a common origin. At the same time, the data indicated that modern industrial oil rose cultivation is based on a very narrow genepool and that oil rose collections contain many genetically identical accessions. The study of long-term vegetative propagation of the Damask roses also reveals high somatic stability for the microsatellite loci analyzed. PMID:15947904

  13. Population genetic structure and migration patterns of Liriomyza sativae in China: moderate subdivision and no Bridgehead effect revealed by microsatellites.

    PubMed

    Tang, X-T; Ji, Y; Chang, Y-W; Shen, Y; Tian, Z-H; Gong, W-R; Du, Y-Z

    2016-02-01

    While Liriomyza sativae (Diptera: Agromyzidae), an important invasive pest of ornamentals and vegetables has been found in China for the past two decades, few studies have focused on its genetics or route of invasive. In this study, we collected 288 L. sativae individuals across 12 provinces to explore its population genetic structure and migration patterns in China using seven microsatellites. We found relatively low levels of genetic diversity but moderate population genetic structure (0.05 < F ST < 0.15) in L. sativae from China. All populations deviated significantly from the Hardy-Weinberg equilibrium due to heterozygote deficiency. Molecular variance analysis revealed that more than 89% of variation was among samples within populations. A UPGMA dendrogram revealed that SH and GXNN populations formed one cluster separate from the other populations, which is in accordance with STRUCTURE and GENELAND analyses. A Mantel test indicated that genetic distance was not correlated to geographic distance (r = -0.0814, P = 0.7610), coupled with high levels of gene flow (M = 40.1-817.7), suggesting a possible anthropogenic influence on the spread of L. sativae in China and on the effect of hosts. The trend of asymmetrical gene flow was from southern to northern populations in general and did not exhibit a Bridgehead effect during the course of invasion, as can be seen by the low genetic diversity of southern populations. PMID:26615869

  14. Crystallization of the c[subscript 14]-rotor of the chloroplast ATP synthase reveals that it contains pigments

    SciTech Connect

    Varco-Merth, Benjamin; Fromme, Raimund; Wang, Meitian; Fromme, Petra

    2008-08-27

    The ATP synthase is one of the most important enzymes on earth as it couples the transmembrane electrochemical potential of protons to the synthesis of ATP from ADP and inorganic phosphage, providing the main ATP source of almost all higher life on earth. During ATP synthesis, stepwise protonation of a conserved carboxylate on each protein subunit of an oligomeric ring of 10--15 c-subunits is commonly thought to drive rotation of the rotor moiety (c{sub 10-14}{gamma}{sup {epsilon}}) relative to stator moiety ({alpha}{sub 3}{beta}{sub 3}{delta}ab{sub 2}). Here we report the isolation and crystallization of the c{sub 14}-ring of subunit c from the spinach chloroplast enzyme diffracting as far as 2.8 {angstrom}. Though ATP synthase was not previously know to contain any pigments, the crystals of the c-subunit possessed a strong yellow color. The pigment analysis revaled that they contain 1 chlorophyll and 2 carotenoids, thereby showing for the first time that the chloroplast ATP synthase contains cofactors, leading to the question of the possible roles of the functions of the pigments in the chloroplast ATP synthase.

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

    PubMed Central

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

    2014-01-01

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

  16. Genetic diversity and population structure of the critically endangered Yangtze finless porpoise (Neophocaena asiaeorientalis asiaeorientalis) as revealed by mitochondrial and microsatellite DNA.

    PubMed

    Chen, Minmin; Zheng, Jinsong; Wu, Min; Ruan, Rui; Zhao, Qingzhong; Wang, Ding

    2014-01-01

    Ecological surveys have indicated that the population of the critically endangered Yangtze finless porpoise (YFP, Neophocaena asiaeorientalis asiaeorientalis) is becoming increasingly small and fragmented, and will be at high risk of extinction in the near future. Genetic conservation of this population will be an important component of the long-term conservation effort. We used a 597 base pair mitochondrial DNA (mtDNA) control region and 11 microsatellite loci to analyze the genetic diversity and population structure of the YFP. The analysis of both mtDNA and microsatellite loci suggested that the genetic diversity of the YFP will possibly decrease in the future if the population keeps declining at a rapid rate, even though these two types of markers revealed different levels of genetic diversity. In addition, mtDNA revealed strong genetic differentiation between one local population, Xingchang-Shishou (XCSS), and the other five downstream local populations; furthermore, microsatellite DNA unveiled fine but significant genetic differentiation between three of the local populations (not only XCSS but also Poyang Lake (PY) and Tongling (TL)) and the other local populations. With an increasing number of distribution gaps appearing in the Yangtze main steam, the genetic differentiation of local populations will likely intensify in the future. The YFP is becoming a genetically fragmented population. Therefore, we recommend attention should be paid to the genetic conservation of the YFP. PMID:24968271

  17. Genetic Diversity and Population Structure of the Critically Endangered Yangtze Finless Porpoise (Neophocaena asiaeorientalis asiaeorientalis) as Revealed by Mitochondrial and Microsatellite DNA

    PubMed Central

    Chen, Minmin; Zheng, Jinsong; Wu, Min; Ruan, Rui; Zhao, Qingzhong; Wang, Ding

    2014-01-01

    Ecological surveys have indicated that the population of the critically endangered Yangtze finless porpoise (YFP, Neophocaena asiaeorientalis asiaeorientalis) is becoming increasingly small and fragmented, and will be at high risk of extinction in the near future. Genetic conservation of this population will be an important component of the long-term conservation effort. We used a 597 base pair mitochondrial DNA (mtDNA) control region and 11 microsatellite loci to analyze the genetic diversity and population structure of the YFP. The analysis of both mtDNA and microsatellite loci suggested that the genetic diversity of the YFP will possibly decrease in the future if the population keeps declining at a rapid rate, even though these two types of markers revealed different levels of genetic diversity. In addition, mtDNA revealed strong genetic differentiation between one local population, Xingchang–Shishou (XCSS), and the other five downstream local populations; furthermore, microsatellite DNA unveiled fine but significant genetic differentiation between three of the local populations (not only XCSS but also Poyang Lake (PY) and Tongling (TL)) and the other local populations. With an increasing number of distribution gaps appearing in the Yangtze main steam, the genetic differentiation of local populations will likely intensify in the future. The YFP is becoming a genetically fragmented population. Therefore, we recommend attention should be paid to the genetic conservation of the YFP. PMID:24968271

  18. A microsatellite linkage map of striped bass (Morone saxatilis) reveals conserved synteny with the hree-spined stickleback (Gasterosteus aculeatus)

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Background: The striped bass (Morone saxatilis) and its relatives (genus Morone) are of great importance to fisheries and aquaculture in North America. As part of a collaborative effort to employ molecular genetic technologies in striped bass breeding programs, nearly 500 microsatellite markers were...

  19. Genetic structuring in a relictual population of screaming hairy armadillo (Chaetophractus vellerosus) in Argentina revealed by a set of novel microsatellite loci.

    PubMed

    Nardelli, Maximiliano; Ibáñez, Ezequiel Alejandro; Dobler, Dara; Justy, Fabienne; Delsuc, Frédéric; Abba, Agustín Manuel; Cassini, Marcelo Hernán; Túnez, Juan Ignacio

    2016-08-01

    The screaming hairy armadillo (Chaetophractus vellerosus) is a mammal species containing disjunct and isolated populations. In order to assess the effect of habitat fragmentation and geographic isolation, we developed seven new microsatellite loci isolated from low-coverage genome shotgun sequencing data for this species. Among these loci, six microsatellites were found to be polymorphic with 8-26 alleles per locus detected across 69 samples analyzed from a relictual population of the species located in the northeast of the Buenos Aires Province (Argentina). Mean allelic richness and polymorphic information content were 15 and 0.75, with observed and expected heterozygosities ranging from 0.40 to 0.67 and 0.58 to 0.90, respectively. All loci showed departures from Hardy-Weinberg equilibrium. The analysis of population structure in this relictual population revealed three groups of individuals that are genetically differentiated. These newly developed microsatellites will constitute a very useful tool for the estimation of genetic diversity and structure, population dynamics, social structure, parentage and mating system in this little-studied armadillo species. Such genetic data will be particularly helpful for the development of conservation strategies for this isolated population and also for the endangered Bolivian populations previously recognized as a distinct species (Chaetophractus nationi). PMID:27406582

  20. Genetic structure of Columbia River redband trout populations in the Kootenai River drainage, Montana, revealed by microsatellite and allozyme loci

    USGS Publications Warehouse

    Knudsen, K.-L.; Muhlfeld, C.C.; Sage, G.K.; Leary, R.F.

    2002-01-01

    We describe the genetic divergence among 10 populations of redband trout Oncorhynchus mykiss gairdneri from the upper Columbia River drainage. Resident redband trout from two watersheds in the Kootenai River drainage and hatchery stocks of migratory Kamloops redband trout from Kootenay Lake, British Columbia, were analyzed using allele frequency data from microsatellite and allozyme loci. The Kamloops populations have significantly different allele frequencies from those of the Kootenai River drainage. Of the total genetic variation detected in the resident redband trout, 40.7% (microsatellites) and 15.5% (allozymes) were due to differences between populations from the two Kootenai River watersheds. The divergence among populations within each watershed, however, was less than 3.5% with both techniques. Our data indicate that watershed-specific broodstocks of redband trout are needed by fisheries managers for reintroduction or the supplementation of populations at risk of extinction.

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

    NASA Astrophysics Data System (ADS)

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

    2011-09-01

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

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

    PubMed

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

    2011-09-01

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

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

    PubMed

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

    2008-09-30

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

  4. Nuclear mutations that block group II RNA splicing in maize chloroplasts reveal several intron classes with distinct requirements for splicing factors.

    PubMed Central

    Jenkins, B D; Kulhanek, D J; Barkan, A

    1997-01-01

    To elucidate mechanisms that regulate chloroplast RNA splicing in multicellular plants, we sought nuclear mutations in maize that result in chloroplast splicing defects. Evidence is presented for two nuclear genes whose function is required for the splicing of group II introns in maize chloroplasts. A mutation in the crs1 (for chloroplast RNA splicing 1) gene blocks the splicing of only the atpF intron, whereas a mutation in the crs2 gene blocks the splicing of many chloroplast introns. In addition, a correlation was observed between the absence of plastid ribosomes and the failure to splice several chloroplast introns. Our results suggest that a chloroplast-encoded factor and a nuclear-encoded factor whose activity requires crs2 function facilitate the splicing of distinct sets of group II introns. These two genetically defined intron sets also differ with regard to intron structure: one set consists of only subgroup IIA introns and the other of only subgroup IIB introns. Therefore, it is likely that distinct splicing factors recognize subgroup-specific features of intron structure or facilitate subgroup-specific aspects of the splicing reaction. Of the 12 pre-mRNA introns in the maize chloroplast genome, only one is normally spliced in both crs2 mutants and in mutants lacking plastid ribosomes, indicating that few, if any, of the group II introns in the chloroplast genome undergo autocatalytic splicing in vivo. PMID:9090875

  5. Posttranslational Modification of Maize Chloroplast Pyruvate Orthophosphate Dikinase Reveals the Precise Regulatory Mechanism of Its Enzymatic Activity.

    PubMed

    Chen, Yi-Bo; Lu, Tian-Cong; Wang, Hong-Xia; Shen, Jie; Bu, Tian-Tian; Chao, Qing; Gao, Zhi-Fang; Zhu, Xin-Guang; Wang, Yue-Feng; Wang, Bai-Chen

    2014-04-01

    In C4 plants, pyruvate orthophosphate dikinase (PPDK) activity is tightly dark/light regulated by reversible phosphorylation of an active-site threonine (Thr) residue; this process is catalyzed by PPDK regulatory protein (PDRP). Phosphorylation and dephosphorylation of PPDK lead to its inactivation and activation, respectively. Here, we show that light intensity rather than the light/dark transition regulates PPDK activity by modulating the reversible phosphorylation at Thr-527 (previously termed Thr-456) of PPDK in maize (Zea mays). The amount of PPDK (unphosphorylated) involved in C4 photosynthesis is indeed strictly controlled by light intensity, despite the high levels of PPDK protein that accumulate in mesophyll chloroplasts. In addition, we identified a transit peptide cleavage site, uncovered partial amino-terminal acetylation, and detected phosphorylation at four serine (Ser)/Thr residues, two of which were previously unknown in maize. In vitro experiments indicated that Thr-527 and Ser-528, but not Thr-309 and Ser-506, are targets of PDRP. Modeling suggests that the two hydrogen bonds between the highly conserved residues Ser-528 and glycine-525 are required for PDRP-mediated phosphorylation of the active-site Thr-527 of PPDK. Taken together, our results suggest that the regulation of maize plastid PPDK isoform (C4PPDK) activity is much more complex than previously reported. These diverse regulatory pathways may work alone or in combination to fine-tune C4PPDK activity in response to changes in lighting. PMID:24710069

  6. The ultrastructure and flexibility of thylakoid membranes in leaves and isolated chloroplasts as revealed by small-angle neutron scattering.

    PubMed

    Unnep, R; Zsiros, O; Solymosi, K; Kovács, L; Lambrev, P H; Tóth, T; Schweins, R; Posselt, D; Székely, N K; Rosta, L; Nagy, G; Garab, G

    2014-09-01

    We studied the periodicity of the multilamellar membrane system of granal chloroplasts in different isolated plant thylakoid membranes, using different suspension media, as well as on different detached leaves and isolated protoplasts-using small-angle neutron scattering. Freshly isolated thylakoid membranes suspended in isotonic or hypertonic media, containing sorbitol supplemented with cations, displayed Bragg peaks typically between 0.019 and 0.023Å(-1), corresponding to spatially and statistically averaged repeat distance values of about 275-330 Å⁻¹. Similar data obtained earlier led us in previous work to propose an origin from the periodicity of stroma thylakoid membranes. However, detached leaves, of eleven different species, infiltrated with or soaked in D2O in dim laboratory light or transpired with D2O prior to measurements, exhibited considerably smaller repeat distances, typically between 210 and 230 Å⁻¹, ruling out a stromal membrane origin. Similar values were obtained on isolated tobacco and spinach protoplasts. When NaCl was used as osmoticum, the Bragg peaks of isolated thylakoid membranes almost coincided with those in the same batch of leaves and the repeat distances were very close to the electron microscopically determined values in the grana. Although neutron scattering and electron microscopy yield somewhat different values, which is not fully understood, we can conclude that small-angle neutron scattering is a suitable technique to study the periodic organization of granal thylakoid membranes in intact leaves under physiological conditions and with a time resolution of minutes or shorter. We also show here, for the first time on leaves, that the periodicity of thylakoid membranes in situ responds dynamically to moderately strong illumination. This article is part of a special issue entitled: photosynthesis research for sustainability: keys to produce clean energy. PMID:24508217

  7. High genetic divergence in miniature breeds of Japanese native chickens compared to Red Junglefowl, as revealed by microsatellite analysis.

    PubMed

    Tadano, R; Nishibori, M; Imamura, Y; Matsuzaki, M; Kinoshita, K; Mizutani, M; Namikawa, T; Tsudzuki, M

    2008-02-01

    A wide diversity of domesticated chicken breeds exist due to artificial selection on the basis of human interests. Miniature variants (bantams) are eminently illustrative of the large changes from ancestral junglefowls. In this report, the genetic characterization of seven Japanese miniature chicken breeds and varieties, together with institute-kept Red Junglefowl, was conducted by means of typing 40 microsatellites located on 21 autosomes. We drew focus to genetic differentiation between the miniature chicken breeds and Red Junglefowl in particular. A total of 305 alleles were identified: 27 of these alleles (8.9%) were unique to the Red Junglefowl with high frequencies (>20%). Significantly high genetic differences (F(ST)) were obtained between Red Junglefowl and all other breeds with a range of 0.3901-0.5128. Individual clustering (constructed from combinations of the proportion of shared alleles and the neighbour-joining method) indicated high genetic divergence among breeds including Red Junglefowl. There were also individual assignments on the basis of the Bayesian and distance-based approaches. The microsatellite differences in the miniature chicken breeds compared to the presumed wild ancestor reflected the phenotypic diversity among them, indicating that each of these miniature chicken breeds is a unique gene pool. PMID:18254737

  8. Genetic Variability of Wild Cherry (Prunus avium L.) Seed Stands in Slovenia as Revealed by Nuclear Microsatellite Loci

    PubMed Central

    Jarni, Kristjan; De Cuyper, Bart; Brus, Robert

    2012-01-01

    Microsatellite markers were used to describe the genetic variability of four seed stands of wild cherry (Prunus avium L.). One hundred and thirty one individuals were genotyped at ten nuclear microsatellite loci. Total genetic diversity was high (HE = 0.704), while differences between stands were small but significant (FST = 0.053, G′ST = 0.234). There was a significant amount of clonal reproduction in one stand, with only 11 genotypes identified among 36 trees. One stand showed a significant excess (FIS = −0.044) of heterozygosity, and one showed a deficit (FIS = 0.044). Our results demonstrate the importance of taking into account the biological and genetic characteristics of species in forest management, especially when determining a new seed stand. The small genetic differences found between seed stands indicate that a large number of stands are not required. However, they should be carefully selected and should possess adequate genetic variability to ensure low relatedness between seed trees. PMID:22911762

  9. Microsatellite development and flow cytometry in the African tree genus Afzelia (Fabaceae, Caesalpinioideae) reveal a polyploid complex1

    PubMed Central

    Donkpegan, Armel S. L.; Doucet, Jean-Louis; Dainou, Kasso; Hardy, Olivier J.

    2015-01-01

    • Premise of the study: Microsatellites were developed in the vulnerable African rainforest tree Afzelia bipindensis to investigate gene flow patterns. • Methods and Results: Using 454 GS-FLX technique, 16 primer sets were identified and optimized, leading to 11 polymorphic and readable markers displaying each six to 25 alleles in a population. Up to four alleles per individual were found in each of the loci, without evidence of fixed heterozygosity, suggesting an autotetraploid genome. Cross-amplification succeeded for all loci in the African rainforest species A. pachyloba and A. bella, which appeared tetraploid, and for most loci in the African woodland species A. africana and A. quanzensis, which appeared diploid, but failed in the Asian species A. xylocarpa. Flow cytometry confirmed the suspected differences in ploidy. • Conclusions: African Afzelia species are diploid or tetraploid, a situation rarely documented in tropical trees. These newly developed microsatellites will help in the study of their mating system and gene flow patterns. PMID:25606356

  10. Integrative Omics Analysis Reveals Post-Transcriptionally Enhanced Protective Host Response in Colorectal Cancers with Microsatellite Instability

    PubMed Central

    2015-01-01

    Microsatellite instability (MSI) is a frequent and clinically relevant molecular phenotype in colorectal cancer. MSI cancers have favorable survival compared with microsatellite stable cancers (MSS), possibly due to the pronounced tumor-infiltrating lymphocytes observed in MSI cancers. Consistent with the strong immune response that MSI cancers trigger in the host, previous transcriptome expression studies have identified mRNA signatures characteristic of immune response in MSI cancers. However, proteomics features of MSI cancers and the extent to which the mRNA signatures are reflected at the protein level remain largely unknown. Here, we performed a comprehensive comparison of global proteomics profiles between MSI and MSS colorectal cancers in The Cancer Genome Atlas (TCGA) cohort. We found that protein signatures of MSI are also associated with increased immunogenicity. To reliably quantify post-transcription regulation in MSI cancers, we developed a resampling-based regression method by integrative modeling of transcriptomics and proteomics data sets. Compared with the popular simple method, which detects post-transcriptional regulation by either identifying genes differentially expressed at the mRNA level but not at the protein level or vice versa, our method provided a quantitative, more sensitive, and accurate way to identify genes subject to differential post-transcriptional regulation. With this method, we demonstrated that post-transcriptional regulation, coordinating protein expression with key players, initiates de novo and enhances protective host response in MSI cancers. PMID:26680540

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

    PubMed Central

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

    2008-01-01

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

  12. Comparative Microsatellite Typing of New World Leishmania infantum Reveals Low Heterogeneity among Populations and Its Recent Old World Origin

    PubMed Central

    Kuhls, Katrin; Alam, Mohammad Zahangir; Cupolillo, Elisa; Ferreira, Gabriel Eduardo M.; Mauricio, Isabel L.; Oddone, Rolando; Feliciangeli, M. Dora; Wirth, Thierry; Miles, Michael A.; Schönian, Gabriele

    2011-01-01

    Leishmania infantum (syn. L. chagasi) is the causative agent of visceral leishmaniasis (VL) in the New World (NW) with endemic regions extending from southern USA to northern Argentina. The two hypotheses about the origin of VL in the NW suggest (1) recent importation of L. infantum from the Old World (OW), or (2) an indigenous origin and a distinct taxonomic rank for the NW parasite. Multilocus microsatellite typing was applied in a survey of 98 L. infantum isolates from different NW foci. The microsatellite profiles obtained were compared to those of 308 L. infantum and 20 L. donovani strains from OW countries previously assigned to well-defined populations. Two main populations were identified for both NW and OW L. infantum. Most of the NW strains belonged to population 1, which corresponded to the OW MON-1 population. However, the NW population was much more homogeneous. A second, more heterogeneous, population comprised most Caribbean strains and corresponded to the OW non-MON-1 population. All Brazilian L. infantum strains belonged to population 1, although they represented 61% of the sample and originated from 9 states. Population analysis including the OW L. infantum populations indicated that the NW strains were more similar to MON-1 and non-MON-1 sub-populations of L. infantum from southwest Europe, than to any other OW sub-population. Moreover, similarity between NW and Southwest European L. infantum was higher than between OW L. infantum from distinct parts of the Mediterranean region, Middle East and Central Asia. No correlation was found between NW L. infantum genotypes and clinical picture or host background. This study represents the first continent-wide analysis of NW L. infantum population structure. It confirmed that the agent of VL in the NW is L. infantum and that the parasite has been recently imported multiple times to the NW from southwest Europe. PMID:21666787

  13. Comparative microsatellite typing of new world leishmania infantum reveals low heterogeneity among populations and its recent old world origin.

    PubMed

    Kuhls, Katrin; Alam, Mohammad Zahangir; Cupolillo, Elisa; Ferreira, Gabriel Eduardo M; Mauricio, Isabel L; Oddone, Rolando; Feliciangeli, M Dora; Wirth, Thierry; Miles, Michael A; Schönian, Gabriele

    2011-06-01

    Leishmania infantum (syn. L. chagasi) is the causative agent of visceral leishmaniasis (VL) in the New World (NW) with endemic regions extending from southern USA to northern Argentina. The two hypotheses about the origin of VL in the NW suggest (1) recent importation of L. infantum from the Old World (OW), or (2) an indigenous origin and a distinct taxonomic rank for the NW parasite. Multilocus microsatellite typing was applied in a survey of 98 L. infantum isolates from different NW foci. The microsatellite profiles obtained were compared to those of 308 L. infantum and 20 L. donovani strains from OW countries previously assigned to well-defined populations. Two main populations were identified for both NW and OW L. infantum. Most of the NW strains belonged to population 1, which corresponded to the OW MON-1 population. However, the NW population was much more homogeneous. A second, more heterogeneous, population comprised most Caribbean strains and corresponded to the OW non-MON-1 population. All Brazilian L. infantum strains belonged to population 1, although they represented 61% of the sample and originated from 9 states. Population analysis including the OW L. infantum populations indicated that the NW strains were more similar to MON-1 and non-MON-1 sub-populations of L. infantum from southwest Europe, than to any other OW sub-population. Moreover, similarity between NW and Southwest European L. infantum was higher than between OW L. infantum from distinct parts of the Mediterranean region, Middle East and Central Asia. No correlation was found between NW L. infantum genotypes and clinical picture or host background. This study represents the first continent-wide analysis of NW L. infantum population structure. It confirmed that the agent of VL in the NW is L. infantum and that the parasite has been recently imported multiple times to the NW from southwest Europe. PMID:21666787

  14. Genetic variability, differentiation, and founder effect in golden jackals (Canis aureus) from Serbia as revealed by mitochondrial DNA and nuclear microsatellite loci.

    PubMed

    Zachos, Frank E; Cirovic, Dusko; Kirschning, Julia; Otto, Marthe; Hartl, Günther B; Petersen, Britt; Honnen, Ann-Christin

    2009-04-01

    We analyzed 121 golden jackals (Canis aureus) from six sample sites in Serbia with regard to genetic variability and differentiation as revealed by mitochondrial control region sequences and eight nuclear microsatellite loci. There was no variation at all in the mtDNA sequences, and nuclear variability was very low (average observed and expected heterozygosity of 0.29 and 0.34, respectively). This is in line with the considerable recent range expansion of this species in the Balkans and indicates a strong founder effect in the recently established Serbian population. We did not find evidence of differentiation between the northeastern jackals and those from the plain of Srem or those in between. F-statistics and Bayesian Structure analyses, however, were indicative of a low degree of overall differentiation in the Serbian population. A vagrant Austrian jackal that was also analyzed was genetically indistinguishable from its Serbian conspecifics. PMID:19169806

  15. Microsatellite markers reveal population structure and low gene flow among collections of Bactrocera cucurbitae (Diptera: Tephritidae) in Asia.

    PubMed

    Wu, Yi; Li, Yunlong; Ruiz-Arce, Raul; McPheron, Bruce A; Wu, Jiajiao; Li, Zhihong

    2011-06-01

    The melon fruit fly, Bactrocera cucurbitae (Coquillett) (Diptera: Tephritidae), is widespread agricultural pest, and it is known to have the potential to establish invasive populations in various tropical and subtropical areas. Despite the economic risk associated with a putative stable presence of this fly, the population genetics of this pest have remained relatively unexplored in Asia, the main area for distribution of this pest. The goals for this study were to employ nuclear markers to examine geographic collections for population genetic structure and quantify the extent of gene flow within these Southeast Asian and Chinese populations. To achieve these goals, we used 12 polymorphic microsatellite markers. A low level of genetic diversity was found among collections from China and higher levels were seen in Southeast Asia collections. Three genetically distinct groups, Southeast Asia, southwest China, and southeast China, were recovered by Bayesian model-based clustering methods, the phylogenetic reconstruction and the principal coordinate analysis. The Mantel test clearly shows geographical distance contributed in the genetic structuring of B. cucurbitae's populations. No recent bottlenecks for any of the populations examined. The results of clustering, migration analyses, and Mantel test, strongly suggest that the regional structure observed may be due to geographical factors such as mountains, rivers, and islands. We found a high rate of migration in some sites from the southwest China region (cluster 1) and the southeast China region (cluster 2), suggesting that China-Guangdong-Guangzhou (GZ) may be the center of melon fruit fly in the southeast China region. PMID:21735930

  16. Microsatellite Analysis of Museum Specimens Reveals Historical Differences in Genetic Diversity between Declining and More Stable Bombus Species

    PubMed Central

    Maebe, Kevin; Meeus, Ivan; Ganne, Maarten; De Meulemeester, Thibaut; Biesmeijer, Koos; Smagghe, Guy

    2015-01-01

    Worldwide most pollinators, e.g. bumblebees, are undergoing global declines. Loss of genetic diversity can play an essential role in these observed declines. In this paper, we investigated the level of genetic diversity of seven declining Bombus species and four more stable species with the use of microsatellite loci. Hereto we genotyped a unique collection of museum specimens. Specimens were collected between 1918 and 1926, in 6 provinces of the Netherlands which allowed us to make interspecific comparisons of genetic diversity. For the stable species B. pascuorum, we also selected populations from two additional time periods: 1949–1955 and 1975–1990. The genetic diversity and population structure in B. pascuorum remained constant over the three time periods. However, populations of declining bumblebee species showed a significantly lower genetic diversity than co-occurring stable species before their major declines. This historical difference indicates that the repeatedly observed reduced genetic diversity in recent populations of declining bumblebee species is not caused solely by the decline itself. The historically low genetic diversity in the declined species may be due to the fact that these species were already rare, making them more vulnerable to the major drivers of bumblebee decline. PMID:26061732

  17. Microsatellite markers reveal chimeric origin of redesignated chromosome 4A of wheat from Triticum urartu and other species.

    PubMed

    Vasu, K; Aghaee-Sarbarzel; Dhaliwal, H S

    2001-08-01

    Although a new nomenclature has been adopted for wheat in which chromosome 4A (4AO) has been renamed 4B (4BN) and chromosome 4B (4BO) has been renamed 4A (4AN), their specific origin remains uncertain. The use of wheat microsatellite (WMS) markers mapped to chromosomes 4AN and 4BN in a set of polyploid wheats and diploid genome donors has unequivocally indicated that the entire short arm of 4AN, some part of 4ANL. and a segment of 4BNL were derived from Triticum urartu. The presence of a T. urartu-specific allele at locus gwm368 on 4BNL and of an Aegilops speltoides allele at locus gwm397 on 4ANL suggests the possibility of a reciprocal translocation between 4ANL and 4BNL. The subcentromeric and telomeric regions of 4ANL corresponding to heterochromatic C-bands were derived neither from diploid wheats nor from Ae. speltoides or Aegilops longissima. PMID:11550897

  18. Genetic diversity and parentage in farmer selections of cacao from Southern Sulawesi, Indonesia revealed by microsatellite markers.

