Plant Diversity 2011, 33(4) 365-375 DOI:   10.3724/SP.J.1143.2011.10202  ISSN: 2095-0845 CN: 53-1217/Q

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Keywords
Phylogenomics
Chloroplast genome
Next-generation sequencing
Long-branch attraction
Authors
ZHANG Yun-Jie
LI De-Zhu
PubMed
Article by Zhang, Y. J.
Article by Li, D. Z.

Advances in Phylogenomics Based on Complete Chloroplast Genomes

 ZHANG  Yun-Jie, LI  De-Zhu

Key Laboratory of Biodiversity and Biogeography, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China

Abstract

Phylogenomics is a new synthesized discipline which combines genomics with phylogenetics. Phylogenomics based on chloroplast genomes has shown many great advantages in plant phylogenetic research in recent years, providing resolutions for phylogeny of some taxonomically difficult groups of plants. However, there are some problems coming along with chloroplast phylogenomics as well. In this review, the application prospects and potential problems of chloroplast phylogenomics in plant phylogenetic reconstruction were discussed based on recent phylogenomic case studies. The influence of nextgeneration sequencing on chloroplast phylogenomics was also discussed.

Keywords Phylogenomics   Chloroplast genome   Next-generation sequencing   Long-branch attraction  
Received 2010-11-15 Revised  Online: 2010-12-01 
DOI: 10.3724/SP.J.1143.2011.10202
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Adachi J, Waddell PJ, Martin W et al., 2000. Plastid genome phylogeny and a model of amino acid substitution for proteins encoded by chloroplast DNA[J]. Journal of Molecular Evolution, 50 (4): 348—358
Aguinaldo AMA, Turbeville JM, Linford LS et al., 1997. Evidence for a clade of nematodes, arthropods and other moulting animals[J]. Nature, 387 (6632): 489—493
Barkman TJ, Chenery G, McNeal JR et al.,  2000. Independent and combined analyses of sequences from all three genomic compartments converge on the root of flowering plant phylogeny[J]. Proceedings of the National Academy of Sciences, 97 (24): 13166—13171
Bergsten J, 2005. A review of longbranch attraction[J]. Cladistics, 21 (2): 163—193
Bowe LM, Coat G, DePamphilis CW, 2000. Phylogeny of seed plants based on all three genomic compartments: extant gymnosperms are monophyletic and Gnetales′ closest relatives are conifers[J]. Proceedings of the National Academy of Sciences of the United States of America, 97 (8): 4092—4097
Brinkmann H, Philippe H, 1999. Archaea sister group of Bacteria? Indications from tree reconstruction artifacts in ancient phylogenies[J]. Molecular Biology and Evolution, 16 (6): 817—825
Burleigh JG, Hilu KW, Soltis DE, 2009. Inferring phylogenies with incomplete data sets: a 5gene, 567taxon analysis of angiosperms[J]. BMC Evolutionary Biology, 9 (1): 61
Cai Z, Guisinger M, Kim HG et al., 2008. Extensive reorganization of the plastid genome of Trifolium subterraneum (Fabaceae) is associated with numerous repeated sequences and novel DNA insertions[J]. Journal of Molecular Evolution, 67 (6): 696—704
Chase MW, Soltis DE, Olmstead RG et al., 1993. Phylogenetics of seed plants: an analysis of nucleotide sequences from the plastid gene rbcL[J]. Annals of the Missouri Botanical Garden, 80 (3): 528—580
Chaw SM, Chang CC, Chen HL et al., 2004. Dating the monocotdicot divergence and the origin of core eudicots using whole chloroplast genomes[J]. Journal of Molecular Evolution, 58 (4): 424—441
