chloroplast dna


Summary: Deoxyribonucleic acid that makes up the genetic material of CHLOROPLASTS.

Top Publications

  1. Wang L, Abbott R, Zheng W, Chen P, Wang Y, Liu J. History and evolution of alpine plants endemic to the Qinghai-Tibetan Plateau: Aconitum gymnandrum (Ranunculaceae). Mol Ecol. 2009;18:709-21 pubmed publisher
    ..Here, we report a survey of chloroplast DNA (cpDNA) and nuclear ribosomal internal transcribed spacer (ITS) DNA variation aimed at exploring the ..
  2. Minami M, Nishio K, Ajioka Y, Kyushima H, Shigeki K, Kinjo K, et al. Identification of Curcuma plants and curcumin content level by DNA polymorphisms in the trnS-trnfM intergenic spacer in chloroplast DNA. J Nat Med. 2009;63:75-9 pubmed publisher
    ..accurate plant identification method, molecular analysis based on polymorphisms of the nucleotide sequence of chloroplast DNA (cpDNA) was performed in order to distinguish four Curcuma species: C. longa, C. aromatica, C...
  3. Su Y, Smith G, Saunders R. Phylogeny of the basal angiosperm genus Pseuduvaria (Annonaceae) inferred from five chloroplast DNA regions, with interpretation of morphological character evolution. Mol Phylogenet Evol. 2008;48:188-206 pubmed publisher
    ..relationships within the magnoliid basal angiosperm genus Pseuduvaria (Annonaceae) are investigated using chloroplast DNA sequences from five regions: psbA-trnH spacer, trnL-F, matK, rbcL, and atpB-rbcL spacer...
  4. Saski C, Lee S, Fjellheim S, Guda C, Jansen R, Luo H, et al. Complete chloroplast genome sequences of Hordeum vulgare, Sorghum bicolor and Agrostis stolonifera, and comparative analyses with other grass genomes. Theor Appl Genet. 2007;115:571-90 pubmed
    ..Phylogenetic trees based on DNA sequences of 61 protein-coding genes of 38 taxa using both maximum parsimony and likelihood methods provide moderate support for a sister relationship between the subfamilies Erhartoideae and Pooideae...
  5. Yang F, Li Y, Ding X, Wang X. Extensive population expansion of Pedicularis longiflora (Orobanchaceae) on the Qinghai-Tibetan Plateau and its correlation with the Quaternary climate change. Mol Ecol. 2008;17:5135-45 pubmed publisher
    ..The possible relationships among geographic genetic structure, climatic change and species diversification in Pedicularis are also discussed...
  6. Wang Y, Li X, Guo J, Guo Z, Li S, Zhao G. Chloroplast DNA phylogeography of Clintoniaudensis Trautv. & Mey. (Liliaceae) in East Asia. Mol Phylogenet Evol. 2010;55:721-32 pubmed publisher
    ..amp; Mey. (Liliaceae) inferred from two types of chloroplast DNA markers, polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) and DNA sequences...
  7. Dobes C, Paule J. A comprehensive chloroplast DNA-based phylogeny of the genus Potentilla (Rosaceae): implications for its geographic origin, phylogeography and generic circumscription. Mol Phylogenet Evol. 2010;56:156-75 pubmed publisher
    A reconstruction of phylogenetic relationships based on three chloroplast DNA markers comprising 98 species of the genus Potentilla and 15 additional genera from the tribe Potentilleae (Rosaceae) is presented...
  8. Hirao T, Watanabe A, Kurita M, Kondo T, Takata K. Complete nucleotide sequence of the Cryptomeria japonica D. Don. chloroplast genome and comparative chloroplast genomics: diversified genomic structure of coniferous species. BMC Plant Biol. 2008;8:70 pubmed publisher
  9. Barthet M, Hilu K. Evaluating evolutionary constraint on the rapidly evolving gene matK using protein composition. J Mol Evol. 2008;66:85-97 pubmed
    ..The results of this study demonstrate evolutionary constraint on MATK, identify three regions of functional importance, show highly conserved secondary structure, and support the putative function of MATK as a group II intron maturase. ..

