Genomes and Genes
Summary: Deoxyribonucleic acid that makes up the genetic material of CHLOROPLASTS.
Publications267 found, 100 shown here
- Accumulation of chloroplast DNA sequences on the Y chromosome of Silene latifoliaEduard Kejnovsky
Laboratory of Plant Developmental Genetics, Institute of Biophysics, Academy of Sciences of the Czech Republic, CZ 612 65, Brno, Czech Republic
Genetica 128:167-75. 2006..Sequence analysis revealed higher divergence of a non-genic region of the chloroplast sequences located on the Y chromosome while genic regions tested showed only very low (max 0.9%) divergence from their chloroplast homologues...
- Complete chloroplast genome sequences from Korean ginseng (Panax schinseng Nees) and comparative analysis of sequence evolution among 17 vascular plantsKi Joong Kim
School of Life Sciences and Biotechnology, Korea University, Seoul 136 701, Korea
DNA Res 11:247-61. 2004..30 tRNA genes, 4 rRNA genes, and 5 conserved open reading frames [ycfs]), however, are identical with the chloroplast DNA of N. tabacum. Sixteen genes contain one intron while two genes have two introns...
- Chloroplast genome (cpDNA) of Cycas taitungensis and 56 cp protein-coding genes of Gnetum parvifolium: insights into cpDNA evolution and phylogeny of extant seed plantsChung Shien Wu
Research Center for Biodiversity, Academia Sinica, Taipei, Taiwan
Mol Biol Evol 24:1366-79. 2007..More cpDNA data from non-Pinaceae conifers are necessary to justify whether the gnetifer or gnepines hypothesis is valid and to generate solid structural evidence for the monophyly of extant gymnosperms...
- Dynamics and evolution of the inverted repeat-large single copy junctions in the chloroplast genomes of monocotsRui Jiang Wang
South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
BMC Evol Biol 8:36. 2008..Therefore, we compared the organizations of genes flanking two IR-LSC junctions in 123 angiosperm representatives to uncover the evolutionary dynamics of IR-LSC junctions in basal angiosperms and monocots...
- Multiple origins of cultivated grapevine (Vitis vinifera L. ssp. sativa) based on chloroplast DNA polymorphismsR Arroyo-Garcia
Departamento de Genética Molecular de Plantas, Centro Nacional de Biotecnologia, CSIC, C Darwin 3, 28049 Madrid, Spain
Mol Ecol 15:3707-14. 2006..Indeed, over 70% of the Iberian Peninsula cultivars display chlorotypes that are only compatible with their having derived from western sylvestris populations...
- The Chlamydomonas reinhardtii plastid chromosome: islands of genes in a sea of repeatsJude E Maul
Boyce Thompson Institute for Plant Research, Cornell University, Ithaca, New York 14853, USA
Plant Cell 14:2659-79. 2002..Together, our results reveal a dynamic and unusual plastid genome whose existence in a model organism will allow its features to be tested functionally...
- Methods for obtaining and analyzing whole chloroplast genome sequencesRobert K Jansen
Section of Integrative Biology, The University of Texas at Austin, Institute of Cellular and Molecular Biology, Austin, Texas 78712 0253, USA
Methods Enzymol 395:348-84. 2005....
- The chloroplast genome sequence of the green alga Pseudendoclonium akinetum (Ulvophyceae) reveals unusual structural features and new insights into the branching order of chlorophyte lineagesJean Francois Pombert
Departement de Biochimie et de Microbiologie, Universite Laval, Quebec G1K 7P4, Canada
Mol Biol Evol 22:1903-18. 2005..We report the 195,867-bp chloroplast DNA (cpDNA) sequence of Pseudendoclonium akinetum (Ulvophyceae), a member of the class that has not been ..
- Comparative organization of chloroplast, mitochondrial and nuclear diversity in plant populationsRemy J Petit
INRA, UMR Biodiversity, Genes and Ecosystems, 69 route d Arcachon, F 33612 Cestas cedex, France
Mol Ecol 14:689-701. 2005..We have compiled studies of genetic structure based on chloroplast DNA (cpDNA), mitochondrial DNA (mtDNA) and nuclear markers in seed plants...
- Comparative phylogeography and postglacial colonization routes in EuropeP Taberlet
Laboratoire de Biologie des populations d Altitude, CNRS UMR 5553, Universite Joseph Fourier, Grenoble, France
Mol Ecol 7:453-64. 1998..As a consequence, molecular genetics so far appears to be of limited use in dating Quaternary events...
- The chloroplast genome sequence of Chara vulgaris sheds new light into the closest green algal relatives of land plantsMonique Turmel
Departement de Biochimie et de Microbiologie, Universite Laval, Quebec, Canada
Mol Biol Evol 23:1324-38. 2006..Analyses of genome rearrangements based on inversions predicted no alteration in gene order during the transition from charophycean green algae to land plants...
- The two largest chloroplast genome-encoded open reading frames of higher plants are essential genesA Drescher
Institut fur Biologie III, Universitat Freiburg, Schänzlestrabetae 1, D 79104 Freiburg, Germany
Plant J 22:97-104. 2000..These findings suggest that ycf1 and ycf2 are functional genes and encode products that are essential for cell survival. The two reading frames are thus the first higher plant chloroplast genes identified as being indispensable...