Chaw SM, Parkinson CL, Cheng Y et al., 2000. Seed plant phylogeny inferred from all three plant genomes: monophyly of extant gymnosperms and origin of Gnetales from conifers[J]. Proceedings of the National Academy of Sciences of the United States of America, 97 (8): 4086—4091
Chaw SM, Zharkikh A, Sung HM et al., 1997. Molecular phylogeny of extant gymnosperms and seed plant evolution: analysis of nuclear 18S rRNA sequences[J]. Molecular Biology and Evolution, 14 (1): 56—68
Chu KH, Qi J, Yu ZG et al.,  2004. Origin and phylogeny of chloroplasts revealed by a simple correlation analysis of complete genomes[J]. Molecular Biology and Evolution, 21 (1): 200—206
Clegg MT, Gaut BS, Learn GH et al., 1994. Rates and patterns of chloroplast DNA evolution[J]. Proceedings of the National Academy of Sciences of the United States of America, 91 (15): 6795—6801
Corriveau JL, Coleman AW, 1988. Rapid screening method to detect potential biparental inheritance of plastid DNA and results for over 200 angiosperm species[J]. American Journal of Botany, 75 (10): 1443—1458
Cosner ME, Jansen RK, Moret BME et al., 2000. An empirical comparison of phylogenetic methods on chloroplast gene order data in Campanulaceae[A]. In: Sankoff D, Nadeau JH eds. Comparative Genomics: Empirical and Analytical Approaches to Gene Order Dynamics, Map Alignment, and the Evolution of Gene Families[M]. Dordrecht: Kluwer Academic Publishers, 99—121
Cosner ME, Jansen RK, Palmer JD et al., 1997. The highly rearranged chloroplast genome of Trachelium caeruleum (Campanulaceae): multiple inversions, inverted repeat expansion and contraction, transposition, insertions/deletions, and several repeat families[J]. Current Genetics, 31 (5): 419—429
Cosner ME, Raubeson LA, Jansen RK, 2004. Chloroplast DNA rearrangements in Campanulaceae: phylogenetic utility of highly rearranged genomes[J]. BMC Evolutionary Biology, 4 (1): 27
Cronn R, Liston A, Parks M et al., 2008. Multiplex sequencing of plant chloroplast genomes using Solexa sequencingbysynthesis technology[J]. Nucleic Acids Research, 36 (19): e122
Delsuc F, Brinkmann H, Philippe H, 2005. Phylogenomics and the reconstruction of the tree of life[J]. Nature Reviews Genetics, 6 (5): 361—375
de Queiroz A, Donoghue MJ, Kim J, 1995. Separate versus combined analysis of phylogenetic evidence[J]. Annual Review of Ecology and Systematics, 26 (1): 657—681
Doyle JA, 2006. Seed ferns and the origin of angiosperms[J]. The Journal of the Torrey Botanical Society, 133 (1): 169—209
Eisen JA, 1998. Phylogenomics: improving functional predictions for uncharacterized genes by evolutionary analysis[J]. Genome research, 8 (3): 163—167
Eisen JA, Hanawalt PC, 1999. A phylogenomic study of DNA repair genes, proteins, and processes[J]. Mutation Research, 435 (3): 171—213
Felsenstein J, 1978. Cases in which parsimony or compatibility methods will be positively misleading[J]. Systematic Biology, 27 (4): 401—410
Goremykin VV, HirschErnst KI, Wolfl S et al., 2003. Analysis of the Amborella trichopoda chloroplast genome sequence suggests that Amborella is not a basal angiosperm[J]. Molecular Biology and Evolution, 20 (9): 1499—1505
Goremykin VV, HirschErnst KI, Wolfl S et al., 2004. The chloroplast genome of Nymphaea alba: wholegenome analyses and the problem of identifying the most basal angiosperm[J]. Molecular Biology and Evolution, 21 (7): 1445—1454