More Information


  1. Wang R, Cheng C, Chang C, Wu C, Su T, Chaw S. Dynamics and evolution of the inverted repeat-large single copy junctions in the chloroplast genomes of monocots. BMC Evol Biol. 2008;8:36 pubmed publisher
    ..Further study is needed to unravel the evolutionary significance of IR expansion in more recently diverged monocots...
  2. Muir G, Filatov D. A selective sweep in the chloroplast DNA of dioecious silene (section Elisanthe). Genetics. 2007;177:1239-47 pubmed
    ..genes compared to Y-linked and autosomal genes suggest that intra- and inter-specific subdivision in the chloroplast DNA may have been eroded by a selective sweep that has crossed the S. latifolia and S. dioica species boundary.
  3. Fehrer J, Gemeinholzer B, Chrtek J, Bräutigam S. Incongruent plastid and nuclear DNA phylogenies reveal ancient intergeneric hybridization in Pilosella hawkweeds (Hieracium, Cichorieae, Asteraceae). Mol Phylogenet Evol. 2007;42:347-61 pubmed
    ..These chloroplast capture events, the first of which involved a now extinct haplotype, are the most likely explanation for the observed incongruencies between plastid and nuclear DNA markers. ..
  4. Koch M, Dobes C, Kiefer C, Schmickl R, Klimes L, Lysak M. Supernetwork identifies multiple events of plastid trnF(GAA) pseudogene evolution in the Brassicaceae. Mol Biol Evol. 2007;24:63-73 pubmed
    ..The phylogenetic distribution of microstructural changes for the trnL-F region supports ancient patterns of divergence in crucifer evolution for some but not all gene loci. ..
  5. Bausher M, Singh N, Lee S, Jansen R, Daniell H. The complete chloroplast genome sequence of Citrus sinensis (L.) Osbeck var 'Ridge Pineapple': organization and phylogenetic relationships to other angiosperms. BMC Plant Biol. 2006;6:21 pubmed
    ..Phylogenetic analyses resolve relationships among several major clades of angiosperms and provide strong support for the monophyly of the eurosid II clade and the position of the Sapindales sister to the Brassicales/Malvales. ..
  6. Sheppard A, Ayliffe M, Blatch L, Day A, Delaney S, Khairul Fahmy N, et al. Transfer of plastid DNA to the nucleus is elevated during male gametogenesis in tobacco. Plant Physiol. 2008;148:328-36 pubmed publisher
    ..The results suggest a new explanation for the occurrence of uniparental inheritance in eukaryotes. ..
  7. Fazekas A, Burgess K, Kesanakurti P, Graham S, Newmaster S, Husband B, et al. Multiple multilocus DNA barcodes from the plastid genome discriminate plant species equally well. PLoS ONE. 2008;3:e2802 pubmed publisher
  8. de Cambiaire J, Otis C, Lemieux C, Turmel M. The complete chloroplast genome sequence of the chlorophycean green alga Scenedesmus obliquus reveals a compact gene organization and a biased distribution of genes on the two DNA strands. BMC Evol Biol. 2006;6:37 pubmed
    ..The five complete chloroplast DNA (cpDNA) sequences currently available for representatives of these classes display considerable variability ..
  9. Drouin G, Daoud H, Xia J. Relative rates of synonymous substitutions in the mitochondrial, chloroplast and nuclear genomes of seed plants. Mol Phylogenet Evol. 2008;49:827-31 pubmed publisher
  10. Jaffé B, Kovacs K, Andras C, Bodi Z, Liu Z, Fray R. Methylation of chloroplast DNA does not affect viability and maternal inheritance in tobacco and may provide a strategy towards transgene containment. Plant Cell Rep. 2008;27:1377-84 pubmed publisher
  11. Leong Pock Tsy J, Lumaret R, Mayne D, Vall A, Abutaba Y, Sagna M, et al. Chloroplast DNA phylogeography suggests a West African centre of origin for the baobab, Adansonia digitata L. (Bombacoideae, Malvaceae). Mol Ecol. 2009;18:1707-15 pubmed publisher
    ..We analysed the polymerase chain reaction-restriction fragment length polymorphism of five chloroplast DNA fragments obtained from 344 individuals of A...