    PubMed

    Dinarti, Diny; Susilo, Agung W; Meinhardt, Lyndel W; Ji, Kun; Motilal, Lambert A; Mischke, Sue; Zhang, Dapeng

    2015-12-01

    Indonesia is the third largest cocoa-producing country in the world. Knowledge of genetic diversity and parentage of farmer selections is important for effective selection and rational deployment of superior cacao clones in farmers' fields. We assessed genetic diversity and parentage of 53 farmer selections of cacao in Sulawesi, Indonesia, using 152 international clones as references. Cluster analysis, based on 15 microsatellite markers, showed that these Sulawesi farmer selections are mainly comprised of hybrids derived from Trinitario and two Upper Amazon Forastero groups. Bayesian assignment and likelihood-based parentage analysis further demonstrated that only a small number of germplasm groups, dominantly Trinitario and Parinari, contributed to these farmer selections, in spite of diverse parental clones having been used in the breeding program and seed gardens in Indonesia since the 1950s. The narrow parentage predicts a less durable host resistance to cacao diseases. Limited access of the farmers to diverse planting materials or the strong preference for large pods and large bean size by local farmers, may have affected the selection outcome. Diverse sources of resistance, harbored in different cacao germplasm groups, need to be effectively incorporated to broaden the on-farm diversity and ensure sustainable cacao production in Sulawesi. PMID:26719747

  19. Genetic diversity and parentage in farmer selections of cacao from Southern Sulawesi, Indonesia revealed by microsatellite markers

    PubMed Central

    Dinarti, Diny; Susilo, Agung W.; Meinhardt, Lyndel W.; Ji, Kun; Motilal, Lambert A.; Mischke, Sue; Zhang, Dapeng

    2015-01-01

    Indonesia is the third largest cocoa-producing country in the world. Knowledge of genetic diversity and parentage of farmer selections is important for effective selection and rational deployment of superior cacao clones in farmers’ fields. We assessed genetic diversity and parentage of 53 farmer selections of cacao in Sulawesi, Indonesia, using 152 international clones as references. Cluster analysis, based on 15 microsatellite markers, showed that these Sulawesi farmer selections are mainly comprised of hybrids derived from Trinitario and two Upper Amazon Forastero groups. Bayesian assignment and likelihood-based parentage analysis further demonstrated that only a small number of germplasm groups, dominantly Trinitario and Parinari, contributed to these farmer selections, in spite of diverse parental clones having been used in the breeding program and seed gardens in Indonesia since the 1950s. The narrow parentage predicts a less durable host resistance to cacao diseases. Limited access of the farmers to diverse planting materials or the strong preference for large pods and large bean size by local farmers, may have affected the selection outcome. Diverse sources of resistance, harbored in different cacao germplasm groups, need to be effectively incorporated to broaden the on-farm diversity and ensure sustainable cacao production in Sulawesi. PMID:26719747

  20. Genetic diversity and phylogenetic relationship among Tunisian cactus species (Opuntia) as revealed by random amplified microsatellite polymorphism markers.

    PubMed

    Bendhifi Zarroug, M; Baraket, G; Zourgui, L; Souid, S; Salhi Hannachi, A

    2015-01-01

    Opuntia ficus indica is one of the most economically important species in the Cactaceae family. Increased interest in this crop stems from its potential contribution to agricultural diversification, application in the exploitation of marginal lands, and utility as additional income sources for farmers. In Tunisia, O. ficus indica has been affected by drastic genetic erosion resulting from biotic and abiotic stresses. Thus, it is imperative to identify and preserve this germplasm. In this study, we focused on the use of random amplified microsatellite polymorphisms to assess genetic diversity among 25 representatives of Tunisian Opuntia species maintained in the collection of the National Institute of Agronomic Research of Tunisia. Seventy-two DNA markers were screened to discriminate accessions using 16 successful primer combinations. The high percentage of polymorphic band (100%), the resolving power value (5.68), the polymorphic information content (0.94), and the marker index (7.2) demonstrated the efficiency of the primers tested. Therefore, appropriate cluster analysis used in this study illustrated a divergence among the cultivars studied and exhibited continuous variation that occurred independently of geographic origin. O. ficus indica accessions did not cluster separately from the other cactus pear species, indicating that their current taxonomical classifications are not well aligned with their genetic variability or locality of origin. PMID:25730081

  1. High genetic differentiation of Aegla longirostri (Crustacea, Decapoda, Anomura) populations in southern Brazil revealed by multi-loci microsatellite analysis.

    PubMed

    Bartholomei-Santos, M L; Roratto, P A; Santos, S

    2011-01-01

    Species with a broad distribution rarely have the same genetic make-up throughout their entire range. In some cases, they may constitute a cryptic complex consisting of a few species, each with a narrow distribution, instead of a single-, widely distributed species. These differences can have profound impacts for biodiversity conservation planning. The genetic differentiation of four populations of Aegla longirostri, a freshwater crab found in two geographically isolated basins in Rio Grande do Sul State, Brazil, was investigated by analyzing pentanucleotide multi-loci microsatellites in a heteroduplex assay. Although no morphological differences were evident, we found significant genetic differentiation among the four populations, based on F(ST) values and clustering analysis. This high level of differentiation may be indicative of cryptic species in these populations. If this hypothesis is correct, then the species occurring in the Ibicuí-Mirim River, at the southern limit of the Atlantic Rain Forest, would be under threat, considering its very restricted distribution. PMID:22179994

  2. High genetic diversity in gametophyte clones of Undaria pinnatifida from Vladivostok, Dalian and Qingdao revealed using microsatellite analysis

    NASA Astrophysics Data System (ADS)

    Shan, Tifeng; Pang, Shaojun; Liu, Feng; Xu, Na; Zhao, Xiaobo; Gao, Suqin

    2012-03-01

    Breeding practice for Undaria pinnatifida (Harvey) Suringar requires the screening of a large number of offspring from gametophyte crossings to obtain an elite variety for large-scale cultivation. To better understand the genetic relationships of different gametophyte cultures isolated from different sources, 20 microsatellite loci were screened and 53 gametophyte clone cultures analyzed for U. pinnatifida isolated from wild sporophytes in Vladivostok, Russia and from cultivated sporophytes from Dalian and Qingdao, China. One locus was abandoned because of poor amplification. At the sex-linked locus of Up-AC-2A8, 3 alleles were detected in 25 female gametophyte clones, with sizes ranging from 307 to 316 bp. At other loci, 3 to 7 alleles were detected with an average of 4.5 alleles per locus. The average number of alleles at each locus was 1.3 and 3.7 for Russian and Chinese gametophyte clones, respectively. The average gene diversity for Russian, Chinese, and for the combined total of gametophyte clones was 0.1, 0.4, and 0.5, respectively. Russian gametophyte clones had unique alleles at 7 out of the 19 loci. In cluster analysis, Russian and Chinese gametophyte clones were separated into two different groups according to genetic distance. Overall, high genetic diversity was detected in gametophyte clones isolated from the two countries. These gametophyte cultures were believed to be appropriate parental materials for conducting breeding programs in the future.

  3. Proteomic Insight into the Response of Arabidopsis Chloroplasts to Darkness

    PubMed Central

    Wang, Jing; Yu, Qingbo; Xiong, Haibo; Wang, Jun; Chen, Sixue; Yang, Zhongnan; Dai, Shaojun

    2016-01-01

    Chloroplast function in photosynthesis is essential for plant growth and development. It is well-known that chloroplasts respond to various light conditions. However, it remains poorly understood about how chloroplasts respond to darkness. In this study, we found 81 darkness-responsive proteins in Arabidopsis chloroplasts under 8 h darkness treatment. Most of the proteins are nucleus-encoded, indicating that chloroplast darkness response is closely regulated by the nucleus. Among them, 17 ribosome proteins were obviously reduced after darkness treatment. The protein expressional patterns and physiological changes revealed the mechanisms in chloroplasts in response to darkness, e.g., (1) inhibition of photosystem II resulted in preferential cyclic electron flow around PSI; (2) promotion of starch degradation; (3) inhibition of chloroplastic translation; and (4) regulation by redox and jasmonate signaling. The results have improved our understanding of molecular regulatory mechanisms in chloroplasts under darkness. PMID:27137770

  4. Comparative Proteomics of Thellungiella halophila Leaves from Plants Subjected to Salinity Reveals the Importance of Chloroplastic Starch and Soluble Sugars in Halophyte Salt Tolerance*

    PubMed Central

    Wang, Xuchu; Chang, Lili; Wang, Baichen; Wang, Dan; Li, Pinghua; Wang, Limin; Yi, Xiaoping; Huang, Qixing; Peng, Ming; Guo, Anping

    2013-01-01

    Thellungiella halophila, a close relative of Arabidopsis, is a model halophyte used to study plant salt tolerance. The proteomic/physiological/transcriptomic analyses of Thellungiella plant leaves subjected to different salinity levels, reported herein, indicate an extraordinary ability of Thellungiella to adapt to large concentrations of exogenous saline by compartmentalizing Na+ into cell vacuoles and accumulating proline and soluble sugars as organic osmolytes. Salinity stress stimulated the accumulation of starch in chloroplasts, which resulted in a greatly increased content of starch and total sugars in leaves. Comparative proteomics of Thellungiella leaves identified 209 salt-responsive proteins. Among these, the sequences of 108 proteins were strongly homologous to Arabidopsis protein sequences, and 30 had previously been identified as Thellungiella proteins. Functional classification of these proteins into 16 categories indicated that the majority are involved in carbohydrate metabolism, followed by those involved in energy production and conversion, and then those involved in the transport of inorganic ions. Pathway analysis revealed that most of the proteins are involved in starch and sucrose metabolism, carbon fixation, photosynthesis, and glycolysis. Of these processes, the most affected were starch and sucrose metabolism, which might be pivotal for salt tolerance. The gene expression patterns of the 209 salt-responsive proteins revealed through hierarchical clustering of microarray data and the expression patterns of 29 Thellungiella genes evaluated via quantitative RT-PCR were similar to those deduced via proteomic analysis, which underscored the possibility that starch and sucrose metabolism might play pivotal roles in determining the salt tolerance ability of Thellungiella. Our observations enabled us to propose a schematic representation of the systematic salt-tolerance phenotype in Thellungiella and suggested that the increased accumulation of

  5. Large scale comparative proteomics of a chloroplast Clp protease mutant reveals folding stress, altered protein homeostasis, and feedback regulation of metabolism.

    PubMed

    Zybailov, Boris; Friso, Giulia; Kim, Jitae; Rudella, Andrea; Rodríguez, Verenice Ramírez; Asakura, Yukari; Sun, Qi; van Wijk, Klaas J

    2009-08-01

    The clpr2-1 mutant is delayed in development due to reduction of the chloroplast ClpPR protease complex. To understand the role of Clp proteases in plastid biogenesis and homeostasis, leaf proteomes of young seedlings of clpr2-1 and wild type were compared using large scale mass spectrometry-based quantification using an LTQ-Orbitrap and spectral counting with significance determined by G-tests. Virtually only chloroplast-localized proteins were significantly affected, indicating that the molecular phenotype was confined to the chloroplast. A comparative chloroplast stromal proteome analysis of fully developed plants was used to complement the data set. Chloroplast unfoldase ClpB3 was strongly up-regulated in both young and mature leaves, suggesting widespread and persistent protein folding stress. The importance of ClpB3 in the clp2-1 mutant was demonstrated by the observation that a CLPR2 and CLPB3 double mutant was seedling-lethal. The observed up-regulation of chloroplast chaperones and protein sorting components further illustrated destabilization of protein homeostasis. Delayed rRNA processing and up-regulation of a chloroplast DEAD box RNA helicase and polynucleotide phosphorylase, but no significant change in accumulation of ribosomal subunits, suggested a bottleneck in ribosome assembly or RNA metabolism. Strong up-regulation of a chloroplast translational regulator TypA/BipA GTPase suggested a specific response in plastid gene expression to the distorted homeostasis. The stromal proteases PreP1,2 were up-regulated, likely constituting compensation for reduced Clp protease activity and possibly shared substrates between the ClpP and PreP protease systems. The thylakoid photosynthetic apparatus was decreased in the seedlings, whereas several structural thylakoid-associated plastoglobular proteins were strongly up-regulated. Two thylakoid-associated reductases involved in isoprenoid and chlorophyll synthesis were up-regulated reflecting feedback from rate

  6. Large Scale Comparative Proteomics of a Chloroplast Clp Protease Mutant Reveals Folding Stress, Altered Protein Homeostasis, and Feedback Regulation of Metabolism*

    PubMed Central

    Zybailov, Boris; Friso, Giulia; Kim, Jitae; Rudella, Andrea; Rodríguez, Verenice Ramírez; Asakura, Yukari; Sun, Qi; van Wijk, Klaas J.

    2009-01-01

    The clpr2-1 mutant is delayed in development due to reduction of the chloroplast ClpPR protease complex. To understand the role of Clp proteases in plastid biogenesis and homeostasis, leaf proteomes of young seedlings of clpr2-1 and wild type were compared using large scale mass spectrometry-based quantification using an LTQ-Orbitrap and spectral counting with significance determined by G-tests. Virtually only chloroplast-localized proteins were significantly affected, indicating that the molecular phenotype was confined to the chloroplast. A comparative chloroplast stromal proteome analysis of fully developed plants was used to complement the data set. Chloroplast unfoldase ClpB3 was strongly up-regulated in both young and mature leaves, suggesting widespread and persistent protein folding stress. The importance of ClpB3 in the clp2-1 mutant was demonstrated by the observation that a CLPR2 and CLPB3 double mutant was seedling-lethal. The observed up-regulation of chloroplast chaperones and protein sorting components further illustrated destabilization of protein homeostasis. Delayed rRNA processing and up-regulation of a chloroplast DEAD box RNA helicase and polynucleotide phosphorylase, but no significant change in accumulation of ribosomal subunits, suggested a bottleneck in ribosome assembly or RNA metabolism. Strong up-regulation of a chloroplast translational regulator TypA/BipA GTPase suggested a specific response in plastid gene expression to the distorted homeostasis. The stromal proteases PreP1,2 were up-regulated, likely constituting compensation for reduced Clp protease activity and possibly shared substrates between the ClpP and PreP protease systems. The thylakoid photosynthetic apparatus was decreased in the seedlings, whereas several structural thylakoid-associated plastoglobular proteins were strongly up-regulated. Two thylakoid-associated reductases involved in isoprenoid and chlorophyll synthesis were up-regulated reflecting feedback from rate

  7. The impact of selection on population genetic structure in the clam Meretrix petechialis revealed by microsatellite markers.

    PubMed

    Lu, Xia; Wang, Hongxia; Li, Yan; Liu, Baozhong

    2016-02-01

    The aim of our work is to evaluate the impact of mass selection on genetic structure in artificially closed populations of the clam Meretrix petechialis. In the present study, we performed mass selection over four generations (from 2004 to 2010) on two clam populations [shell features of purple lines (SP) and black dots (SB)] and analyzed their temporal genetic variation and structure using microsatellite makers. The two closed populations originated from the natural Shandong population (SD); thus, a natural SD population (10SD) was used to detect the current genetic structure after 6 years of natural selection. The results showed that the genetic diversity of the four generations of SB and SP was gradually reduced but remained at relatively high levels (SB, A = 18.9.4-16.8, Ho = 0.7389-0.6971, and He = 0.8897-0.8591; SP, A = 20.0-17.8, Ho = 0.7512-0.7043, and He = 0.8938-0.8625), which has not been reduced compared with that of the 10SD population (A = 17.8, Ho = 0.6803, and He = 0.8302). The Ne estimates for the two populations were almost at the same levels as the actual numbers of parental individuals. In addition, a low inbreeding coefficient was detected in the two populations (SB, 0.00201-0.00639; SP, 0.00176-0.00541). Based on the results, the present mass selection has not made a large impact on the population genetic structure of the closed populations. The present investigation provides important information for the development of management strategies for genetic breeding of the clam. PMID:26586137

  8. Heterogeneous genetic structure in a Fagus crenata population in an old-growth beech forest revealed by microsatellite markers.

    PubMed

    Asuka, Y; Tomaru, N; Nisimura, N; Tsumura, Y; Yamamoto, S

    2004-05-01

    The within-population genetic structure of Fagus crenata in a 4-ha plot (200 x 200 m) of an old-growth beech forest was analysed using microsatellite markers. To assess the genetic structure, Moran's I spatial autocorrelation coefficient was calculated. Correlograms of Moran's I showed significant positive values less than 0.100 for short-distance classes, indicating weak genetic structure. The genetic structure within the population is created by limited seed dispersal, and is probably weakened by overlapping seed shadow, secondary seed dispersal, extensive pollen flow and the thinning process. Genetic structure was detected in a western subplot of 50 x 200 m with immature soils and almost no dwarf bamboos (Sasa spp.), where small and intermediate-sized individuals were distributed in aggregations with high density because of successful regeneration. By contrast, genetic structure was not found in an eastern subplot of the same size with mature soils and Sasa cover, where successful regeneration was prevented, and the density of the small and intermediate-sized individuals was low. Moreover, genetic structure of individuals in a small-size class (diameter at breast height < 12 cm) was more obvious than in a large-size class (diameter at breast height >/= 12 cm). The apparent genetic structure detected in the 4-ha plot was therefore probably the result of the structure in the western portion of the plot and in small and intermediate-sized individuals that successfully regenerated under the favourable environment. The heterogeneity in genetic structure presumably reflects variation in the density that should be affected by differences in regeneration dynamics associated with heterogeneity in environmental conditions. PMID:15078459

  9. Microsatellites reveal a strong subdivision of genetic structure in Chinese populations of the mite Tetranychus urticae Koch (Acari: Tetranychidae)

    PubMed Central

    2012-01-01

    Background Two colour forms of the two-spotted spider mite (Tetranychus urticae Koch) coexist in China: a red (carmine) form, which is considered to be native and a green form which is considered to be invasive. The population genetic diversity and population genetic structure of this organism were unclear in China, and there is a controversy over whether they constitute distinct species. To address these issues, we genotyped a total of 1,055 individuals from 18 red populations and 7 green populations in China using eight microsatellite loci. Results We identified 109 alleles. We found a highly significant genetic differentiation among the 25 populations (global FST = 0.506, global FST {ENA} = 0.473) and a low genetic diversity in each population. In addition, genetic diversity of the red form mites was found to be higher than the green form. Pearson correlations between statistics of variation (AR and HE) and geographic coordinates (latitude and longitude) showed that the genetic diversity of the red form was correlated with latitude. Using Bayesian clustering, we divided the Chinese mite populations into five clades which were well congruent with their geographic distributions. Conclusions Spider mites possess low levels of genetic diversity, limit gene flow between populations and significant and IBD (isolation by distance) effect. These factors in turn contribute to the strong subdivision of genetic structure. In addition, population genetic structure results don't support the separation of the two forms of spider mite into two species. The morphological differences between the two forms of mites may be a result of epigenetic effects. PMID:22348504

  10. Genetic structuring and transfer of marine dinoflagellate Cochlodinium polykrikoides in Japanese and Korean coastal waters revealed by microsatellites.

    PubMed

    Nagai, S; Nishitani, G; Sakamoto, S; Sugaya, T; Lee, C K; Kim, C H; Itakura, S; Yamaguchi, M

    2009-06-01

    To determine the process of population expansion and ascertain the origin of the Sea of Japan population, in a noxious red tide forming dinoflagellate Cochlodinium polykrikoides, 13 samples, isolated from 11 different localities in Japanese and Korean coasts, were analysed using 10 polymorphic microsatellites. Analyses by nonmetric multidimensional scaling plots of pairwise F(ST), global amova, and genetic admixture analysis identified three clusters--the Sea of Japan populations, Yatsushiro Sea (Kumamoto Pref.) populations, and other populations--indicating genetic structuring of the 13 samples into three distinct populations. In the proportion of shared alleles by pairwise individuals (P(SAxy)) analyses between the Sea of Japan and the other samples, P(SAxy) was extremely low compared with that among the Sea of Japan or among other samples, indicating that a large genetic barrier has occurred between the populations. No significant relationship of isolation-by-distance patterns and almost no genetic distance were detected between pairwise samples of the Sea of Japan, although there is a maximal distance of > 600 km between samples. In addition, P(SAxy) data among the samples were extremely high compared with those among other samples, clearly showing that a large-scale transfer from west to east has occurred via the Tushima Warm Current. In the P(SAxy) data of the Seto Inland Sea and Pacific samples, individuals showing relatively high P(SAxy) were concentrated in the three areas of Nagasaki, Harima, and Mie, suggesting that frequent transfer may have occurred by human-assisted dispersal, although Nagasaki and Mie are separated by a distance of approximately 700 km. PMID:19457209

  11. Chloroplast evolution, structure and functions

    PubMed Central

    Jensen, Poul Erik

    2014-01-01

    In this review, we consider a selection of recent advances in chloroplast biology. These include new findings concerning chloroplast evolution, such as the identification of Chlamydiae as a third partner in primary endosymbiosis, a second instance of primary endosymbiosis represented by the chromatophores found in amoebae of the genus Paulinella, and a new explanation for the longevity of captured chloroplasts (kleptoplasts) in sacoglossan sea slugs. The controversy surrounding the three-dimensional structure of grana, its recent resolution by tomographic analyses, and the role of the CURVATURE THYLAKOID1 (CURT1) proteins in supporting grana formation are also discussed. We also present an updated inventory of photosynthetic proteins and the factors involved in the assembly of thylakoid multiprotein complexes, and evaluate findings that reveal that cyclic electron flow involves NADPH dehydrogenase (NDH)- and PGRL1/PGR5-dependent pathways, both of which receive electrons from ferredoxin. Other topics covered in this review include new protein components of nucleoids, an updated inventory of the chloroplast proteome, new enzymes in chlorophyll biosynthesis and new candidate messengers in retrograde signaling. Finally, we discuss the first successful synthetic biology approaches that resulted in chloroplasts in which electrons from the photosynthetic light reactions are fed to enzymes derived from secondary metabolism. PMID:24991417

  12. Metabolic engineering of the chloroplast genome reveals that the yeast ArDH gene confers enhanced tolerance to salinity and drought in plants.

    PubMed

    Khan, Muhammad Sarwar; Kanwal, Benish; Nazir, Shahid

    2015-01-01

    Osmoprotectants stabilize proteins and membranes against the denaturing effect of high concentrations of salts and other harmful solutes. In yeast, arabitol dehydrogenase (ArDH) reduces D-ribulose to D-arabitol where D-ribulose is derived by dephosphorylating D-ribulose-5-PO4 in the oxidized pentose pathway. Osmotolerance in plants could be developed through metabolic engineering of chloroplast genome by introducing genes encoding polyols since chloroplasts offer high level transgene expression and containment. Here, we report that ArDH expression in tobacco chloroplasts confers tolerance to NaCl (up to 400 mM). Transgenic plants compared to wild type (WT) survived for only 4-5 weeks on 400 mM NaCl whereas plants remained green and grew normal on concentrations up to 350 mM NaCl. Further, a-week-old seedlings were also challenged with poly ethylene glycol (PEG, up to 6%) in the liquid medium, considering that membranes and proteins are protected under stress conditions due to accumulation of arabitol in chloroplasts. Seedlings were tolerant to 6% PEG, suggesting that ARDH enzyme maintains integrity of membranes in chloroplasts under drought conditions via metabolic engineering. Hence, the gene could be expressed in agronomic plants to withstand abiotic stresses. PMID:26442039

  13. Metabolic engineering of the chloroplast genome reveals that the yeast ArDH gene confers enhanced tolerance to salinity and drought in plants

    PubMed Central

    Khan, Muhammad Sarwar; Kanwal, Benish; Nazir, Shahid

    2015-01-01

    Osmoprotectants stabilize proteins and membranes against the denaturing effect of high concentrations of salts and other harmful solutes. In yeast, arabitol dehydrogenase (ArDH) reduces D-ribulose to D-arabitol where D-ribulose is derived by dephosphorylating D-ribulose-5-PO4 in the oxidized pentose pathway. Osmotolerance in plants could be developed through metabolic engineering of chloroplast genome by introducing genes encoding polyols since chloroplasts offer high level transgene expression and containment. Here, we report that ArDH expression in tobacco chloroplasts confers tolerance to NaCl (up to 400 mM). Transgenic plants compared to wild type (WT) survived for only 4–5 weeks on 400 mM NaCl whereas plants remained green and grew normal on concentrations up to 350 mM NaCl. Further, a-week-old seedlings were also challenged with poly ethylene glycol (PEG, up to 6%) in the liquid medium, considering that membranes and proteins are protected under stress conditions due to accumulation of arabitol in chloroplasts. Seedlings were tolerant to 6% PEG, suggesting that ARDH enzyme maintains integrity of membranes in chloroplasts under drought conditions via metabolic engineering. Hence, the gene could be expressed in agronomic plants to withstand abiotic stresses. PMID:26442039

  14. Population structure of North American beluga whales (Delphinapterus leucas) based on nuclear DNA microsatellite variation and contrasted with the population structure revealed by mitochondrial DNA variation

    PubMed

    Gladden; Ferguson; Friesen; Clayton

    1999-03-01

    Beluga whales (Delphinapterus leucas) in North American waters migrate seasonally between wintering areas in broken pack ice and summering locations in estuaries and other open water areas in the Arctic and sub-Arctic. Results from our previous investigation of beluga whale mitochondrial DNA (mtDNA) revealed genetic heterogeneity among beluga from different summering locations that was interpreted as representing a high degree of summering site philopatry. However, mtDNA is maternally inherited and does not reflect mating that may occur among beluga from different summering locations in wintering areas or during annual migrations. To test the possibility that breeding occurs among beluga from different summering locations, genetic variability at five nuclear DNA (nDNA) microsatellite loci was examined in the same animals tested in the mtDNA study. Beluga samples (n = 640) were collected between 1984 and 1994 from 24 sites across North America, mostly during the summer. Whales from the various sites were categorized into eight summering locations as identified by mtDNA analysis, as well as four hypothesized wintering areas: Bering Sea, Hudson Strait (Hudson Strait, Labrador Sea, southwest Davis Strait), Baffin Bay (North Water, east Davis Strait), and St Lawrence River. Microsatellite allele frequencies indicated genetic homogeneity among animals from summering sites believed to winter together but differentiation among whales from some of the wintering areas. In particular, beluga from western North America (Bering Sea) were clearly distinguished from beluga from eastern North America (Hudson Strait, Baffin Bay, and St Lawrence River). Based upon the combined data set, the population of North American beluga whales was divided into two evolutionarily significant units. However, the population may be further subdivided into management units to reflect distinct groups of beluga at summering locations. PMID:10199005

  15. Chloroplast DNA Phylogeography Reveals Repeated Range Expansion in a Widespread Aquatic Herb Hippuris vulgaris in the Qinghai-Tibetan Plateau and Adjacent Areas

    PubMed Central

    Sun, Shan-Shan; Gituru, Robert Wahiti; Wang, Qing-Feng

    2013-01-01

    Background The Qinghai-Tibetan Plateau (QTP) is one of the most extensive habitats for alpine plants in the world. Climatic oscillations during the Quaternary ice age had a dramatic effect on species ranges on the QTP and the adjacent areas. However, how the distribution ranges of aquatic plant species shifted on the QTP in response to Quaternary climatic changes remains almost unknown. Methodology and Principal Findings We studied the phylogeography and demographic history of the widespread aquatic herb Hippuris vulgaris from the QTP and adjacent areas. Our sampling included 385 individuals from 47 natural populations of H. vulgaris. Using sequences from four chloroplast DNA (cpDNA) non-coding regions, we distinguished eight different cpDNA haplotypes. From the cpDNA variation in H. vulgaris, we found a very high level of population differentiation (GST = 0.819) but the phylogeographical structure remained obscure (NST = 0.853>GST = 0.819, P>0.05). Phylogenetic analyses revealed two main cpDNA haplotype lineages. The split between these two haplotype groups can be dated back to the mid-to-late Pleistocene (ca. 0.480 Myr). Mismatch distribution analyses showed that each of these had experienced a recent range expansion. These two expansions (ca. 0.12 and 0.17 Myr) might have begun from the different refugees before the Last Glacial Maximum (LGM). Conclusions/Significance This study initiates a research on the phylogeography of aquatic herbs in the QTP and for the first time sheds light on the response of an alpine aquatic seed plant species in the QTP to Quaternary climate oscillations. PMID:23565290

  16. Chloroplast-Specific in Vivo Ca2+ Imaging Using Yellow Cameleon Fluorescent Protein Sensors Reveals Organelle-Autonomous Ca2+ Signatures in the Stroma.