Graybeal A, 1998. Is it better to add taxa or characters to a difficult phylogenetic problem ?[J]. Systematic Biology, 47 (1): 9—17
Hajibabaei M, Xia J, Drouin G, 2006. Seed plant phylogeny: Gnetophytes are derived conifers and a sister group to Pinaceae[J]. Molecular Phylogenetics and Evolution, 40 (1): 208—217
Hendy MD, Penny D, 1989. A framework for the quantitative study of evolutionary trees[J]. Systematic Biology, 38 (4): 297—309
Hillis DM, 1996. Inferring complex phylogenies[J]. Nature, 383: 130—131
Hillis DM, 1998. Taxonomic sampling, phylogenetic accuracy, and investigator bias[J]. Systematic Biology, 47 (1): 3—8
Hilu KW, Borsch T, Muller K et al., 2003. Angiosperm phylogeny based on matK sequence information[J]. American Journal of Botany, 90 (12): 1758—1776
Huelsenbeck JP, 1997. Is the Felsenstein zone a fly trap?[J]. Systematic Biology, 46 (1): 69—74
Jansen RK, Cai Z, Raubeson LA et al., 2007. Analysis of 81 genes from 64 plastid genomes resolves relationships in angiosperms and identifies genomescale evolutionary patterns[J]. Proceedings of the National Academy of Sciences, 104 (49): 19369—19374
Jansen RK, Kaittanis C, Saski C et al., 2006. Phylogenetic analyses of Vitis (Vitaceae) based on complete chloroplast genome sequences: effects of taxon sampling and phylogenetic methods on resolving relationships among rosids[J]. BMC Evolutionary Biology, 6 (1): 32
Jansen RK, Raubeson LA, Boore JL et al., 2005. Methods for obtaining and analyzing whole chloroplast genome sequences[J]. Methods in Enzymology, 395: 348—384
Jeffroy O, Brinkmann H, Delsuc F et al., 2006. Phylogenomics: the beginning of incongruence?[J]. Trends in Genetics, 22 (4): 225—231
Kim J, Kim W, Cunningham CW, 1999. A new perspective on lower metazoan relationships from 18S rDNA sequences[J]. Molecular Biology and Evolution, 16: 423—427
Knox EB, Downie SR, Palmer JD, 1993. Chloroplast genome rearrangements and the evolution of giant lobelias from herbaceous ancestors[J]. Molecular Biology and Evolution, 10 (2):414—430
Knox EB, Palmer JD, 1999. The chloroplast genome arrangement of Lobelia thuliniana (Lobeliaceae): expansion of the inverted repeat in an ancestor of the Campanulales[J]. Plant Systematics and Evolution, 214 (1):49—64
Lake JA, 1987. A rateindependent technique for analysis of nucleic acid sequences: evolutionary parsimony[J]. Molecular Biology and Evolution, 4(2): 167—191
LeebensMack J, Raubeson LA, Cui L et al., 2005. Identifying the basal angiosperm node in chloroplast genome phylogenies: sampling one′s way out of the Felsenstein zone[J]. Molecular Biology and Evolution, 22 (10): 1948—1963
Lemieux C, Otis C, Turmel M, 2007. A clade uniting the green algae Mesostigma viride and Chlorokybus atmophyticus represents the deepest branch of the Streptophyta in chloroplast genomebased phylogenies[J]. BMC biology, 5 (1): 2
Li W, Olmstead R, 1997. Molecular Evolution[M]. Sunderland, MA: Sinauer Associates
Lockhart PJ, Penny D, Soltis DE et al., 2005. The place of Amborella within the radiation of angiosperms[J]. Trends in Plant Science, 10 (5): 201—202
Lockhart P, Steel M, 2005. A tale of two processes[J]. Systematic Biology, 54 (6): 948—951
Lonsdale DM, Brears T, Hodge TP et al., 1988. The plant mitochondrial genome: homologous recombination as a mechanism for generating heterogeneity[J]. Philosophical Transactions of the Royal Society of London Series B, 319 (1193): 149—163