- Use of DNA barcodes to identify flowering plantsW John Kress
Department of Botany and Laboratories of Analytical Biology, National Museum of Natural History, Smithsonian Institution, P O Box 37012, Washington, DC 20013 7012
Proc Natl Acad Sci U S A 102:8369-74. 2005....
- A two-locus global DNA barcode for land plants: the coding rbcL gene complements the non-coding trnH-psbA spacer regionW John Kress
Department of Botany, National Museum of Natural History, Smithsonian Institution, Washington, DC, United States of America
PLoS ONE 2:e508. 2007..This low rate has complicated the trade-off in finding a locus that is universal and readily sequenced and has sufficiently high sequence divergence at the species-level...
- The plastid chromosome of spinach (Spinacia oleracea): complete nucleotide sequence and gene organizationC Schmitz-Linneweber
, , Germany
Plant Mol Biol 45:307-15. 2001..A detailed transcript study of one of the latter (ycf15) shows that these loci may be transcribed, but do not constitute protein-coding genes...
- Complete chloroplast DNA sequence of the moss Physcomitrella patens: evidence for the loss and relocation of rpoA from the chloroplast to the nucleusChika Sugiura
Center for Gene Research, Nagoya University, Chikusa, Nagoya 464 8602, Japan
Nucleic Acids Res 31:5324-31. 2003The complete chloroplast DNA sequence (122 890 bp) of the moss Physcomitrella patens has been determined. The genome contains 83 protein, 31 tRNA and four rRNA genes, and a pseudogene...
- The chloroplast genomes of the green algae Pedinomonas minor, Parachlorella kessleri, and Oocystis solitaria reveal a shared ancestry between the Pedinomonadales and ChlorellalesMonique Turmel
Departement de Biochimie et de Microbiologie, Universite Laval, Québec Québec Canada
Mol Biol Evol 26:2317-31. 2009..Our results further emphasize the importance of secondary reduction at both the cellular and genome levels during chlorophyte evolution...
- The rice nuclear genome continuously integrates, shuffles, and eliminates the chloroplast genome to cause chloroplast-nuclear DNA fluxMitsuhiro Matsuo
Center for Gene Research, Nagoya University, Nagoya 464 8602, Japan
Plant Cell 17:665-75. 2005....
- Nucleotide substitution rates in legume chloroplast DNA depend on the presence of the inverted repeatAntoinette S Perry
Department of Genetics, Smurfit Institute, University of Dublin, Trinity College, Dublin 2, Ireland
J Mol Evol 55:501-8. 2002..We propose that this acceleration is a direct result of the decrease in the copy number of the sequence, rather than an intrinsic property of the genes normally located in the IR...
- Molecular analysis of plant migration and refugia in the ArcticR J Abbott
Division of Environmental and Evolutionary Biology, Harold Mitchell Building, School of Biology, University of St Andrews, St Andrews, Fife KY16 9TH, UK
Science 289:1343-6. 2000..A phylogenetic analysis of chloroplast DNA variation in the purple saxifrage (Saxifraga oppositifolia) indicates that this plant first occurred in the ..
- Analysis of Acorus calamus chloroplast genome and its phylogenetic implicationsVadim V Goremykin
Institut für Spezielle Botanik, Universitat Jena, Jena, Germany
Mol Biol Evol 22:1813-22. 2005..Hence, we remain agnostic regarding phylogenetic relationships among basal angiosperm lineages...
- Evolution of reduced and compact chloroplast genomes (cpDNAs) in gnetophytes: selection toward a lower-cost strategyChung Shien Wu
School of Forestry and Resource Conservation, National Taiwan University, Taipei, Taiwan
Mol Phylogenet Evol 52:115-24. 2009..The smallest C-values in gnetophyte nuclear DNAs and the competitive or resource-poor situations encountered by gnetophytes further suggest a critical need for an economic strategy...
- Comparative analysis of the complete sequence of the plastid genome of Parthenium argentatum and identification of DNA barcodes to differentiate Parthenium species and linesShashi Kumar
Crop Improvement and Utilization Research Unit, Western Regional Research Center, ARS, USDA, Albany, CA 94710, USA
BMC Plant Biol 9:131. 2009..Chloroplast-specific DNA barcodes were developed for identification of Parthenium species and lines...
- History and evolution of alpine plants endemic to the Qinghai-Tibetan Plateau: Aconitum gymnandrum (Ranunculaceae)Liuyang Wang
Institute of Molecular Ecology, MOE Key Laboratory of Arid and Grassland Ecology, School of Life Science, Lanzhou University, Lanzhou 730000, Gansu, China
Mol Ecol 18:709-21. 2009..Here, we report a survey of chloroplast DNA (cpDNA) and nuclear ribosomal internal transcribed spacer (ITS) DNA variation aimed at exploring the ..
- Many parallel losses of infA from chloroplast DNA during angiosperm evolution with multiple independent transfers to the nucleusR S Millen
Department of Environmental, Population, and Organismic Biology, University of Colorado, Boulder, Colorado 80309, USA
Plant Cell 13:645-58. 2001..Considering this and the many separate losses of infA from chloroplast DNA, the gene has probably been transferred many more times, making infA by far the most mobile chloroplast gene ..
- Increasing phylogenetic resolution at low taxonomic levels using massively parallel sequencing of chloroplast genomesMatthew Parks
Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331, USA
BMC Biol 7:84. 2009..Is it possible to efficiently apply massively parallel sequencing to increase phylogenetic resolution at low taxonomic levels?..
