Plastid genome sequencing, comparative genomics, and phylogenomics: Current status and prospects
Tóm tắt
Từ khóa
Tài liệu tham khảo
Becker, 2009, Streptophyte algae and the origin of embryophytes, Annals of Botany, 103, 999, 10.1093/aob/mcp044
Belanger, 2006, Distinctive architecture of the chloroplast genome in the chlorophycean green alga Stigeoclonium helveticum, Molecular Genetics and Genomics, 276, 464, 10.1007/s00438-006-0156-2
Braukmann, 2009, Loss of all plastid ndh genes in Gnetales and conifers: extent and evolutionary significance for the seed plant phylogeny, Current Genetics, 55, 323, 10.1007/s00294-009-0249-7
Brinkmann, 2008, Animal phylogeny and large-scale sequencing: progress and pitfalls, Journal of Systematics and Evolution, 46, 274
Brouard, 2008, 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 transfer, BMC Genomics, 9, 290, 10.1186/1471-2164-9-290
Cai, 2008, Extensive reorganization of the plastid genome of Trifolium subterraneum (Fabaceae) is associated with numerous repeated sequences and novel DNA insertions, Journal of Molecular Evolution, 67, 696, 10.1007/s00239-008-9180-7
Cantino, 2007, Towards a phylogenetic nomenclature of Tracheophyta, Taxon, 56, 822, 10.2307/25065864
Chang, 2006, The chloroplast genome of Phalaenopsis aphrodite (Orchidaceae): comparative analysis of evolutionary rate with that of grasses and its phylogenetic implications, Molecular Biology and Evolution, 23, 279, 10.1093/molbev/msj029
Chumley, 2006, The complete chloroplast genome sequence of Pelargonium x hortorum: organization and evolution of the largest and most highly rearranged chloroplast genome of land plants, Molecular Biology and Evolution, 23, 2175, 10.1093/molbev/msl089
Crane, 1985, Phylogenetic analysis of seed plants and the origin of angiosperms, Annals of the Missouri Botanical Garden, 72, 716, 10.2307/2399221
Crane, 1985, Phylogenetic relationships in seed plants, Cladistics, 1, 329, 10.1111/j.1096-0031.1985.tb00432.x
Cronn, 2008, Multiplex sequencing of plant chloroplast genomes using Solexa sequencing-by-synthesis technology, Nucleic Acids Researchearch, 36, e122, 10.1093/nar/gkn502
Daniell, 2006, Complete chloroplast genome sequences of Solanum bulbocastanum, Solanum lycopersicum and comparative analyses with other Solanaceae genomes, Theoretical and Applied Genetics, 112, 1503, 10.1007/s00122-006-0254-x
de Koning, 2006, The complete plastid genome sequence of the parasitic green alga Helicosporidium sp. is highly reduced and structured, BMC Biology, 4, 12, 10.1186/1741-7007-4-12
Delsuc, 2005, Phylogenomics and the reconstruction of the tree of life, Nature Reviews Genetics, 6, 361, 10.1038/nrg1603
dePamphilis, 1990, Loss of photosynthetic and chlororespiratory genes from the plastid genome of a parasitic flowering plant, Nature, 348, 337, 10.1038/348337a0
Donoghue, 1994, Progress and prospects in reconstructing plant phylogeny, Annals of the Missouri Botanical Garden, 81, 405, 10.2307/2399898
Doyle, 1986, Seed plant phylogeny and the origin of angiosperms: an experimental cladistic approach, The Botanical Review, 52, 321, 10.1007/BF02861082
Doyle, 1996, Seed plant phylogeny and the relationships of gnetales, International Journal of Plant Sciences, 157, S3, 10.1086/297401
Edgar, 2004, MUSCLE: a multiple sequence alignment method with reduced time and space complexity, BMC Bioinformatics, 5, 113, 10.1186/1471-2105-5-113
Erickson, 2008, DNA barcoding in land plants: developing standards to quantify and maximize success, Taxon, 57, 1304, 10.1002/tax.574020
Fazekas, 2008, Multiple multilocus DNA barcodes from the plastid genome discriminate plant species equally well, PLoS ONE, 3, e2802, 10.1371/journal.pone.0002802