  12. Kim Y, Park C, Kim K. Complete chloroplast DNA sequence from a Korean endemic genus, Megaleranthis saniculifolia, and its evolutionary implications. Mol Cells. 2009;27:365-81 pubmed publisher
    The chloroplast DNA sequences of Megaleranthis saniculifolia, an endemic and monotypic endangered plant species, were completed in this study (GenBank FJ597983). The genome is 159,924 bp in length...
  13. Shimizu Inatsugi R, Lihová J, Iwanaga H, Kudoh H, Marhold K, Savolainen O, et al. The allopolyploid Arabidopsis kamchatica originated from multiple individuals of Arabidopsis lyrata and Arabidopsis halleri. Mol Ecol. 2009;18:4024-48 pubmed publisher
    ..The haplotypes of low-copy nuclear genes in Japan suggest independent polyploidization events rather than introgression. Our findings suggest that self-compatibility and gene silencing occurred independently in different origins...
  14. Jaramillo Correa J, Beaulieu J, Ledig F, Bousquet J. Decoupled mitochondrial and chloroplast DNA population structure reveals Holocene collapse and population isolation in a threatened Mexican-endemic conifer. Mol Ecol. 2006;15:2787-800 pubmed
    ..Additional mtDNA sequence analysis confirmed that P. martinezii (Patterson) is not conspecific with P. chihuahuana, and thus deserves separate conservation efforts. ..
  15. Kahlau S, Aspinall S, Gray J, Bock R. Sequence of the tomato chloroplast DNA and evolutionary comparison of solanaceous plastid genomes. J Mol Evol. 2006;63:194-207 pubmed publisher
    ..Comparison of the two genotypes (IPA-6, bred in South America, and Ailsa Craig, bred in Europe) revealed no nucleotide differences, suggesting that the plastomes of modern tomato cultivars display very little, if any, sequence variation...
  16. Kumagai M, Wang L, Ueda S. Genetic diversity and evolutionary relationships in genus Oryza revealed by using highly variable regions of chloroplast DNA. Gene. 2010;462:44-51 pubmed publisher
    We studied the phylogeny of the genus Oryza using chloroplast DNA sequences...
  17. Turmel M, Otis C, Lemieux C. The chloroplast genome sequence of Chara vulgaris sheds new light into the closest green algal relatives of land plants. Mol Biol Evol. 2006;23:1324-38 pubmed
    ..Analyses of genome rearrangements based on inversions predicted no alteration in gene order during the transition from charophycean green algae to land plants...
  18. Heinrichs J, Hentschel J, Bombosch A, Fiebig A, Reise J, Edelmann M, et al. One species or at least eight? Delimitation and distribution of Frullania tamarisci (L.) Dumort. s. l. (Jungermanniopsida, Porellales) inferred from nuclear and chloroplast DNA markers. Mol Phylogenet Evol. 2010;56:1105-14 pubmed publisher
    ..Our findings support frequent short-distance migration, rare successful long-distance dispersal events, extinction and recolonization as an explanation for the range formation in these Frullania species...
  19. Bendich A. Mitochondrial DNA, chloroplast DNA and the origins of development in eukaryotic organisms. Biol Direct. 2010;5:42 pubmed publisher
    ..One of the biochemical properties required for stemness to emerge from a population of cells might be the metabolic quiescence that protects organellar DNA from oxidative stress. ..
  20. Roark L, Hui A, Donnelly L, Birchler J, Newton K. Recent and frequent insertions of chloroplast DNA into maize nuclear chromosomes. Cytogenet Genome Res. 2010;129:17-23 pubmed publisher
    ..We have examined chloroplast DNA insertions in maize chromosomes using fluorescence in situ hybridization (FISH)...
  21. Minnhagen S, Carvalho W, Salomon P, Janson S. Chloroplast DNA content in Dinophysis (Dinophyceae) from different cell cycle stages is consistent with kleptoplasty. Environ Microbiol. 2008;10:2411-7 pubmed publisher
    ..Together these findings strongly suggest that D. norvegica does not possess the ability for plastid replication. ..