- Long branch attraction, taxon sampling, and the earliest angiosperms: Amborella or monocots?Sasa Stefanovic
Department of Biology, Indiana University, Bloomington, IN 47405, USA
BMC Evol Biol 4:35. 2004..We hypothesized that this conflict reflects a misrooting of angiosperms resulting from inadequate taxon sampling, inappropriate phylogenetic methodology, and rapid evolution in the grass lineage used to represent monocots...
- Chloroplast DNA rearrangements in Campanulaceae: phylogenetic utility of highly rearranged genomesMary E Cosner
Department of Plant Biology, Ohio State University, Columbus OH 43210, USA
BMC Evol Biol 4:27. 2004..However, chloroplast genomes of Campanulaceae represent an exception and phylogenetic analyses solely based on chloroplast rearrangement characters support a reasonably well-resolved tree...
- Generation and evolutionary fate of insertions of organelle DNA in the nuclear genomes of flowering plantsChristos Noutsos
Abteilung für Pflanzenzüchtung und Genetik, Max Planck Institut fur Zuchtungsforschung, D 50829 Köln, Germany
Genome Res 15:616-28. 2005..Deletion of organelle DNA at these loci is essentially balanced by insertions of nonorganelle DNA. Deletions are associated with the removal of DNA between perfect repeats, indicating that they originate by replication slippage...
- Transfer of plastid DNA to the nucleus is elevated during male gametogenesis in tobaccoAnna E Sheppard
School of Molecular and Biomedical Science, University of Adelaide, South Australia 5005, Australia
Plant Physiol 148:328-36. 2008..The results suggest a new explanation for the occurrence of uniparental inheritance in eukaryotes...
- Multiple multilocus DNA barcodes from the plastid genome discriminate plant species equally wellAron J Fazekas
Department of Integrative Biology, University of Guelph, Guelph, Ontario, Canada
PLoS ONE 3:e2802. 2008....
- The complete chloroplast DNA sequence of the green alga Oltmannsiellopsis viridis reveals a distinctive quadripartite architecture in the chloroplast genome of early diverging ulvophytesJean Francois Pombert
Departement de Biochimie et de Microbiologie, Universite Laval, Quebec, Canada
BMC Biol 4:3. 2006..The four complete chloroplast DNA (cpDNA) sequences presently available for representatives of these classes have revealed extensive ..
- Nuclear and chloroplast DNA reassessment of the origin of Indian potato varieties and its implications for the origin of the early European potatoD M Spooner
USDA ARS, Department of Horticulture, University of Wisconsin, 1575 Linden Drive, Madison, WI 53706 1590, USA
Theor Appl Genet 110:1020-6. 2005..These results lead us to reexamine the hypothesis that early introductions of potato to Europe were solely from the Andes...
- Chloroplast DNA content in Dinophysis (Dinophyceae) from different cell cycle stages is consistent with kleptoplastySusanna Minnhagen
Department of Natural Sciences, University of Kalmar, 39182 Kalmar, Sweden
Environ Microbiol 10:2411-7. 2008..Together these findings strongly suggest that D. norvegica does not possess the ability for plastid replication...
- One species or at least eight? Delimitation and distribution of Frullania tamarisci (L.) Dumort. s. l. (Jungermanniopsida, Porellales) inferred from nuclear and chloroplast DNA markersJochen Heinrichs
Georg August University, Albrecht von Haller Institute of Plant Sciences, Department of Systematic Botany, Untere Karspüle 2, 37073 Gottingen, Germany
Mol Phylogenet Evol 56:1105-14. 2010..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...
- Historical range expansion determines the phylogenetic diversity introduced during contemporary species invasionDouglas R Taylor
Department of Biology, University of Virginia, Charlottesville, Virginia 22904 4328, USA
Evolution 61:334-45. 2007..We used chloroplast DNA (cpDNA) gene genealogies and coalescent methods to study two congeneric plants, Silene latifolia and S...
- Chloroplast DNA sequence of the green alga Oedogonium cardiacum (Chlorophyceae): unique genome architecture, derived characters shared with the Chaetophorales and novel genes acquired through horizontal transferJean Simon Brouard
Departement de Biochimie et de Microbiologie, Universite Laval, Quebec, QC G1V 0A6, Canada
BMC Genomics 9:290. 2008..and to expand our understanding of chloroplast genome evolution, we have undertaken the sequencing of chloroplast DNA (cpDNA) from representative taxa...
- Mitochondrial DNA of Vitis vinifera and the issue of rampant horizontal gene transferVadim V Goremykin
Istituto Agrario San Michele all Adige Research Center, San Michele all Adige TN, Italy
Mol Biol Evol 26:99-110. 2009..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...
- Chloroplast DNA variation in the Quercus affinis-Q. laurina complex in Mexico: geographical structure and associations with nuclear and morphological variationA Gonzalez-Rodriguez
Centro de Investigaciones en Ecosistemas, Universidad Nacional Autonoma de Mexico, Antigua Carretera a Pátzcuaro No 8701, Col Ex Hacienda de San José de la Huerta, Morelia, 58190 Michoacán, Mexico
Mol Ecol 13:3467-76. 2004The geographical distribution of chloroplast DNA (cpDNA) variation in 39 populations of two hybridizing Mexican red oaks, Quercus affinis and Q...
- Complete chloroplast DNA sequence from a Korean endemic genus, Megaleranthis saniculifolia, and its evolutionary implicationsYoung Kyu Kim
School of Life Sciences, Korea University, Seoul 136 701, Korea
Mol Cells 27:365-81. 2009The 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...