Funk, 2007, Complete DNA sequences of the plastid genomes of two parasitic flowering plant species, Cuscuta reflexa and Cuscuta gronovii, BMC Plant Biology, 7, 45, 10.1186/1471-2229-7-45
Gao, 2009, Complete chloroplast genome sequence of a tree fern Alsophila spinulosa: insights into evolutionary changes in fern chloroplast genomes, BMC Evolutionary Biology, 9, 130, 10.1186/1471-2148-9-130
Goffinet, 2009, Bryophyte biology
Goffinet, 2007, Distribution and phylogenetic significance of the 71-kb inversion in the plastid genome in Funariidae (Bryophyta), Annals of Botany, 99, 747, 10.1093/aob/mcm010
Goremykin, 2003, Analysis of the Amborella trichopoda chloroplast genome sequence suggests that Amborella is not a basal angiosperm, Molecular Biology and Evolution, 20, 1499, 10.1093/molbev/msg159
Goremykin, 2004, The chloroplast genome of Nymphaea alba: whole-genome analyses and the problem of identifying the most basal angiosperm, Molecular Biology and Evolution, 21, 1445, 10.1093/molbev/msh147
Graham, 2000, Utility of 17 chloroplast genes for inferring the phylogeny of the basal angiosperms, American Journal of Botany, 87, 1712, 10.2307/2656749
Groth-Malonek, 2005, Ancestors of trans-splicing mitochondrial introns support serial sister group relationships of hornworts and mosses with vascular plants, Molecular Biology and Evolution, 22, 117, 10.1093/molbev/msh259
Haberle, 2008, Extensive rearrangements in the chloroplast genome of Trachelium caeruleum are associated with repeats and tRNA genes, Journal of Molecular Evolution, 66, 350, 10.1007/s00239-008-9086-4
Hasebe, 1992, Gene localization on the chloroplast DNA of the maiden hair fern; Adiantum capillus-veneris, Journal of Plant Research, 105, 413
Hilu, 2003, Angiosperm phylogeny based on matK sequence information, American Journal of Botany, 90, 1758, 10.3732/ajb.90.12.1758
Hirao, 2008, Complete nucleotide sequence of the Cryptomeria japonica D. Don. chloroplast genome and comparative chloroplast genomics: diversified genomic structure of coniferous species, BMC Plant Biology, 8, 70, 10.1186/1471-2229-8-70
Hiratsuka, 1989, The complete sequence of the rice (Oryza sativa) chloroplast genome: intermolecular recombination between distinct tRNA genes accounts for a major plastid DNA inversion during the evolution of the cereals, Molecular Genetics and Genomics, 217, 185, 10.1007/BF02464880
Hollingsworth, 2009, A DNA barcode for land plants, Proceedings of the National Academy of Sciences USA, 106, 12794, 10.1073/pnas.0905845106
Jansen, 2007, Analysis of 81 genes from 64 plastid genomes resolves relationships in angiosperms and identifies genome-scale evolutionary patterns, Proceedings of the National Academy of Sciences USA, 104, 19369, 10.1073/pnas.0709121104
Jansen, 2006, Phylogenetic analyses of Vitis (Vitaceae) based on complete chloroplast genome sequences: effects of taxon sampling and phylogenetic methods on resolving relationships among rosids, BMC Evolutionary Biology, 6, 32, 10.1186/1471-2148-6-32
Jeffroy, 2006, Phylogenomics: the beginning of incongruence?, Trends in Genetics, 22, 225, 10.1016/j.tig.2006.02.003
Karol, 2001, The closest living relatives of land plants, Science, 294, 2351, 10.1126/science.1065156
Kelch, 2004, Molecular systematics of bryophytes, 3
Kim, 2004, Complete chloroplast genome sequences from Korean ginseng (Panax schinseng Nees) and comparative analysis of sequence evolution among 17 vascular plants, DNA Research, 11, 247, 10.1093/dnares/11.4.247
Krause, 2008, From chloroplasts to “cryptic” plastids: evolution of plastid genomes in parasitic plants, Current Genetics, 54, 111, 10.1007/s00294-008-0208-8