  22. Erixon P, Oxelman B. Reticulate or tree-like chloroplast DNA evolution in Sileneae (Caryophyllaceae)?. Mol Phylogenet Evol. 2008;48:313-25 pubmed publisher
    Despite sampling of up to 25kb of chloroplast DNA sequence from 24 species in Sileneae a number of nodes in the phylogeny remain poorly supported and it is not expected that additional sequence sampling will converge to a reliable ..
  23. Jansen R, Kaittanis C, Saski C, Lee S, Tomkins J, Alverson A, et al. Phylogenetic analyses of Vitis (Vitaceae) based on complete chloroplast genome sequences: effects of taxon sampling and phylogenetic methods on resolving relationships among rosids. BMC Evol Biol. 2006;6:32 pubmed
    ..We sequenced the complete chloroplast genome of Vitis vinifera and used these data to assess relationships among 27 angiosperms, including nine taxa of rosids...
  24. Guo X, Ruan S, Hu W, Cai D, Fan L. Chloroplast DNA insertions into the nuclear genome of rice: the genes, sites and ages of insertion involved. Funct Integr Genomics. 2008;8:101-8 pubmed
    ..In this study, a total of 45 chloroplast DNA insertions more than 2 kb in length were detected in rice nuclear genome...
  25. Taberlet P, Coissac E, Pompanon F, Gielly L, Miquel C, Valentini A, et al. Power and limitations of the chloroplast trnL (UAA) intron for plant DNA barcoding. Nucleic Acids Res. 2007;35:e14 pubmed
  26. Frajman B, Oxelman B. Reticulate phylogenetics and phytogeographical structure of Heliosperma (Sileneae, Caryophyllaceae) inferred from chloroplast and nuclear DNA sequences. Mol Phylogenet Evol. 2007;43:140-55 pubmed
    ..The morphological differentiation into high elevation, mainly widely distributed taxa, and low elevation narrow endemics is not correlated with the molecular data, and is possibly a result of ecological differentiation...
  27. Robbens S, Derelle E, Ferraz C, Wuyts J, Moreau H, Van de Peer Y. The complete chloroplast and mitochondrial DNA sequence of Ostreococcus tauri: organelle genomes of the smallest eukaryote are examples of compaction. Mol Biol Evol. 2007;24:956-68 pubmed
    ..Phylogenetic analyses based on a concatenated alignment of cp, mt, and nuclear genes confirm the position of O. tauri within the Prasinophyceae, an early branch of the Chlorophyta. ..
  28. Natcheva R, Cronberg N. Recombination and introgression of nuclear and chloroplast genomes between the peat mosses, Sphagnum capillifolium and Sphagnum quinquefarium. Mol Ecol. 2007;16:811-8 pubmed
    ..Further evolutionary and phylogenetic consequences of restricted interspecific gene exchange are discussed. ..
  29. Lee H, Jansen R, Chumley T, Kim K. Gene relocations within chloroplast genomes of Jasminum and Menodora (Oleaceae) are due to multiple, overlapping inversions. Mol Biol Evol. 2007;24:1161-80 pubmed
    ..However, their genome organization is surprisingly similar despite the distant relationship of these 2 angiosperm families...
  30. Van Droogenbroeck B, Kyndt T, Romeijn Peeters E, Van Thuyne W, Goetghebeur P, Romero motochi J, et al. Evidence of natural hybridization and introgression between Vasconcellea species (Caricaceae) from southern Ecuador revealed by chloroplast, mitochondrial and nuclear DNA markers. Ann Bot. 2006;97:793-805 pubmed
    ..The aim of this paper is to examine individuals of these three taxa and of individuals from the closely related species V. parviflora and V. weberbaueri, which all inhabit a hybrid zone in southern Ecuador...
  31. Jaramillo Correa J, Aguirre Planter E, Khasa D, Eguiarte L, Piñero D, Furnier G, et al. Ancestry and divergence of subtropical montane forest isolates: molecular biogeography of the genus Abies (Pinaceae) in southern México and Guatemala. Mol Ecol. 2008;17:2476-90 pubmed publisher
    ..In contrast, variation at three paternally inherited chloroplast DNA microsatellites was high. Chloroplast genetic differentiation was lower (G(ST) = 0.402; R(ST) = 0...