- Decoupled mitochondrial and chloroplast DNA population structure reveals Holocene collapse and population isolation in a threatened Mexican-endemic coniferJuan P Jaramillo-Correa
Chaire de recherche du Canada en génomique forestière et environnementale and Centre de recherche en biologie forestière, Pavillon Charles Eugène Marchand, Universite Laval, Quebec, Canada
Mol Ecol 15:2787-800. 2006..Additional mtDNA sequence analysis confirmed that P. martinezii (Patterson) is not conspecific with P. chihuahuana, and thus deserves separate conservation efforts...
- The complete chloroplast and mitochondrial DNA sequence of Ostreococcus tauri: organelle genomes of the smallest eukaryote are examples of compactionSteven Robbens
Department of Plant Systems Biology, Flanders Institute for Biotechnology VIB, Ghent University, Ghent, Belgium
Mol Biol Evol 24:956-68. 2007..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...
- Range-wide patterns of nuclear and chloroplast DNA diversity in Vriesea gigantea (Bromeliaceae), a neotropical forest speciesC Palma-Silva
Departamento de Genetica, IB UFRGS, Rio Grande do Sul, Porto Alegre, Brazil
Heredity (Edinb) 103:503-12. 2009..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...
- Mitochondrial DNA, chloroplast DNA and the origins of development in eukaryotic organismsArnold J Bendich
Department of Biology, University of Washington, Seattle, WA 98195 5325, USA
Biol Direct 5:42. 2010..The advantage here is realized at the level of the mitochondrion and chloroplast...
- Diverse plant and animal genetic records from Holocene and Pleistocene sedimentsEske Willerslev
Department of Evolutionary Biology, Zoological Institute, University of Copenhagen, Universitetsparken 15, Denmark DK 2100 Ø
Science 300:791-5. 2003..Therefore, many sedimentary deposits may contain unique, and widespread, genetic records of paleoenvironments...
- Chloroplast DNA supports a hypothesis of glacial refugia over postglacial recolonization in disjunct populations of black pine (Pinus nigra) in western EuropeZara Afzal-Rafii
IMEP, UMR 6116 CNRS, Université d Aix Marseille III, 13397 Marseille Cedex 20, France
Mol Ecol 16:723-36. 2007..than having been re-colonized in the postglacial period, genetic variation was assessed using a suite of 10 chloroplast DNA microsatellites...
- Polymerase chain reaction-single strand conformation polymorphism analyses of nuclear and chloroplast DNA provide evidence for recombination, multiple introductions and nascent speciation in the Caulerpa taxifolia complexI Meusnier
Laboratoire de Genetique et Evolution des Populations Vegetales, UPRESA CNRS 8016, Bat SN2, Universite de Lille I, 59655 Villeneuve d Ascq cedex, France
Mol Ecol 11:2317-25. 2002..C. taxifolia is clearly a complex of genetically and ecologically differentiated sibling species or subspecies...
- The phylogeny of the Pentaschistis clade (Danthonioideae, Poaceae) based on chloroplast DNA, and the evolution and loss of complex charactersC Galley
Institute of Systematic Botany, University of Zurich, Zollikerstrasse 107, Ch 8008 Zurich, Switzerland
Evolution 61:864-84. 2007We construct a species-level phylogeny for the Pentaschistis clade based on chloroplast DNA, from the following regions: trnL-F, trnT-L, atpB-rbcL, rpL16, and trnD-psbA...
- Identification of Curcuma plants and curcumin content level by DNA polymorphisms in the trnS-trnfM intergenic spacer in chloroplast DNAMotoyasu Minami
Department of Environmental Biology, College of Bioscience and Biotechnology, Chubu University, 1200 Matsumoto cho, Kasugai, Aichi, 487 8501, Japan
J Nat Med 63:75-9. 2009..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...
- Molecular phylogeny and systematics of the banana family (Musaceae) inferred from multiple nuclear and chloroplast DNA fragments, with a special reference to the genus MusaLin feng Li
Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
Mol Phylogenet Evol 57:1-10. 2010....
- Range shifts of Potentilla fruticosa on the Qinghai-Tibetan Plateau during glacial and interglacial periods revealed by chloroplast DNA sequence variationA Shimono
Environmental Biology Division, National Institute for Environmental Studies, Tsukuba, Ibaraki, Japan
Heredity (Edinb) 104:534-42. 2010..Thus, the interior region acted as a refugium and greatly contributed to the diversification of P. fruticosa...
- The chloroplast genome of Phalaenopsis aphrodite (Orchidaceae): comparative analysis of evolutionary rate with that of grasses and its phylogenetic implicationsChing Chun Chang
Institute of Biotechnology, National Cheng Kung University, Tainan, Taiwan
Mol Biol Evol 23:279-91. 2006..We demonstrated that these conflicting angiosperm phylogenies are most probably linked to the transitional sites at all codon positions, especially at the third one where the strong base-composition bias and saturation effect take place...
- Milestones in chloroplast genetic engineering: an environmentally friendly era in biotechnologyHenry Daniell
Dept of Molecular Biology and Microbiology, University of Central Florida, Orlando, FL 32826 3227, USA
Trends Plant Sci 7:84-91. 2002....