    PubMed

    Loro, Giovanna; Wagner, Stephan; Doccula, Fabrizio Gandolfo; Behera, Smrutisanjita; Weinl, Stefan; Kudla, Joerg; Schwarzländer, Markus; Costa, Alex; Zottini, Michela

    2016-08-01

    In eukaryotes, subcellular compartments such as mitochondria, the endoplasmic reticulum, lysosomes, and vacuoles have the capacity for Ca(2+) transport across their membranes to modulate the activity of compartmentalized enzymes or to convey specific cellular signaling events. In plants, it has been suggested that chloroplasts also display Ca(2+) regulation. So far, monitoring of stromal Ca(2+) dynamics in vivo has exclusively relied on using the luminescent Ca(2+) probe aequorin. However, this technique is limited in resolution and can only provide a readout averaged over chloroplast populations from different cells and tissues. Here, we present a toolkit of Arabidopsis (Arabidopsis thaliana) Ca(2+) sensor lines expressing plastid-targeted FRET-based Yellow Cameleon (YC) sensors. We demonstrate that the probes reliably report in vivo Ca(2+) dynamics in the stroma of root plastids in response to extracellular ATP and of leaf mesophyll and guard cell chloroplasts during light-to-low-intensity blue light illumination transition. Applying YC sensing of stromal Ca(2+) dynamics to single chloroplasts, we confirm findings of gradual, sustained stromal Ca(2+) increases at the tissue level after light-to-low-intensity blue light illumination transitions, but monitor transient Ca(2+) spiking as a distinct and previously unknown component of stromal Ca(2+) signatures. Spiking was dependent on the availability of cytosolic Ca(2+) but not synchronized between the chloroplasts of a cell. In contrast, the gradual sustained Ca(2+) increase occurred independent of cytosolic Ca(2+), suggesting intraorganellar Ca(2+) release. We demonstrate the capacity of the YC sensor toolkit to identify novel, fundamental facets of chloroplast Ca(2+) dynamics and to refine the understanding of plastidial Ca(2+) regulation. PMID:27252306

  17. Fluorescence Properties of Guard Cell Chloroplasts

    PubMed Central

    Zeiger, Eduardo; Armond, Paul; Melis, Anastasios

    1981-01-01

    The presence of chloroplasts in guard cells from leaf epidermis, coleoptile, flowers, and albino portions of variegated leaves was established by incident fluorescence microscopy, thus confirming the notion that guard cell chloroplasts are remarkably conserved. Room temperature emission spectra from a few chloroplasts in a single guard cell of Vicia faba showed one major peak at around 683 nanometers. Low-temperature (77 K) emission spectra from peels of albino portions of Chlorophytum comosum leaves and from mesophyll chloroplasts of green parts of the same leaves showed major peaks at around 687 and 733 nanometers, peaks usually attributed to photosystem II and photosystem I pigment systems, respectively. Spectra of peels of V. faba leaves showed similar peaks. However, fluorescence microscopy revealed that the Vicia peels, as well as those from Allium cepa and Tulipa sp., were contaminated with non-guard cell chloroplasts which were practically undetectable under bright field illumination. These observations pose restrictions on the use of epidermal peels as a source of isolated guard cell chloroplasts. Studies on the 3-(3,4-dichlorophenyl)-1,1-dimethylurea-sensitive variable fluorescence kinetics of uncontaminated epidermal peels of C. comosum indicated that guard cell chloroplasts operate a normal, photosystem II-dependent, linear electron transport. The above properties in combination with their reported inability to fix CO2 photosynthetically may render the guard cell chloroplasts optimally suited to supply the reducing and high-energy phosphate equivalents needed to sustain active ion transport during stomatal opening in daylight. PMID:16661620

  18. Insights into chloroplast biogenesis and development.

    PubMed

    Pogson, Barry J; Ganguly, Diep; Albrecht-Borth, Verónica

    2015-09-01

    In recent years many advances have been made to obtain insight into chloroplast biogenesis and development. In plants several plastids types exist such as the proplastid (which is the progenitor of all plastids), leucoplasts (group of colourless plastids important for storage including elaioplasts (lipids), amyloplasts (starch) or proteinoplasts (proteins)), chromoplasts (yellow to orange-coloured due to carotenoids, in flowers or in old leaves as gerontoplasts), and the green chloroplasts. Chloroplasts are indispensable for plant development; not only by performing photosynthesis and thus rendering the plant photoautotrophic, but also for biochemical processes (which in some instances can also take place in other plastids types), such as the synthesis of pigments, lipids, and plant hormones and sensing environmental stimuli. Although we understand many aspects of these processes there are gaps in our understanding of the establishment of functional chloroplasts and their regulation. Why is that so? Even though chloroplast function is comparable in all plants and most of the algae, ferns and moss, detailed analyses have revealed many differences, specifically with respect to its biogenesis. As an update to our prior review on the genetic analysis of chloroplast biogenesis and development [1] herein we will focus on recent advances in Angiosperms (monocotyledonous and dicotyledonous plants) that provide novel insights and highlight the challenges and prospects for unravelling the regulation of chloroplast biogenesis specifically during the establishment of the young plants. This article is part of a Special Issue entitled: Chloroplast Biogenesis. PMID:25667967

  19. REDUCTION OF SPECIES IN THE WILD POTATO SOLANUM SECTION PETOTA SERIES LONGIPEDICELLATA: AFLP, RAPD AND CHLOROPLAST SSR DATA.

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Species boundaries were assessed with three molecular markers (AFLPs, RAPDs, chloroplast microsatellites, also known as chloroplast single sequence repeats [cpSSRs]) for all six species of wild potatoes (Solanum L. section Petota Dumort.) assigned to ser. Longipedicellata: S. fendleri, S. hjertingii...

  20. Establishment of Monitoring Methods for Autophagy in Rice Reveals Autophagic Recycling of Chloroplasts and Root Plastids during Energy Limitation1[OPEN

    PubMed Central

    Hidema, Jun; Wada, Shinya; Kondo, Eri; Kurusu, Takamitsu; Kuchitsu, Kazuyuki; Makino, Amane; Ishida, Hiroyuki

    2015-01-01

    Autophagy is an intracellular process leading to vacuolar or lysosomal degradation of cytoplasmic components in eukaryotes. Establishment of proper methods to monitor autophagy was a key step in uncovering its role in organisms, such as yeast (Saccharomyces cerevisiae), mammals, and Arabidopsis (Arabidopsis thaliana), in which chloroplastic proteins were found to be recycled by autophagy. Chloroplast recycling has been predicted to function in nutrient remobilization for growing organs or grain filling in cereal crops. Here, to develop our understanding of autophagy in cereals, we established monitoring methods for chloroplast autophagy in rice (Oryza sativa). We generated transgenic rice-expressing fluorescent protein (FP) OsAuTophaGy8 (OsATG8) fusions as autophagy markers. FP-ATG8 signals were delivered into the vacuolar lumen in living cells of roots and leaves mainly as vesicles corresponding to autophagic bodies. This phenomenon was not observed upon the addition of wortmannin, an inhibitor of autophagy, or in an ATG7 knockout mutant. Markers for the chloroplast stroma, stromal FP, and FP-labeled Rubisco were delivered by a type of autophagic body called the Rubisco-containing body (RCB) in the same manner. RCB production in excised leaves was suppressed by supply of external sucrose or light. The release of free FP caused by autophagy-dependent breakdown of FP-labeled Rubisco was induced during accelerated senescence in individually darkened leaves. In roots, nongreen plastids underwent both RCB-mediated and entire organelle types of autophagy. Therefore, our newly developed methods to monitor autophagy directly showed autophagic degradation of leaf chloroplasts and root plastids in rice plants and its induction during energy limitation. PMID:25717038

  1. 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

  2. Whole Chloroplast Genome Sequencing in Fragaria Using Deep Sequencing: A Comparison of Three Methods

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Chloroplast sequences previously investigated in Fragaria revealed low amounts of variation. Deep sequencing technologies enable economical sequencing of complete chloroplast genomes. These sequences can potentially provide robust phylogenetic resolution, even at low taxonomic levels within plant gr...

  3. Genetic Differentiation and Genetic Diversity of Castanopsis (Fagaceae), the Dominant Tree Species in Japanese Broadleaved Evergreen Forests, Revealed by Analysis of EST-Associated Microsatellites

    PubMed Central

    Aoki, Kyoko; Ueno, Saneyoshi; Kamijo, Takashi; Setoguchi, Hiroaki; Murakami, Noriaki; Kato, Makoto; Tsumura, Yoshihiko

    2014-01-01

    The broadleaved evergreen forests of the East Asian warm temperate zone are characterised by their high biodiversity and endemism, and there is therefore a need to extend our understanding of its genetic diversity and phylogeographic patterns. Castanopsis (Fagaceae) is one of the dominant tree species in the broadleaved evergreen forests of Japan. In this study we investigate the genetic diversity, genetic structure and leaf epidermal morphology of 63 natural populations of C. sieboldii and C. cuspidata, using 32 Expressed Sequence Tag associated microsatellites. The overall genetic differentiation between populations was low (GST = 0.069 in C. sieboldii and GST = 0.057 in C. cuspidata). Neighbor-joining tree and Bayesian clustering analyses revealed that the populations of C. sieboldii and C. cuspidata were genetically clearly differentiated, a result which is consistent with the morphology of their epidermal cell layers. This suggests that C. sieboldii and C. cuspidata should be treated as independent species, although intermediate morphologies are often observed, especially at sites where the two species coexist. The higher level of genetic diversity observed in the Kyushu region (for both species) and the Ryukyu Islands (for C. sieboldii) is consistent with the available fossil pollen data for Castanopsis-type broadleaved evergreen trees during the Last Glacial Maximum and suggests the existence of refugia for Castanopsis forests in southern Japan. Within the C. sieboldii populations, Bayesian clustering analyses detected three clusters, in the western and eastern parts of the main islands and in the Ryukyu Islands. The west-east genetic differentiation observed for this species in the main islands, a pattern which is also found in several plant and animal species inhabiting Castanopsis forests in Japan, suggests that they have been isolated from each other in the western and eastern populations for an extended period of time, and may imply the

  4. Genetic differentiation and genetic diversity of Castanopsis (Fagaceae), the dominant tree species in Japanese broadleaved evergreen forests, revealed by analysis of EST-associated microsatellites.

    PubMed

    Aoki, Kyoko; Ueno, Saneyoshi; Kamijo, Takashi; Setoguchi, Hiroaki; Murakami, Noriaki; Kato, Makoto; Tsumura, Yoshihiko

    2014-01-01

    The broadleaved evergreen forests of the East Asian warm temperate zone are characterised by their high biodiversity and endemism, and there is therefore a need to extend our understanding of its genetic diversity and phylogeographic patterns. Castanopsis (Fagaceae) is one of the dominant tree species in the broadleaved evergreen forests of Japan. In this study we investigate the genetic diversity, genetic structure and leaf epidermal morphology of 63 natural populations of C. sieboldii and C. cuspidata, using 32 Expressed Sequence Tag associated microsatellites. The overall genetic differentiation between populations was low (GST = 0.069 in C. sieboldii and GST = 0.057 in C. cuspidata). Neighbor-joining tree and Bayesian clustering analyses revealed that the populations of C. sieboldii and C. cuspidata were genetically clearly differentiated, a result which is consistent with the morphology of their epidermal cell layers. This suggests that C. sieboldii and C. cuspidata should be treated as independent species, although intermediate morphologies are often observed, especially at sites where the two species coexist. The higher level of genetic diversity observed in the Kyushu region (for both species) and the Ryukyu Islands (for C. sieboldii) is consistent with the available fossil pollen data for Castanopsis-type broadleaved evergreen trees during the Last Glacial Maximum and suggests the existence of refugia for Castanopsis forests in southern Japan. Within the C. sieboldii populations, Bayesian clustering analyses detected three clusters, in the western and eastern parts of the main islands and in the Ryukyu Islands. The west-east genetic differentiation observed for this species in the main islands, a pattern which is also found in several plant and animal species inhabiting Castanopsis forests in Japan, suggests that they have been isolated from each other in the western and eastern populations for an extended period of time, and may imply the

  5. Genetic structure and relationships within and between cultivated and wild sorghum (Sorghum bicolor (L.) Moench) in Kenya as revealed by microsatellite markers.

    PubMed

    Mutegi, E; Sagnard, F; Semagn, K; Deu, M; Muraya, M; Kanyenji, B; de Villiers, S; Kiambi, D; Herselman, L; Labuschagne, M

    2011-03-01

    Understanding the extent and partitioning of diversity within and among crop landraces and their wild/weedy relatives constitutes the first step in conserving and unlocking their genetic potential. This study aimed to characterize the genetic structure and relationships within and between cultivated and wild sorghum at country scale in Kenya, and to elucidate some of the underlying evolutionary mechanisms. We analyzed at total of 439 individuals comprising 329 cultivated and 110 wild sorghums using 24 microsatellite markers. We observed a total of 295 alleles across all loci and individuals, with 257 different alleles being detected in the cultivated sorghum gene pool and 238 alleles in the wild sorghum gene pool. We found that the wild sorghum gene pool harbored significantly more genetic diversity than its domesticated counterpart, a reflection that domestication of sorghum was accompanied by a genetic bottleneck. Overall, our study found close genetic proximity between cultivated sorghum and its wild progenitor, with the extent of crop-wild divergence varying among cultivation regions. The observed genetic proximity may have arisen primarily due to historical and/or contemporary gene flow between the two congeners, with differences in farmers' practices explaining inter-regional gene flow differences. This suggests that deployment of transgenic sorghum in Kenya may lead to escape of transgenes into wild-weedy sorghum relatives. In both cultivated and wild sorghum, genetic diversity was found to be structured more along geographical level than agro-climatic level. This indicated that gene flow and genetic drift contributed to shaping the contemporary genetic structure in the two congeners. Spatial autocorrelation analysis revealed a strong spatial genetic structure in both cultivated and wild sorghums at the country scale, which could be explained by medium- to long-distance seed movement. PMID:21153801

  6. The selective biotin tagging and thermolysin proteolysis of chloroplast outer envelope proteins reveals information on protein topology and association into complexes

    PubMed Central

    Hardré, Hélène; Kuhn, Lauriane; Albrieux, Catherine; Jouhet, Juliette; Michaud, Morgane; Seigneurin-Berny, Daphné; Falconet, Denis; Block, Maryse A.; Maréchal, Eric

    2014-01-01

    The understanding of chloroplast function requires the precise localization of proteins in each of its sub-compartments. High-sensitivity mass spectrometry has allowed the inventory of proteins in thylakoid, stroma, and envelope fractions. Concerning membrane association, proteins can be either integral or peripheral or even soluble proteins bound transiently to a membrane complex. We sought a method providing information at the surface of the outer envelope membrane (OEM), based on specific tagging with biotin or proteolysis using thermolysin, a non-membrane permeable protease. To evaluate this method, envelope, thylakoid, and stroma proteins were separated by two-dimensional electrophoresis and analyzed by immunostaining and mass spectrometry. A short selection of proteins associated to the chloroplast envelope fraction was checked after superficial treatments of intact chloroplasts. We showed that this method could allow the characterization of OEM embedded proteins facing the cytosol, as well as peripheral and soluble proteins associated via tight or lose interactions. Some stromal proteins were associated with biotinylated spots and analyzes are still needed to determine whether polypeptides were tagged prior import or if they co-migrated with OEM proteins. This method also suggests that some proteins associated with the inner envelope membrane (IEM) might need the integrity of a trans-envelope (IEM–OEM) protein complex (e.g., division ring-forming components) or at least an intact OEM partner. Following this evaluation, proteomic analyzes should be refined and the putative role of inter-membrane space components stabilizing trans-envelope complexes demonstrated. For future comprehensive studies, perspectives include the dynamic analyses of OEM proteins and IEM–OEM complexes in various physiological contexts and using virtually any other purified membrane organelle. PMID:24999344

  7. Effects of cyclosis on chloroplast-cytoplasm interactions revealed with localized lighting in Characean cells at rest and after electrical excitation.

    PubMed

    Bulychev, Alexander A; Dodonova, Svetlana O

    2011-09-01

    Cytoplasmic streaming in Characean internodes enables rapid intracellular transport and facilitates interactions between spatially remote cell regions. Cyclosis-mediated distant interactions might be particularly noticeable under nonuniform illumination, in the vicinity of light-shade borders where metabolites are transported between functionally distinct cell regions. In support of this notion, chlorophyll fluorescence parameters assessed on a microscopic area of Chara corallina internodal cells (area of inspection, AOI) responded to illumination of nearby regions in asymmetric manner depending on the vector of cytoplasmic streaming. When a beam of white light was applied through a 400-μm optic fiber upstream of AOI with regard to the direction of cytoplasmic streaming, non-photochemical quenching (NPQ) developed after a lag period in AOI exposed to moderate intensity light. Conversely, no NPQ was induced in the same cell area when the beam position was shifted to an equal distance downstream of AOI. Light-response curves for the efficiency of photosystem II electron transport in chloroplasts differed markedly depending on the illumination pattern (whole-cell versus small area illumination) but these differences were eliminated after the inhibition of cytoplasmic streaming with cytochalasin B. Localized illumination promoted chloroplast fluorescence responses to electrical plasmalemma excitation at high light intensities, which contrasts to the requirement of low to moderate irradiances for observation of the stimulus-response coupling under whole-cell illumination. The results indicate that different photosynthetic capacities of chloroplasts under general and localized illumination are related to lateral transport of nonevenly distributed cytoplasmic components between the cell parts with dominant photosynthetic and respiratory metabolism. PMID:21708122

  8. The knockdown of chloroplastic ascorbate peroxidases reveals its regulatory role in the photosynthesis and protection under photo-oxidative stress in rice.

    PubMed

    Caverzan, Andréia; Bonifacio, Aurenivia; Carvalho, Fabricio E L; Andrade, Claudia M B; Passaia, Gisele; Schünemann, Mariana; Maraschin, Felipe Dos Santos; Martins, Marcio O; Teixeira, Felipe K; Rauber, Rafael; Margis, Rogério; Silveira, Joaquim Albenisio Gomes; Margis-Pinheiro, Márcia

    2014-01-01

    The inactivation of the chloroplast ascorbate peroxidases (chlAPXs) has been thought to limit the efficiency of the water-water cycle and photo-oxidative protection under stress conditions. In this study, we have generated double knockdown rice (Oryza sativa L.) plants in both OsAPX7 (sAPX) and OsAPX8 (tAPX) genes, which encode chloroplastic APXs (chlAPXs). By employing an integrated approach involving gene expression, proteomics, biochemical and physiological analyses of photosynthesis, we have assessed the role of chlAPXs in the regulation of the protection of the photosystem II (PSII) activity and CO2 assimilation in rice plants exposed to high light (HL) and methyl violagen (MV). The chlAPX knockdown plants were affected more severely than the non-transformed (NT) plants in the activity and structure of PSII and CO2 assimilation in the presence of MV. Although MV induced significant increases in pigment content in the knockdown plants, the increases were apparently not sufficient for protection. Treatment with HL also caused generalized damage in PSII in both types of plants. The knockdown and NT plants exhibited differences in photosynthetic parameters related to efficiency of utilization of light and CO2. The knockdown plants overexpressed other antioxidant enzymes in response to the stresses and increased the GPX activity in the chloroplast-enriched fraction. Our data suggest that a partial deficiency of chlAPX expression modulate the PSII activity and integrity, reflecting the overall photosynthesis when rice plants are subjected to acute oxidative stress. However, under normal growth conditions, the knockdown plants exhibit normal phenotype, biochemical and physiological performance. PMID:24268165

  9. Chloroplast and Cytoplasmic Enzymes

    PubMed Central

    Anderson, Louise E.; Pacold, Ivan

    1972-01-01

    Several peaks of aldolase activity are found in the isoelectric focusing pattern of pea (Pisum sativum) leaf chloroplast extracts. One peak, separated by 0.5 pH unit from the major chloroplast aldolase peak, is found when cytoplasmic extracts are focused. The chloroplast and cytoplasmic enzymes have a pH 7.4 optimum with fructose 1,6-diphosphate. The Michaelis constant for fructose-1,6-diphosphate is 19 μM for the chloroplast, 21 μM for the cytoplasmic enzyme, and for sedoheptulose 1,7-diphosphate, 8 μM for the chloroplast enzyme, 18 μM for the cytoplasmic enzyme. Both enzymes are inhibited by d-glyceraldehyde 3-phosphate and by ribulose 1,5-diphosphate. The similarity in the catalytic properties of the isoenzymes suggests that both enzymes have an amphibolic role in carbon metabolism in the green leaf. PMID:16657968

  10. Posttranslational Modifications of Chloroplast Proteins: An Emerging Field1

    PubMed Central

    2015-01-01

    Posttranslational modifications of proteins are key effectors of enzyme activity, protein interactions, targeting, and turnover rate, but despite their importance, they are still poorly understood in plants. Although numerous reports have revealed the regulatory role of protein phosphorylation in photosynthesis, various other protein modifications have been identified in chloroplasts only recently. It is known that posttranslational Nα-acetylation occurs in both nuclear- and plastid-encoded chloroplast proteins, but the physiological significance of this acetylation is not yet understood. Lysine acetylation affects the localization and activity of key metabolic enzymes, and it may work antagonistically or cooperatively with lysine methylation, which also occurs in chloroplasts. In addition, tyrosine nitration may help regulate the repair cycle of photosystem II, while N-glycosylation determines enzyme activity of chloroplastic carbonic anhydrase. This review summarizes the progress in the research field of posttranslational modifications of chloroplast proteins and points out the importance of these modifications in the regulation of chloroplast metabolism. PMID:25911530

  11. Action of Nalidixic Acid on Chloroplast Replication in Euglena gracilis.

    PubMed

    Lyman, H; Jupp, A S; Larrinua, I

    1975-02-01

    The role of light in nalidixic acid bleaching of Euglena gracilis var. bacillaris was investigated. The kinetics of loss of the chloroplast-associated DNA and the sensitivity of chloroplast replication to ultraviolet light was followed during treatment with nalidixic acid. By using the mutant P(4)ZUL, and 3-(3,4-dichlorophenyl)-, 1-dimethylurea, it was demonstrated that the requirement for light was a functioning photosynthetic electron transport system. Ultracentifugal analysis showed a substantial decrease in chloroplast-associated DNA after 6 hours of treatment with nalidixic acid. Ultraviolet target analysis revealed that the number of chloroplast genomes per cell had been reduced. The possible role of light and implications of the reduction in chloroplast genomes for chloroplast replication are discussed. PMID:16659089

  12. Posttranslational Modifications of Chloroplast Proteins: An Emerging Field.

    PubMed

    Lehtimäki, Nina; Koskela, Minna M; Mulo, Paula

    2015-07-01

    Posttranslational modifications of proteins are key effectors of enzyme activity, protein interactions, targeting, and turnover rate, but despite their importance, they are still poorly understood in plants. Although numerous reports have revealed the regulatory role of protein phosphorylation in photosynthesis, various other protein modifications have been identified in chloroplasts only recently. It is known that posttranslational N(α)-acetylation occurs in both nuclear- and plastid-encoded chloroplast proteins, but the physiological significance of this acetylation is not yet understood. Lysine acetylation affects the localization and activity of key metabolic enzymes, and it may work antagonistically or cooperatively with lysine methylation, which also occurs in chloroplasts. In addition, tyrosine nitration may help regulate the repair cycle of photosystem II, while N-glycosylation determines enzyme activity of chloroplastic carbonic anhydrase. This review summarizes the progress in the research field of posttranslational modifications of chloroplast proteins and points out the importance of these modifications in the regulation of chloroplast metabolism. PMID:25911530

  13. Auxin and chloroplast movements.

    PubMed

    Eckstein, Aleksandra; Krzeszowiec, Weronika; Waligórski, Piotr; Gabryś, Halina

    2016-03-01

    Auxin is involved in a wide spectrum of physiological processes in plants, including responses controlled by the blue light photoreceptors phototropins: phototropic bending and stomatal movement. However, the role of auxin in phototropin-mediated chloroplast movements has never been studied. To address this question we searched for potential interactions between auxin and the chloroplast movement signaling pathway using different experimental approaches and two model plants, Arabidopsis thaliana and Nicotiana tabacum. We observed that the disturbance of auxin homeostasis by shoot decapitation caused a decrease in chloroplast movement parameters, which could be rescued by exogenous auxin application. In several cases, the impairment of polar auxin transport, by chemical inhibitors or in auxin carrier mutants, had a similar negative effect on chloroplast movements. This inhibition was not correlated with changes in auxin levels. Chloroplast relocations were also affected by the antiauxin p-chlorophenoxyisobutyric acid and mutations in genes encoding some of the elements of the SCF(TIR1)-Aux/IAA auxin receptor complex. The observed changes in chloroplast movement parameters are not prominent, which points to a modulatory role of auxin in this process. Taken together, the obtained results suggest that auxin acts indirectly to regulate chloroplast movements, presumably by regulating gene expression via the SCF(TIR1)-Aux/IAA-ARF pathway. Auxin does not seem to be involved in controlling the expression of phototropins. PMID:26467664

  14. Complete Chloroplast Genome Sequence of Holoparasite Cistanche deserticola (Orobanchaceae) Reveals Gene Loss and Horizontal Gene Transfer from Its Host Haloxylon ammodendron (Chenopodiaceae)

    PubMed Central

    Qiao, Qin; Ren, Zhumei; Zhao, Jiayuan; Yonezawa, Takahiro; Hasegawa, Masami; Crabbe, M. James C; Li, Jianqiang; Zhong, Yang

    2013-01-01

    Background The central function of chloroplasts is to carry out photosynthesis, and its gene content and structure are highly conserved across land plants. Parasitic plants, which have reduced photosynthetic ability, suffer gene losses from the chloroplast (cp) genome accompanied by the relaxation of selective constraints. Compared with the rapid rise in the number of cp genome sequences of photosynthetic organisms, there are limited data sets from parasitic plants. Principal Findings/Significance Here we report the complete sequence of the cp genome of Cistanche deserticola, a holoparasitic desert species belonging to the family Orobanchaceae. The cp genome of C. deserticola is greatly reduced both in size (102,657 bp) and in gene content, indicating that all genes required for photosynthesis suffer from gene loss and pseudogenization, except for psbM. The striking difference from other holoparasitic plants is that it retains almost a full set of tRNA genes, and it has lower dN/dS for most genes than another close holoparasitic plant, E. virginiana, suggesting that Cistanche deserticola has undergone fewer losses, either due to a reduced level of holoparasitism, or to a recent switch to this life history. We also found that the rpoC2 gene was present in two copies within C. deserticola. Its own copy has much shortened and turned out to be a pseudogene. Another copy, which was not located in its cp genome, was a homolog of the host plant, Haloxylon ammodendron (Chenopodiaceae), suggesting that it was acquired from its host via a horizontal gene transfer. PMID:23554920

  15. Nanophotonics of Chloroplasts for Bio-Inspired Solar Energy Materials

    NASA Astrophysics Data System (ADS)

    Gourley, Paul L.; Gourley, Cheryl R.

    2011-03-01

    In the search for new energy sources, lessons can be learned from chloroplast photonics. The nano-architecture of chloroplasts is remarkably well-adapted to mediate sunlight interactions for efficient energy conversion. We carried out experiments with chloroplasts isolated from spinach and leaf lettuce to elucidate the relationship between nano-architecture, biomolecular composition and photonic properties. We obtained high-resolution microscopic images of single chloroplasts to identify geometries of chloroplasts and interior grana. We performed micro-spectroscopy to identify strengths of absorption and fluorescence transitions and related them to broadband reflectance and transmittance spectra of whole leaf structures. Finally, the nonlinear optical properties were investigated with nanolaser spectroscopy by placing chloroplasts into micro-resonators and optically pumping. These spectra reveal chloroplast photonic modes and allow measurement of single chloroplast light scattering cross section, polarizability, and refractive index. The nanolaser spectra recorded at increasing pump powers enabled us to observe non-linear optics, photon dynamics, and stimulated emission from single chloroplasts. All of these experiments provide insight into plant photonics and inspiration of paradigms for synthetic biomaterials to harness sunlight in new ways.

  16. Identification of chloroplast genome loci suitable for high-resolution phylogeographic studies of Colocasia esculenta (L.) Schott (Araceae) and closely related taxa.

    PubMed

    Ahmed, Ibrar; Matthews, Peter J; Biggs, Patrick J; Naeem, Muhammad; McLenachan, Patricia A; Lockhart, Peter J

    2013-09-01

    Recently, we reported the chloroplast genome-wide association of oligonucleotide repeats, indels and nucleotide substitutions in aroid chloroplast genomes. We hypothesized that the distribution of oligonucleotide repeat sequences in a single representative genome can be used to identify mutational hotspots and loci suitable for population genetic, phylogenetic and phylogeographic studies. Using information on the location of oligonucleotide repeats in the chloroplast genome of taro (Colocasia esculenta), we designed 30 primer pairs to amplify and sequence polymorphic loci. The primers have been tested in a range of intra-specific to intergeneric comparisons, including ten taro samples (Colocasia esculenta) from diverse geographical locations, four other Colocasia species (C. affinis, C. fallax, C. formosana, C. gigantea) and three other aroid genera (represented by Remusatia vivipara, Alocasia brisbanensis and Amorphophallus konjac). Multiple sequence alignments for the intra-specific comparison revealed nucleotide substitutions (point mutations) at all 30 loci and microsatellite polymorphisms at 14 loci. The primer pairs reported here reveal levels of genetic variation suitable for high-resolution phylogeographic and evolutionary studies of taro and other closely related aroids. Our results confirm that information on repeat distribution can be used to identify loci suitable for such studies, and we expect that this approach can be used in other plant groups. PMID:23718317

  17. Mitochondrial and microsatellite DNA markers reveal a Balkan origin for the highly invasive horse-chestnut leaf miner Cameraria ohridella (Lepidoptera, Gracillariidae).