  32. Wills D, Burke J. Chloroplast DNA variation confirms a single origin of domesticated sunflower (Helianthus annuus L.). J Hered. 2006;97:403-8 pubmed
  33. Hosaka K, Sanetomo R. Comparative differentiation in mitochondrial and chloroplast DNA among cultivated potatoes and closely related wild species. Genes Genet Syst. 2009;84:371-8 pubmed
    ..accessions of seven cultivated and 32 wild potato species previously characterized by nuclear DNA (nDNA) and chloroplast DNA (ctDNA) marker analyses were employed to the mitochondrial DNA (mtDNA) marker analysis...
  34. Palma Silva C, Lexer C, Paggi G, Barbara T, Bered F, Bodanese Zanettini M. Range-wide patterns of nuclear and chloroplast DNA diversity in Vriesea gigantea (Bromeliaceae), a neotropical forest species. Heredity (Edinb). 2009;103:503-12 pubmed publisher
    ..The link between patterns of genetic and species diversity supports the hypothesis that both were shaped by the same biogeographic processes, triggered by the climatic oscillations of the Pleistocene. ..
  35. Goremykin V, Salamini F, Velasco R, Viola R. Mitochondrial DNA of Vitis vinifera and the issue of rampant horizontal gene transfer. Mol Biol Evol. 2009;26:99-110 pubmed publisher
    ..We also report that analysis of sequences shared by both chloroplast and mitochondrial genomes provides evidence for a previously unknown gene transfer route from the mitochondrion to the chloroplast. ..
  36. Kaplan Z, Fehrer J. Molecular evidence for a natural primary triple hybrid in plants revealed from direct sequencing. Ann Bot. 2007;99:1213-22 pubmed
    ..gramineus, P. lucens and P. perfoliatus, whereas chloroplast DNA identified P. perfoliatus as the female parent...
  37. Chacón J, Madriñán S, Debouck D, Rodriguez F, Tohme J. Phylogenetic patterns in the genus Manihot (Euphorbiaceae) inferred from analyses of nuclear and chloroplast DNA regions. Mol Phylogenet Evol. 2008;49:260-7 pubmed publisher
    ..The low levels of variation observed in the DNA regions sampled suggest a recent and explosive diversification of the genus, which is confirmed by our age estimates. ..
  38. Svab Z, Maliga P. Exceptional transmission of plastids and mitochondria from the transplastomic pollen parent and its impact on transgene containment. Proc Natl Acad Sci U S A. 2007;104:7003-8 pubmed
  39. Meudt H, Bayly M. Phylogeographic patterns in the Australasian genus Chionohebe (Veronica s.l., Plantaginaceae) based on AFLP and chloroplast DNA sequences. Mol Phylogenet Evol. 2008;47:319-38 pubmed publisher
    ..Analyses of chloroplast DNA (cpDNA) revealed eight haplotypes in Chionohebe, but these did not correspond to current taxonomy or ..
  40. Okaura T, Quang N, Ubukata M, Harada K. Phylogeographic structure and late Quaternary population history of the Japanese oak Quercus mongolica var. crispula and related species revealed by chloroplast DNA variation. Genes Genet Syst. 2007;82:465-77 pubmed
    ..The difference in genetic structure between the northeastern and southwestern regions indicates a difference in the history of migration and recolonization in Japan during the last glacial period...
  41. Nettel A, Dodd R, Afzal Rafii Z, Tovilla Hernández C. Genetic diversity enhanced by ancient introgression and secondary contact in East Pacific black mangroves. Mol Ecol. 2008;17:2680-90 pubmed publisher
    ..analysis of the internal transcribed spacer region (ITS) of the nuclear ribosomal DNA and intergenic chloroplast DNA; we also tested for current hybridization by population level analysis of nuclear microsatellites...
  42. Li L, Häkkinen M, Yuan Y, Hao G, Ge X. Molecular phylogeny and systematics of the banana family (Musaceae) inferred from multiple nuclear and chloroplast DNA fragments, with a special reference to the genus Musa. Mol Phylogenet Evol. 2010;57:1-10 pubmed publisher
  43. Gamage D, de Silva M, Inomata N, Yamazaki T, Szmidt A. Comprehensive molecular phylogeny of the sub-family Dipterocarpoideae (Dipterocarpaceae) based on chloroplast DNA sequences. Genes Genet Syst. 2006;81:1-12 pubmed
    ..of the sub-family Dipterocarpoideae using the trnL-trnF spacer, trnL intron and the matK gene sequences of chloroplast DNA (cpDNA)...