- Structural features of a wheat plastome as revealed by complete sequencing of chloroplast DNAY Ogihara
Kihara Institute for Biological Research and Graduate School of Integrated Science, Yokohama City University, Yokohama 244 0813, Japan
Mol Genet Genomics 266:740-6. 2002Structural features of the wheat plastome were clarified by comparison of the complete sequence of wheat chloroplast DNA with those of rice and maize chloroplast genomes...
- Repeated range expansion and glacial endurance of Potentilla glabra (Rosaceae) in the Qinghai-Tibetan plateauLiu Yang Wang
Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, The Chinese Academy of Sciences, Xining 810001, China
J Integr Plant Biol 51:698-706. 2009..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...
- Evidences for multiple maternal lineages of Caryocar brasiliense populations in the Brazilian Cerrado based on the analysis of chloroplast DNA sequences and microsatellite haplotype variationRosane G Collevatti
Pós Graduação em Ciências Genômicas, Universidade Catolica de Brasilia, SGAN 916, Mod B, Brasilia, DF Brasil 70790 160
Mol Ecol 12:105-15. 2003..the endangered tree species Caryocar brasiliense based on variability in two classes of maternally inherited chloroplast DNA sequences with different rates of molecular evolution...
- A chloroplast genealogy of hordeum (poaceae): Long-term persisting haplotypes, incomplete lineage sorting, regional extinction, and the consequences for phylogenetic inferenceSabine S Jakob
Leibniz Institute of Plant Genetics and Crop Science IPK, D 06466 Gatersleben, Germany
Mol Biol Evol 23:1602-12. 2006..We conclude that the described phenomena are not restricted to Hordeum and that the knowledge of the chloroplast relationships within a genus is indispensable to prevent misinterpretation of phylogeographic data within single species...
- Contrasting phylogeographical patterns between mainland and island taxa of the Pinus luchuensis complexY C Chiang
Department of Life Sciences, Pingtung University of Science and Technology, Taiwan
Mol Ecol 15:765-79. 2006..In this study, paternally transmitted chloroplast DNA (cpDNA) and maternally transmitted mitochondrial DNA (mtDNA) were used to estimate population structure and ..
- High-frequency gene transfer from the chloroplast genome to the nucleusSandra Stegemann
Westfalische Wilhelms Universitat Munster, Institut für Biochemie und Biotechnologie der Pflanzen, Hindenburgplatz 55, D 48143 Munster, Germany
Proc Natl Acad Sci U S A 100:8828-33. 2003....
- Power and limitations of the chloroplast trnL (UAA) intron for plant DNA barcodingPierre Taberlet
Laboratoire d Ecologie Alpine, CNRS UMR 5553, Universite Joseph Fourier, BP 53, 38041 Grenoble Cedex 9, France
Nucleic Acids Res 35:e14. 2007....
- RecA maintains the integrity of chloroplast DNA molecules in ArabidopsisBeth A Rowan
Department of Biology, University of Washington, Seattle, WA 91895 USA
J Exp Bot 61:2575-88. 2010..The effects on chloroplast DNA (cpDNA) structure of two nuclear-encoded, chloroplast-targeted homologues of RecA in Arabidopsis were ..
- Complete nucleotide sequence of the Cryptomeria japonica D. Don. chloroplast genome and comparative chloroplast genomics: diversified genomic structure of coniferous speciesTomonori Hirao
Institute of Wood Technology, Akita Prefectural University, 11 1 Kaieisaka, Noshiro, Akita 016 0876, Japan
BMC Plant Biol 8:70. 2008....
- Chloroplast DNA phylogeography of Cunninghamia konishii (Cupressaceae), an endemic conifer of TaiwanS Y Lu
Division of Forest Biology, Taiwan Forestry Research Institute, Taipei
Genome 44:797-807. 2001..restricted to mainland China and Taiwan, based on sequences of the trnD-trnT noncoding spacer of the chloroplast DNA. Maternal inheritance of chloroplasts was determined experimentally. No paternal leakage was detected...
- Relative rates of synonymous substitutions in the mitochondrial, chloroplast and nuclear genomes of seed plantsGuy Drouin
Département de biologie et Centre de recherche avancée en génomique environnementale, Université d Ottawa, 30 Marie Curie, Ottawa, Ontario, Canada
Mol Phylogenet Evol 49:827-31. 2008....
- Glacial refugia: hotspots but not melting pots of genetic diversityRemy J Petit
Institut National de la Recherche Agronomique, UMR Biodiversité, Génes et Ecosystémes, F 33612 Cestas, France
Science 300:1563-5. 2003..To test this hypothesis, we studied chloroplast DNA variation in 22 widespread European trees and shrubs sampled in the same forests...
- The origin of populations of Arabidopsis thaliana in China, based on the chloroplast DNA sequencesPing Yin
National Laboratory of Protein Engineering and Plant Genetic Engineering, Peking Yale Joint Center for Plant Molecular Genetics and Agrobiotechnology, College of Life Sciences, Peking University, Beijing, China
BMC Plant Biol 10:22. 2010..thaliana are very few. In this study, chloroplast DNA sequence variability was used to infer phylogenetic relationships among Arabidopsis thaliana accessions from ..
- Recurrent nuclear DNA introgression accompanies chloroplast DNA exchange between two eucalypt speciesG E McKinnon
School of Plant Science, University of Tasmania, Private Bag 55, Hobart, Tasmania 7001, Australia
Mol Ecol 19:1367-80. 2010..globulus is correlated with spatial proximity to E. cordata, but departs from expectations based on AFLP marker frequency in E. cordata, indicating that selection may be governing the persistence of introgressed fragments in E. globulus...