Kress, 2009, Plant DNA barcodes and a community phylogeny of a tropical forest dynamics plot in Panama, Proceedings of the National Academy of Sciences USA, 106, 18621, 10.1073/pnas.0909820106
Kugita, 2003, The complete nucleotide sequence of the hornwort (Anthoceros formosae) chloroplast genome: insight into the earliest land plants, Nucleic Acids Research, 31, 716, 10.1093/nar/gkg155
Kurtz, 2001, REPuter: the manifold applications of repeat analysis on a genomic scale, Nucleic Acids Research, 29, 4633, 10.1093/nar/29.22.4633
Lee, 2007, Gene relocations within chloroplast genomes of Jasminum and Menodora (Oleaceae) are due to multiple, overlapping inversions, Molecular Biology and Evolution, 24, 1161, 10.1093/molbev/msm036
Leebens-Mack, 2005, Identifying the basal angiosperm node in chloroplast genome phylogenies: sampling one's way out of the Felsenstein zone, Molecular Biology and Evolution, 22, 1948, 10.1093/molbev/msi191
Lemieux, 2007, A clade uniting the green algae Mesostigma viride and Chlorokybus atmophyticus represents the deepest branch of the Streptophyta in chloroplast genome-based phylogenies, BMC Biology, 5, 2, 10.1186/1741-7007-5-2
Lung, 2006, Identification of small non-coding RNAs from mitochondria and chloroplasts, Nucleic Acids Research, 34, 3842, 10.1093/nar/gkl448
Mardanov, 2008, Complete sequence of the duckweed (Lemna minor) chloroplast genome: structural organization and phylogenetic relationships to other angiosperms, Journal of Molecular Evolution, 66, 555, 10.1007/s00239-008-9091-7
Martin, 2005, Chloroplast genome phylogenetics: why we need independent approaches to plant molecular evolution, Trends in Plant Science, 10, 203, 10.1016/j.tplants.2005.03.007
Martin, 1998, Gene transfer to the nucleus and the evolution of chloroplasts, Nature, 393, 162, 10.1038/30234
Mathews, 2009, Phylogenetic relationships among seed plants: persistent questions and the limits of molecular data, American Journal of Botany, 96, 228, 10.3732/ajb.0800178
Mathews, 1999, The root of angiosperm phylogeny inferred from duplicate phytochrome genes, Science, 286, 947, 10.1126/science.286.5441.947
Maul, 2002, The Chlamydomonas reinhardtii plastid chromosome: islands of genes in a sea of repeats, Plant Cell, 14, 2659, 10.1105/tpc.006155
Mayor, 2000, VISTA: visualizing global DNA sequence alignments of arbitrary length, Bioinformatics, 16, 1046, 10.1093/bioinformatics/16.11.1046
McCourt, 2004, Charophyte algae and land plant origins, Trends in Ecology & Evolution, 19, 661, 10.1016/j.tree.2004.09.013
McCoy, 2008, The complete plastid genome sequence of Welwitschia mirabilis: an unusually compact plastome with accelerated divergence rates, BMC Evolutionary Biology, 8, 130, 10.1186/1471-2148-8-130
McNeal, 2007, Complete plastid genome sequences suggest strong selection for retention of photosynthetic genes in the parasitic plant genus Cuscuta, BMC Plant Biology, 7, 57, 10.1186/1471-2229-7-57
McNeal, 2009, Parallel loss of plastid introns and their maturase in the genus Cuscuta, PLoS ONE, 4, e5982, 10.1371/journal.pone.0005982
Millen, 2001, Many parallel losses of infA from chloroplast DNA during angiosperm evolution with multiple independent transfers to the nucleus, Plant Cell, 13, 645, 10.1105/tpc.13.3.645
Mishler, 2009, Bryophyte biology, 173
Moore, 2007, Using plastid genome-scale data to resolve enigmatic relationships among basal angiosperms, Proceedings of the National Academy of Sciences USA, 104, 19363, 10.1073/pnas.0708072104
Moore, 2006, Rapid and accurate pyrosequencing of angiosperm plastid genomes, BMC Plant Biology, 6, 17, 10.1186/1471-2229-6-17
