Chloroplast DNA Structural Variation, Phylogeny, and Age of Divergence among Diploid Cotton Species

被引：37

作者：

Chen, Zhiwen ^{[1
]}

Feng, Kun ^{[2
]}

Grover, Corrinne E. ^{[3
]}

Li, Pengbo ^{[1
]}

Liu, Fang ^{[2
]}

Wang, Yumei ^{[1
]}

Xu, Qin ^{[1
]}

Shang, Mingzhao ^{[2
]}

Zhou, Zhongli ^{[2
]}

Cai, Xiaoyan ^{[2
]}

Wang, Xingxing ^{[2
]}

Wendel, Jonathan F. ^{[3
]}

Wang, Kunbo ^{[2
]}

Hua, Jinping ^{[1
]}

机构：

[1] China Agr Univ, Beijing Key Lab Crop Genet Improvement, Minist Educ, Key Lab Crop Heterosis & Utilizat,Dept Plant Gene, Beijing 100193, Peoples R China

[2] Chinese Acad Agr Sci, Inst Cotton Res, State Key Lab Cotton Biol, Anyang 455000, Henan, Peoples R China

[3] Iowa State Univ, Dept Ecol Evolut & Organismal Biol, Ames, IA 50011 USA

来源：

PLOS ONE | 2016年 / 11卷 / 06期

基金：

中国国家自然科学基金;

关键词：

MULTIPLE SEQUENCE ALIGNMENT; GENOME SEQUENCE; EVOLUTIONARY HISTORY; MAXIMUM-LIKELIHOOD; GOSSYPIUM-HIRSUTUM; PROVIDES INSIGHTS; GENUS GOSSYPIUM; NUCLEOTIDE; CHARACTERS; ORGANIZATION;

D O I：

10.1371/journal.pone.0157183

中图分类号：

O [数理科学和化学]; P [天文学、地球科学]; Q [生物科学]; N [自然科学总论];

学科分类号：

07 ; 0710 ; 09 ;

摘要：

The cotton genus (Gossypium spp.) contains 8 monophyletic diploid genome groups (A, B, C, D, E, F, G, K) and a single allotetraploid clade (AD). To gain insight into the phylogeny of Gossypium and molecular evolution of the chloroplast genome in this group, we performed a comparative analysis of 19 Gossypium chloroplast genomes, six reported here for the first time. Nucleotide distance in non-coding regions was about three times that of coding regions. As expected, distances were smaller within than among genome groups. Phylogenetic topologies based on nucleotide and indel data support for the resolution of the 8 genome groups into 6 clades. Phylogenetic analysis of indel distribution among the 19 genomes demonstrates contrasting evolutionary dynamics in different clades, with a parallel genome downsizing in two genome groups and a biased accumulation of insertions in the clade containing the cultivated cottons leading to large (for Gossypium) chloroplast genomes. Divergence time estimates derived from the cpDNA sequence suggest that the major diploid clades had diverged approximately 10 to 11 million years ago. The complete nucleotide sequences of 6 cpDNA genomes are provided, offering a resource for cytonuclear studies in Gossypium.

引用

页数：16

共 73 条

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