LyonsWeiler J, Hoelzer GA, 1997. Escaping from the felsenstein zone by detecting long branches in phylogenetic Data[J]. Molecular Phylogenetics and Evolution, 8 (3): 375—384
Magallón S, Castillo A, 2009. Angiosperm diversification through time[J]. American Journal of Botany, 96 (1): 349—365
Magallón S, Crane PR, Herendeen PS, 1999. Phylogenetic pattern, diversity, and diversification of eudicots[J]. Annals of the Missouri Botanical Garden, 86 (2): 297—372
Moore MJ, Dhingra A, Soltis PS et al., 2006. Rapid and accurate pyrosequencing of angiosperm plastid genomes[J]. BMC Plant Biology, 6 (1): 17
Moore MJ, Soltis PS, Bell CD et al., 2010. Phylogenetic analysis of 83 plastid genes further resolves the early diversification of eudicots[J]. Proceedings of the National Academy of Sciences, 107 (10): 4623—4628
Nei M, Kumar S, 2000. Molecular Evolution and Phylogenetics[M]. New York: Oxford University Press
Nickrent DL, Parkinson CL, Palmer JD et al., 2000. Multigene phylogeny of land plants with special reference to bryophytes and the earliest land plants[J]. Molecular Biology and Evolution, 17 (12): 1885—1895
Nozaki H, Ohta N, Matsuzaki M et al.,  2003. Phylogeny of plastids based on cladistic analysis of gene loss inferred from complete plastid genome sequences[J]. Journal of Molecular Evolution, 57 (4): 377—382
Palmer JD, 1992. Mitochondrial DNA in plant systematics: applications and limitations[A]. In: Soltis PS, Soltis DE, Doyle JJ eds. Molecular Systematics of Plants[M]. New York: Chapman and Hall, 36—49
Palmer JD, Herbon LA, 1988. Plant mitochondrial DNA evolved rapidly in structure, but slowly in sequence[J]. Journal of Molecular Evolution, 28 (1): 87—97
Parks M, Cronn R, Liston A, 2009. Increasing phylogenetic resolution at low taxonomic levels using massively parallel sequencing of chloroplast genomes[J]. BMC biology, 7 (1): 84
Philippe H, Lartillot N, Brinkmann H, 2005. Multigene analyses of bilaterian animals corroborate the monophyly of Ecdysozoa, Lophotrochozoa, and Protostomia[J]. Molecular Biology and Evolution, 22 (5): 1246—1253
Phillips MJ, Delsuc F, Penny D, 2004. Genomescale phylogeny and the detection of systematic biases[J]. Molecular Biology and Evolution, 21 (7): 1455—1458
Pombert JF, Otis C, Lemieux C et al., 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[J]. Molecular Biology and Evolution, 22 (9): 1903—1918
Qiu YL, Dombrovska O, Lee J et al., 2005. Phylogenetic analyses of basal angiosperms based on nine plastid, mitochondrial, and nuclear genes[J]. International Journal of Plant Sciences, 166 (5): 815—842
Savolainen V, Chase MW, Hoot SB et al., 2000. Phylogenetics of flowering plants based on combined analysis of plastid atpB and rbcL gene sequences[J]. Systematic Biology, 49 (2): 306—362
Shendure J, Ji H, 2008. Nextgeneration DNA sequencing[J]. Nature biotechnology, 26 (10): 1135—1145
Soltis DE, Senters AE, Zanis MJ et al., 2003. Gunnerales are sister to other core eudicots: implications for the evolution of pentamery[J]. American Journal of Botany, 90 (3): 461—470
Soltis DE, Albert VA, Savolainen V et al., 2004. Genomescale data, angiosperm relationships, and ‘ending incongruence’: a cautionary tale in phylogenetics[J]. Trends in plant science, 9 (10): 477—483
Soltis DE, Soltis PS, 2004. Amborella not a “basal angiosperm”? Not so fast[J]. American Journal of Botany, 91 (6): 997—1001