Nixon, 1994, A reevaluation of seed plant phylogeny, Annals of the Missouri Botanical Garden, 81, 484, 10.2307/2399901
Ohyama, 1986, Chloroplast gene organization deduced from complete sequence of liverwort Marchantia polymorpha chloroplast DNA, Nature, 322, 572, 10.1038/322572a0
Ovcharenko, 2004, zPicture: dynamic alignment and visualization tool for analyzing conservation profiles, Genome Research, 14, 472, 10.1101/gr.2129504
Parks, 2009, Increasing phylogenetic resolution at low taxonomic levels using massively parallel sequencing of chloroplast genomes, BMC Biology, 7, 84, 10.1186/1741-7007-7-84
Philippe, 2005, Phylogenomics, Annual Review of Ecology, Evolution, and Systematics, 36, 541, 10.1146/annurev.ecolsys.35.112202.130205
Phillips, 2004, Genome-scale phylogeny and the detection of systematic biases, Molecular Biology and Evolution, 21, 1455, 10.1093/molbev/msh137
Pombert, 2006, The complete chloroplast DNA sequence of the green alga Oltmannsiellopsis viridis reveals a distinctive quadripartite architecture in the chloroplast genome of early diverging ulvophytes, BMC Biology, 4, 3, 10.1186/1741-7007-4-3
Pombert, 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 lineages, Molecular Biology and Evolution, 22, 1903, 10.1093/molbev/msi182
Pryer, 2001, Horsetails and ferns are a monophyletic group and the closest living relatives to seed plants, Nature, 409, 618, 10.1038/35054555
Pryer, 2002, Deciding among green plants for whole genome studies, Trends in Plant Science, 7, 550, 10.1016/S1360-1385(02)02375-0
Pryer, 2004, Phylogeny and evolution of ferns (monilophytes) with a focus on the early leptosporangiate divergences, American Journal of Botany, 91, 1582, 10.3732/ajb.91.10.1582
Qiu, 2008, Phylogeny and evolution of charophytic algae and land plants, Journal of Systematics and Evolution, 46, 287
Qiu, 1999, The earliest angiosperms: evidence from mitochondrial, plastid and nuclear genomes, Nature, 402, 404, 10.1038/46536
Qiu, 2007, A nonflowering land plant phylogeny inferred from nucleotide sequences of seven chloroplast, mitochondrial, and nuclear genes, International Journal of Plant Sciences, 168, 691, 10.1086/513474
Qiu, 2006, The deepest divergences in land plants inferred from phylogenomic evidence, Proceedings of the National Academy of Sciences USA, 103, 15511, 10.1073/pnas.0603335103
Raubeson, 1992, Chloroplast DNA evidence on the ancient evolutionary split in vascular land plants, Science, 255, 1697, 10.1126/science.255.5052.1697
Raubeson, 2005, Plant diversity and evolution: genotypic and phenotypic variation in higher plants, 45, 10.1079/9780851999043.0045
Raubeson, 1995, Insights into fern evolution from mapping chloroplast genomes, American Fern Journal, 85, 193, 10.2307/1547809
Raubeson, 2007, Comparative chloroplast genomics: analyses including new sequences from the angiosperms Nuphar advena and Ranunculus macranthus, BMC Genomics, 8, 174, 10.1186/1471-2164-8-174
Robbens, 2007, The complete chloroplast and mitochondrial DNA sequence of Ostreococcus tauri: organelle genomes of the smallest eukaryote are examples of compaction, Molecular Biology and Evolution, 24, 956, 10.1093/molbev/msm012
Rodriguez-Ezpeleta, 2007, Phylogenetic analyses of nuclear, mitochondrial, and plastid multigene data sets support the placement of Mesostigma in the Streptophyta, Molecular Biology and Evolution, 24, 723, 10.1093/molbev/msl200
Rokas, 2000, Rare genomic changes as a tool for phylogenetics, Trends in Ecology & Evolution, 15, 454, 10.1016/S0169-5347(00)01967-4
Rokas, 2003, Genome-scale approaches to resolving incongruence in molecular phylogenies, Nature, 425, 798, 10.1038/nature02053