- Complete chloroplast genome sequences of Hordeum vulgare, Sorghum bicolor and Agrostis stolonifera, and comparative analyses with other grass genomesChristopher Saski
Clemson University Genomics Institute, Clemson University, Biosystems Research Complex, 51 New Cherry Street, Clemson, SC 29634, USA
Theor Appl Genet 115:571-90. 2007..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...
- Chloroplast DNA variation and postglacial recolonization of common ash (Fraxinus excelsior L.) in EuropeM Heuertz
Centre de Recherche Public Gabriel Lippmann, CREBS Research Unit, 162 a, av de la Faïencerie, L 1511 Luxembourg, Luxembourg
Mol Ecol 13:3437-52. 2004..A low chloroplast DNA mutation rate, a low effective population size in glacial refugia related to ash's life history traits, as ..
- Chloroplast DNA microsatellite analysis supports a polyphyletic origin for barleyJ L Molina-Cano
Centre UdL IRTA, Av Rovira Roure 177, 25189, Lleida, Spain
Theor Appl Genet 110:613-9. 2005Five barley chloroplast DNA microsatellites (cpSSRs) were used to study genetic relationships among a set of 186 barley accessions-34 Hordeum vulgare ssp...
- Phylogeographical variation of chloroplast DNA in holm oak (Quercus ilex L.)R Lumaret
Centre d Ecologie Fonctionnelle et Evolutive, Centre National de la Recherche Scientifique, 1919 Route de Mende, F 34293 Montpellier Cedex05, France
Mol Ecol 11:2327-36. 2002Variation in the lengths of restriction fragments (RFLPs) of the whole chloroplast DNA molecule was studied in 174 populations of Quercus ilex L. sampled over the entire distribution of this evergreen and mainly Mediterranean oak species...
- Phylogeny of the paleotropical fern genus Lepisorus (Polypodiaceae, Polypodiopsida) inferred from four chloroplast DNA regionsLi Wang
State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, The Chinese Academy of Sciences, Beijing, China
Mol Phylogenet Evol 54:211-25. 2010..The variation of chromosome numbers is largely due to a single aneuploidy event instead of a stepwise reduction during the evolutionary history of this genus...
- Phylogenetic analysis reveals five independent transfers of the chloroplast gene rbcL to the mitochondrial genome in angiospermsMichael P Cummings
The Josephine Bay Paul Center for Comparative Molecular Biology and Evolution, Marine Biological Laboratory, 7 MBL Street, Woods Hole, MA 02543 1015, USA
Curr Genet 43:131-8. 2003....
- A comprehensive chloroplast DNA-based phylogeny of the genus Potentilla (Rosaceae): implications for its geographic origin, phylogeography and generic circumscriptionChristoph Dobes
Department of Pharmacognosy, Pharmacobotany, University of Vienna, Vienna, Austria
Mol Phylogenet Evol 56:156-75. 2010A 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...
- A fragment of chloroplast DNA was transferred horizontally, probably from non-eudicots, to mitochondrial genome of PhaseolusMagdalena Woloszynska
Institute of Biochemistry and Molecular Biology, Department of Cell Molecular Biology, University of Wroclaw, Wroclaw, Poland
Plant Mol Biol 56:811-20. 2004..This is the first example of horizontal transfer of a chloroplast sequence to the mitochondrial genome in higher plants...
- Recombination diversifies chloroplast trnF pseudogenes in Arabidopsis lyrataS W Ansell
Department of Botany, The Natural History Museum, London, UK
J Evol Biol 20:2400-11. 2007....
- Phylogenetic analysis of North American Elymus and the monogenomic Triticeae (Poaceae) using three chloroplast DNA data setsRoberta J Mason-Gamer
The University of Idaho, Department of Biological Sciences, Moscow, ID 83844 3051, USA
Genome 45:991-1002. 2002..We analyze new and previously published chloroplast DNA data from Elymus and from most of the monogenomic genera of the Triticeae in an attempt to identify the ..
- Phylogeographic structure of the chloroplast DNA gene pool in North American Boechera--a genus and continental-wide perspectiveChristiane Kiefer
Heidelberg Institute of Plant Sciences, Department Biodiversity and Plant Systematics, University of Heidelberg, Im Neuenheimer Feld 345, D 69120 Heidelberg, Germany
Mol Phylogenet Evol 52:303-11. 2009..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...
- Strand asymmetry and codon usage bias in the chloroplast genome of Euglena gracilisB R Morton
Department of Biological Sciences, Barnard College, Columbia University, 3009 Broadway, New York, NY 10027, USA
Proc Natl Acad Sci U S A 96:5123-8. 1999....
- Impact of ice ages on circumpolar molecular diversity: insights from an ecological key speciesI G Alsos
Tromsø Museum, University of Tromsø, NO 9037 Tromsø, Norway
Mol Ecol 14:2739-53. 2005..Eighteen chloroplast DNA haplotypes were observed in and among 122 populations, grouping into three main lineages which probably ..
- Phylogenetic patterns in the genus Manihot (Euphorbiaceae) inferred from analyses of nuclear and chloroplast DNA regionsJuliana Chacón
Laboratorio de Botánica y Sistemática, Universidad de Los Andes, Apartado Aereo 4976, Bogota, D C, Colombia
Mol Phylogenet Evol 49:260-7. 2008..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...