    PubMed

    Valade, R; Kenis, M; Hernandez-Lopez, A; Augustin, S; Mari Mena, N; Magnoux, E; Rougerie, R; Lakatos, F; Roques, A; Lopez-Vaamonde, C

    2009-08-01

    Biological invasions usually start with a small number of founder individuals. These founders are likely to represent a small fraction of the total genetic diversity found in the source population. Our study set out to trace genetically the geographical origin of the horse-chestnut leafminer, Cameraria ohridella, an invasive microlepidopteran whose area of origin is still unkown. Since its discovery in Macedonia 25 years ago, this insect has experienced an explosive westward range expansion, progressively colonizing all of Central and Western Europe. We used cytochrome oxidase I sequences (DNA barcode fragment) and a set of six polymorphic microsatellites to assess the genetic variability of C. ohridella populations, and to test the hypothesis that C. ohridella derives from the southern Balkans (Albania, Macedonia and Greece). Analysis of mtDNA of 486 individuals from 88 localities allowed us to identify 25 geographically structured haplotypes. In addition, 480 individuals from 16 populations from Europe and the southern Balkans were genotyped for 6 polymorphic microsatellite loci. High haplotype diversity and low measures of nucleotide diversities including a significantly negative Tajima's D indicate that C. ohridella has experienced rapid population expansion during its dispersal across Europe. Both mtDNA and microsatellites show a reduction in genetic diversity of C. ohridella populations sampled from artificial habitats (e.g. planted trees in public parks, gardens, along roads in urban or sub-urban areas) across Europe compared with C. ohridella sampled in natural stands of horse-chestnuts in the southern Balkans. These findings suggest that European populations of C. ohridella may indeed derive from the southern Balkans. PMID:19627490

  18. Intercontinental long-distance dispersal of Canellaceae from the New to the Old World revealed by a nuclear single copy gene and chloroplast loci.

    PubMed

    Müller, Sebastian; Salomo, Karsten; Salazar, Jackeline; Naumann, Julia; Jaramillo, M Alejandra; Neinhuis, Christoph; Feild, Taylor S; Wanke, Stefan

    2015-03-01

    Canellales, a clade consisting of Winteraceae and Canellaceae, represent the smallest order of magnoliid angiosperms. The clade shows a broad distribution throughout the Southern Hemisphere, across a diverse range of dry to wet tropical forests. In contrast to their sister-group, Winteraceae, the phylogenetic relations and biogeography within Canellaceae remain poorly studied. Here we present the phylogenetic relationships of all currently recognized genera of Canellales with a special focus on the Old World Canellaceae using a combined dataset consisting of the chloroplast trnK-matK-trnK-psbA and the nuclear single copy gene mag1 (Maigo 1). Within Canellaceae we found high statistical support for the monophyly of Warburgia and Cinnamosma. However, we also found relationships that differ from previous studies. Cinnamodendron splitted into two clades, a South American clade and a second clade confined to the Antilles and adjacent areas. Cinnamodendron from the Antilles, as well as Capsicodendron, South American Cinnamodendron and Pleodendron were not monophyletic. Consequently, Capsicodendron should be included in the South American Cinnamodendron clade and the genus Pleodendron merged with the Cinnamodendron clade from the Antilles. We also found that Warburgia (restricted to mainland eastern Africa) together with the South American Cinnamodendron and Capsicodendron are sister to the Malagasy genus Cinnamosma. In addition to the unexpected geographical relationships, both biogeographic and molecular clock analyses suggest vicariance, extinction, and at least one intercontinental long-distance-dispersal event. Our dating result contrasts previous work on Winteraceae. Diversification of Winteraceae took place in the Paleocene, predating the Canellaceae diversification by 13 MA in the Eocene. The phylogenetic relationships for Canellaceae supported here offer a solid framework for a future taxonomic revision of the Canellaceae. PMID:25579657

  19. The complete chloroplast genome sequence of Panax quinquefolius (L.).

    PubMed

    Kim, Kyunghee; Lee, Sang-Choon; Lee, Junki; Kim, Nam-Hoon; Jang, Woojong; Yang, Tae-Jin

    2016-07-01

    The complete chloroplast genome sequence of Panax quinquefolius, an important medicinal herb, was generated by de novo assembly with low-coverage whole-genome sequence data and manual correction. A circular 156 088-bp chloroplast genome showed typical chloroplast genome structure comprising a large single copy region of 86 095 bp, a small single copy region of 17 993 bp, and a pair of inverted repeats of 26 000 bp. The chloroplast genome had 87 protein-coding genes, 37 tRNA genes, and eight rRNA genes. Phylogenetic analysis with the chloroplast genome revealed that P. quinquefolius is much closer to P. ginseng than P. notoginseng. PMID:26162051

  20. Multiplexed Fragaria Chloroplast Genome Sequencing

    Technology Transfer Automated Retrieval System (TEKTRAN)

    A method to sequence multiple chloroplast genomes that uses the sequencing depth of ultra high throughput sequencing technologies was recently described. Sequencing complete chloroplast genomes can resolve phylogenetic relationships at low taxonomic levels and identify point mutations and indels tha...

  1. Microsatellite and mitochondrial markers reveal strong gene flow barriers for Anopheles farauti in the Solomon Archipelago: implications for malaria vector control.

    PubMed

    Ambrose, Luke; Cooper, Robert D; Russell, Tanya L; Burkot, Thomas R; Lobo, Neil F; Collins, Frank H; Hii, Jeffrey; Beebe, Nigel W

    2014-03-01

    Anopheles farauti is the primary malaria vector throughout the coastal regions of the Southwest Pacific. A shift in peak biting time from late to early in the night occurred following widespread indoor residue spraying of dichlorodiphenyltrichloro-ethane (DDT) and has persisted in some island populations despite the intervention ending decades ago. We used mitochondrial cytochrome oxidase I (COI) sequence data and 12 newly developed microsatellite markers to assess the population genetic structure of this malaria vector in the Solomon Archipelago. With geographically distinct differences in peak A. farauti night biting time observed in the Solomon Archipelago, we tested the hypothesis that strong barriers to gene flow exist in this region. Significant and often large fixation index (FST) values were found between different island populations for the mitochondrial and nuclear markers, suggesting highly restricted gene flow between islands. Some discordance in the location and strength of genetic breaks was observed between the mitochondrial and microsatellite markers. Since early night biting A. farauti individuals occur naturally in all populations, the strong gene flow barriers that we have identified in the Solomon Archipelago lend weight to the hypothesis that the shifts in peak biting time from late to early night have appeared independently in these disconnected island populations. For this reason, we suggest that insecticide impregnated bed nets and indoor residue spraying are unlikely to be effective as control tools against A. farauti occurring elsewhere, and if used, will probably result in peak biting time behavioural shifts similar to that observed in the Solomon Islands. PMID:24440418

  2. Multilocus microsatellite typing revealed high genetic variability of Leishmania donovani strains isolated during and after a Kala-azar epidemic in Libo Kemkem district, northwest Ethiopia.

    PubMed

    Gelanew, Tesfaye; Cruz, Israel; Kuhls, Katrin; Alvar, Jorge; Cañavate, Carmen; Hailu, Asrat; Schönian, Gabriele

    2011-06-01

    In 2004, an outbreak of kala-azar (KA) occurred for the first time in Libo Kemkem district, in the highland area of northwest Ethiopia. In order to track the possible origins of the outbreak parasites, we have investigated 19 strains of Leishmania donovani that were collected during (n = 6) and after (n = 13) the outbreak by using 14 highly polymorphic microsatellite markers. Unique microsatellite profiles were obtained for all strains from Libo Kemkem. When compared to those of L. donovani strains from different Ethiopian, Kenyan and Sudanese foci, by genetic distance and Bayesian clustering model analyses, most strains from Libo Kemkem grouped with strains from: (i) Humera and Metema in the lowlands and Belessa in the highland of Ethiopia, and (ii) Sudan, at different hierarchal levels. The strains from Libo Kemkem district were assigned at least to three genetically distinct clusters (A, B1 and B2) of which only one, cluster B2, consisted exclusively of strains from Libo Kemkem. The fact that most of the outbreak strains were found to be related to strains from well-known KA foci in northwest Ethiopia and Sudan might suggest multiple introductions of L. donovani strains from these foci into Libo Kemkem district. PMID:21382503

  3. Chloroplast Proteases: Updates on Proteolysis within and across Suborganellar Compartments.

    PubMed

    Nishimura, Kenji; Kato, Yusuke; Sakamoto, Wataru

    2016-08-01

    Chloroplasts originated from the endosymbiosis of ancestral cyanobacteria and maintain transcription and translation machineries for around 100 proteins. Most endosymbiont genes, however, have been transferred to the host nucleus, and the majority of the chloroplast proteome is composed of nucleus-encoded proteins that are biosynthesized in the cytosol and then imported into chloroplasts. How chloroplasts and the nucleus communicate to control the plastid proteome remains an important question. Protein-degrading machineries play key roles in chloroplast proteome biogenesis, remodeling, and maintenance. Research in the past few decades has revealed more than 20 chloroplast proteases, which are localized to specific suborganellar locations. In particular, two energy-dependent processive proteases of bacterial origin, Clp and FtsH, are central to protein homeostasis. Processing endopeptidases such as stromal processing peptidase and thylakoidal processing peptidase are involved in the maturation of precursor proteins imported into chloroplasts by cleaving off the amino-terminal transit peptides. Presequence peptidases and organellar oligopeptidase subsequently degrade the cleaved targeting peptides. Recent findings have indicated that not only intraplastidic but also extraplastidic processive protein-degrading systems participate in the regulation and quality control of protein translocation across the envelopes. In this review, we summarize current knowledge of the major chloroplast proteases in terms of type, suborganellar localization, and diversification. We present details of these degradation processes as case studies according to suborganellar compartment (envelope, stroma, and thylakoids). Key questions and future directions in this field are discussed. PMID:27288365

  4. Why have chloroplasts developed a unique motility system?

    PubMed Central

    Suetsugu, Noriyuki; Dolja, Valerian V

    2010-01-01

    Organelle movement in plants is dependent on actin filaments with most of the organelles being transported along the actin cables by class XI myosins. Although chloroplast movement is also actin filament-dependent, a potential role of myosin motors in this process is poorly understood. Interestingly, chloroplasts can move in any direction and change the direction within short time periods, suggesting that chloroplasts use the newly formed actin filaments rather than preexisting actin cables. Furthermore, the data on myosin gene knockouts and knockdowns in Arabidopsis and tobacco do not support myosins' XI role in chloroplast movement. Our recent studies revealed that chloroplast movement and positioning are mediated by the short actin filaments localized at chloroplast periphery (cp-actin filaments) rather than cytoplasmic actin cables. The accumulation of cp-actin filaments depends on kinesin-like proteins, KAC1 and KAC2, as well as on a chloroplast outer membrane protein CHUP1. We propose that plants evolved a myosin XI-independent mechanism of the actin-based chloroplast movement that is distinct from the mechanism used by other organelles. PMID:20855973

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

    PubMed

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

    2013-01-01

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

  6. Interaction of Chloroplasts with Inhibitors

    PubMed Central

    Ridley, Stuart M.

    1983-01-01

    Several effects on pea (Pisum sativum L. var Onwards) chloroplasts of a new diphenylether herbicide, fomesafen (5-[2-chloro-4-trifluoromethyl-phenoxy]-N-methanesulfonyl-2 -nitrobenzamide) have been compared with those of a herbicide of related structure, nitrofluorfen (2-chloro-1-[4-nitrophenoxy]-4-[trifluoromethyl]benzene). Although both compounds produce the same light-dependent symptoms of desiccation and chlorosis indicative of a common primary mechanism of action, this study is concerned with a more broadly based investigation of different effects on the electron transport system. Comparisons have also been made with other compounds interacting with the chloroplast. Unlike nitrofluorfen, fomesafen has little effect as an inhibitor of electron flow or energy transfer. Both compounds have the ability to stimulate superoxide production through a functional electron transport system, and this involves specifically the p-nitro substituent. The stimulation, which is not likely to be an essential part of the primary herbicidal effect, is diminished under conditions that remove the coupling factor. Evidence suggests that both diphenylethers may be able to bind to the coupling factor, and kinetic studies reveal this for dibromothymoquinone as well. Such a binding site might be an important feature in allowing the primary effect of the diphenylether herbicides to be expressed. PMID:16663025

  7. Microsatellite instability in bladder cancer.

    PubMed

    Gonzalez-Zulueta, M; Ruppert, J M; Tokino, K; Tsai, Y C; Spruck, C H; Miyao, N; Nichols, P W; Hermann, G G; Horn, T; Steven, K

    1993-12-01

    Somatic instability at microsatellite repeats was detected in 6 of 200 transitional cell carcinomas of the bladder. Instabilities were apparent as changes in (GT)n repeat lengths on human chromosome 9 for four tumors and as alterations in a (CAG)n repeat in the androgen receptor gene on the X chromosome for three tumors. Single locus alterations were detected in three tumors, while three other tumors revealed changes in two or more loci. In one tumor we found microsatellite instability in all five loci analyzed on chromosome 9. The alterations detected were either minor 2-base pair changes or larger (> 2 base pairs) alterations in repeat length. All six tumors were low stage (Ta-T1), suggesting that these alterations can occur early in bladder tumorigenesis. PMID:8242615

  8. Complex hybridization dynamics between golden-winged and blue-winged warblers (Vermivora chrysoptera and Vermivora pinus) revealed by AFLP, microsatellite, intron and mtDNA markers.

    PubMed

    Vallender, R; Robertson, R J; Friesen, V L; Lovette, I J

    2007-05-01

    Blue-winged (Vermivora pinus) and golden-winged warblers (Vermivora chrysoptera) have an extensive mosaic hybrid zone in eastern North America. Over the past century, the general trajectory has been a rapid replacement of chrysoptera by pinus in a broad, northwardly moving area of contact. Previous mtDNA-based studies on these species' hybridization dynamics have yielded variable results: asymmetric and rapid introgression from pinus into chrysoptera in some areas and bidirectional maternal gene flow in others. To further explore the hybridization genetics of this otherwise well-studied complex, we surveyed variation in three nuclear DNA marker types--microsatellites, introns, and a panel of amplified fragment length polymorphisms (AFLPs)--with the goal of generating a multilocus assay of hybrid introgression. All markers were first tested on birds from phenotypically and mitochondrially pure parental-type populations from outside the hybrid zone. Searches for private alleles and assignment test approaches found no combination of microsatellite or intron markers that could separate the parental populations, but seven AFLP characters exhibited significant frequency differences among them. We then used the AFLP markers to examine the extent and pattern of introgression in a population where pinus-phenotype individuals have recently invaded a region that previously supported only a chrysoptera-phenotype population. Despite the low frequency of phenotypic hybrids at this location, the AFLP data suggest that almost a third of the phenotypically pure chrysoptera have introgressed genotypes, indicating the presence of substantial cryptic hybridization in the history of this species. The evidence for extensive cryptic introgression, combined with the lack of differentiation at other nuclear loci, cautions against hybrid assessments based on single markers or on phenotypic traits that are likely to be determined by a small number of loci. Considered in concert, these

  9. Genetic Structure of Aedes aegypti in Australia and Vietnam Revealed by Microsatellite and Exon Primed Intron Crossing Markers Suggests Feasibility of Local Control Options

    PubMed Central

    ENDERSBY, N. M.; HOFFMANN, A. A.; WHITE, V. L.; LOWENSTEIN, S.; RITCHIE, S.; JOHNSON, P. H.; RAPLEY, L. P.; RYAN, P. A.; NAM, V. S.; YEN, N. T.; KITTIYAPONG, P.; WEEKS, A. R.

    2009-01-01

    The distribution of Aedes aegypti (L.) in Australia is currently restricted to northern Queensland, but it has been more extensive in the past. In this study, we evaluate the genetic structure of Ae. aegypti populations in Australia and Vietnam and consider genetic differentiation between mosquitoes from these areas and those from a population in Thailand. Six microsatellites and two exon primed intron crossing markers were used to assess isolation by distance across all populations and also within the Australian sample. Investigations of founder effects, amount of molecular variation between and within regions and comparison of FST values among Australian and Vietnamese populations were made to assess the scale of movement of Ae. aegypti. Genetic control methods are under development for mosquito vector populations including the dengue vector Ae. aegypti. The success of these control methods will depend on the population structure of the target species including population size and rates of movement among populations. Releases of modified mosquitoes could target local populations that show a high degree of isolation from surrounding populations, potentially allowing new variants to become established in one region with eventual dispersal to other regions. PMID:19769038

  10. Microsatellite variation reveals weak genetic structure and retention of genetic variability in threatened Chinook salmon (Oncorhynchus tshawytscha) within a Snake River watershed

    USGS Publications Warehouse

    Neville, Helen; Issacs, Frank B.; Thurow, Russel; Dunham, J.B.; Rieman, B.

    2007-01-01

    Pacific salmon (Oncorhynchus spp.) have been central to the development of management concepts associated with evolutionarily significant units (ESUs), yet there are still relatively few studies of genetic diversity within threatened and endangered ESUs for salmon or other species. We analyzed genetic variation at 10 microsatellite loci to evaluate spatial population structure and genetic variability in indigenous Chinook salmon (Oncorhynchus tshawytscha) across a large wilderness basin within a Snake River ESU. Despite dramatic 20th century declines in abundance, these populations retained robust levels of genetic variability. No significant genetic bottlenecks were found, although the bottleneck metric (M ratio) was significantly correlated with average population size and variability. Weak but significant genetic structure existed among tributaries despite evidence of high levels of gene flow, with the strongest genetic differentiation mirroring the physical segregation of fish from two sub-basins. Despite the more recent colonization of one sub-basin and differences between sub-basins in the natural level of fragmentation, gene diversity and genetic differentiation were similar between sub-basins. Various factors, such as the (unknown) genetic contribution of precocial males, genetic compensation, lack of hatchery influence, and high levels of current gene flow may have contributed to the persistence of genetic variability in this system in spite of historical declines. This unique study of indigenous Chinook salmon underscores the importance of maintaining natural populations in interconnected and complex habitats to minimize losses of genetic diversity within ESUs.

  11. Transposon-induced nuclear mutations that alter chloroplast gene expression

    SciTech Connect

    Barkan, A.

    1992-01-01

    The goal of this project is to use mutant phenotypes as a guide to nuclear genes that determine the timing and localization of chloroplast development The immediate goals are to identify nuclear mutants with defects in chloroplast gene expression from maize lines harboring active Mu transposons; characterize their phenotypes to determine the precise defect in gene expression; clone several of the most interesting mutations by exploiting the transposon tag; and use the clones to further define the roles of these genes in modulating chloroplast gene expression. Three mutants were described earlier that had global defects in chloroplast gene expression. We have found that two of these mutations are allelic. Both alleles have global defects in chloroplast translation initiation, as revealed by the failure to assemble chloroplast mRNAs into polysomes. We have isolated and characterized three new mutants from Mu lines that have novel defects in chloroplast RNA metabolism. We are now ready to begin the task of cloning several of these genes, by using the Mu transposon tag.

  12. Chloroplast-like transfer RNA genes expressed in wheat mitochondria.

    PubMed Central

    Joyce, P B; Gray, M W

    1989-01-01

    In the course of a systematic survey of wheat mitochondrial tRNA genes, we have sequenced chloroplast-like serine (trnS-GGA), phenylalanine (trnF-GAA) and cysteine (trnC-GCA) tRNA genes and their flanking regions. These genes are remnants of 'promiscuous' chloroplast DNA that has been incorporated into wheat mtDNA in the course of its evolution. Each gene differs by one or a few nucleotides from the authentic chloroplast homolog previously characterized in wheat or other plants, and each could potentially encode a functional tRNA whose secondary structure shows no deviations from the generalized model. To determine whether these chloroplast-like tRNA genes are actually expressed, wheat mitochondrial tRNAs were resolved by a series of polyacrylamide gel electrophoreses, after being specifically end-labeled in vitro by 3'-CCA addition mediated by wheat tRNA nucleotidyltransferase. Subsequent direct RNA sequence analysis identified prominent tRNA species corresponding to the mitochondrial and not the chloroplast trnS, trnF and trnC genes. This analysis also revealed chloroplast-like elongator methionine, asparagine and tryptophan tRNAs. Our results suggest that at least some chloroplast-like tRNA genes in wheat mtDNA are transcribed, with transcripts undergoing processing, post-transcriptional modification and 3'-CCA addition, to produce mature tRNAs that may participate in mitochondrial protein synthesis. Images PMID:2762145

  13. The complete chloroplast genome sequence of Zanthoxylum piperitum.

    PubMed

    Lee, Jonghoon; Lee, Hyeon Ju; Kim, Kyunghee; Lee, Sang-Choon; Sung, Sang Hyun; Yang, Tae-Jin

    2016-09-01

    The complete chloroplast genome sequence of Zanthoxylum piperitum, a plant species with useful aromatic oils in family Rutaceae, was generated in this study by de novo assembly with whole-genome sequence data. The chloroplast genome was 158 154 bp in length with a typical quadripartite structure containing a pair of inverted repeats of 27 644 bp, separated by large single copy and small single copy of 85 340 bp and 17 526 bp, respectively. The chloroplast genome harbored 112 genes consisting of 78 protein-coding genes 30 tRNA genes and 4 rRNA genes. Phylogenetic analysis of the complete chloroplast genome sequences with those of known relatives revealed that Z. piperitum is most closely related to the Citrus species. PMID:26260183

  14. Pb-Induced Avoidance-Like Chloroplast Movements in Fronds of Lemna trisulca L.

    PubMed Central

    Samardakiewicz, Sławomir; Krzeszowiec-Jeleń, Weronika; Bednarski, Waldemar; Jankowski, Artur; Suski, Szymon; Gabryś, Halina; Woźny, Adam

    2015-01-01

    Lead ions are particularly dangerous to the photosynthetic apparatus, but little is known about the effects of trace metals, including Pb, on regulation of chloroplast redistribution. In this study a new effect of lead on chloroplast distribution patterns and movements was demonstrated in mesophyll cells of a small-sized aquatic angiosperm Lemna trisulca L. (star duckweed). An analysis of confocal microscopy images of L. trisulca fronds treated with lead (15 μM Pb2+, 24 h) in darkness or in weak white light revealed an enhanced accumulation of chloroplasts in the profile position along the anticlinal cell walls, in comparison to untreated plants. The rearrangement of chloroplasts in their response to lead ions in darkness was similar to the avoidance response of chloroplasts in plants treated with strong white light. Transmission electron microscopy X-ray microanalysis showed that intracellular chloroplast arrangement was independent of the location of Pb deposits, suggesting that lead causes redistribution of chloroplasts, which looks like a light-induced avoidance response, but is not a real avoidance response to the metal. Furthermore, a similar redistribution of chloroplasts in L. trisulca cells in darkness was observed also under the influence of exogenously applied hydrogen peroxide (H2O2). In addition, we detected an enhanced accumulation of endogenous H2O2 after treatment of plants with lead. Interestingly, H2O2-specific scavenger catalase partly abolished the Pb-induced chloroplast response. These results suggest that H2O2 can be involved in the avoidance-like movement of chloroplasts induced by lead. Analysis of photometric measurements revealed also strong inhibition (but not complete) of blue-light-induced chloroplast movements by lead. This inhibition may result from disturbances in the actin cytoskeleton, as we observed fragmentation and disappearance of actin filaments around chloroplasts. Results of this study show that the mechanisms of the toxic

  15. Pb-induced avoidance-like chloroplast movements in fronds of Lemna trisulca L.

    PubMed

    Samardakiewicz, Sławomir; Krzeszowiec-Jeleń, Weronika; Bednarski, Waldemar; Jankowski, Artur; Suski, Szymon; Gabryś, Halina; Woźny, Adam

    2015-01-01

    Lead ions are particularly dangerous to the photosynthetic apparatus, but little is known about the effects of trace metals, including Pb, on regulation of chloroplast redistribution. In this study a new effect of lead on chloroplast distribution patterns and movements was demonstrated in mesophyll cells of a small-sized aquatic angiosperm Lemna trisulca L. (star duckweed). An analysis of confocal microscopy images of L. trisulca fronds treated with lead (15 μM Pb2+, 24 h) in darkness or in weak white light revealed an enhanced accumulation of chloroplasts in the profile position along the anticlinal cell walls, in comparison to untreated plants. The rearrangement of chloroplasts in their response to lead ions in darkness was similar to the avoidance response of chloroplasts in plants treated with strong white light. Transmission electron microscopy X-ray microanalysis showed that intracellular chloroplast arrangement was independent of the location of Pb deposits, suggesting that lead causes redistribution of chloroplasts, which looks like a light-induced avoidance response, but is not a real avoidance response to the metal. Furthermore, a similar redistribution of chloroplasts in L. trisulca cells in darkness was observed also under the influence of exogenously applied hydrogen peroxide (H2O2). In addition, we detected an enhanced accumulation of endogenous H2O2 after treatment of plants with lead. Interestingly, H2O2-specific scavenger catalase partly abolished the Pb-induced chloroplast response. These results suggest that H2O2 can be involved in the avoidance-like movement of chloroplasts induced by lead. Analysis of photometric measurements revealed also strong inhibition (but not complete) of blue-light-induced chloroplast movements by lead. This inhibition may result from disturbances in the actin cytoskeleton, as we observed fragmentation and disappearance of actin filaments around chloroplasts. Results of this study show that the mechanisms of the toxic

  16. Flow cytometric analysis and microsatellite genotyping reveal extensive DNA content variation in Trypanosoma cruzi populations and expose contrasts between natural and experimental hybrids

    PubMed Central

    Lewis, Michael D.; Llewellyn, Martin S.; Gaunt, Michael W.; Yeo, Matthew; Carrasco, Hernán J.; Miles, Michael A.