Roper, 2007, The complete plastid genome sequence of Angiopteris evecta (G. Forst.) Hoffm. (Marattiaceae), American Fern Journal, 97, 95, 10.1640/0002-8444(2007)97[95:TCPGSO]2.0.CO;2
Saski, 2005, Complete chloroplast genome sequence of Glycine max and comparative analyses with other legume genomes, Plant Molecular Biology, 59, 309, 10.1007/s11103-005-8882-0
Schwartz, 2000, PipMaker - a web server for aligning two genomic DNA sequences, Genome Research, 10, 577, 10.1101/gr.10.4.577
Shinozaki, 1986, The complete nucleotide sequence of the tobacco chloroplast genome: its gene organization and expression, The EMBO Journal, 5, 2043, 10.1002/j.1460-2075.1986.tb04464.x
Smith, 2009, Unparalleled GC content in the plastid DNA of Selaginella, Plant Molecular Biology, 71, 627, 10.1007/s11103-009-9545-3
Soltis, 2009, Floral variation and floral genetics in basal angiosperms, American Journal of Botany, 96, 110, 10.3732/ajb.0800182
Steane, 2005, Complete nucleotide sequence of the chloroplast genome from the Tasmanian blue gum, Eucalyptus globulus (Myrtaceae), DNA Research, 12, 215, 10.1093/dnares/dsi006
Stein, 1992, Structural rearrangements of the chloroplast genome provide an important phylogenetic link in ferns, Proceedings of the National Academy of Sciences USA, 89, 1856, 10.1073/pnas.89.5.1856
Stirewalt, 1995, Nucleotide sequence of the cyanelle genome from Cyanophora paradoxa, Plant Molecular Biology Reporter, 13, 327, 10.1007/BF02669186
Sugiura, 2003, Complete chloroplast DNA sequence of the moss Physcomitrella patens: evidence for the loss and relocation of rpoA from the chloroplast to the nucleus, Nucleic Acids Research, 31, 5324, 10.1093/nar/gkg726
Sugiura, 2004, Plastid transformation reveals that moss tRNAArg-CCG is not essential for plastid function, The Plant Journal, 40, 314, 10.1111/j.1365-313X.2004.02202.x
Sugiura, 2003, History of chloroplast genomics, Photosynthesis Research, 76, 371, 10.1023/A:1024913304263
Tesler, 2002, GRIMM: genome rearrangements web server, Bioinformatics, 18, 492, 10.1093/bioinformatics/18.3.492
Timme, 2007, A comparative analysis of the Lactuca and Helianthus (Asteraceae) plastid genomes: identification of divergent regions and categorization of shared repeats, American Journal of Botany, 94, 302, 10.3732/ajb.94.3.302
Timmis, 2004, Endosymbiotic gene transfer: organelle genomes forge eukaryotic chromosomes, Nature Reviews Genetics, 5, 123, 10.1038/nrg1271
Tsuji, 2007, The chloroplast genome from a lycophyte (microphyllophyte), Selaginella uncinata, has a unique inversion, transpositions and many gene losses, Journal of Plant Research, 120, 281, 10.1007/s10265-006-0055-y
Turmel, 2009, The chloroplast genomes of the green algae Pyramimonas, Monomastix, and Pycnococcus shed new light on the evolutionary history of prasinophytes and the origin of the secondary chloroplasts of Euglenids, Molecular Biology and Evolution, 26, 631, 10.1093/molbev/msn285
Turmel, 1999, The complete chloroplast DNA sequence of the green alga Nephroselmis olivacea: insights into the architecture of ancestral chloroplast genomes, Proceedings of the National Academy of Sciences USA, 96, 10248, 10.1073/pnas.96.18.10248
Turmel, 2002, The chloroplast and mitochondrial genome sequences of the charophyte Chaetosphaeridium globosum: insights into the timing of the events that restructured organelle DNAs within the green algal lineage that led to land plants, Proceedings of the National Academy of Sciences USA, 99, 11275, 10.1073/pnas.162203299
Turmel, 2003, The mitochondrial genome of Chara vulgaris: insights into the mitochondrial DNA architecture of the last common ancestor of green algae and land plants, Plant Cell, 15, 1888, 10.1105/tpc.013169
