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Phylogenetic relationships and genome divergence among the AA- genome species of the genus Oryza as revealed by 53 nuclear genes and 16 intergenic regions
Zhu, Ting1,2; Xu, Ping-Zhen1; Liu, Jiang-Peng1; Peng, Sheng1; Mo, Xin-Chun1,2; Gao, Li-Zhi1
Corresponding AuthorGao,LZ (reprint author),Chinese Acad Sci,Kunming Inst Bot,Plant Germplasm & Genom Ctr,Germplasm Bank Wild Species Southwest China,Kunming 650204,Peoples R China. ; zhuting@mail.kib.ac.cn ; Xupzh@mail.kib.ac.cn ; Liujiangpeng@mail.kib.ac.cn ; Pengsh@mail.kib.ac.cn ; Moxinchun@mail.kib.ac.cn ; lgao@mail.kib.ac.cn
2014
Source PublicationMOLECULAR PHYLOGENETICS AND EVOLUTION
ISSN1055-7903
Volume70Pages:348-361
AbstractRapid radiations have long been regarded as the most challenging issue for elucidating poorly resolved phylogenies in evolutionary biology. The eight diploid AA- genome species in the genus Oryza represent a typical example of a closely spaced series of recent speciation events in plants. However, questions regarding when and how they diversified have long been an issue of extensive interest but remain a mystery. Here, a data set comprising >60 kb of 53 singleton fragments and 16 intergenic regions is used to perform phylogenomic analyses of all eight AA- genome species plus four diploid Oryza species with BB-, CC-, EE- and GG- genomes. We fully reconstruct phylogenetic relationships of AA- genome species with confidence. Oryza meridionalis, native to Australia, is found to be the earliest divergent lineage around 2.93 mya, whereas O. punctata, a BB- genome species, serves as the best outgroup to distinguish their phylogenetic relationships. They separated from O. punctata approximately 9.11 mya during the Miocene epoch, and subsequently radiated to generate the entire AA- genome lineage diversity. The success in resolving the phylogeny of AA- genome species highlights the potential of phylogenomics to determine their divergence and evolutionary histories. (C) 2013 Elsevier Inc. All rights reserved.
KeywordOryza Aa-genome Phylogenomics Genome Divergence Evolutionary History Rapid Recent Speciation
Subject AreaBiochemistry & Molecular Biology ; Evolutionary Biology ; Genetics & Heredity
DOI10.1016/j.ympev.2013.10.008
Indexed BySCI
Language英语
WOS Research AreaBiochemistry & Molecular Biology ; Evolutionary Biology ; Genetics & Heredity
WOS SubjectBiochemistry & Molecular Biology ; Evolutionary Biology ; Genetics & Heredity
WOS IDWOS:000328441100034
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Document Type期刊论文
Identifierhttp://ir.kib.ac.cn/handle/151853/17949
Collection中国西南野生生物种质资源库
Affiliation1.Chinese Acad Sci, Kunming Inst Bot, Plant Germplasm & Genom Ctr, Germplasm Bank Wild Species Southwest China, Kunming 650204, Peoples R China
2.Univ Chinese Acad Sci, Beijing 100039, Peoples R China
Recommended Citation
GB/T 7714
Zhu, Ting,Xu, Ping-Zhen,Liu, Jiang-Peng,et al. Phylogenetic relationships and genome divergence among the AA- genome species of the genus Oryza as revealed by 53 nuclear genes and 16 intergenic regions[J]. MOLECULAR PHYLOGENETICS AND EVOLUTION,2014,70:348-361.
APA Zhu, Ting,Xu, Ping-Zhen,Liu, Jiang-Peng,Peng, Sheng,Mo, Xin-Chun,&Gao, Li-Zhi.(2014).Phylogenetic relationships and genome divergence among the AA- genome species of the genus Oryza as revealed by 53 nuclear genes and 16 intergenic regions.MOLECULAR PHYLOGENETICS AND EVOLUTION,70,348-361.
MLA Zhu, Ting,et al."Phylogenetic relationships and genome divergence among the AA- genome species of the genus Oryza as revealed by 53 nuclear genes and 16 intergenic regions".MOLECULAR PHYLOGENETICS AND EVOLUTION 70(2014):348-361.
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