系统发育基因组学研究进展

doi:10.3724/SP.J.1005.2014.0669

[an error occurred while processing this directive]

HEREDITAS(Beijing) ›› 2014, Vol. 36 ›› Issue (7): 669-678.doi: 10.3724/SP.J.1005.2014.0669

• Reviews • Previous Articles Next Articles

Advances in phylogenomics

Zhangqun Wang¹, Zengyan Xie², Yingfan Cai³, Kunxian Shu², Feifei Huang²

1. College of Computer Science and Technology, Chongqing University of Posts and Telecommunications, Chongqing 400065, China;
2. College of Bio-information, Chongqing University of Posts and Telecommunications, Chongqing 400065, China;
3. School of Life Science, Henan University, Kaifeng 475001, China

Received:2013-10-28 Online:2014-07-20 Published:2014-06-23

Abstract

Abstract: Phylogenomics is a new phylogenetic field that aims to rebuild phylogenetic relationship of organisms using whole genome data. It can effectively eliminate the impact of horizontal gene transfer and variant evolutionary rates on phylogeny. According to the genome data type they are based on, these methods can be classified into five groups: multi-gene based, gene content based, gene order based, K-string based, and metabolic pathway based. The mechanism, speed, accuracy, applicable range and their application of these methods are summarized. The prospects of phylogenomics and challenges that it is faced with are also discussed.

Key words: phylogeny, phylogenetic tree, phylogenomics, gene content, K-string

Zhangqun Wang, Zengyan Xie, Yingfan Cai, Kunxian Shu, Feifei Huang. Advances in phylogenomics[J]. HEREDITAS(Beijing), 2014, 36(7): 669-678.

References

[1] SL, Giordano R, Colbert AM, Karr TL, Robertson HM. 16S rRNA phylogenetic analysis of the bacterial endosymbionts associated with cytoplasmic incompatibility in insects. Proc Natl Acad Sci USA , 1992, 89(7): 2699- 2702.
[2] U, Pommerening-Röser A, Juretschko S, Schmid MC, Koops HP, Wagner M. Phylogeny of all recognized species of ammonia oxidizers based on comparative 16S rRNA and amoA sequence analysis: implications for molecular diversity surveys. Appl Environ Microb , 2000, 66(12): 5368-5382.
[3] SB, Moberg KD, Maxson LR. Tetrapod phylogeny inferred from 18S and 28S ribosomal RNA sequences and a review of the evidence for amniote relationships. Mol Biol Evol , 1990, 7(6): 607-633.
[4] 郭茂祖. 系统发生树构建技术综述. 电子学报, 2006, 34(11): 2047-2052.
[5] WF, Logsdon JM Jr. Archaeal genomics: do archaea have a mixed heritage? Curr Biol , 1998, 8(6): R209- R211.
[6] WF. Phylogenetic classification and the universal tree. Science , 1999, 284(5423): 2124-2128.
[7] MA, Bork P. Measuring genome evolution. Proc Natl Acad Sci USA , 1998, 95(11): 5849-5856.
[8] JH, Rosenberg NA. Discordance of species trees with their most likely gene trees. PLoS Genet , 2006, 2(5): e68.
[9] S, Liu L, Edwards SV, Wu SY. Resolving conflict in eutherian mammal phylogeny using phylogenomics and the multispecies coalescent model. Proc Natl Acad Sci USA , 2012, 109(37): 14942-14947.
[10] B, Bork P, Huynen MA. Genome phylogeny based on gene content. Nat Genet , 1999, 21(1): 108-110.
[11] BM, Wang LS, Warnow T, Wyman SK. New approaches for reconstructing phylogenies from gene order data. Bioinformatics , 2001, 17(Suppl.1): S165-S173.
[12] C, Steel M. A supertree method for rooted trees. Discrete Appl Math , 2000, 105(1-3): 147-158.
[13] BL, Qi J. Prokaryote phylogeny without sequence alignment: from avoidance signature to composition distance. J Bioinform Comput Biol , 2004, 2(1): 1-19.
[14] 张亚平. 系统发育基因组学——重建生命之树的一条迷人途径. 遗传, 2006, 28(11): 1445-1450.
[15] T, Gevers D, Van de Peer Y, Vandamme P, Swings J. Towards a prokaryotic genomic taxonomy. FEMS Micr o biol Rev , 2005, 29(2): 147-167.
[16] 孙啸. 基于全基因组的系统发生分析. 生物技术, 2003, 13(6): 53-56.
[17] M, Eisen JA. A simple, fast, and accurate method of phylogenomic inference. Genome Biol , 2008, 9(10): R151.
[18] MA. Phylogenetic inference based on matrix representation of trees. Mol Phylogenet Evol , 1992, 1(1): 53-58.
[19] OR, Gittleman JL, Steel MA. The (super) tree of life: procedures, problems, and prospects. Annu Rev Ecol Syst , 2002, 33: 265-289.
[20] BR. Combining trees as a way of combining data sets for phylogenetic inference, and the desirability of combining gene trees. Taxon , 1992, 44(1): 3-10.
[21] ZG, Ye ZQ, Yu L, Shi P. Phylogenomic reconstruction of lactic acid bacteria: an update. BMC Evol Biol , 2011, 11: 1.
[22] PJ. The endosymbiotic origin, diversification and fate of plastids. Philos Trans R Soc Lond B Biol Sci , 2010, 365(1541): 729-748.
[23] A, Gribaldo S. Large-scale phylogenomic analyses indicate a deep origin of primary plastids within cyanobacteria. Mol Biol Evol , 2011, 28(11): 3019-3032.
[24] G, Derelle R, Paps J, Lang BF, Roger AJ, Shalchian-Tabrizi K, Ruiz-Trillo I. Phylogenetic relationships within the Opisthokonta based on phylogenomic analyses of conserved single-copy protein domains. Mol Biol Evol , 2012, 29(2): 531-544.
[25] F, Brinkmann H, Chourrout D, Philippe H. Tunicates and not cephalochordates are the closest living relatives of vertebrates. Nature , 2006, 439(7079): 965-968.
[26] XX, Liang D, Feng YJ, Chen MY, Zhang P. A versatile and highly efficient toolkit including 102 nuclear markers for vertebrate phylogenomics, tested by resolving the higher level relationships of the caudata. Mol Biol Evol , 2013, 30(10): 2235-2248.
[27] XX, Liang D, Wen JZ, Zhang P. Multiple genome alignments facilitate development of NPCL markers: a case study of tetrapod phylogeny focusing on t