    2009-01-01

    Trypanosoma cruzi exhibits remarkable genetic heterogeneity. This is evident at the nucleotide level but also structurally, in the form of karyotypic variation and DNA content differences between strains. Although natural populations of T. cruzi are predominantly clonal, hybrid lineages (TcIId and TcIIe) have been identified and hybridisation has been demonstrated in vitro, raising the possibility that genetic exchange may continue to shape the evolution of this pathogen. The mechanism of genetic exchange identified in the laboratory is unusual, apparently involving fusion of diploid parents followed by genome erosion. We investigated DNA content diversity in natural populations of T. cruzi in the context of its genetic subdivisions by using flow cytometric analysis and multilocus microsatellite genotyping to determine the relative DNA content and estimate the ploidy of 54 cloned isolates. The maximum difference observed was 47.5% between strain Tu18 cl2 (TcIIb) and strain C8 cl1 (TcI), which we estimated to be equivalent to ∼73 Mb of DNA. Large DNA content differences were identified within and between discrete typing units (DTUs). In particular, the mean DNA content of TcI strains was significantly less than that for TcII strains (P < 0.001). Comparisons of hybrid DTUs TcIId/IIe with corresponding parental DTUs TcIIb/IIc indicated that natural hybrids are predominantly diploid. We also measured the relative DNA content of six in vitro-generated TcI hybrid clones and their parents. In contrast to TcIId/IIe hybrid strains these experimental hybrids comprised populations of sub-tetraploid organisms with mean DNA contents 1.65–1.72 times higher than the parental organisms. The DNA contents of both parents and hybrids were shown to be relatively stable after passage through a mammalian host, heat shock or nutritional stress. The results are discussed in the context of hybridisation mechanisms in both natural and in vitro settings. PMID:19393242

  17. Rapid radiation in spiny lobsters (Palinurus spp) as revealed by classic and ABC methods using mtDNA and microsatellite data

    PubMed Central

    Palero, Ferran; Lopes, Joao; Abelló, Pere; Macpherson, Enrique; Pascual, Marta; Beaumont, Mark A

    2009-01-01

    Background Molecular tools may help to uncover closely related and still diverging species from a wide variety of taxa and provide insight into the mechanisms, pace and geography of marine speciation. There is a certain controversy on the phylogeography and speciation modes of species-groups with an Eastern Atlantic-Western Indian Ocean distribution, with previous studies suggesting that older events (Miocene) and/or more recent (Pleistocene) oceanographic processes could have influenced the phylogeny of marine taxa. The spiny lobster genus Palinurus allows for testing among speciation hypotheses, since it has a particular distribution with two groups of three species each in the Northeastern Atlantic (P. elephas, P. mauritanicus and P. charlestoni) and Southeastern Atlantic and Southwestern Indian Oceans (P. gilchristi, P. delagoae and P. barbarae). In the present study, we obtain a more complete understanding of the phylogenetic relationships among these species through a combined dataset with both nuclear and mitochondrial markers, by testing alternative hypotheses on both the mutation rate and tree topology under the recently developed approximate Bayesian computation (ABC) methods. Results Our analyses support a North-to-South speciation pattern in Palinurus with all the South-African species forming a monophyletic clade nested within the Northern Hemisphere species. Coalescent-based ABC methods allowed us to reject the previously proposed hypothesis of a Middle Miocene speciation event related with the closure of the Tethyan Seaway. Instead, divergence times obtained for Palinurus species using the combined mtDNA-microsatellite dataset and standard mutation rates for mtDNA agree with known glaciation-related processes occurring during the last 2 my. Conclusion The Palinurus speciation pattern is a typical example of a series of rapid speciation events occurring within a group, with very short branches separating different species. Our results support the

  18. WHITE PANICLE1, a Val-tRNA Synthetase Regulating Chloroplast Ribosome Biogenesis in Rice, Is Essential for Early Chloroplast Development1[OPEN

    PubMed Central

    Wang, Chunming; Zheng, Ming; Lyu, Jia; Xu, Yang; Li, Xiaohui; Niu, Mei; Long, Wuhua; Wang, Di; Wang, Yihua; Wan, Jianmin

    2016-01-01

    Chloroplasts and mitochondria contain their own genomes and transcriptional and translational systems. Establishing these genetic systems is essential for plant growth and development. Here we characterized a mutant form of a Val-tRNA synthetase (OsValRS2) from Oryza sativa that is targeted to both chloroplasts and mitochondria. A single base change in OsValRS2 caused virescent to albino phenotypes in seedlings and white panicles at heading. We therefore named this mutant white panicle 1 (wp1). Chlorophyll autofluorescence observations and transmission electron microscopy analyses indicated that wp1 mutants are defective in early chloroplast development. RNA-seq analysis revealed that expression of nuclear-encoded photosynthetic genes is significantly repressed, while expression of many chloroplast-encoded genes also changed significantly in wp1 mutants. Western-blot analyses of chloroplast-encoded proteins showed that chloroplast protein levels were reduced in wp1 mutants, although mRNA levels of some genes were higher in wp1 than in wild type. We found that wp1 was impaired in chloroplast ribosome biogenesis. Taken together, our results show that OsValRS2 plays an essential role in chloroplast development and regulating chloroplast ribosome biogenesis. PMID:26839129

  19. Chloroplast ribosomes and protein synthesis.

    PubMed Central

    Harris, E H; Boynton, J E; Gillham, N W

    1994-01-01

    Consistent with their postulated origin from endosymbiotic cyanobacteria, chloroplasts of plants and algae have ribosomes whose component RNAs and proteins are strikingly similar to those of eubacteria. Comparison of the secondary structures of 16S rRNAs of chloroplasts and bacteria has been particularly useful in identifying highly conserved regions likely to have essential functions. Comparative analysis of ribosomal protein sequences may likewise prove valuable in determining their roles in protein synthesis. This review is concerned primarily with the RNAs and proteins that constitute the chloroplast ribosome, the genes that encode these components, and their expression. It begins with an overview of chloroplast genome structure in land plants and algae and then presents a brief comparison of chloroplast and prokaryotic protein-synthesizing systems and a more detailed analysis of chloroplast rRNAs and ribosomal proteins. A description of the synthesis and assembly of chloroplast ribosomes follows. The review concludes with discussion of whether chloroplast protein synthesis is essential for cell survival. PMID:7854253

  20. The complete chloroplast genome of Cynara humilis.

    PubMed

    Curci, Pasquale Luca; Sonnante, Gabriella

    2016-07-01

    The complete chloroplast genome of the wild thistle Cynara humilis L. (Asteraceae) is presented in this study. The genome is 152,585 bp in length and has a quadripartite structure composed by a large single-copy (LSC) of 83,622 bp, a small single-copy (SSC) of 18,651 bp and two inverted repeats (IRb/a) of 25,156 bp each. The GC content corresponds to 37.7%. The amount of unique genes is 114, in which 17 are duplicated in the IRs, for a total of 131 genes. A maximum parsimony phylogenetic analysis revealed that C. humilis chloroplast genome is closely related to that of the globe artichoke within the Carduoideae subfamily. PMID:25812057

  1. Complete Chloroplast Genome of Nicotiana otophora and its Comparison with Related Species

    PubMed Central

    Asaf, Sajjad; Khan, Abdul L.; Khan, Abdur R.; Waqas, Muhammad; Kang, Sang-Mo; Khan, Muhammad A.; Lee, Seok-Min; Lee, In-Jung

    2016-01-01

    Nicotiana otophora is a wild parental species of Nicotiana tabacum, an interspecific hybrid of Nicotiana tomentosiformis and Nicotiana sylvestris. However, N. otophora is least understood as an alternative paternal donor. Here, we compared the fully assembled chloroplast (cp) genome of N. otophora and with those of closely related species. The analysis showed a cp genome size of 156,073 bp and exhibited a typical quadripartite structure, which contains a pair of inverted repeats separated by small and large single copies, containing 163 representative genes, with 165 microsatellites distributed unevenly throughout the genome. Comparative analysis of a gene with known function across Nicotiana species revealed 76 protein-coding sequences, 20 tRNA sequences, and 3 rRNA sequence shared between the cp genomes. The analysis revealed that N. otophora is a sister species to N. tomentosiformis within the Nicotiana genus, and Atropha belladonna and Datura stramonium are their closest relatives. These findings provide a valuable analysis of the complete N. otophora cp genome, which can identify species, elucidate taxonomy, and reconstruct the phylogeny of genus Nicotiana. PMID:27379132

  2. A Nucleus-Encoded Chloroplast Protein YL1 Is Involved in Chloroplast Development and Efficient Biogenesis of Chloroplast ATP Synthase in Rice

    PubMed Central

    Chen, Fei; Dong, Guojun; Wu, Limin; Wang, Fang; Yang, Xingzheng; Ma, Xiaohui; Wang, Haili; Wu, Jiahuan; Zhang, Yanli; Wang, Huizhong; Qian, Qian; Yu, Yanchun

    2016-01-01

    Chloroplast ATP synthase (cpATPase) is an importance thylakoid membrane-associated photosynthetic complex involved in the light-dependent reactions of photosynthesis. In this study, we isolated and characterized a rice (Oryza sativa) mutant yellow leaf 1 (yl1), which exhibits chlorotic leaves throughout developmental stages. The YL1 mutation showed reduced chlorophyll contents, abnormal chloroplast morphology, and decreased photochemical efficiency. Moreover, YL1 deficiency disrupts the expression of genes associated with chloroplast development and photosynthesis. Molecular and genetic analyses revealed that YL1 is a nucleus-encoded protein with a predicted transmembrane domain in its carboxyl-terminus that is conserved in the higher plant kingdom. YL1 localizes to chloroplasts and is preferentially expressed in green tissues containing chloroplasts. Immunoblot analyses showed that inactivation of YL1 leads to drastically reduced accumulation of AtpA (α) and AtpB (β), two core subunits of CF1αβ subcomplex of cpATPase, meanwhile, a severe decrease (ca. 41.7%) in cpATPase activity was observed in the yl1-1 mutant compared with the wild type. Furthermore, yeast two-hybrid and bimolecular fluorescence complementation assays revealed a specific interaction between YL1 and AtpB subunit of cpATPase. Taken together, our results suggest that YL1 is a plant lineage-specific auxiliary factor involved in the biogenesis of the cpATPase complex, possibly via interacting with the β-subunit. PMID:27585744

  3. A Nucleus-Encoded Chloroplast Protein YL1 Is Involved in Chloroplast Development and Efficient Biogenesis of Chloroplast ATP Synthase in Rice.

    PubMed

    Chen, Fei; Dong, Guojun; Wu, Limin; Wang, Fang; Yang, Xingzheng; Ma, Xiaohui; Wang, Haili; Wu, Jiahuan; Zhang, Yanli; Wang, Huizhong; Qian, Qian; Yu, Yanchun

    2016-01-01

    Chloroplast ATP synthase (cpATPase) is an importance thylakoid membrane-associated photosynthetic complex involved in the light-dependent reactions of photosynthesis. In this study, we isolated and characterized a rice (Oryza sativa) mutant yellow leaf 1 (yl1), which exhibits chlorotic leaves throughout developmental stages. The YL1 mutation showed reduced chlorophyll contents, abnormal chloroplast morphology, and decreased photochemical efficiency. Moreover, YL1 deficiency disrupts the expression of genes associated with chloroplast development and photosynthesis. Molecular and genetic analyses revealed that YL1 is a nucleus-encoded protein with a predicted transmembrane domain in its carboxyl-terminus that is conserved in the higher plant kingdom. YL1 localizes to chloroplasts and is preferentially expressed in green tissues containing chloroplasts. Immunoblot analyses showed that inactivation of YL1 leads to drastically reduced accumulation of AtpA (α) and AtpB (β), two core subunits of CF1αβ subcomplex of cpATPase, meanwhile, a severe decrease (ca. 41.7%) in cpATPase activity was observed in the yl1-1 mutant compared with the wild type. Furthermore, yeast two-hybrid and bimolecular fluorescence complementation assays revealed a specific interaction between YL1 and AtpB subunit of cpATPase. Taken together, our results suggest that YL1 is a plant lineage-specific auxiliary factor involved in the biogenesis of the cpATPase complex, possibly via interacting with the β-subunit. PMID:27585744

  4. Amino acid incorporation by ribosomes and polyribosomes from wheat chloroplasts.

    PubMed

    Hadziyev, D; Zalik, S

    1970-01-01

    Sucrose-gradient and analytical ultracentrifugation showed that chloroplast polyribosomes from 4-day-old seedlings had mono-, di-, tri-, tetra- and traces of penta-ribosomes, in contrast with those from 7-day-old seedlings in which only the mono-, di- and traces of tri-ribosomes were present. Without Mg(2+) the polyribosomes dissociated into ribosomal subunits. The rate of l-[U-(14)C]phenylalanine incorporation was threefold greater for preparations from 4- than from 7-day-old seedlings. Incorporation by the latter was stimulated by polyuridylic acid. The rates of incorporation were similar whether the reaction mixture contained chloroplast or wheat-germ transfer RNA and amino acid synthetases purified on methylated albumin-on-kieselguhr and Sephadex G-75 columns respectively. The cofactor requirement was the same as for isolated intact chloroplasts. Osmotic rupture of chloroplasts with and without Triton X-100 revealed the presence of free and bound ribosomes. Free single ribosomes isolated by osmotic shrinkage or prepared by pancreatic ribonuclease digestion of chloroplast polyribosomes had negligible incorporation activity. This activity was increased by washing or by polyuridylic acid, but was still only a fraction of that given by polyribosomes. A comparison of incorporation activity of chloroplast polyribosomes with those from the surrounding cytoplasm showed the former to be 20 times more active. PMID:5411422

  5. Genetic Analysis of Chloroplast Translation

    SciTech Connect

    Barkan, Alice

    2005-08-15

    The assembly of the photosynthetic apparatus requires the concerted action of hundreds of genes distributed between the two physically separate genomes in the nucleus and chloroplast. Nuclear genes coordinate this process by controlling the expression of chloroplast genes in response to developmental and environmental cues. However, few regulatory factors have been identified. We used mutant phenotypes to identify nuclear genes in maize that modulate chloroplast translation, a key control point in chloroplast gene expression. This project focused on the nuclear gene crp1, required for the translation of two chloroplast mRNAs. CRP1 is related to fungal proteins involved in the translation of mitochondrial mRNAs, and is the founding member of a large gene family in plants, with {approx}450 members. Members of the CRP1 family are defined by a repeated 35 amino acid motif called a ''PPR'' motif. The PPR motif is closely related to the TPR motif, which mediates protein-protein interactions. We and others have speculated that PPR tracts adopt a structure similar to that of TPR tracts, but with a substrate binding surface adapted to bind RNA instead of protein. To understand how CRP1 influences the translation of specific chloroplast mRNAs, we sought proteins that interact with CRP1, and identified the RNAs associated with CRP1 in vivo. We showed that CRP1 is associated in vivo with the mRNAs whose translation it activates. To explore the functions of PPR proteins more generally, we sought mutations in other PPR-encoding genes: mutations in the maize PPR2 and PPR4 were shown to disrupt chloroplast ribosome biogenesis and chloroplast trans-splicing, respectively. These and other results suggest that the nuclear-encoded PPR family plays a major role in modulating the expression of the chloroplast genome in higher plants.

  6. Post-transcriptional control of cell type-specific gene expression in bundle sheath and mesophyll chloroplasts of Amaranthus hypochondriacus.

    PubMed

    Boinski, J J; Wang, J L; Xu, P; Hotchkiss, T; Berry, J O

    1993-06-01

    Plants that utilize the highly efficient C4 photosynthetic pathway possess two types of specialized leaf cells, the mesophyll and bundle sheath. In mature leaves of amaranth, a dicotyledonous C4 plant, ribulose 1,5-bisphosphate carboxylase (Rubisco) is localized specifically to the chloroplasts of bundle sheath cells, and is not present in the chloroplasts of mesophyll cells. The cell type-specific expression of the chloroplast-encoded Rubisco large subunit (rbcL) gene, and other representative chloroplastic genes, was investigated by using separated bundle sheath and mesophyll chloroplasts prepared from mature amaranth leaves. One-dimensional SDS-polyacrylamide gel electrophoresis revealed several differences in the polypeptide compositions of the two chloroplast types. Western analysis demonstrated that, as in the intact leaves, the Rubisco LSU polypeptide was present only in chloroplast preparations from bundle sheath cells. Pyruvate orthophosphate dikinase (PPdK), a nuclear-encoded chloroplastic enzyme, was found only in the mesophyll chloroplast preparations. rbcL mRNA was present only in the bundle sheath chloroplast preparations, whereas transcripts for the chloroplast-encoded psbA, psaA-B, and rpl2 genes were present in both chloroplast types. Although the rbcL message accumulated only in bundle sheath chloroplasts, run-on transcription analysis indicated that the rbcL gene was transcribed in both bundle sheath and mesophyll chloroplast preparations. Therefore, differential rbcL gene expression in the isolated C4 chloroplasts is regulated, at least in part, at the post-transcriptional level. Possibly this control is mediated by differential processing or stabilization of the rbcL transcript. PMID:8329680

  7. WHIRLY1 is a major organizer of chloroplast nucleoids

    PubMed Central

    Krupinska, Karin; Oetke, Svenja; Desel, Christine; Mulisch, Maria; Schäfer, Anke; Hollmann, Julien; Kumlehn, Jochen; Hensel, Götz

    2014-01-01

    WHIRLY1 is an abundant protein of chloroplast nucleoids, which has also been named pTAC-1 with regard to its detection in the proteome of transcriptionally active chromosomes (TAC). In barley primary foliage leaves, expression of the WHIRLY1 gene is highest at the base whereas protein accumulation is highest in the middle of the leaf where young developing chloroplasts are found. In order to elucidate the function of WHIRLY1 in chloroplast nucleoids, transgenic barley plants with an RNAi-mediated knock-down of the HvWHIRLY1 gene (RNAi-W1) were generated. The homozygous RNAi-W1-7 plants, barely containing traces of the WHIRLY1 protein, were chosen for detailed analyses of nucleoids. Nucleic acid specific-staining with YO-PRO®-1 revealed that in comparison to wild type chloroplasts, which have multiple small nucleoids attached to thylakoids, chloroplasts of the transgenic plants contain large irregularly formed patches of DNA besides nucleoids that are similar in size and shape to those of wild type chloroplasts. In large electron lucent areas, filamentous structures were detected by conventional transmission electron microscopy. Analyses of ptDNA levels by both DNA dot-blot hybridization and quantitative PCR showed that leaves of the transgenic plants have a two- to three-fold higher level of ptDNA than the wild type. The higher ptDNA level in RNAi-W1 plants coincided with an enhanced expression of the gene encoding a putative organelle targeted DNA polymerase in the mid part of primary foliage leaves. Furthermore, overexpression of the barley WHIRLY1 gene in E. coli cells revealed a higher compaction of bacterial nucleoids. These results suggest that WHIRLY1 belongs to the group of plastid nucleoid associated proteins (ptNAP) having a function in compacting a subpopulation of chloroplast nucleoids thereby affecting DNA replication. PMID:25237316

  8. Dynamics of Chloroplast Translation during Chloroplast Differentiation in Maize

    PubMed Central

    Chotewutmontri, Prakitchai; Barkan, Alice

    2016-01-01

    Chloroplast genomes in land plants contain approximately 100 genes, the majority of which reside in polycistronic transcription units derived from cyanobacterial operons. The expression of chloroplast genes is integrated into developmental programs underlying the differentiation of photosynthetic cells from non-photosynthetic progenitors. In C4 plants, the partitioning of photosynthesis between two cell types, bundle sheath and mesophyll, adds an additional layer of complexity. We used ribosome profiling and RNA-seq to generate a comprehensive description of chloroplast gene expression at four stages of chloroplast differentiation, as displayed along the maize seedling leaf blade. The rate of protein output of most genes increases early in development and declines once the photosynthetic apparatus is mature. The developmental dynamics of protein output fall into several patterns. Programmed changes in mRNA abundance make a strong contribution to the developmental shifts in protein output, but output is further adjusted by changes in translational efficiency. RNAs with prioritized translation early in development are largely involved in chloroplast gene expression, whereas those with prioritized translation in photosynthetic tissues are generally involved in photosynthesis. Differential gene expression in bundle sheath and mesophyll chloroplasts results primarily from differences in mRNA abundance, but differences in translational efficiency amplify mRNA-level effects in some instances. In most cases, rates of protein output approximate steady-state protein stoichiometries, implying a limited role for proteolysis in eliminating unassembled or damaged proteins under non-stress conditions. Tuned protein output results from gene-specific trade-offs between translational efficiency and mRNA abundance, both of which span a large dynamic range. Analysis of ribosome footprints at sites of RNA editing showed that the chloroplast translation machinery does not generally

  9. Novel microsatellite control system

    SciTech Connect

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

    1996-12-31

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

  10. Arabidopsis chloroplast chaperonin 10 is a calmodulin-binding protein

    NASA Technical Reports Server (NTRS)

    Yang, T.; Poovaiah, B. W.

    2000-01-01

    Calcium regulates diverse cellular activities in plants through the action of calmodulin (CaM). By using (35)S-labeled CaM to screen an Arabidopsis seedling cDNA expression library, a cDNA designated as AtCh-CPN10 (Arabidopsis thaliana chloroplast chaperonin 10) was cloned. Chloroplast CPN10, a nuclear-encoded protein, is a functional homolog of E. coli GroES. It is believed that CPN60 and CPN10 are involved in the assembly of Rubisco, a key enzyme involved in the photosynthetic pathway. Northern analysis revealed that AtCh-CPN10 is highly expressed in green tissues. The recombinant AtCh-CPN10 binds to CaM in a calcium-dependent manner. Deletion mutants revealed that there is only one CaM-binding site in the last 31 amino acids of the AtCh-CPN10 at the C-terminal end. The CaM-binding region in AtCh-CPN10 has higher homology to other chloroplast CPN10s in comparison to GroES and mitochondrial CPN10s, suggesting that CaM may only bind to chloroplast CPN10s. Furthermore, the results also suggest that the calcium/CaM messenger system is involved in regulating Rubisco assembly in the chloroplast, thereby influencing photosynthesis. Copyright 2000 Academic Press.

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

    PubMed Central

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

    2005-01-01

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

  12. Molecular Diversity and Population Structure of a Worldwide Collection of Cultivated Tetraploid Alfalfa (Medicago sativa subsp. sativa L.) Germplasm as Revealed by Microsatellite Markers

    PubMed Central

    Qiang, Haiping; Chen, Zhihong; Zhang, Zhengli; Wang, Xuemin; Gao, Hongwen; Wang, Zan

    2015-01-01

    Information on genetic diversity and population structure of a tetraploid alfalfa collection might be valuable in effective use of the genetic resources. A set of 336 worldwide genotypes of tetraploid alfalfa (Medicago sativa subsp. sativa L.) was genotyped using 85 genome-wide distributed SSR markers to reveal the genetic diversity and population structure in the alfalfa. Genetic diversity analysis identified a total of 1056 alleles across 85 marker loci. The average expected heterozygosity and polymorphism information content values were 0.677 and 0.638, respectively, showing high levels of genetic diversity in the cultivated tetraploid alfalfa germplasm. Comparison of genetic characteristics across chromosomes indicated regions of chromosomes 2 and 3 had the highest genetic diversity. A higher genetic diversity was detected in alfalfa landraces than that of wild materials and cultivars. Two populations were identified by the model-based population structure, principal coordinate and neighbor-joining analyses, corresponding to China and other parts of the world. However, lack of strictly correlation between clustering and geographic origins suggested extensive germplasm exchanges of alfalfa germplasm across diverse geographic regions. The quantitative analysis of the genetic diversity and population structure in this study could be useful for genetic and genomic analysis and utilization of the genetic variation in alfalfa breeding. PMID:25901573

  13. Middle-Upper Pleistocene climate changes shaped the divergence and demography of Cycas guizhouensis (Cycadaceae): Evidence from DNA sequences and microsatellite markers

    PubMed Central

    Feng, Xiuyan; Zheng, Ying; Gong, Xun

    2016-01-01

    Climatic oscillations in the Pleistocene have had profound effects on the demography and genetic diversity of many extant species. Cycas guizhouensis Lan & R.F. Zou is an endemic and endangered species in Southwest China that is primarily distributed along the valleys of the Nanpan River. In this study, we used four chloroplast DNAs (cpDNA), three nuclear genes (nDNA) and 13 microsatellite (SSR) loci to investigate the genetic structure, divergence time and demographic history of 11 populations of C. guizhouensis. High genetic diversity and high levels of genetic differentiation among the populations were observed. Two evolutionary units were revealed based on network and Structure analysis. The divergence time estimations suggested that haplotypes of C. guizhouensis were diverged during the Middle-Upper Pleistocene. Additionally, the demographic histories deduced from different DNA sequences were discordant, but overall indicated that C. guizhouensis had experienced a recent population expansion during the post-glacial period. Microsatellite data revealed that there was a contraction in effective population size in the past. These genetic features allow conservation measures to be taken to ensure the protection of this endangered species from extinction. PMID:27270859

  14. Middle-Upper Pleistocene climate changes shaped the divergence and demography of Cycas guizhouensis (Cycadaceae): Evidence from DNA sequences and microsatellite markers.

    PubMed

    Feng, Xiuyan; Zheng, Ying; Gong, Xun

    2016-01-01

    Climatic oscillations in the Pleistocene have had profound effects on the demography and genetic diversity of many extant species. Cycas guizhouensis Lan &R.F. Zou is an endemic and endangered species in Southwest China that is primarily distributed along the valleys of the Nanpan River. In this study, we used four chloroplast DNAs (cpDNA), three nuclear genes (nDNA) and 13 microsatellite (SSR) loci to investigate the genetic structure, divergence time and demographic history of 11 populations of C. guizhouensis. High genetic diversity and high levels of genetic differentiation among the populations were observed. Two evolutionary units were revealed based on network and Structure analysis. The divergence time estimations suggested that haplotypes of C. guizhouensis were diverged during the Middle-Upper Pleistocene. Additionally, the demographic histories deduced from different DNA sequences were discordant, but overall indicated that C. guizhouensis had experienced a recent population expansion during the post-glacial period. Microsatellite data revealed that there was a contraction in effective population size in the past. These genetic features allow conservation measures to be taken to ensure the protection of this endangered species from extinction. PMID:27270859

  15. Comparison of intraspecific, interspecific and intergeneric chloroplast diversity in Cycads.

    PubMed

    Jiang, Guo-Feng; Hinsinger, Damien Daniel; Strijk, Joeri Sergej

    2016-01-01

    Cycads are among the most threatened plant species. Increasing the availability of genomic information by adding whole chloroplast data is a fundamental step in supporting phylogenetic studies and conservation efforts. Here, we assemble a dataset encompassing three taxonomic levels in cycads, including ten genera, three species in the genus Cycas and two individuals of C. debaoensis. Repeated sequences, SSRs and variations of the chloroplast were analyzed at the intraspecific, interspecific and intergeneric scale, and using our sequence data, we reconstruct a phylogenomic tree for cycads. The chloroplast was 162,094 bp in length, with 133 genes annotated, including 87 protein-coding, 37 tRNA and 8 rRNA genes. We found 7 repeated sequences and 39 SSRs. Seven loci showed promising levels of variations for application in DNA-barcoding. The chloroplast phylogeny confirmed the division of Cycadales in two suborders, each of them being monophyletic, revealing a contradiction with the current family circumscription and its evolution. Finally, 10 intraspecific SNPs were found. Our results showed that despite the extremely restricted distribution range of C. debaoensis, using complete chloroplast data is useful not only in intraspecific studies, but also to improve our understanding of cycad evolution and in defining conservation strategies for this emblematic group. PMID:27558458

  16. The complete chloroplast genome of Capsicum frutescens (Solanaceae)1

    PubMed Central

    Shim, Donghwan; Raveendar, Sebastin; Lee, Jung-Ro; Lee, Gi-An; Ro, Na-Young; Jeon, Young-Ah; Cho, Gyu-Taek; Lee, Ho-Sun; Ma, Kyung-Ho; Chung, Jong-Wook

    2016-01-01

    Premise of the study: We report the complete sequence of the chloroplast genome of Capsicum frutescens (Solanaceae), a species of chili pepper. Methods and Results: Using an Illumina platform, we sequenced the chloroplast genome of C. frutescens. The total length of the genome is 156,817 bp, and the overall GC content is 37.7%. A pair of 25,792-bp inverted repeats is separated by small (17,853 bp) and large (87,380 bp) single-copy regions. The C. frutescens chloroplast genome encodes 132 unique genes, including 87 protein-coding genes, 37 transfer RNA (tRNA) genes, and eight ribosomal RNA (rRNA) genes. Of these, seven genes are duplicated in the inverted repeats and 12 genes contain one or two introns. Comparative analysis with the reference chloroplast genome revealed 125 simple sequence repeat motifs and 34 variants, mostly located in the noncoding regions. Conclusions: The complete chloroplast genome sequence of C. frutescens reported here is a valuable genetic resource for Capsicum species. PMID:27213127

  17. Comparison of intraspecific, interspecific and intergeneric chloroplast diversity in Cycads

    PubMed Central

    Jiang, Guo-Feng; Hinsinger, Damien Daniel; Strijk, Joeri Sergej

    2016-01-01

    Cycads are among the most threatened plant species. Increasing the availability of genomic information by adding whole chloroplast data is a fundamental step in supporting phylogenetic studies and conservation efforts. Here, we assemble a dataset encompassing three taxonomic levels in cycads, including ten genera, three species in the genus Cycas and two individuals of C. debaoensis. Repeated sequences, SSRs and variations of the chloroplast were analyzed at the intraspecific, interspecific and intergeneric scale, and using our sequence data, we reconstruct a phylogenomic tree for cycads. The chloroplast was 162,094 bp in length, with 133 genes annotated, including 87 protein-coding, 37 tRNA and 8 rRNA genes. We found 7 repeated sequences and 39 SSRs. Seven loci showed promising levels of variations for application in DNA-barcoding. The chloroplast phylogeny confirmed the division of Cycadales in two suborders, each of them being monophyletic, revealing a contradiction with the current family circumscription and its evolution. Finally, 10 intraspecific SNPs were found. Our results showed that despite the extremely restricted distribution range of C. debaoensis, using complete chloroplast data is useful not only in intraspecific studies, but also to improve our understanding of cycad evolution and in defining conservation strategies for this emblematic group. PMID:27558458

  18. The complete chloroplast genome of Schrenkiella parvula (Brassicaceae).

    PubMed

    He, Qi; Hao, Guoqian; Wang, Xiaojuan; Bi, Hao; Li, Yuanshuo; Guo, Xinyi; Ma, Tao

    2016-09-01

    Schrenkiella parvula is an Arabidopsis-related model species used here for studying plant stress tolerance. In this study, the complete chloroplast genome sequence of S. parvula has been reported for the first time. The total length of the chloroplast genome was 153 979 bp, which had a typical quadripartite structure. The annotated plastid genome includes 87 protein-coding genes, 39 tRNA genes and 8 ribosomal RNA genes. The evolutionary relationships revealed by our phylogenetic analysis indicated that S. parvula is closer to the Brassiceae species when compared with Eutrema salsugineum. PMID:26260181

  19. Circadian oscillations of cytosolic and chloroplastic free calcium in plants

    NASA Technical Reports Server (NTRS)

    Johnson, C. H.; Knight, M. R.; Kondo, T.; Masson, P.; Sedbrook, J.; Haley, A.; Trewavas, A.