Turmel, 2005, The complete chloroplast DNA sequences of the charophycean green algae Staurastrum and Zygnema reveal that the chloroplast genome underwent extensive changes during the evolution of the Zygnematales, BMC Biology, 3, 22, 10.1186/1741-7007-3-22
Turmel, 2006, The chloroplast genome sequence of Chara vulgaris sheds new light into the closest green algal relatives of land plants, Molecular Biology and Evolution, 23, 1324, 10.1093/molbev/msk018
Turmel, 2009, The chloroplast genomes of the green algae Pedinomonas minor, Parachlorella kessleri and Oocystis solitaria reveal a shared ancestry between the Pedinomonadales and Chlorellales, Molecular Biology and Evolution, 26, 2317, 10.1093/molbev/msp138
Turmel, 2007, The green algal ancestry of land plants as revealed by the chloroplast genome, International Journal of Plant Sciences, 168, 679, 10.1086/513470
Wakasugi, 1997, Complete nucleotide sequence of the chloroplast genome from the green alga Chlorella vulgaris: the existence of genes possibly involved in chloroplast division, Proceedings of the National Academy of Sciences USA, 94, 5967, 10.1073/pnas.94.11.5967
Wakasugi, 1998, Complete nucleotide sequence of the plastid genome from a fern, Psilotum nudum, Endocytobiosis and Cell Research, 13, 147
Wakasugi, 1994, Loss of all ndh genes as determined by sequencing the entire chloroplast genome of the black pine Pinus thunbergii, Proceedings of the National Academy of Sciences USA, 91, 9794, 10.1073/pnas.91.21.9794
Wakasugi, 2001, The genomics of land plant chloroplasts: Gene content and alteration of genomic information by RNA editing, Photosynthesis Research, 70, 107, 10.1023/A:1013892009589
Wickett, 2008, Functional gene losses occur with minimal size reduction in the plastid genome of the parasitic liverwort Aneura mirabilis, Molecular Biology and Evolution, 25, 393, 10.1093/molbev/msm267
Wojciechowski, 2000, Advances in legume systematics, 277
Wolf, 2005, The first complete chloroplast genome sequence of a lycophyte, Huperzia lucidula (Lycopodiaceae), Gene, 350, 117, 10.1016/j.gene.2005.01.018
Wolf, 2003, Complete nucleotide sequence of the chloroplast genome from a leptosporangiate fern, Adiantum capillus-veneris L, DNA Research, 10, 59, 10.1093/dnares/10.2.59
Wolfe, 1992, Function and evolution of a minimal plastid genome from a nonphotosynthetic parasitic plant, Proceedings of the National Academy of Sciences USA, 89, 10648, 10.1073/pnas.89.22.10648
Wu, 2009, Evolution of reduced and compact chloroplast genomes (cpDNAs) in gnetophytes: Selection toward a lower-cost strategy, Molecular Phylogenetics and Evolution, 52, 115, 10.1016/j.ympev.2008.12.026
Wu, 2007, Chloroplast genome (cpDNA) of Cycas taitungensis and 56 cp protein-coding genes of Gnetum parvifolium: insights into cpDNA evolution and phylogeny of extant seed plants, Molecular Biology and Evolution, 24, 1366, 10.1093/molbev/msm059
Wu, 2009, Complete nucleotide sequence of Dendrocalamus latiflorus and Bambusa oldhamii chloroplast genomes, Tree Physiology, 29, 847, 10.1093/treephys/tpp015
Yue, 2008, Gene rearrangement analysis and ancestral order inference from chloroplast genomes with inverted repeat, BMC Genomics, 9, S25, 10.1186/1471-2164-9-S1-S25
Zanis, 2002, The root of the angiosperms revisited, Proceedings of the National Academy of Sciences USA, 99, 6848, 10.1073/pnas.092136399
Zou, 2008, Analysis of 142 genes resolves the rapid diversification of the rice genus, Genome Biology, 9, R49, 10.1186/gb-2008-9-3-r49
Zwickl, 2006, Genetic algorithm approaches for the phylogenetic analysis of large biological sequence datasets under the maximum likelihood criterion