Metrics

Comments

www.chinagene.cn
备案号：京ICP备09063187号

Advances in phylogenomics

PDF (PC)

Knowledge

Abstract

Cite this article

share this article

References

Related Articles 15

Recommended Articles

Metrics

Comments

[1]	Wenchao Zou, Linlin Shen, Jianguo Shen, Wei Cai, Jiasui Zhan, Fangluan Gao. A multigene phylogentic analysis of Potato virus Y and its application in strain identification [J]. Hereditas(Beijing), 2017, 39(10): 918-929.
[2]	Huazhao Yuan, Mizhen Zhao, Weimin Wu, HongMei Yu, Yaming Qian, Zhuangwei Wang, Xicheng Wang. Genome-wide identification and expression analysis of auxin-related gene families in grape [J]. HEREDITAS(Beijing), 2015, 37(7): 720-730.
[3]	Wuhe Jike,Zefeng Wu,Sanhong Fan,Xuguang Xi. Structure and evolution of the eukaryotic FANCJ-like proteins [J]. HEREDITAS(Beijing), 2015, 37(2): 204-213.
[4]	Xuejuan Li, Yuan Huang, Fumin Lei. Comparative and phylogenomic analyses on mitochondrial genomes of Arborophila species [J]. HEREDITAS(Beijing), 2014, 36(9): 912-920.
[5]	Xue Yu, Hong Yu, Lingfeng Kong, Qi Li. Phylogenetic analysis of tyrosinase gene family in the Pacific oyster (Crassostrea gigas Thunberg) [J]. HEREDITAS, 2014, 36(2): 135-144.
[6]	Haysa Ayelhan, Yan Guo, Wei Meng, Tianyan Yang, Yanwu Ma. Phylogeny and divergence time estimation of Schizothoracinae fishes in Xinjiang [J]. HEREDITAS(Beijing), 2014, 36(10): 1013-1020.
[7]	CAO Lian-Fei, NIU De-Fang, HE Shao-Yu, KUANG Hai-Ou, HU Fu-Liang. Phylogenetic relationships of honey bees (Hymenoptera: Apinae) in-ferred from mitochondrial and nuclear DNA sequences [J]. HEREDITAS, 2012, 34(8): 1057-1063.
[8]	YANG Ze-Min, CHEN Wei-Wen. Molecular phylogeny analysis of full-length vacA and cagA genes from Helicobacter pylori [J]. HEREDITAS, 2012, 34(7): 863-871.
[9]	. Phylogenetic relationships among Orthoptera insect groups based on complete sequences of 16S ribosomal RNA [J]. HEREDITAS, 2012, 34(5): 597-608.
[10]	LI Juan, ZHANG Ke-Qin. Genetic diversity of microorganisms [J]. HEREDITAS, 2012, 34(11): 1399-1408.
[11]	WANG Jin-Feng, ZHANG Ya-Ping, YU Li. Summary of phylogeny in family Felidae of Carnivora [J]. HEREDITAS, 2012, 34(11): 1365-1378.
[12]	. Sequencing and analysis of the complete mitochondrial genome of the King Cobra, Ophiophagus hannah (Serpents: Elapidae) [J]. HEREDITAS, 2010, 32(7): 719-725.
[13]	CHEN Juan, TUN Wen-Wu, JIE Xiao-Chi, GUO Man-Cai, YUAN Zhi-Fa. A new alignment-free sequence analysis based on the distribution of K-tuple [J]. HEREDITAS, 2010, 32(6): 606-612.
[14]	JIANG Wen-Ping, LI Jia-Le, ZHENG Run-Ling, HONG Gui-Ling. Analysis of complete mitochondrial genome of Cristaria plicata [J]. HEREDITAS, 2010, 32(2): 153-162.
[15]	PI Yan, LIN Juan, HOU Rong, SHEN Da-Leng, JIANG Ke-Ji, QIAO Shou-Yi. Development research of the genetics textbook in Chinese universities [J]. HEREDITAS, 2009, 31(1): 109-112.