    1995-01-01

    Tobacco and Arabidopsis plants, expressing a transgene for the calcium-sensitive luminescent protein apoaequorin, revealed circadian oscillations in free cytosolic calcium that can be phase-shifted by light-dark signals. When apoaequorin was targeted to the chloroplast, circadian chloroplast calcium rhythms were likewise observed after transfer of the seedlings to constant darkness. Circadian oscillations in free calcium concentrations can be expected to control many calcium-dependent enzymes and processes accounting for circadian outputs. Regulation of calcium flux is therefore fundamental to the organization of circadian systems.

  20. The complete chloroplast genome sequence of Dieffenbachia seguine (Araceae).

    PubMed

    Wang, Bin; Han, Limin; Chen, Chen; Wang, Zhezhi

    2016-07-01

    The nucleotide sequence of the chloroplast genome from Dieffenbachia seguine is the first to have complete genome sequence from genus of Dieffenbachia family Araceae. The genome size is 163 699 bp in length, with 36.4% GC content. A pair of inverted repeats (IRs, 25 235 bp) is separated by a large single copy region (LSC, 90 780 bp) and a small single copy region (SSC, 22 449 bp). The chloroplast genome contains 113 unique genes, 88 protein-coding genes, 37 tRNA genes, and four rRNA genes. In these genes, 16 genes contained single intron and two genes composed of double introns. A maximum likelihood phylogenetic analysis using complete chloroplast genome revealed that Dieffenbachia seguine belongs to the Araceae family of the Arecidae group, which is conform to the traditional classification. PMID:26153749

  1. The complete chloroplast genome sequence of Alocasia macrorrhizos.

    PubMed

    Wang, Bin; Han, Limin

    2016-09-01

    The complete chloroplast sequence of Alocasia macrorrhizos is 154 995 bp in length, containing a pair of inverted repeats of 25 944 bp separated by a large single-copy (LSC) region and a small single-copy (SSC) region of 87 366 bp and 15 741 bp, respectively. The chloroplast genome encodes 132 predicted functional genes, including 87 protein-coding genes, four ribosomal RNA genes, and 37 transfer RNA genes, 18 of which are duplicated in the inverted repeat regions. In these genes, 16 genes contained single intron and two genes comprising double introns. A maximum-likelihood phylogenetic analysis using complete chloroplast genome revealed that A. macrorrhizos does not belong to Araceae family, which infers that the A. macrorrhizos is distant from the species in Araceae family. PMID:26258514

  2. Evolution of Chloroplast J Proteins

    PubMed Central

    Chiu, Chi-Chou; Chen, Lih-Jen; Su, Pai-Hsiang; Li, Hsou-min

    2013-01-01

    Hsp70 chaperones are involved in multiple biological processes and are recruited to specific processes by designated J domain-containing cochaperones, or J proteins. To understand the evolution and functions of chloroplast Hsp70s and J proteins, we identified the Arabidopsis chloroplast J protein constituency using a combination of genomic and proteomic database searches and individual protein import assays. We show that Arabidopsis chloroplasts have at least 19 J proteins, the highest number of confirmed J proteins for any organelle. These 19 J proteins are classified into 11 clades, for which cyanobacteria and glaucophytes only have homologs for one clade, green algae have an additional three clades, and all the other 7 clades are specific to land plants. Each clade also possesses a clade-specific novel motif that is likely used to interact with different client proteins. Gene expression analyses indicate that most land plant-specific J proteins show highly variable expression in different tissues and are down regulated by low temperatures. These results show that duplication of chloroplast Hsp70 in land plants is accompanied by more than doubling of the number of its J protein cochaperones through adding new J proteins with novel motifs, not through duplications within existing families. These new J proteins likely recruit chloroplast Hsp70 to perform tissue specific functions related to biosynthesis rather than to stress resistance. PMID:23894646

  3. The complete chloroplast genome sequence of Dendropanax morbifera (Léveillé).

    PubMed

    Kim, Kyunghee; Lee, Sang-Choon; Yang, Tae-Jin

    2016-07-01

    The complete chloroplast genome sequence of Dendropanax morbifera, an economically and medicinally important endemic tree species in Korea, was obtained by de novo assembly with whole-genome sequence data and manual correction. A circular 156 366-bp chloroplast genome showed typical chloroplast genome structure comprising a large single copy region of 86 475 bp, a small single copy region of 18 125 bp, and a pair of inverted repeats of 25 883 bp. The chloroplast genome harbored 87 protein-coding genes. Phylogenetic analysis with the chloroplast genome revealed that D. morbifera is most closely related to Dendropanax dentiger, an evergreen tree species in China and Southeastern Asia. PMID:26153746

  4. Induction and Segregation of Chloroplast Mutations in Vegetative Cell Cultures of Chlamydomonas Reinhardtii

    PubMed Central

    Lee, Robert W.; Haughn, George W.

    1980-01-01

    The single chloroplast of the alga Chlamydomonas reinhardtii contains at least 100 copies of the chloroplast chromosome. It is not known how the chloroplast (or cell) becomes homoplasmic for a mutation that arises in one of these copies. Under suitable selection conditions, clones with chloroplast mutations for streptomycin resistance induced by methyl methanesulfonate can be recovered with direct plating after mutagenesis. Using an adaptation of the Luria-Delbrück fluctuation test, mutagenized cultures grown on nonselective liquid medium for seven to nine doublings show negligible proliferation of cells capable of forming such mutant colonies. In contrast, cells among the same cultures with reduced nuclear mutations conferring streptomycin resistance reveal considerable clonal propagation prior to plating on selection medium. Reconstruction growth-rate experiments show no reduced growth of cells with chloroplast mutations relative to either wild-type cells or to those with nuclear mutations. We propose that newly arising chloroplast mutations and their copies are usually transmitted to only one daughter cell for several cell generations by reductional divisions of the chloroplast genome. In the absence of recombination and mixing, such a reductional partition of chloroplast alleles would readily permit the formation of homoplasmic lines without the need for selection. PMID:17249064

  5. Chloroplast Proteases: Updates on Proteolysis within and across Suborganellar Compartments1[OPEN

    PubMed Central

    Nishimura, Kenji

    2016-01-01

    Chloroplasts originated from the endosymbiosis of ancestral cyanobacteria and maintain transcription and translation machineries for around 100 proteins. Most endosymbiont genes, however, have been transferred to the host nucleus, and the majority of the chloroplast proteome is composed of nucleus-encoded proteins that are biosynthesized in the cytosol and then imported into chloroplasts. How chloroplasts and the nucleus communicate to control the plastid proteome remains an important question. Protein-degrading machineries play key roles in chloroplast proteome biogenesis, remodeling, and maintenance. Research in the past few decades has revealed more than 20 chloroplast proteases, which are localized to specific suborganellar locations. In particular, two energy-dependent processive proteases of bacterial origin, Clp and FtsH, are central to protein homeostasis. Processing endopeptidases such as stromal processing peptidase and thylakoidal processing peptidase are involved in the maturation of precursor proteins imported into chloroplasts by cleaving off the amino-terminal transit peptides. Presequence peptidases and organellar oligopeptidase subsequently degrade the cleaved targeting peptides. Recent findings have indicated that not only intraplastidic but also extraplastidic processive protein-degrading systems participate in the regulation and quality control of protein translocation across the envelopes. In this review, we summarize current knowledge of the major chloroplast proteases in terms of type, suborganellar localization, and diversification. We present details of these degradation processes as case studies according to suborganellar compartment (envelope, stroma, and thylakoids). Key questions and future directions in this field are discussed. PMID:27288365

  6. [Study of Chloroplast DNA Polymorphism in the Sunflower (Helianthus L.)].

    PubMed

    Markina, N V; Usatov, A V; Logacheva, M D; Azarin, K V; Gorbachenko, C F; Kornienko, I V; Gavrilova, V A; Tihobaeva, V E

    2015-08-01

    The polymorphism of microsatellite loci of chloroplast genome in six Helianthus species and 46 lines of cultivated sunflower H. annuus (17 CMS lines and 29 Rf-lines) were studied. The differences between species are confined to four SSR loci. Within cultivated forms of the sunflower H. annuus, the polymorphism is absent. A comparative analysis was performed on sequences of the cpDNA inbred line 3629, line 398941 of the wild sunflower, and the American line HA383 H. annuus. As a result, 52 polymorphic loci represented by 27 SSR and 25 SNP were found; they can be used for genotyping of H. annuus samples, including cultural varieties: twelve polymorphic positions, of which eight are SSR and four are SNP. PMID:26601486

  7. Isolation of chloroplastic phosphoglycerate kinase

    SciTech Connect

    Macioszek, J.; Anderson, L.E. ); Anderson, J.B. )

    1990-09-01

    We report here a method for the isolation of high specific activity phosphoglycerate kinase (EC 2.7.2.3) from chloroplasts. The enzyme has been purified over 200-fold from pea (Pisum sativum L.) stromal extracts to apparent homogeneity with 23% recovery. Negative cooperativity is observed with the two enzyme phosphoglycerate kinase/glyceraldehyde-3-P dehydrogenase (EC 1.2.1.13) couple restored from the purified enzymes when NADPH is the reducing pyridine nucleotide, consistent with earlier results obtained with crude chloroplastic extracts. Michaelis Menten kinetics are observed when 3-phosphoglycerate is held constant and phosphoglycerate kinase is varied, which suggests that phosphoglycerate kinase-bound 1,3-bisphosphoglycerate may be the preferred substrate for glyceraldehyde-3-P dehydrogenase in the chloroplast.

  8. Biosynthesis of starch in chloroplasts.

    PubMed

    Nomura, T; Nakayama, N; Murata, T; Akazawa, T

    1967-03-01

    The enzymic synthesis of ADP-glucose and UDP-glucose by chloroplastic pyrophosphorylase of bean and rice leaves has been demonstrated by paper chromatographic techniques. In both tissues, the activity of UDP-glucose-pyrophosphorylase was much higher than ADP-glucose-pyrophosphorylase. Glycerate-3-phosphate, phosphoenolpyruvate and fructose-1,6-diphosphate did not stimulate ADP-glucose formation by a pyrophosphorylation reaction. The major metabolic pathway for UDP-glucose utilization appears to be the synthesis of either sucrose or sucrose-P. On the other hand, a specific precursor role of ADP-glucose for synthesizing chloroplast starch by the ADP-glucose-starch transglucosylase reaction is supported by the coupled enzyme system of ADP-glucose-pyrophosphorylase and transglucosylase, isolated from chloroplasts. None of the glycolytic intermediates stimulated the glucose transfer in the enzyme sequence of reaction system employed. PMID:4292567

  9. Thermal Damage to Chloroplast Envelope Membranes 1

    PubMed Central

    McCain, Douglas C.; Croxdale, Judith; Markley, John L.

    1989-01-01

    Nuclear magnetic resonance was used to detect thermal injury to chloroplasts in vivo. A lesion occurs in the chloroplast envelope membrane at temperatures between 53°C and 57°C, depending on species, leaf condition, and heating rate. The injury is associated with a sudden loss of water from the chloroplast. PMID:16666815

  10. Photomorphogenic Regulation of Chloroplast Replication in Euglena

    PubMed Central

    Srinivas, Usha; Lyman, Harvard

    1980-01-01

    Chloroplast replication in Euglena gracilis is specifically inhibited by ultraviolet light and the effect is photoreactivable. The ability of irradiated cells to be photoreactivated is lost more rapidly if cells are incubated in red light than in darkness. A mutant, Y9ZNa1L, which lacks the red-blue photomorphogenic system regulating chloroplast synthesis does not show the red-light-enhanced loss of photoreactivability. Another mutant, Y11P27ZD which has the red-blue system, but lacks the blue-light system also regulating chloroplast synthesis, shows the red-light effect. The red-light effect is seen in a mutant of photosynthetic electron transport, P4ZUL, which rules out a product of photosynthesis as a mediator of the effect. Inhibitors of protein synthesis on chloroplast ribosomes do not prevent the red-light-enhanced loss of chloroplast DNA. Chloroplast DNA is lost rapidly when UV-irradiated cells are incubated in red light, showing that the loss of photoreactivability is due to the loss of the substrate for photoreactivation, chloroplast DNA. Therefore, the red-blue photomorphogenic system is activating a chloroplast DNA-specific nuclease(s). A model is proposed for a light-mediated mechanism regulating the amount of chloroplast DNA: blue light would promote chloroplast DNA synthesis; red light would promote its degradation. The photomorphogenic systems regulating chloroplast synthesis might work by activating a chloroplast-specific modification-restriction mechanism. PMID:16661425

  11. Nitrogen control of chloroplast differentiation

    SciTech Connect

    Schmidt, G.W.

    1992-07-01

    This project is directed toward understanding how the availability of nitrogen affects the accumulation of chloroplast pigments and proteins functioning in energy transduction and carbon metabolism. Molecular analyses performed with Chlamydomonas reinhardtii grown in a continuous culture system such that ammonium concentration is maintained at a low steady-state concentration so as to limit cell division. As compared to chloroplasts from cells of non-limiting nitrogen provisions, chloroplasts of N-limited cells are profoundly chlorophyll-deficient but still assimilate carbon for deposition of as starch and as storage lipids. Chlorophyll deficiency arises by limiting accumulation of appropriate nuclear-encoded mRNAs of and by depressed rates of translation of chloroplast mRNAs for apoproteins of reaction centers. Chloroplast translational effects can be partially ascribed to diminished rates of chlorophyll biosynthesis in N-limited cells, but pigment levels are not determinants for expression of the nuclear light-harvesting protein genes. Consequently, other signals that are responsive to nitrogen availability mediate transcriptional or post-transcriptional processes for accumulation of the mRNAs for LHC apoproteins and other mRNAs whose abundance is dependent upon high nitrogen levels. Conversely, limited nitrogen availability promotes accumulation of other proteins involved in carbon metabolism and oxidative electron transport in chloroplasts. Hence, thylakoids of N-limited cells exhibit enhanced chlororespiratory activities wherein oxygen serves as the electron acceptor in a pathway that involves plastoquinone and other electron carrier proteins that remain to be thoroughly characterized. Ongoing and future studies are also outlined.

  12. Student's Microsatellite Project

    NASA Astrophysics Data System (ADS)

    Zelentsov, Victor; Kopik, Anatoliy; Karpenko, Stanislav; Mayorova, Victoria

    2002-01-01

    Nowadays BMSTU Youth space center carries on development of the microsatellite project. The project is based on principles of students direct involvement on all stages of development and maintenance of the satellite. The group of students was organized within the university with purpose of coordination of work at the program. Project current condition The work on creation of an experimental model of the micro satellite is performed. The aim is to define the structure and parameters of on-board devices (mass-overall dimensions characteristics, energy consumption and so on). developed. According to the simplified model an active stabilization system (three orthogonal electro-magnetic coils) and orientation characterization system (sunlight detector and magnitometer) are included in OCS structure. most suitable battery storage, power-supply controlling system. Student micro-satellite program goals 1.Scientific Information gaining in the field of Earth study- using perspective research methods. Studying of new devices behavior in space conditions. 2. Educative a. Students derive real experience of projecting, building of a spacecraft from the point of view of an experimenter, a constructor and a researcher. b. Organization of student's cooperation with key men of aerospace industry and other branches. c. Brainpower and material base preparation for micro-satellite systems' development. d. Attraction of youth interest to the topic, by: - Students' and pupils' groups attraction and involvement in experiments conduction and results processing. - Seminars and lections devoted to Earth study from the space organization - Specific scientific data distribution over World Wide Web. 3. International With purpose of program expansion, the developers' group looks to start of an international project. Within the project new experiments conduction and scientific information exchange are expected. 4. Status Bauman Moscow State Technical University's status improvement in the field

  13. Protein import into chloroplasts requires a chloroplast ATPase

    SciTech Connect

    Pain, D.; Blobel, G.

    1987-05-01

    The authors have transcribed mRNA from a cDNA clone coding for pea ribulose-1,5-bisphosphate carboxylase, translated the mRNA in a wheat germ cell-free system, and studied the energy requirement for posttranslational import of the (/sup 35/S)methionine-labeled protein into the stroma of pea chloroplasts. They found that import depends on ATP hydrolysis within the stroma. Import is not inhibited when H/sup +/, K/sup +/, Na/sup +/, or divalent cation gradients across the chloroplast membranes are dissipated by ionophores, as long as exogenously added ATP is also present during the import reaction. The data suggest that protein import into the chloroplast stroma requires a chloroplast ATPase that does not function to generate a membrane potential for driving the import reaction but that exerts its effect in another, yet-to-be-determined, mode. They have carried out a preliminary characterization of this ATPase regarding its nucleotide specificity and the effects of various ATPase inhibitors.

  14. The novel protein DELAYED PALE-GREENING1 is required for early chloroplast biogenesis in Arabidopsis thaliana.

    PubMed

    Liu, Dong; Li, Weichun; Cheng, Jianfeng

    2016-01-01

    Chloroplast biogenesis is one of the most important subjects in plant biology. In this study, an Arabidopsis early chloroplast biogenesis mutant with a delayed pale-greening phenotype (dpg1) was isolated from a T-DNA insertion mutant collection. Both cotyledons and true leaves of dpg1 mutants were initially albino but gradually became pale green as the plant matured. Transmission electron microscopic observations revealed that the mutant displayed a delayed proplastid-to-chloroplast transition. Sequence and transcription analyses showed that AtDPG1 encodes a putatively chloroplast-localized protein containing three predicted transmembrane helices and that its expression depends on both light and developmental status. GUS staining for AtDPG1::GUS transgenic lines showed that this gene was widely expressed throughout the plant and that higher expression levels were predominantly found in green tissues during the early stages of Arabidopsis seedling development. Furthermore, quantitative real-time RT-PCR analyses revealed that a number of chloroplast- and nuclear-encoded genes involved in chlorophyll biosynthesis, photosynthesis and chloroplast development were substantially down-regulated in the dpg1 mutant. These data indicate that AtDPG1 plays an essential role in early chloroplast biogenesis, and its absence triggers chloroplast-to-nucleus retrograde signalling, which ultimately down-regulates the expression of nuclear genes encoding chloroplast-localized proteins. PMID:27160321

  15. The novel protein DELAYED PALE-GREENING1 is required for early chloroplast biogenesis in Arabidopsis thaliana

    PubMed Central

    Liu, Dong; Li, Weichun; Cheng, Jianfeng

    2016-01-01

    Chloroplast biogenesis is one of the most important subjects in plant biology. In this study, an Arabidopsis early chloroplast biogenesis mutant with a delayed pale-greening phenotype (dpg1) was isolated from a T-DNA insertion mutant collection. Both cotyledons and true leaves of dpg1 mutants were initially albino but gradually became pale green as the plant matured. Transmission electron microscopic observations revealed that the mutant displayed a delayed proplastid-to-chloroplast transition. Sequence and transcription analyses showed that AtDPG1 encodes a putatively chloroplast-localized protein containing three predicted transmembrane helices and that its expression depends on both light and developmental status. GUS staining for AtDPG1::GUS transgenic lines showed that this gene was widely expressed throughout the plant and that higher expression levels were predominantly found in green tissues during the early stages of Arabidopsis seedling development. Furthermore, quantitative real-time RT-PCR analyses revealed that a number of chloroplast- and nuclear-encoded genes involved in chlorophyll biosynthesis, photosynthesis and chloroplast development were substantially down-regulated in the dpg1 mutant. These data indicate that AtDPG1 plays an essential role in early chloroplast biogenesis, and its absence triggers chloroplast-to-nucleus retrograde signalling, which ultimately down-regulates the expression of nuclear genes encoding chloroplast-localized proteins. PMID:27160321

  16. Mutational dynamics of aroid chloroplast genomes.

    PubMed

    Ahmed, Ibrar; Biggs, Patrick J; Matthews, Peter J; Collins, Lesley J; Hendy, Michael D; Lockhart, Peter J

    2012-01-01

    A characteristic feature of eukaryote and prokaryote genomes is the co-occurrence of nucleotide substitution and insertion/deletion (indel) mutations. Although similar observations have also been made for chloroplast DNA, genome-wide associations have not been reported. We determined the chloroplast genome sequences for two morphotypes of taro (Colocasia esculenta; family Araceae) and compared these with four publicly available aroid chloroplast genomes. Here, we report the extent of genome-wide association between direct and inverted repeats, indels, and substitutions in these aroid chloroplast genomes. We suggest that alternative but not mutually exclusive hypotheses explain the mutational dynamics of chloroplast genome evolution. PMID:23204304

  17. The complete chloroplast genome provides insight into the evolution and polymorphism of Panax ginseng

    PubMed Central

    Zhao, Yongbing; Yin, Jinlong; Guo, Haiyan; Zhang, Yuyu; Xiao, Wen; Sun, Chen; Wu, Jiayan; Qu, Xiaobo; Yu, Jun; Wang, Xumin; Xiao, Jingfa

    2015-01-01

    Panax ginseng C.A. Meyer (P. ginseng) is an important medicinal plant and is often used in traditional Chinese medicine. With next generation sequencing (NGS) technology, we determined the complete chloroplast genome sequences for four Chinese P. ginseng strains, which are Damaya (DMY), Ermaya (EMY), Gaolishen (GLS), and Yeshanshen (YSS). The total chloroplast genome sequence length for DMY, EMY, and GLS was 156,354 bp, while that for YSS was 156,355 bp. Comparative genomic analysis of the chloroplast genome sequences indicate that gene content, GC content, and gene order in DMY are quite similar to its relative species, and nucleotide sequence diversity of inverted repeat region (IR) is lower than that of its counterparts, large single copy region (LSC) and small single copy region (SSC). A comparison among these four P. ginseng strains revealed that the chloroplast genome sequences of DMY, EMY, and GLS were identical and YSS had a 1-bp insertion at base 5472. To further study the heterogeneity in chloroplast genome during domestication, high-resolution reads were mapped to the genome sequences to investigate the differences at the minor allele level; 208 minor allele sites with minor allele frequencies (MAF) of ≥0.05 were identified. The polymorphism site numbers per kb of chloroplast genome sequence for DMY, EMY, GLS, and YSS were 0.74, 0.59, 0.97, and 1.23, respectively. All the minor allele sites located in LSC and IR regions, and the four strains showed the same variation types (substitution base or indel) at all identified polymorphism sites. Comparison results of heterogeneity in the chloroplast genome sequences showed that the minor allele sites on the chloroplast genome were undergoing purifying selection to adapt to changing environment during domestication process. A study of P. ginseng chloroplast genome with particular focus on minor allele sites would aid in investigating the dynamics on the chloroplast genomes and different P. ginseng strains

  18. Comparative chromatography of chloroplast pigment

    NASA Technical Reports Server (NTRS)

    Grandolfo, M.; Sherma, J.; Strain, H. H.

    1969-01-01

    Methods for isolation of low concentration pigments of the cocklebur species are described. The methods entail two step chromatography so that the different sorption properties of the various pigments in varying column parameters can be utilized. Columnar and thin layer methods are compared. Many conditions influence separability of the chloroplasts.

  19. Increasing tomato fruit quality by enhancing fruit chloroplast function. A double-edged sword?

    PubMed

    Cocaliadis, Maria Florencia; Fernández-Muñoz, Rafael; Pons, Clara; Orzaez, Diego; Granell, Antonio

    2014-08-01

    Fruits are generally regarded as photosynthate sinks as they rely on energy provided by sugars transported from leaves to carry out the highly demanding processes of development and ripening; eventually these imported photosynthates also contribute to the fruit organoleptic properties. Three recent reports have revealed, however, that transcriptional factors enhancing chloroplast development in fruit may result in higher contents not only of tomato fruit-specialized metabolites but also of sugars. In addition to suggesting new ways to improve fruit quality by fortifying fruit chloroplasts and plastids, these results prompted us to re-evaluate the importance of the contribution of chloroplasts/photosynthesis to fruit development and ripening. PMID:24723405

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

    PubMed

    Slettan, A; Olsaker, I; Lie, O

    1997-06-01

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

  1. Phototropin encoded by a single-copy gene mediates chloroplast photorelocation movements in the liverwort Marchantia polymorpha.

    PubMed

    Komatsu, Aino; Terai, Mika; Ishizaki, Kimitsune; Suetsugu, Noriyuki; Tsuboi, Hidenori; Nishihama, Ryuichi; Yamato, Katsuyuki T; Wada, Masamitsu; Kohchi, Takayuki

    2014-09-01

    Blue-light-induced chloroplast photorelocation movement is observed in most land plants. Chloroplasts move toward weak-light-irradiated areas to efficiently absorb light (the accumulation response) and escape from strong-light-irradiated areas to avoid photodamage (the avoidance response). The plant-specific kinase phototropin (phot) is the blue-light receptor for chloroplast movements. Although the molecular mechanisms for chloroplast photorelocation movement have been analyzed, the overall aspects of signal transduction common to land plants are still unknown. Here, we show that the liverwort Marchantia polymorpha exhibits the accumulation and avoidance responses exclusively induced by blue light as well as specific chloroplast positioning in the dark. Moreover, in silico and Southern-blot analyses revealed that the M. polymorpha genome encodes a single PHOT gene, MpPHOT, and its knockout line displayed none of the chloroplast photorelocation movements, indicating that the sole MpPHOT gene mediates all types of movement. Mpphot was localized on the plasma membrane and exhibited blue-light-dependent autophosphorylation both in vitro and in vivo. Heterologous expression of MpPHOT rescued the defects in chloroplast movement of phot mutants in the fern Adiantum capillus-veneris and the seed plant Arabidopsis (Arabidopsis thaliana). These results indicate that Mpphot possesses evolutionarily conserved regulatory activities for chloroplast photorelocation movement. M. polymorpha offers a simple and versatile platform for analyzing the fundamental processes of phototropin-mediated chloroplast photorelocation movement common to land plants. PMID:25096976

  2. Microsatellites in Pursuit of Microbial Genome Evolution

    PubMed Central

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

    2016-01-01

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

  3. cpDNA microsatellite markers for Lemna minor (Araceae): Phylogeographic implications1

    PubMed Central

    Wani, Gowher A.; Shah, Manzoor A.; Reshi, Zafar A.; Atangana, Alain R.; Khasa, Damase P.

    2014-01-01

    • Premise of the study: A lack of genetic markers impedes our understanding of the population biology of Lemna minor. Thus, the development of appropriate genetic markers for L. minor promises to be highly useful for population genetic studies and for addressing other life history questions regarding the species. • Methods and Results: For the first time, we characterized nine polymorphic and 24 monomorphic chloroplast microsatellite markers in L. minor using DNA samples of 26 individuals sampled from five populations in Kashmir and of 17 individuals from three populations in Quebec. Initially, we designed 33 primer pairs, which were tested on genomic DNA from natural populations. Nine loci provided markers with two alleles. Based on genotyping of the chloroplast DNA fragments from 43 sampled individuals, we identified one haplotype in Quebec and 11 haplotypes in Kashmir, of which one occurs in 56% of the genotypes, one in 8%, and nine in 4%, respectively. There was a maximum of two alleles per locus. • Conclusions: These new chloroplast microsatellite markers for L. minor and haplotype distribution patterns indicate a complex phylogeographic history that merits further investigation. PMID:25202636

  4. Formation of putative chloroplast cytochromes in isolated developing pea chloroplasts

    SciTech Connect

    Thaver, S.S.; Bhava, D.; Castelfranco, P.A.

    1986-04-01

    In addition to chlorophyll-protein complexes, other proteins were labeled when isolated developing pea chloroplasts were incubated with (/sup 14/C)-5-aminolevulinic acid (/sup 14/C)-ALA. The major labeled band (M/sub r/ = 43 kDa by LDS-PAGE) was labeled even in the presence of chloramphenicol. Heme-dependent peroxidase activity (as detected by the tetramethyl benzidine-H/sub 2/O/sub 2/ stain) was not visibly associated with this band. The radioactive band was stable to heat, 5% HCl in acetone, and was absent if the incubation with (/sup 14/C)-5-aminolevulinic acid was carried out in the presence of N-methyl protoporphyrin IX dimethyl ester (a specific inhibitor of ferrochelatase). Organic solvent extraction procedures for the enrichment of cytochrome f from chloroplast membranes also extracted this unknown labeled product. It was concluded that this labeled product was probably a c-type cytochrome. The effect of exogenous iron, iron chelators, gabaculine (an inhibitor of ALA synthesis) and other incubation conditions upon the in vitro formation of putative chloroplast cytochromes will be discussed.