- Chloroplast DNA variation confirms a single origin of domesticated sunflower (Helianthus annuus L.)David M Wills
Department of Biological Sciences, Vanderbilt University, VU Station B 351634, Nashville, TN 37235, USA
J Hered 97:403-8. 2006....
- Chloroplast DNA phylogeography of Clintoniaudensis Trautv. & Mey. (Liliaceae) in East AsiaYi Ling Wang
Key Laboratory of Resource Biology and Biotechnology in Western China Ministry of Education, College of Life Sciences, Northwest University, Xi an 710069, PR China
Mol Phylogenet Evol 55:721-32. 2010..amp; Mey. (Liliaceae) inferred from two types of chloroplast DNA markers, polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) and DNA sequences...
- Relationships in Ananas and other related genera using chloroplast DNA restriction site variationM F Duval
EMBRAPA Recursos Geneticos e Biotecnologia, Brasilia, Brazil
Genome 46:990-1004. 2003b>Chloroplast DNA (cpDNA) diversity was examined using PCR-RFLP to study phylogenetic relationships in Ananas and related genera...
- Late Quaternary history of Hippophaë rhamnoides L. (Elaeagnaceae) inferred from chalcone synthase intron (Chsi) sequences and chloroplast DNA variationIgor V Bartish
Department of Phanerogamic Botany, Swedish Museum of Natural History, PO Box 50007, S 10405 Stockholm, Sweden
Mol Ecol 15:4065-83. 2006..We used sequence variation at the nuclear chalcone synthase intron (Chsi), in conjunction with chloroplast DNA-restriction fragment length polymorphism data, to investigate the intraspecific phylogeny, phylogeographic ..
- Utility of selected non-coding chloroplast DNA sequences for lineage assessment of Musa interspecific hybridsSasivimon Swangpol
Biological Sciences Program, Chulalongkorn University, Phayathai Road, Pathumwan, Bangkok 10330, Thailand
J Biochem Mol Biol 40:577-87. 2007..Until thoroughly identified in other members of Musaceae and Zingiberales clade, utility of this inverted repeat as phylogenetic marker in these taxa are cautioned...
- Tribal and subtribal delimitation and phylogeny of the Cardueae (Asteraceae): a combined nuclear and chloroplast DNA analysisNúria Garcia-Jacas
Botanical Institute of Barcelona C S I C Ajuntament de Barcelona, Av Muntanyans, S N, E 08038 Barcelona, Spain
Mol Phylogenet Evol 22:51-64. 2002..of the internal transcribed spaces (ITS) of the nuclear ribosomal DNA genes and the matK gene of the chloroplast DNA of a broad representation of the tribe to examine (1) the phylogeny of the tribe, (2) the position of ..
- Genetic identification of cinnamon (Cinnamomum spp.) based on the trnL-trnF chloroplast DNAMareshige Kojoma
Izu Experimental Station for Medicinal Plants, National Institute of Health Sciences, Shizuoka, Japan
Planta Med 68:94-6. 2002Genetic identification among cinnamon species was studied by analyzing nucleotide sequences of chloroplast DNA from four species (Cinnamomum cassia, C. zeylanicum, C. burmannii and C. sieboldii)...
- Molecular phylogenetics of the sexually deceptive orchid genus Ophrys (Orchidaceae) based on nuclear and chloroplast DNA sequencesM Soliva
Geobotanical Institute, ETH Zurich, Zollikerstrasse 107, Zurich, CH 8008, Switzerland
Mol Phylogenet Evol 20:78-88. 2001....
- Invasion of Lepidium draba (Brassicaceae) in the western United States: distributions and origins of chloroplast DNA haplotypesJohn F Gaskin
Northern Plains Agricultural Research Laboratory, USDA ARS, P O Box 463, Sidney, MT 59270 USA
Mol Ecol 14:2331-41. 2005..In this study, we investigated a highly variable chloroplast DNA (cpDNA) marker for populations of the weed Lepidium draba (Brassicaceae) in its native Eurasian and invasive ..
- Spatial pattern of chloroplast DNA variation of Cyclobalanopsis glauca in Taiwan and East AsiaSophie S F Huang
National Taiwan University, Department of Botany, Roosevelt Road, Section 4, Taipei, Taiwan 106
Mol Ecol 11:2349-58. 2002This study examined the spatial pattern of chloroplast DNA (cpDNA) variation in Cyclobalanopsis glauca (Thunb. ex Murray) Oerst...
- Quantitative assessment of heteroplasmy levels in Senecio vulgaris chloroplast DNAJuerg E Frey
Agroscope FAW Waedenswil, Department of Plant Protection, Molecular Diagnostics Laboratory, Swiss Federal Research Station for Horticulture, CH8820 Wädenswil, Switzerland
Genetica 123:255-61. 2005Heteroplasmy in coding chloroplast DNA was only recently shown to occur and was so far not quantitatively assessed...
- Molecular authentication of 21 Korean artemisia species (Compositae) by polymerase chain reaction-restriction fragment length polymorphism based on trnL-F region of chloroplast DNAJeong Hoon Lee
Department of Herbal Crop Research, NIHHS, RDA, Eumseong 369 873, Republic of Korea
Biol Pharm Bull 32:1912-6. 2009..chain reaction-restriction fragment length polymorphism) technique based on the trnL-F sequences in chloroplast DNA. Five different banding patterns were generated from 21 Artemisia species using HinfI restriction enzyme. A...