  44. Rowan B, Oldenburg D, Bendich A. RecA maintains the integrity of chloroplast DNA molecules in Arabidopsis. J Exp Bot. 2010;61:2575-88 pubmed publisher
    ..The effects on chloroplast DNA (cpDNA) structure of two nuclear-encoded, chloroplast-targeted homologues of RecA in Arabidopsis were ..
  45. Matsuoka Y, Takumi S, Kawahara T. Natural variation for fertile triploid F1 hybrid formation in allohexaploid wheat speciation. Theor Appl Genet. 2007;115:509-18 pubmed
    ..turgidum. Implications of our findings on how natural variation in the ability of Ae. tauschii to express those postzygotic reproductive phenotypes diversified and contributed to the speciation of T. aestivum are discussed. ..
  46. Yin P, Kang J, He F, Qu L, Gu H. The origin of populations of Arabidopsis thaliana in China, based on the chloroplast DNA sequences. BMC Plant Biol. 2010;10:22 pubmed publisher
    ..thaliana are very few. In this study, chloroplast DNA sequence variability was used to infer phylogenetic relationships among Arabidopsis thaliana accessions from ..
  47. Lemieux C, Otis C, Turmel M. A clade uniting the green algae Mesostigma viride and Chlorokybus atmophyticus represents the deepest branch of the Streptophyta in chloroplast genome-based phylogenies. BMC Biol. 2007;5:2 pubmed
    ..Here, we describe the complete chloroplast DNA (cpDNA) sequence of the early-diverging charophycean alga Chlorokybus atmophyticus and present chloroplast ..
  48. Wang L, Ikeda H, Liu T, Wang Y, Liu J. Repeated range expansion and glacial endurance of Potentilla glabra (Rosaceae) in the Qinghai-Tibetan plateau. J Integr Plant Biol. 2009;51:698-706 pubmed publisher
    ..Our findings based on available limited samples support that multiple refugia of a few cold-enduring species had been maintained in the QTP platform during LGM and/or previous glacial stages...
  49. Gutman B, Niyogi K. Evidence for base excision repair of oxidative DNA damage in chloroplasts of Arabidopsis thaliana. J Biol Chem. 2009;284:17006-12 pubmed publisher
    ..fluorescent protein fusions showed that all three are targeted to the chloroplast and co-localized with chloroplast DNA in nucleoids...
  50. Kiefer C, Dobes C, Sharbel T, Koch M. Phylogeographic structure of the chloroplast DNA gene pool in North American Boechera--a genus and continental-wide perspective. Mol Phylogenet Evol. 2009;52:303-11 pubmed publisher
    ..Unrelated from taxon identity we can show that the evolutionary lineages detected have a different phylogeographic history in terms of glacial refugia and recently recolonised areas. ..
  51. de Cambiaire J, Otis C, Turmel M, Lemieux C. The chloroplast genome sequence of the green alga Leptosira terrestris: multiple losses of the inverted repeat and extensive genome rearrangements within the Trebouxiophyceae. BMC Genomics. 2007;8:213 pubmed
    ..The intriguing similarities of the derived features exhibited by Leptosira cpDNA and its chlorophycean counterparts suggest that the same evolutionary forces shaped the IR-lacking chloroplast genomes in these two algal lineages. ..
  52. Ansell S, Schneider H, Pedersen N, Grundmann M, Russell S, Vogel J. Recombination diversifies chloroplast trnF pseudogenes in Arabidopsis lyrata. J Evol Biol. 2007;20:2400-11 pubmed
  53. Kress W, Erickson D. A two-locus global DNA barcode for land plants: the coding rbcL gene complements the non-coding trnH-psbA spacer region. PLoS ONE. 2007;2:e508 pubmed
    ..A combination of the non-coding trnH-psbA spacer region and a portion of the coding rbcL gene is recommended as a two-locus global land plant barcode that provides the necessary universality and species discrimination. ..