  5. A Brassica napus Lipase Locates at the Membrane Contact Sites Involved in Chloroplast Development

    PubMed Central

    Tan, Xiaoli; Wang, Qiuye; Tian, Baoxia; Zhang, Henan; Lu, Daoli; Zhou, Jia

    2011-01-01

    Background Fatty acids synthesized in chloroplast are transported to endoplasmic reticulum (ER) for triacylglycerols (TAGs) resembling. The development of chloroplast also requires lipids trafficking from ER to chloroplast. The membrane contact sites (MCSs) between ER and chloroplast has been demonstrated to be involved for the trafficking of lipids and proteins. Lipids trafficking between ER and chloroplast is often accompanied by lipids interconversion. However, it is rarely known how lipids interconversion happens during their trafficking. Methodology/Principal Findings We cloned a lipase gene from Brassica napus L., designated as BnCLIP1. Green fluorescence protein (GFP)-tagged BnCLIP1 was shown to locate at the MCSs between ER and chloroplasts in tobacco leaves. Heterogeneous expression of BnCLIP1 in Saccharomyces cerevisiae (pep4) reduced the total amount of fatty acid. Gas chromatography-mass spectrometry (GC-MS) analysis revealed that the truncated BnCLIP1 had a substrate preference for C16:0 lipids in Saccharomyces cerevisiae (pep4). To probe the physiological function of BnCLIP1, two Brassica napus lines with different oil-content were introduced to investigate the transcript patterns of BnCLIP1 during seed development. Intriguingly, the transcript level of BnCLIP1 was found to be immediately up-regulated during the natural seed senescence of both lines; the transcription response of BnCLIP1 in the high oil-content seeds was faster than the lower ones, suggesting a potential role of BnCLIP1 in affecting seed oil synthesis via regulating chloroplast integrity. Further researches showed that chemical disruption of leaf chloroplast also activated the transcription of BnCLIP1. Conclusions/Significance The findings of this study show that BnCLIP1 encodes a lipase, localizes at the MCSs and involves in chloroplast development. PMID:22046373

  6. Reinvestigation of the triplet-minus-singlet spectrum of chloroplasts

    NASA Astrophysics Data System (ADS)

    Jávorfi, T.; Garab, G.; Razi Naqvi, K.

    2000-01-01

    A comparison of the triplet-minus-singlet (TmS) absorption spectrum of spinach chloroplasts, recorded some thirty years ago, with the more recently published TmS spectrum of isolated Chl a/ b LHCII (light-harvesting complexes associated with photosystem II of higher plants) shows that the two spectra are very similar, which is to be expected, since only the carotenoid pigments contribute to each spectrum. Be that as it may, the comparison also reveals a dissimilarity: photoexcitation of the sample does, or does not, affect the absorbance in the Qy region (650-700 nm), depending on whether the sample is a suspension of chloroplasts or of isolated LHCII. The Qy-signal in the TmS spectrum of LHCII decays, it should be noted, at the same rate as the rest of the difference spectrum, and its most prominent feature is a negative peak. As the carotenoids do not absorb in the Qy region, the presence of a signal in this region calls for an explanation: van der Vos, Carbonera and Hoff, the first to find as well as fathom the phenomenon, attributed the Qy-signal to a change, in the absorption spectrum of a chlorophyll a (Chl a) molecule, brought about by the presence of triplet excitation on a neighbouring carotenoid (Car). The difference in the behaviours of chloroplasts and LHCII, if reproducible, would imply that the Car triplets which give rise to the TmS spectrum of chloroplasts do not influence the absorption spectra of their Chl a neighbours. With a view to reaching a firm conclusion about this vexed issue, spinach chloroplasts and thylakoids have been examined with the aid of the same kinetic spectrometer as that used for investigating LHCII; the TmS spectra of both chloroplasts and thylakoids contain prominent bleaching signals centred at 680 nm, and the triplet decay time in each case is comparable to that of the Chl a/ b LHCII triplets. Results pertaining to other closely related systems are recalled, and it is concluded that, so far as the overall appearance of the

  7. Characterization of microsatellite DNA libraries from three mealybug species and development of microsatellite markers for Pseudococcus viburni (Hemiptera: Pseudococcidae).

    PubMed

    Correa, M C G; Zaviezo, T; Le Maguet, J; Herrbach, E; Malausa, T

    2014-04-01

    Mealybugs (Hemiptera: Pseudococcidae) are important pests for crops worldwide. Different species, cryptic taxa under the same species name or even populations within a species can differ in biological characteristics, such as phenology, resistance to insecticides, virus transmission and susceptibility to natural enemies. Therefore, their management efficacy depends on their accurate identification. Microsatellite genetic markers are efficient in revealing the fine-scale taxonomic status of insects, both at inter- and intra-specific level. Despite their potential uses, microsatellites have been developed only for one mealybug species so far. Hence, it is unclear whether microsatellites may be useful to assess mealybug population differentiation and structuring. In this work, we tested the feasibility of developing microsatellite markers in mealybugs by: (i) producing and characterizing microsatellite DNA libraries for three species: Pseudococcus viburni, Pseudococcus comstocki and Heliococcus bohemicus, and (ii) by developing and testing markers for Ps. viburni. The obtained libraries contained balanced percentages of dinucleotide (ranging from 15 to 25%) and trinucleotide (from 5 to 17%) motifs. The marker setup for Ps. viburni was successful, although 70% of the primers initially tested were discarded for a lack of polymorphism. Finally, 25 markers were combined in two multiplex polymerase chain reactions with 21 displaying no evidence of deviation from Hardy-Weinberg equilibrium. Ps. viburni markers were tested on one population from France and one from Chile. The markers revealed a significant genetic differentiation between the two populations with an Fst estimate of 0.266. PMID:24345408

  8. Contrasts between the phylogeographic patterns of chloroplast and nuclear DNA highlight a role for pollen-mediated gene flow in preventing population divergence in an East Asian temperate tree.

    PubMed

    Bai, Wei-Ning; Wang, Wen-Ting; Zhang, Da-Yong

    2014-12-01

    Plant phylogeographic studies in East Asia have provided support for the biogeographic hypothesis that the complex landforms and climate of this region have provided substantial opportunities for allopatric speciation. However, most of these studies have been based on maternally inherited chloroplast DNA (cpDNA) markers and were therefore unable to reveal the role of pollen-mediated gene flow in preventing population divergence. Here, we investigate the phylogeography of the Chinese walnut Juglans cathayensis, a temperate deciduous tree widely distributed across disjunct montane sites in subtropical China. We genotyped 19 populations using seven cpDNA fragments and ten nuclear microsatellite loci and modeled the ecological niche of J. cathayensis. CpDNA analysis identified a total of nine haplotypes, and each of the 19 sampled populations was fixed for a single haplotype, displaying a prominent phylogeographic structure. The results of ecological niche modeling indicated that J. cathayensis populations survived the last glaciation in situ, although they were probably more fragmented than today. In contrast, we detected a much weaker, but nonetheless clear, genetic structure based on nuclear microsatellite data. Our study demonstrates how extensive pollen flow can erase the genetic imprint of long-term refugial isolation in maternal lineages, effectively preventing population differentiation in temperate, particularly wind-pollinated, forest trees in subtropical China. PMID:25196588

  9. Comparative analyses of chloroplast genome data representing nine green algae in Sphaeropleales (Chlorophyceae, Chlorophyta).

    PubMed

    Fučíková, Karolina; Lewis, Louise A; Lewis, Paul O

    2016-06-01

    The chloroplast genomes of green algae are highly variable in their architecture. In this article we summarize gene content across newly obtained and published chloroplast genomes in Chlorophyceae, including new data from nine of species in Sphaeropleales (Chlorophyceae, Chlorophyta). We present genome architecture information, including genome synteny analysis across two groups of species. Also, we provide a phylogenetic tree obtained from analysis of gene order data for species in Chlorophyceae with fully sequenced chloroplast genomes. Further analyses and interpretation of the data can be found in "Chloroplast phylogenomic data from the green algal order Sphaeropleales (Chlorophyceae, Chlorophyta) reveal complex patterns of sequence evolution" (Fučíková et al., In review) [1]. PMID:27054159

  10. Sequence analysis and protein import studies of an outer chloroplast envelope polypeptide.

    PubMed Central

    Salomon, M; Fischer, K; Flügge, U I; Soll, J

    1990-01-01

    A chloroplast outer envelope membrane protein was cloned and sequenced and from the sequence it was possible to deduce a polypeptide of 6.7 kDa. It has only one membrane-spanning region; the C terminus extends into the cytosol, whereas the N terminus is exposed to the space between the two envelope membranes. The protein was synthesized in an in vitro transcription-translation system to study its routing into isolated chloroplasts. The import studies revealed that the 6.7-kDa protein followed a different and heretofore undescribed translocation pathway in the respect that (i) it does not have a cleavable transit sequence, (ii) it does not require ATP hydrolysis for import, and (iii) protease-sensitive components that are responsible for recognition of precursor proteins destined for the inside of the chloroplasts are not involved in routing the 6.7-kDa polypeptide to the outer chloroplast envelope. Images PMID:2377616

  11. The complete chloroplast genome sequence of an important medicinal plant Cynanchum wilfordii (Maxim.) Hemsl. (Apocynaceae).

    PubMed

    Park, Hyun-Seung; Kim, Kyu-Yeob; Kim, Kyunghee; Lee, Sang-Choon; Lee, Junki; Seong, Rack Seon; Shim, Young Hun; Sung, Sang Hyun; Yang, Tae-Jin

    2016-09-01

    Cynanchum wilfordii (Maxim.) Hemsl. is a traditional medicinal herb belonging to the Asclepiadoideae subfamily, whose dried roots have been used as traditional medicine in Asia. The complete chloroplast genome of C. wilfordii was generated by de novo assembly using the small amount of whole genome sequencing data. The chloroplast genome of C. wilfordii was 161 241 bp long, composed of large single copy region (91 995 bp), small single copy region (19 930 bp) and a pair of inverted repeat regions (24 658 bp). The overall GC contents of the chloroplast genome was 37.8%. A total of 114 genes were annotated, which included 80 protein-coding genes, 30 tRNA genes and 4 rRNA genes. Phylogenetic analysis with the reported chloroplast genomes revealed that C. wilfordii is most closely related to Asclepias nivea (Caribbean milkweed) and Asclepias syriaca (common milkweed) within the Asclepiadoideae subfamily. PMID:26358391

  12. A microsatellite genetic linkage map of human chromosome 18

    SciTech Connect

    Straub, R.E.; Speer, M.C.; Luo, Ying; Ott, J.; Gilliam, T.C. ); Rojas, K.; Overhauser, J. )

    1993-01-01

    We isolated nine new microsatellite markers from chromosome 18 and further characterized and mapped eight microsatellites developed in other laboratories. We have constructed a framework linkage map of chromosome 18 that includes 14 microsatellite markers (12 dinucleotide and 2 tetranucleotide) and 2 RFLP markers. Cytogenetic localization for the microsatellites was performed by PCR amplification of IS somatic cell hybrids containing different deletions of chromosome 18. Twelve of the microsatellites and one of the RFLPs have heterozygosities greater than 70%. The average heterozygosity of the markers included in the map is 72%. In addition, we have made provisional placements of 3 more microsatellite markers and 2 more RFLP markers. The map lengths (in Kosambi centimorgans) are as follows: sex-averaged, 109.3 cM; male, 72.4 cM; female, 161.2 cM. The average distance between markers in the sex-averaged map is 7.3 cM, and the largest gap between markers is 16.7 cM. Analysis of the data for differences in the female:male map distance ratio revealed significant evidence for a constant difference in the ratio (X[sup 2]=32.25; df = 1; P < 0.001; ratio = 2.5:1). Furthermore, there was significant evidence in favor of a variable female:male map distance ratio across the chromosome compared to a constant distance ratio (X[sup 2] = 27.78; df = 14; P = 0.015). To facilitate their use in genomic screening for disease genes, all of the microsatellite markers used here can be amplified under standard PCR conditions, and most can be used in duplex PCR reactions. 36 refs., 3 figs., 4 tabs.

  13. Essential role of VIPP1 in chloroplast envelope maintenance in Arabidopsis.

    PubMed

    Zhang, Lingang; Kato, Yusuke; Otters, Stephanie; Vothknecht, Ute C; Sakamoto, Wataru

    2012-09-01

    VESICLE-INDUCING PROTEIN IN PLASTIDS1 (VIPP1), proposed to play a role in thylakoid biogenesis, is conserved in photosynthetic organisms and is closely related to Phage Shock Protein A (PspA), which is involved in plasma membrane integrity in Escherichia coli. This study showed that chloroplasts/plastids in Arabidopsis thaliana vipp1 knockdown and knockout mutants exhibit a unique morphology, forming balloon-like structures. This altered morphology, as well as lethality of vipp1, was complemented by expression of VIPP1 fused to green fluorescent protein (VIPP1-GFP). Several lines of evidence show that the balloon chloroplasts result from chloroplast swelling related to osmotic stress, implicating VIPP1 in the maintenance of plastid envelopes. In support of this, Arabidopsis VIPP1 rescued defective proton leakage in an E. coli pspA mutant. Microscopy observation of VIPP1-GFP in transgenic Arabidopsis revealed that VIPP1 forms large macrostructures that are integrated into various morphologies along the envelopes. Furthermore, live imaging revealed that VIPP1-GFP is highly mobile when chloroplasts are subjected to osmotic stress. VIPP1-GFP showed dynamic movement in the transparent area of spherical chloroplasts, as the fluorescent molecules formed filament-like structures likely derived from disassembly of the large VIPP1 complex. Collectively, our data demonstrate that VIPP1 is a multifunctional protein in chloroplasts that is critically important for envelope maintenance. PMID:23001039

  14. The Conserved Endoribonuclease YbeY Is Required for Chloroplast Ribosomal RNA Processing in Arabidopsis1

    PubMed Central

    Liu, Jinwen; Zhou, Wenbin; Liu, Guifeng; Yang, Chuanping; Sun, Yi; Wu, Wenjuan; Cao, Shenquan; Wang, Chong; Hai, Guanghui; Wang, Zhifeng; Bock, Ralph; Huang, Jirong

    2015-01-01

    Maturation of chloroplast ribosomal RNAs (rRNAs) comprises several endoribonucleolytic and exoribonucleolytic processing steps. However, little is known about the specific enzymes involved and the cleavage steps they catalyze. Here, we report the functional characterization of the single Arabidopsis (Arabidopsis thaliana) gene encoding a putative YbeY endoribonuclease. AtYbeY null mutants are seedling lethal, indicating that AtYbeY function is essential for plant growth. Knockdown plants display slow growth and show pale-green leaves. Physiological and ultrastructural analyses of atybeY mutants revealed impaired photosynthesis and defective chloroplast development. Fluorescent microcopy analysis showed that, when fused with the green fluorescence protein, AtYbeY is localized in chloroplasts. Immunoblot and RNA gel-blot assays revealed that the levels of chloroplast-encoded subunits of photosynthetic complexes are reduced in atybeY mutants, but the corresponding transcripts accumulate normally. In addition, atybeY mutants display defective maturation of both the 5′ and 3′ ends of 16S, 23S, and 4.5S rRNAs as well as decreased accumulation of mature transcripts from the transfer RNA genes contained in the chloroplast rRNA operon. Consequently, mutant plants show a severe deficiency in ribosome biogenesis, which, in turn, results in impaired plastid translational activity. Furthermore, biochemical assays show that recombinant AtYbeY is able to cleave chloroplast rRNAs as well as messenger RNAs and transfer RNAs in vitro. Taken together, our findings indicate that AtYbeY is a chloroplast-localized endoribonuclease that is required for chloroplast rRNA processing and thus for normal growth and development. PMID:25810095

  15. Light modulation of glyceraldehyde-3-phosphate dehydrogenase and glucose-6-phosphate dehydrogenase by photosynthetic electron flow in pea chloroplasts

    SciTech Connect

    Akamba, L.M.; Anderson, L.E.

    1981-02-01

    Light activation of NADP-linked glyceraldehyde-3-P dehydrogenase (EC 1.2.1.13) and light inactivation of glucose-6-P dehydrogenase (EC 1.1.1.49) appear to be modulated within pea leaf chloroplasts by mediators which are reduced by photosynthetic electron flow from the photosystem I reaction center. Dichlorophenyl-1,1-dimethylurea inhibition of this modulation can be completely reversed by ascorbate plus 2,6-dichlorophenolindophenol in broken chloroplasts, but not in intact chloroplasts. Intact chloroplasts are impermeable to 2,6-dichlorophenolindophenol at pH 7.5. Studies on the effect of light in reconstituted chloroplasts with photosystem I-enriched particles in the place of whole thylakoids revealed that photosystem I participants in the light modulation of NADP-linked glyceraldehyde-3-P dehydrogenase and of glucose-6-P dehydrogenase.

  16. Endosymbiotic origin and codon bias of the nuclear gene for chloroplast glyceraldehyde-3-phosphate dehydrogenase from maize.

    PubMed

    Brinkmann, H; Martinez, P; Quigley, F; Martin, W; Cerff, R

    1987-01-01

    The nuclei of plant cells harbor genes for two types of glyceraldehyde-3-phosphate dehydrogenases (GAPDH) displaying a sequence divergence corresponding to the prokaryote/eukaryote separation. This strongly supports the endosymbiotic theory of chloroplast evolution and in particular the gene transfer hypothesis suggesting that the gene for the chloroplast enzyme, initially located in the genome of the endosymbiotic chloroplast progenitor, was transferred during the course of evolution into the nuclear genome of the endosymbiotic host. Codon usage in the gene for chloroplast GAPDH of maize is radically different from that employed by present-day chloroplasts and from that of the cytosolic (glycolytic) enzyme from the same cell. This reveals the presence of subcellular selective pressures which appear to be involved in the optimization of gene expression in the economically important graminaceous monocots. PMID:3131533

  17. Chloroplast genome sequencing analysis of Heterosigma akashiwo CCMP452 (West Atlantic) and NIES293 (West Pacific) strains

    PubMed Central

    Cattolico, Rose Ann; Jacobs, Michael A; Zhou, Yang; Chang, Jean; Duplessis, Melinda; Lybrand, Terry; McKay, John; Ong, Han Chuan; Sims, Elizabeth; Rocap, Gabrielle

    2008-01-01

    Background Heterokont algae form a monophyletic group within the stramenopile branch of the tree of life. These organisms display wide morphological diversity, ranging from minute unicells to massive, bladed forms. Surprisingly, chloroplast genome sequences are available only for diatoms, representing two (Coscinodiscophyceae and Bacillariophyceae) of approximately 18 classes of algae that comprise this taxonomic cluster. A universal challenge to chloroplast genome sequencing studies is the retrieval of highly purified DNA in quantities sufficient for analytical processing. To circumvent this problem, we have developed a simplified method for sequencing chloroplast genomes, using fosmids selected from a total cellular DNA library. The technique has been used to sequence chloroplast DNA of two Heterosigma akashiwo strains. This raphidophyte has served as a model system for studies of stramenopile chloroplast biogenesis and evolution. Results H. akashiwo strain CCMP452 (West Atlantic) chloroplast DNA is 160,149 bp in size with a 21,822-bp inverted repeat, whereas NIES293 (West Pacific) chloroplast DNA is 159,370 bp in size and has an inverted repeat of 21,665 bp. The fosmid cloning technique reveals that both strains contain an isomeric chloroplast DNA population resulting from an inversion of their single copy domains. Both strains contain multiple small inverted and tandem repeats, non-randomly distributed within the genomes. Although both CCMP452 and NIES293 chloroplast DNAs contains 197 genes, multiple nucleotide polymorphisms are present in both coding and intergenic regions. Several protein-coding genes contain large, in-frame inserts relative to orthologous genes in other plastids. These inserts are maintained in mRNA products. Two genes of interest in H. akashiwo, not previously reported in any chloroplast genome, include tyrC, a tyrosine recombinase, which we hypothesize may be a result of a lateral gene transfer event, and an unidentified 456 amino acid

  18. Characterization of microsatellite loci isolated in trumpeter swan (Cygnus buccinator)

    USGS Publications Warehouse

    John, J. St; Ransler, F.A.; Quinn, T.W.; Oyler-McCance, S.J.

    2006-01-01

    Primers for 16 microsatellite loci were developed for the trumpeter swan (Cygnus buccinator), a species recovering from a recent population bottleneck. In a screen of 158 individuals, the 16 loci were found to have levels of variability ranging from two to seven alleles. No loci were found to be linked, although two loci repeatedly revealed significant departures from Hardy-Weinberg equilibrium. Amplification in the closely related tundra swan (Cygnus columbianus) was successful for all except one locus. These microsatellite loci will be applicable for population genetic analyses and ultimately aid in management efforts. ?? 2006 The Authors.

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

    PubMed

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

    2009-05-01

    Sixteen polymorphic microsatellite markers were isolated and identified in Zizania latifolia Turcz. (Poaceae), a perennial aquatic plant widespread in Eastern Asia. The microsatellite-enriched library was constructed using the fast isolation by AFLP of sequences containing repeats method. These markers revealed two to 14 alleles, with an average of 5.6 alleles per locus. The observed and expected heterozygosities varied from 0.071 to 0.690 and from 0.174 to 0.812, respectively. These markers will be useful for studying of gene flow and evaluating the genetic diversity of the Zizania latifolia population. PMID:21564779

  20. Characterization of microsatellite loci isolated in Mountain Plover (Charadrius montanus)

    USGS Publications Warehouse

    John, J. St; Kysela, R.F.; Oyler-McCance, S.J.

    2007-01-01

    Primers for 15 microsatellite loci were developed for Mountain Plover, a species whose distribution and abundance have been reduced drastically in the past 30 years. In a screen of 126 individuals collected from four breeding locales across the species' range, levels of polymorphism ranged from two to 13 alleles per locus. No two loci were found to be linked, although one locus revealed significant departures from Hardy-Weinberg equilibrium. These microsatellite loci can be used in population genetic studies, ultimately aiding in management efforts for Mountain Plover. Additionally, these markers can potentially be used in studies investigating the mating system of Mountain Plover. ?? 2007 Blackwell Publishing Ltd.

  1. Microsatellite and Chromosome Evolution of Parthenogenetic Sitobion Aphids in Australia

    PubMed Central

    Sunnucks, P.; England, P. R.; Taylor, A. C.; Hales, D. F.

    1996-01-01

    Single-locus microsatellite variation correlated perfectly with chromosome number in Sitobion miscanthi aphids. The microsatellites were highly heterozygous, with up to 10 alleles per locus in this species. Despite this considerable allelic variation, only seven different S. miscanthi genotypes were discovered in 555 individuals collected from a wide range of locations, hosts and sampling periods. Relatedness between genotypes suggests only two successful colonizations of Australia. There was no evidence for genetic recombination in 555 S. miscanthi so the occurrence of recent sexual reproduction must be near zero. Thus diversification is by mutation and chromosomal rearrangement alone. Since the aphids showed no sexual recombination, microsatellites can mutate without meiosis. Five of seven microsatellite differences were a single repeat unit, and one larger jump is likely. The minimum numbers of changes between karyotypes corresponded roughly one-to-one with microsatellite allele changes, which suggests very rapid chromosomal evolution. A chromosomal fission occurred in a cultured line, and a previously unknown chromosomal race was detected. All 121 diverse S. near fragariae were heterozygous but revealed only one genotype. This species too must have a low rate of sexual reproduction and few colonizations of Australia. PMID:8889535

  2. A Novel Approach for Characterizing Microsatellite Instability in Cancer Cells

    PubMed Central

    Lu, Yuheng; Soong, T. David; Elemento, Olivier

    2013-01-01

    Microsatellite instability (MSI) is characterized by the expansion or contraction of DNA repeat tracts as a consequence of DNA mismatch repair deficiency (MMRD). Accurate detection of MSI in cancer cells is important since MSI is associated with several cancer subtypes and can help inform therapeutic decisions. Although experimental assays have been developed to detect MSI, they typically depend on a small number of known microsatellite loci or mismatch repair genes and have limited reliability. Here, we report a novel genome-wide approach for MSI detection based on the global detection of insertions and deletions (indels) in microsatellites found in expressed genes. Our large-scale analyses of 20 cancer cell lines and 123 normal individuals revealed striking indel features associated with MSI: there is a significant increase of short microsatellite deletions in MSI samples compared to microsatellite stable (MSS) ones, suggesting a mechanistic bias of repair efficiency between insertions and deletions in normal human cells. By incorporating this observation into our MSI scoring metric, we show that our approach can correctly distinguish between MSI and MSS cancer cell lines. Moreover, when we applied this approach to primal tumor samples, our metric is also well consistent with diagnosed MSI status. Thus, our study offers new insight into DNA mismatch repair system, and also provides a novel MSI diagnosis method for clinical oncology with better reliability. PMID:23671654

  3. Diversity of a ribonucleoprotein family in tobacco chloroplasts: two new chloroplast ribonucleoproteins and a phylogenetic tree of ten chloroplast RNA-binding domains.

    PubMed Central

    Ye, L H; Li, Y Q; Fukami-Kobayashi, K; Go, M; Konishi, T; Watanabe, A; Sugiura, M

    1991-01-01

    Two new ribonucleoproteins (RNPs) have been identified from a tobacco chloroplast lysate. These two proteins (cp29A and cp29B) are nuclear-encoded and have a less affinity to single-stranded DNA as compared with three other chloroplast RNPs (cp28, cp31 and cp33) previously isolated. DNA sequencing revealed that both contain two consensus sequence-type homologous RNA-binding domains (CS-RBDs) and a very acidic amino-terminal domain but shorter than that of cp28, cp31 and cp33. Comparison of cp29A and cp29B showed a 19 amino acid insertion in the region separating the two CS-RBDs in cp29B. This insertion results in three tandem repeats of a glycine-rich sequence of 10 amino acids, which is a novel feature in RNPs. The two proteins are encoded by different single nuclear genes and no alternatively spliced transcripts could be identified. We constructed a phylogenetic tree for the ten chloroplast CS-RBDs. These results suggest that there is a sizable RNP family in chloroplasts and the diversity was mainly generated through a series of gene duplications rather than through alternative pre-mRNA splicing. The gene for cp29B contains three introns. The first and second introns interrupt the first CS-RBD and the third intron does the second CS-RBD. The position of the first intron site is the same as that in the human hnRNP A1 protein gene. Images PMID:1721701

  4. Multilocus microsatellite analysis of European and African Candida glabrata isolates.

    PubMed

    Chillemi, V; Lo Passo, C; van Diepeningen, A D; Rharmitt, S; Delfino, D; Cascio, A; Nnadi, N E; Cilo, B D; Sampaio, P; Tietz, H-J; Pemán, J; Criseo, G; Romeo, O; Scordino, F

    2016-06-01

    This study aimed to elucidate the genetic relatedness and epidemiology of 127 clinical and environmental Candida glabrata isolates from Europe and Africa using multilocus microsatellite analysis. Each isolate was first identified using phenotypic and molecular methods and subsequently, six unlinked microsatellite loci were analyzed using automated fluorescent genotyping. Genetic relationships were estimated using the minimum-spanning tree (MStree) method. Microsatellite analyses revealed the existence of 47 different genotypes. The fungal population showed an irregular distribution owing to the over-representation of genetically different infectious haplotypes. The most common genotype was MG-9, which was frequently found in both European and African isolates. In conclusion, the data reported here emphasize the role of specific C. glabrata genotypes in human infections for at least some decades and highlight the widespread distribution of some isolates, which seem to be more able to cause disease than others. PMID:26946511

  5. Exploring mechanisms linked to differentiation and function of dimorphic chloroplasts in the single cell C4 species Bienertia sinuspersici

    PubMed Central

    2014-01-01

    Background In the model single-cell C4 plant Bienertia sinuspersici, chloroplast- and nuclear-encoded photosynthetic enzymes, characteristically confined to either bundle sheath or mesophyll cells in Kranz-type C4 leaves, all occur together within individual leaf chlorenchyma cells. Intracellular separation of dimorphic chloroplasts and key enzymes within central and peripheral compartments allow for C4 carbon fixation analogous to NAD-malic enzyme (NAD-ME) Kranz type species. Several methods were used to investigate dimorphic chloroplast differentiation in B. sinuspersici. Results Confocal analysis revealed that Rubisco-containing chloroplasts in the central compartment chloroplasts (CCC) contained more photosystem II proteins than the peripheral compartment chloroplasts (PCC) which contain pyruvate,Pi dikinase (PPDK), a pattern analogous to the cell type-specific chloroplasts of many Kranz type NAD-ME species. Transient expression analysis using GFP fusion constructs containing various lengths of a B. sinuspersici Rubisco small subunit (RbcS) gene and the transit peptide of PPDK revealed that their import was not specific to either chloroplast type. Immunolocalization showed the rbcL-specific mRNA binding protein RLSB to be selectively localized to the CCC in B. sinuspersici, and to Rubisco-containing BS chloroplasts in the closely related Kranz species Suaeda taxifolia. Comparative fluorescence analyses were made using redox-sensitive and insensitive GFP forms, as well comparative staining using the peroxidase indicator 3,3-diaminobenzidine (DAB), which demonstrated differences in stromal redox potential, with the CCC having a more negative potential than the PCC. Conclusions Both CCC RLSB localization and the differential chloroplast redox state are suggested to have a role in post-transcriptional rbcL expression. PMID:24443986