Steel M, 2005. Should phylogenetic models be trying to ‘fit an elephant’?[J]. Trends in Genetics, 21 (6): 307—309
Stefanovi'c  S, Rice DW, Palmer JD, 2004. Long branch attraction, taxon sampling, and the earliest angiosperms: Amborella or monocots?[J]. BMC Evolutionary Biology, 4 (1): 35
Swofford DL, Olsen GJ, Waddell PJ et al., 1996. Phylogenetic inference[A]. In: Hillis DM, Moritz C, Mable BK eds. Phylogenetic Inference[M]. MA: Sinauer Associates, Sunderland, 407—514
Tangphatsornruang S, Sangsrakru D, Chanprasert J et al., 2010. The chloroplast genome sequence of Mungbean (Vigna radiata) determined by highthroughput pyrosequencing: structural organization and phylogenetic relationships[J]. DNA Research, 17 (1): 11—22
Tian X (田欣), Li DZ (李德铢), 2002. Application of DNA sequences in plant phylogentic study[J]. Acta Botanica Yunnanica (云南植物研究), 24: 170—184
Wakasugi T, Tsudzuki J, Ito S et al., 1994. Loss of all ndh genes as determined by sequencing the entire chloroplast genome of the black pine Pinus thunbergii[J]. Proceedings of the National Academy of Sciences of the United States of America, 91 (21): 9794—9798
Wendel JF, Doyle JJ, 1998. Phylogenetic incongruence: window into genome history and molecular evolution[A]. In: Soltis DE, Soltis PS, Doyle JJ eds. Molecular Systematics of Plants II: DNA sequencing[M]. Boston: Kluwer, 265—296
Whittall JB, Syring J, Parks M et al., 2010. Finding a (pine) needle in a haystack: chloroplast genome sequence divergence in rare and widespread pines[J]. Molecular Ecology, 19 (S1): 100—114
Willson SJ, 1999. A higher order parsimony method to reduce longbranch attraction[J]. Molecular Biology and Evolution, 16: 694—705
Wolfe KH, Morden CW, Palmer JD, 1992. Function and evolution of a minimal plastid genome from a nonphotosynthetic parasitic plant[J]. Proceedings of the National Academy of Sciences of the United States of America, 89 (22): 10648—10652
Wu CS, Wang YN, Liu SM et al., 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[J]. Molecular Biology and Evolution, 24 (6): 1366—1379
Yu L (于黎), Zhang YP (张亚平), 2006. Phylogenomic——An attractive avenue to reconstruct “tree of life”[J]. Hereditas (遗传), 28 (11):1445—1450
Yu ZG, Zhou LQ, Anh VV et al., 2005. Phylogeny of prokaryotes and chloroplasts revealed by a simple composition approach on all protein sequences from complete genomes without sequence alignment[J]. Journal of Molecular Evolution, 60 (4): 538—545
Zeng CX, Zhang YX, Triplett JK et al., 2010. Large multilocus plastid phylogeny of the tribe Arundinarieae (Poaceae: Bambusoideae) reveals ten major lineages and low rate of molecular divergence[J]. Molecular Phylogenetics and Evolution, 56 (2): 821—839
Zhang YJ, Ma PF, Li DZ, 2011. Highthroughput sequencing of six bamboo chloroplast genomes: phylogenetic implications for temperate woody bamboos (Poaceae: Bambusoideae)[J]. PloS ONE, 6 (5): e20596
Zhong B, Yonezawa T, Zhong Y et al., 2009. Episodic evolution and adaptation of chloroplast genomes in ancestral grasses[J]. PloS ONE, 4 (4): e5297
Zhong B, Yonezawa T, Zhong Y et al., 2010. The position of Gnetales among seed plants: overcoming pitfalls of chloroplast phylogenomics[J]. Molecular Biology and Evolution, 27 (12): 2855—2863
Zou XH, Zhang FM, Zhang JG et al., 2008. Analysis of 142 genes resolves the rapid diversification of the rice genus[J]. Genome Biology, 9 (3): R49

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