- Two chloroplast DNA inversions originated simultaneously during the early evolution of the sunflower family (Asteraceae)Ki Joong Kim
School of Life Sciences and Biotechnology, Korea University, Seoul, Korea
Mol Biol Evol 22:1783-92. 2005The chloroplast DNA (cpDNA) inversion in the Asteraceae has been cited as a classic example of using genomic rearrangements for defining major lineages of plants...
- Genetic variation and species identification of Thai Boesenbergia (Zingiberaceae) analyzed by chloroplast DNA polymorphismJiranan Techaprasan
National Center for Genetic Engineering and Biotechnology BIOTEC, 113 Paholyothin Road, Klong 1, Klong Luang, Pathum Thani 12120, Thailand
J Biochem Mol Biol 39:361-70. 2006..74%) were observed in these investigated taxa. The 50% majority-rule consensus tree constructed from combined chloroplast DNA sequences allocated Boesenbergia in this study into 3 different groups...
- Molecular phylogeny of the genus Hordeum using three chloroplast DNA sequencesTomotaro Nishikawa
Genetic Diversity Department, National Institute of Agrobiological Sciences, Tsukuba, Ibaraki, 305 8602, Japan
Genome 45:1157-66. 2002..We used 32 taxa of Hordeum and three chloroplast DNA sequences, matK, atpB-rbcL, and trnL-trnF in the current study...
- Origin and diversification of Hibiscus glaber, species endemic to the oceanic Bonin Islands, revealed by chloroplast DNA polymorphismKoji Takayama
Botanical Gardens, Graduate School of Science, The University of Tokyo, Hakusan 3 7 1, Bunkyo ku, Tokyo 112 0001, Japan
Mol Ecol 14:1059-71. 2005..of the two closely related species on the Bonin Islands, we conducted molecular phylogenetic analyses on chloroplast DNA (cpDNA) sequences...
- Phylogeographical structure revealed by chloroplast DNA variation in Japanese beech (Fagus crenata Blume)T Okaura
Faculty of Agriculture, Ehime University, 3 5 7 Tarumi, Matsuyama, Ehime 790 8566, Japan
Heredity (Edinb) 88:322-9. 2002Intraspecific genetic variation in three non-coding chloroplast DNA (cpDNA) regions (trnT-L and trnL-F spacers, and trnL intron) of Japanese beech (Fagus crenata Blume) was investigated...
- Phylogeographical variation of chloroplast DNA in cork oak (Quercus suber)Roselyne Lumaret
UMR5175, Centre d Ecologie Fonctionnelle et Evolutive, Centre National de la Recherche Scientifique, 1919 Route de Mende, F 34293 Montpellier Cedex 05, France
Ann Bot 96:853-61. 2005..In the last decades, the geographical location of the centre of origin of Quercus suber (cork oak), a strictly western Mediterranean oak species, has been the subject of controversy...
- Amplification of noncoding chloroplast DNA for phylogenetic studies in lycophytes and monilophytes with a comparative example of relative phylogenetic utility from OphioglossaceaeRandall L Small
Department of Ecology and Evolutionary Biology, The University of Tennessee, Knoxville, TN 37996, USA
Mol Phylogenet Evol 36:509-22. 2005..ferns, eusporangiate ferns, Psilotaceae, and Equisetaceae), on the other hand, relatively few noncoding chloroplast DNA regions have been explored...
- Chloroplast DNA base substitutions: an experimental assessmentMonica Guhamajumdar
Department of Plant Biology, Michigan State University, East Lansing, MI, 48824 1312, USA
Mol Genet Genomics 273:177-83. 2005..was carried out to determine directly the frequency and types of spontaneous base substitutions that occur in chloroplast DNA. A target site within the chloroplast 16S rRNA gene of the green alga Chlamydomonas reinhardtii was chosen ..
- PHYLOGENETIC ANALYSIS OF CHLOROPLAST DNA POLYMORPHISMS ISteven Strauss; Fiscal Year: 1990..to twenty restriction endonucleases will be employed for studying variability in the nucleotide sequences of chloroplast DNA. The chloroplast DNA of Douglas-fir will be isolated and cloned, and then used as probe in filter ..
- REPLICATION OF CHLOROPLAST DNAKRISHNA TEWARI; Fiscal Year: 1992The long term goal of the proposal is to identify and purify the proteins involved in the replication of chloroplast DNA (ctDNA) followed by studying in vitro replication using purified proteins...
- MOLECULAR BIOLOGY OF CHLOROPLAST RIBOSOMESDon Bourque; Fiscal Year: 1991..that regulation of expression of chloroplast ribosomal protein genes which are coded by Nicotiana tabacum chloroplast DNA occurs at the level of transcription and translation...
- Expression of Human Therapeutic Proteins in Transgenic Tobacco ChloroplastsHenry Daniell; Fiscal Year: 2010..Successful completion of these studies would make transgenic chloroplasts ideal bioreactors for the production of safe and less expensive therapeutic proteins and open the door for in depth studies of membrane proteins. ..
- SELENIUM AND LUNG CANCER RISKHenry Thompson; Fiscal Year: 2004..In addition, this work has the potential to provide new biomarkers with which to assess lung cancer risk and its modulation. ..
- The molecular basis of reproductive isolationSTUART MCDANIEL; Fiscal Year: 2007..The identification of molecular variants underlying complex traits, like reproductive isolation, opens several new avenues of research into the specific mechanisms of adaptation and speciation. [unreadable] [unreadable]..