  6. Estimating microsatellite based genetic diversity in Rhode Island Red chicken.

    PubMed

    Das, A K; Kumar, S; Rahim, A

    2015-01-01

    This study aimed to estimate microsatellite based genetic diversity in two lines (the selected RIR(S) and control line RIR(C)) of Rhode Island Red (RIR) chicken. Genomic DNA of 24 randomly selected birds maintained at Central Avian Research Institute (India) and 24 microsatellite markers were used. Microsatellite alleles were determined on 6% urea-PAGE, recorded using GelDoc system and the samples were genotyped. Nei's heterozygosity and Botstein's polymorphic information content (PIC) at each microsatellite locus were estimated. Wright's fixation indices and gene flow were estimated using POPGENE software. All the microsatellite loci were polymorphic and the estimated PIC ranged from 0.3648 (MCW0059) to 0.7819 (ADL0267) in RIR(S) and from 0.2392 (MCW0059) to 0.8620 (ADL0136) in RIR(C). Most of the loci were highly informative (PIC>0.50) in the both lines, except for five loci in RIR(S) and six loci in RIR(C) line. Nei's heterozygosity per locus ranged from 0.4800 (MCW0059) to 0.8056 (ADL0267) in RIR(S) and from 0.2778 (MCW0059) to 0.875 (ADL0136) in RIR(C). Out of 24 loci, 15 (62.5%) in RIR(S) and 14 loci (58.33%) in RIR(C) revealed moderate to high negative FIS index indicating heterozygote excess for these loci in corresponding lines, but the rest revealed positive FIS indicating heterozygosity deficiency. A mean FIS across the both lines indicated overall 10.77% heterozygosity deficit and a mean FIT indicated 17.19% inbreeding co-efficient favoring homozygosity over the two lines. The mean FST indicated that 10.18% of the microsatellite variation between the two lines was due to their genetic difference. PMID:27175188

  7. Chloroplasts as functional organelles in animal tissues.

    PubMed

    Trench, R K; Greene, R W; Bystrom, B G

    1969-08-01

    The marine gastropod molluscs Tridachia crispata, Tridachiella diomedea, and Placobranchus ianthobapsus (Sacoglossa, Opisthobranchia) possess free functional chloroplasts within the cells of the digestive diverticula, as determined by observations on ultrastructure, pigment analyses, and experiments on photosynthetic capacity. In the light, the chloroplasts incorporate H(14)CO(3) (-)in situ. Reduced radiocarbon is translocated to various chloroplast-free tissues in the animals. The slugs feed on siphonaceous algae from which the chloroplasts are derived. Pigments from the slugs and from known siphonaceous algae, when separated chromatographically and compared, showed similar components. Absorption spectra of extracts of slugs and algae were very similar. The larvae of the slugs are pigment-free up to the post-veliger stage, suggesting that chloroplasts are acquired de novo. with each new generation. PMID:5792329

  8. The complete chloroplast genome of Torreya fargesii (Taxaceae).

    PubMed

    Tao, Ke; Gao, Lei; Li, Jia; Chen, Shanshan; Su, Yingjuan; Wang, Ting

    2016-09-01

    The complete chloroplast genome sequence of Torreya fargesii (Taxaceae), a relic plant endemic to China, is presented in this study. The genome is 137 075 bp in length, with 35.47% average GC content. One copy of the large inverted repeats is lost from this genome. The T. fargesii chloroplast genome encodes 118 unique genes, in which trnI-CAU, trnQ-UUG, trnN-GUU are duplicated. Protein-coding, tRNA and rRNA genes represent 54.7%, 1.9% and 3.4% of the genome, respectively. There are 17 intron-containing genes, of which 6 are tRNA genes. A maximum likelihood phylogenetic analysis revealed a strong sister relationship between Torreya and Amentotaxus. PMID:27158868

  9. Mutations in SUPPRESSOR OF VARIEGATION1, a Factor Required for Normal Chloroplast Translation, Suppress var2-Mediated Leaf Variegation in Arabidopsis[W

    PubMed Central

    Yu, Fei; Liu, Xiayan; Alsheikh, Muath; Park, Sungsoon; Rodermel, Steve

    2008-01-01

    The Arabidopsis thaliana yellow variegated2 (var2) mutant is variegated due to lack of a chloroplast FtsH-like metalloprotease (FtsH2/VAR2). We have generated suppressors of var2 variegation to gain insight into factors and pathways that interact with VAR2 during chloroplast biogenesis. Here, we describe two such suppressors. Suppression of variegation in the first line, TAG-FN, was caused by disruption of the nuclear gene (SUPPRESSOR OF VARIEGATION1 [SVR1]) for a chloroplast-localized homolog of pseudouridine (Ψ) synthase, which isomerizes uridine to Ψ in noncoding RNAs. svr1 single mutants were epistatic to var2, and they displayed a phenotypic syndrome that included defects in chloroplast rRNA processing, reduced chloroplast translation, reduced chloroplast protein accumulation, and elevated chloroplast mRNA levels. In the second line (TAG-IE), suppression of variegation was caused by a lesion in SVR2, the gene for the ClpR1 subunit of the chloroplast ClpP/R protease. Like svr1, svr2 was epistatic to var2, and clpR1 mutants had a phenotype that resembled svr1. We propose that an impairment of chloroplast translation in TAG-FN and TAG-IE decreased the demand for VAR2 activity during chloroplast biogenesis and that this resulted in the suppression of var2 variegation. Consistent with this hypothesis, var2 variegation was repressed by chemical inhibitors of chloroplast translation. In planta mutagenesis revealed that SVR1 not only played a role in uridine isomerization but that its physical presence was necessary for proper chloroplast rRNA processing. Our data indicate that defects in chloroplast rRNA processing are a common, but not universal, molecular phenotype associated with suppression of var2 variegation. PMID:18599582

  10. Microsatellite-based genetic diversity patterns in disjunct populations of a rare orchid.

    PubMed

    Pandey, Madhav; Richards, Matt; Sharma, Jyotsna

    2015-12-01

    We investigated the patterns of genetic diversity and structure in seven disjunct populations of a rare North American orchid, Cypripedium kentuckiense by including populations that represented the periphery and the center of the its range. Eight nuclear and two chloroplast microsatellites were used. Genetic diversity was low across the sampled populations of C. kentuckiense based on both nuclear (average An = 4.0, Ho = 0.436, He = 0.448) and cpDNA microsatellites (average An = 1.57, Nh = 1.57 and H = 0.133). The number of private alleles ranged from one to four per population with a total of 17 private alleles detected at five nuclear microsatellites. One private allele at one cpDNA microsatellite was also observed. Although the absolute values for nuclear microsatellite based population differentiation were low (Fst = 0.075; ϕPT = 0.24), they were statistically significant. Pairwise Fst values ranged from 0.038 to 0.123 and each comparison was significant. We also detected isolation by distance with nDNA microsatellites based on the Mantel test (r(2) = 0.209, P = 0.05). STRUCTURE analysis and the neighbor joining trees grouped the populations similarly whereby the geographically proximal populations were genetically similar. Our data indicate that the species is genetically depauperate but the diversity is distributed more or less equally across its range. Population differentiation and isolation by distance were detectable, which indicates that genetic isolation is beginning to manifest itself across the range in this rare species. PMID:26481007

  11. Chloroplast Activity and 3'phosphadenosine 5'phosphate Signaling Regulate Programmed Cell Death in Arabidopsis.

    PubMed

    Bruggeman, Quentin; Mazubert, Christelle; Prunier, Florence; Lugan, Raphaël; Chan, Kai Xun; Phua, Su Yin; Pogson, Barry James; Krieger-Liszkay, Anja; Delarue, Marianne; Benhamed, Moussa; Bergounioux, Catherine; Raynaud, Cécile

    2016-03-01

    Programmed cell death (PCD) is a crucial process both for plant development and responses to biotic and abiotic stress. There is accumulating evidence that chloroplasts may play a central role during plant PCD as for mitochondria in animal cells, but it is still unclear whether they participate in PCD onset, execution, or both. To tackle this question, we have analyzed the contribution of chloroplast function to the cell death phenotype of the myoinositol phosphate synthase1 (mips1) mutant that forms spontaneous lesions in a light-dependent manner. We show that photosynthetically active chloroplasts are required for PCD to occur in mips1, but this process is independent of the redox state of the chloroplast. Systematic genetic analyses with retrograde signaling mutants reveal that 3'-phosphoadenosine 5'-phosphate, a chloroplast retrograde signal that modulates nuclear gene expression in response to stress, can inhibit cell death and compromises plant innate immunity via inhibition of the RNA-processing 5'-3' exoribonucleases. Our results provide evidence for the role of chloroplast-derived signal and RNA metabolism in the control of cell death and biotic stress response. PMID:26747283

  12. Rapid Mass Movement of Chloroplasts during Segment Formation of the Calcifying Siphonalean Green Alga, Halimeda macroloba

    PubMed Central

    Larkum, Anthony W. D.; Salih, Anya; Kühl, Michael

    2011-01-01

    Background The calcifying siphonalean green alga, Halimeda macroloba is abundant on coral reefs and is important in the production of calcium carbonate sediments. The process by which new green segments are formed over-night is revealed here for the first time. Methodology/Principal Findings Growth of new segments was visualised by epifluorescence and confocal microscopy and by pulse amplitude modulation (PAM) fluorimetry. Apical colourless proto-segments were initiated on day 1, and formed a loose network of non-calcified, non-septate filaments, containing no chloroplasts. Rapid greening was initiated at dusk by i) the mass movement of chloroplasts into these filaments from the parent segment and ii) the growth of new filaments containing chloroplasts. Greening was usually complete in 3–5 h and certainly before dawn on day 2 when the first signs of calcification were apparent. Mass chloroplast movement took place at a rate of ∼0.65 µm/s. Photosynthetic yield and rate remained low for a period of 1 to several hours, indicating that the chloroplasts were made de novo. Use of the inhibitors colchicine and cytochalasin d indicated that the movement process is dependent on both microtubules and microfilaments. Significance This unusual process involves the mass movement of chloroplasts at a high rate into new segments during the night and rapid calcification on the following day and may be an adaptation to minimise the impact of herbivorous activity. PMID:21750703

  13. Rust fungal effectors mimic host transit peptides to translocate into chloroplasts.

    PubMed

    Petre, Benjamin; Lorrain, Cécile; Saunders, Diane G O; Win, Joe; Sklenar, Jan; Duplessis, Sébastien; Kamoun, Sophien

    2016-04-01

    Parasite effector proteins target various host cell compartments to alter host processes and promote infection. How effectors cross membrane-rich interfaces to reach these compartments is a major question in effector biology. Growing evidence suggests that effectors use molecular mimicry to subvert host cell machinery for protein sorting. We recently identified chloroplast-targeted protein 1 (CTP1), a candidate effector from the poplar leaf rust fungus Melampsora larici-populina that carries a predicted transit peptide and accumulates in chloroplasts and mitochondria. Here, we show that the CTP1 transit peptide is necessary and sufficient for accumulation in the stroma of chloroplasts. CTP1 is part of a Melampsora-specific family of polymorphic secreted proteins. Two members of that family, CTP2 and CTP3, also translocate in chloroplasts in an N-terminal signal-dependent manner. CTP1, CTP2 and CTP3 are cleaved when they accumulate in chloroplasts, while they remain intact when they do not translocate into chloroplasts. Our findings reveal that fungi have evolved effector proteins that mimic plant-specific sorting signals to traffic within plant cells. PMID:26426202

  14. Incongruence between Nuclear and Chloroplast DNA Phylogenies in Pedicularis Section Cyathophora (Orobanchaceae)

    PubMed Central

    Yu, Wen-Bin; Huang, Pan-Hui; Li, De-Zhu; Wang, Hong

    2013-01-01

    Pedicularis section Cyathophora is a monophyletic group characterized by perfoliate leaf and/or bract bases at each node. This section comprises four series, corresponding to four general corolla types of Pedicularis, i.e. toothless, toothed, beaked and long-tubed corollas. In this study, we aim to reconstruct a comprehensive phylogeny of section Cyathophora, and compare phylogenetic incongruence between nuclear and chloroplast datasets. Sixty-seven accessions belonging to section Cyathophora and 9 species for other Pedicularis were sampled, and one nuclear gene (nrITS) and four chloroplast genes (matK, rbcL, trnH-psbA and trnL-F) were sequenced. Phylogenetic analyses show that the topologies and networks inferred from nrITS and the concatenated chloroplast datasets were incongruent, and the nrITS phylogenies and network agreed with the morphology-based taxonomy to some degree. The chloroplast genome of two Sichuan samples of P. cyathophylloides (E4 and E5) may show introgression from an ancestor of P. cyathophylla. Neither the nrITS dataset nor the concatenated chloroplast dataset were able to adequately resolve relationships among species in the series Reges; this is most likely due to incomplete lineage sorting and/or introgression/hybridization. The nrITS phylogeny indicates the beakless (toothed and toothless) and beaked galeas may have evolved independently within section Cyathophora, and the chloroplast phylogeny reveals that the long corolla tube with beaked galea is derived from the short one. PMID:24069353

  15. Microsatellite instability in adenocarcinoma of the prostrate

    SciTech Connect

    Terrell, R.B.; Willie, A.H.; Cheville, J.C.

    1994-09-01

    Instability of tandem repeat sequences (microsatellites) has been reported to play a major etiologic role in familial colon cancer, as well as a potential role in the carcinogenesis of other sporadic neoplasms. These replication errors are the result of faulty DNA excision/repair function controlled at the gene level. In order to examine this phenomenon in prostate cancer, we screened 40 tumors with di-, tri- and tetranucleotide markers spanning eleven chromosomal loci. Microsatellite instability was observed overall in 3 of the 40 cases (7.5%). All changes were identified solely in tetranucleotide sequences (3 of 11 total markers analyzed). One tumor demonstrated repeat length expansions at two loci, while the other tumors did so at a single locus. Both Type 1 (>4 base pairs) and Type II (4 base pairs) mutations were identified. One of these cases also included metastatic nodal disease. Analysis of the metastatic tumor tissue revealed allelic patterns identical to the normal tissue control. A secondary screening of the mutated tumors demonstrated no repeat length alterations in 16 additional markers. A CAG repeat in the androgen receptor (AR) gene was also studied and demonstrated that 3 of 40 (7.5%) tumors contained mutations within this repeat. We concluded that microsatellite instability is uncommon in prostate adenocarcinoma appearing to occur more often in tetranucleotide repeat sequences and in an AR gene repeat. Additionally, these findings suggest that dysfunctional DNA excision/repair mechanisms, as evidenced by the low frequency of replication errors, are unlikely to play a major role in the natural history of prostate cancer.

  16. Characterization of novel microsatellites from Drosophila transversa.

    PubMed

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

    2009-03-01

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

  17. Plastidic Isoprenoid Synthesis during Chloroplast Development 1

    PubMed Central

    Heintze, Adolf; Görlach, Jörn; Leuschner, Carola; Hoppe, Petra; Hagelstein, Petra; Schulze-Siebert, Detlef; Schultz, Gernot

    1990-01-01

    The chloroplast isoprenoid synthesis of very young leaves is supplied by the plastidic CO2 → pyruvate → acetyl-coenzyme A (C3 → C2) metabolism (D Schulze-Siebert, G Schultz [1987] Plant Physiol 84: 1233-1237) and occurs via the plastidic mevalonate pathway. The plastidic C3 → C2 metabolism and/or plastidic mevalonate pathway of barley (Hordeum vulgare L.) seedlings changes from maximal activity at the leaf base (containing developing chloroplasts with incomplete thylakoid stacking but a considerable rate of photosynthetic CO2-fixation) almost to ineffectivity at the leaf tip (containing mature chloroplasts with maximal photosynthetic activity). The ability to import isopentenyl diphosphate from the extraplastidic space gradually increases to substitute for the loss of endogenous intermediate supply for chloroplast isoprenoid synthesis (change from autonomic to division-of-labor stage). Fatty acid synthesis from NaH14CO3 decreases in the same manner as shown for leaf sections and chloroplasts isolated from these. Evidence has been obtained for a drastic decrease of pyruvate decarboxylase-dehydrogenase activity during chloroplast development compared with other anabolic chloroplast pathways (synthesis of aromatic amino acid and branched chain amino acids). The noncompetition of pyruvate and acetate in isotopic dilution studies indicates that both a pyruvate-derived and an acetate-derived compound are simultaneously needed to form introductory intermediates of the mevalonate pathway, presumably acetoacetyl-coenzyme A. PMID:16667567

  18. Blueberry Microsatellite Markers Identify Cranberries

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Forty-six blueberry simple sequence repeat (SSR) markers or microsatellites were tested for the ability to amplify a polymorphic marker in eight American cranberry accessions. Sixteen SSRs resulted in informative and polymorphic SSR primer pairs and were used to fingerprint 16 economically important...

  19. Microsatellites from Conyza canadensis (horseweed)

    Technology Transfer Automated Retrieval System (TEKTRAN)

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

  20. The complexity of chloroplast chaperonins.

    PubMed

    Vitlin Gruber, Anna; Nisemblat, Shahar; Azem, Abdussalam; Weiss, Celeste

    2013-12-01

    Type I chaperonins are large oligomeric protein ensembles that are involved in the folding and assembly of other proteins. Chloroplast chaperonins and co-chaperonins exist in multiple copies of two distinct isoforms that can combine to form a range of labile oligomeric structures. This complex system increases the potential number of chaperonin substrates and possibilities for regulation. The incorporation of unique subunits into the oligomer can modify substrate specificity. Some subunits are upregulated in response to heat shock and some show organ-specific expression, whereas others possess additional functions that are unrelated to their role in protein folding. Accumulating evidence suggests that specific subunits have distinct roles in biogenesis of ribulose-1,5-bisphosphate carboxylase oxygenase (Rubisco). PMID:24035661

  1. Evolution and homoplasy at the Bem6 microsatellite locus in three sweetpotato whitefly (Bemisia tabaci) cryptic species

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The evolution of individual microsatellite loci is often complex and homoplasy is common but often goes undetected. Sequencing alleles at a microsatellite locus can provide a more complete picture of the common evolutionary mechanisms occurring at that locus and can reveal cases of homoplasy. Within...

  2. Chloroplast diversity in a putative hybrid swarm of Ponderosae (Pinaceae).

    PubMed

    Epperson, Bryan K; Telewski, Frank W; Willyard, Ann

    2009-03-01

    The Ponderosae subsection of the genus Pinus contains numerous taxa in disjunct mountain ranges of southern Arizona and New Mexico, differing for several leaf and cone traits, key among which is the number of leaf needles per fascicle. Trees with three needles are often found together with trees having five needles and mixed numbers. One taxonomic hypothesis is that there are swarms of hybrids between P. ponderosa and P. arizonica. A second hypothesis is that there are spatial mixtures of two separate taxa, five-needle P. arizonica and a "taxon X" containing three needle and mixed needle trees. We genotyped chloroplasts in one putative hybrid swarm on Mt. Lemmon using microsatellite markers and show that cpDNA is almost completely differentiated between two separate morphotypes corresponding to P. arizonica and "taxon X." Little if any introgression has occurred on Mt. Lemmon, and the simplest explanation is that little or no effective hybridization has occurred. Further results indicate that not only is taxon X not of hybrid origin, it is more closely related to nonregional Ponderosae other than P. ponderosa and P. arizonica. The results further suggest that other putative hybrid swarms in the region are also spatial mixtures of distinct taxa. PMID:21628225

  3. Plastome Mutations and Recombination Events in Barley Chloroplast Mutator Seedlings.

    PubMed

    Landau, Alejandra; Lencina, Franco; Pacheco, María G; Prina, Alberto R

    2016-05-01

    The barley chloroplast mutator (cpm) is an allele of a nuclear gene that when homozygous induces several types of cytoplasmically inherited chlorophyll deficiencies. In this work, a plastome Targeting Induced Local Lesions in Genomes (TILLING) strategy based on mismatch digestion was used on families that carried the cpm genotype through many generations. Extensive scanning of 33 plastome genes and a few intergenic regions was conducted. Numerous polymorphisms were detected on both genic and intergenic regions. The detected polymorphisms can be accounted for by at least 61 independent mutational events. The vast majority of the polymorphisms originated in substitutions and small indels (insertions/deletions) in microsatellites. The rpl23 and the rps16 genes were the most polymorphic. Interestingly, the variation observed in the rpl23 gene consisted of several combinations of 5 different one nucleotide polymorphisms. Besides, 4 large indels that have direct repeats at both ends were also observed, which appear to be originated from recombinational events. The cpm mutation spectrum suggests that the CPM gene product is probably involved in plastome mismatch repair. The numerous subtle molecular changes that were localized in a wide range of plastome sites show the cpm as a valuable source of plastome variability for plant research and/or plant breeding. Moreover, the cpm mutant appears to be an interesting experimental material for investigating the mechanisms responsible for maintaining the stability of plant organelle DNA. PMID:26774059

  4. ISOLATION AND CHARACTERIZATION OF 15 MICROSATELLITE LOCI FOR Ophicephalus argus Cantor.

    PubMed

    Xiao, M; Xia, H; Bao, F

    2015-10-01

    The isolation and development of 15 polymorphic dinucleotide microsatellite loci were described for Ophicephalus argus from the Huaihe River. All loci were polymorphic in the 30 individuals tested. The number of alleles per variable locus ranged from nine to seventeen, with a mean of 12.00. These novel microsatellite loci showed high level of polymorphism. Observed and expected heterozygosities ranged from 0.793 to 0.929 and from 0.841 to 0.952, respectively. Two loci were found deviated from HWE in the sampled population after Bonferroni correction. These microsatellite loci will be useful for revealing population structure, genetic diversity, and phylogeography of Ophicephalus argus. PMID:27169238

  5. Characterization of microsatellite DNA markers for the alligator snapping turtle, Macrochelys temminckii: Primer note

    USGS Publications Warehouse

    Hackler, J.C.; Van Den Bussche, Ronald A.; Leslie, David M., Jr.

    2007-01-01

    Two trinucleotide and seven tetranucleotide microsatellite loci were isolated from an alligator snapping turtle Macrochelys temminckii. To assess the degree of variability in these nine microsatellite loci, we genotyped 174 individuals collected from eight river drainage basins in the southeastern USA. These markers revealed a moderate degree of allelic diversity (six to 16 alleles per locus) and observed heterozygosity (0.166-0.686). These polymorphic microsatellite loci provide powerful tools for population genetic studies for a species that is afforded some level of conservation protection in every state in which it occurs. ?? 2006 The Authors.

  6. Chloroplasts at work during plant innate immunity.

    PubMed

    Serrano, Irene; Audran, Corinne; Rivas, Susana

    2016-06-01

    The major role played by chloroplasts during light harvesting, energy production, redox homeostasis, and retrograde signalling processes has been extensively characterized. Beyond the obvious link between chloroplast functions in primary metabolism and as providers of photosynthesis-derived carbon sources and energy, a growing body of evidence supports a central role for chloroplasts as integrators of environmental signals and, more particularly, as key defence organelles. Here, we review the importance of these organelles as primary sites for the biosynthesis and transmission of pro-defence signals during plant immune responses. In addition, we highlight interorganellar communication as a crucial process for amplification of the immune response. Finally, molecular strategies used by microbes to manipulate, directly or indirectly, the production/function of defence-related signalling molecules and subvert chloroplast-based defences are also discussed. PMID:26994477

  7. Solar energy conversion by chloroplast photoelectrochemical cells

    NASA Astrophysics Data System (ADS)

    Bhardwaj, R.; Pan, R. L.; Gross, E. L.

    1981-01-01

    A photoelectrochemical cell based on chloroplasts which generates large photovoltages and photocurrents from solar energy is presented. The cell contains broken Type C chloroplasts placed on a filter separating compartments containing an electron acceptor and electron donor with platinum electrodes in each. Photovoltages were observed across a load resistance of 3000 ohms with either flavin mononucleotide or anthroquinone 2-sulphonate as the electron acceptor and dichlorophenol indophenol as the donor, and persisted for 1-2 hr after the light was turned off. The powers and short circuit currents obtained in the chloroplast cells are nearly equal to those obtained in cells based on isolated photosystem I particles. Finally, an efficiency of 2.3% has been measured for the chloroplast contribution to the total power in flavin mononucleotide cells.

  8. Transposon-induced nuclear mutations that alter chloroplast gene expression. Annual report, September 1, 1991--August 31, 1992

    SciTech Connect

    Barkan, A.

    1992-12-31

    The goal of this project is to use mutant phenotypes as a guide to nuclear genes that determine the timing and localization of chloroplast development The immediate goals are to identify nuclear mutants with defects in chloroplast gene expression from maize lines harboring active Mu transposons; characterize their phenotypes to determine the precise defect in gene expression; clone several of the most interesting mutations by exploiting the transposon tag; and use the clones to further define the roles of these genes in modulating chloroplast gene expression. Three mutants were described earlier that had global defects in chloroplast gene expression. We have found that two of these mutations are allelic. Both alleles have global defects in chloroplast translation initiation, as revealed by the failure to assemble chloroplast mRNAs into polysomes. We have isolated and characterized three new mutants from Mu lines that have novel defects in chloroplast RNA metabolism. We are now ready to begin the task of cloning several of these genes, by using the Mu transposon tag.

  9. Transient foreign gene expression in chloroplasts of cultured tobacco cells after biolistic delivery of chloroplast vectors.

    PubMed Central

    Daniell, H; Vivekananda, J; Nielsen, B L; Ye, G N; Tewari, K K; Sanford, J C

    1990-01-01

    Expression of chloramphenicol acetyltransferase (cat) by suitable vectors in chloroplasts of cultured tobacco cells, delivered by high-velocity microprojectiles, is reported here. Several chloroplast expression vectors containing bacterial cat genes, placed under the control of either psbA promoter region from pea (pHD series) or rbcL promoter region from maize (pAC series) have been used in this study. In addition, chloroplast expression vectors containing replicon fragments from pea, tobacco, or maize chloroplast DNA have also been tested for efficiency and duration of cat expression in chloroplasts of tobacco cells. Cultured NT1 tobacco cells collected on filter papers were bombarded with tungsten particles coated with pUC118 (negative control), 35S-CAT (nuclear expression vector), pHD312 (repliconless chloroplast expression vector), and pHD407, pACp18, and pACp19 (chloroplast expression vectors with replicon). Sonic extracts of cells bombarded with pUC118 showed no detectable cat activity in the autoradiograms. Nuclear expression of cat reached two-thirds of the maximal 48 hr after bombardment and the maximal at 72 hr. Cells bombarded with chloroplast expression vectors showed a low level of expression until 48 hr of incubation. A dramatic increase in the expression of cat was observed 24 hr after the addition of fresh medium to cultured cells in samples bombarded with pHD407; the repliconless vector pHD312 showed about 50% of this maximal activity. The expression of nuclear cat and the repliconless chloroplast vector decreased after 72 hr, but a high level of chloroplast cat expression was maintained in cells bombarded with pHD407. Organelle-specific expression of cat in appropriate compartments was checked by introducing various plasmid constructions into tobacco protoplasts by electroporation. Although the nuclear expression vector 35S-CAT showed expression of cat, no activity was observed with any chloroplast vectors. Images PMID:2404285

  10. Indications for Three Independent Domestication Events for the Tea Plant (Camellia sinensis (L.) O. Kuntze) and New Insights into the Origin of Tea Germplasm in China and India Revealed by Nuclear Microsatellites

    PubMed Central

    Meegahakumbura, M. K.; Wambulwa, M. C.; Thapa, K. K.; Li, M. M.; Möller, M.; Xu, J. C.; Yang, J. B.; Liu, B. Y.; Ranjitkar, S.; Liu, J.; Li, D. Z.; Gao, L. M.

    2016-01-01

    Background Tea is the world’s most popular non-alcoholic beverage. China and India are known to be the largest tea producing countries and recognized as the centers for the domestication of the tea plant (Camellia sinensis (L.) O. Kuntze). However, molecular studies on the origin, domestication and relationships of the main teas, China type, Assam type and Cambod type are lacking. Methodology/Principal Findings Twenty-three nuclear microsatellite markers were used to investigate the genetic diversity, relatedness, and domestication history of cultivated tea in both China and India. Based on a total of 392 samples, high levels of genetic diversity were observed for all tea types in both countries. The cultivars clustered into three distinct genetic groups (i.e. China tea, Chinese Assam tea and Indian Assam tea) based on STRUCTURE, PCoA and UPGMA analyses with significant pairwise genetic differentiation, corresponding well with their geographical distribution. A high proportion (30%) of the studied tea samples were shown to possess genetic admixtures of different tea types suggesting a hybrid origin for these samples, including the Cambod type. Conclusions We demonstrate that Chinese Assam tea is a distinct genetic lineage from Indian Assam tea, and that China tea sampled from India was likely introduced from China directly. Our results further indicate that China type tea, Chinese Assam type tea and Indian Assam type tea are likely the result of three independent domestication events from three separate regions across China and India. Our findings have important implications for the conservation of genetic stocks, as well as future breeding programs. PMID:27218820