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Mol Phylogenet Evol. 2017 Jul;112:268-276. doi: 10.1016/j.ympev.2017.04.014. Epub 2017 Apr 13.

Molecular evolution of the plastid genome during diversification of the cotton genus.

Author information

1
Laboratory of Cotton Genetics, Genomics and Breeding, College of Agronomy and Biotechnology/Key Laboratory of Crop Heterosis and Utilization of Ministry of Education/Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China. Electronic address: b1301031@cau.edu.cn.
2
Department of Ecology, Evolution and Organismal Biology, Iowa State University, Ames, IA 50011, USA. Electronic address: corrinne@iastate.edu.
3
Laboratory of Cotton Genetics, Genomics and Breeding, College of Agronomy and Biotechnology/Key Laboratory of Crop Heterosis and Utilization of Ministry of Education/Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China. Electronic address: lpbmhs@126.com.
4
Institute of Cash Crops, Hubei Academy of Agricultural Sciences, Wuhan 430064, Hubei, China. Electronic address: yumeiwang001@126.com.
5
Laboratory of Cotton Genetics, Genomics and Breeding, College of Agronomy and Biotechnology/Key Laboratory of Crop Heterosis and Utilization of Ministry of Education/Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China. Electronic address: niehs@cau.edu.cn.
6
Laboratory of Cotton Genetics, Genomics and Breeding, College of Agronomy and Biotechnology/Key Laboratory of Crop Heterosis and Utilization of Ministry of Education/Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China. Electronic address: yanpeng_zhao@cau.edu.cn.
7
Laboratory of Cotton Genetics, Genomics and Breeding, College of Agronomy and Biotechnology/Key Laboratory of Crop Heterosis and Utilization of Ministry of Education/Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China. Electronic address: 1289526725@qq.com.
8
State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, Henan, China. Electronic address: liufcri@163.com.
9
State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, Henan, China. Electronic address: zhonglizhou@163.com.
10
State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, Henan, China. Electronic address: wxx1991@126.com.
11
State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, Henan, China. Electronic address: kxncai0611@163.com.
12
State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, Henan, China. Electronic address: wkbcri@163.com.
13
Department of Ecology, Evolution and Organismal Biology, Iowa State University, Ames, IA 50011, USA. Electronic address: jfw@iastate.edu.
14
Laboratory of Cotton Genetics, Genomics and Breeding, College of Agronomy and Biotechnology/Key Laboratory of Crop Heterosis and Utilization of Ministry of Education/Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China. Electronic address: jinping_hua@cau.edu.cn.

Abstract

Cotton (Gossypium spp.) is commonly grouped into eight diploid genomic groups, designated A-G and K, and one tetraploid genomic group, namely AD. To gain insight into the phylogeny of Gossypium and molecular evolution of the chloroplast genome duringdiversification, chloroplast genomes (cpDNA) from 6 D-genome and 2 G-genome species of Gossypium (G. armourianum D2-1, G. harknessii D2-2, G. davidsonii D3-d, G. klotzschianum D3-k, G. aridum D4, G. trilobum D8, and G. australe G2, G. nelsonii G3) were newly reported here. In combination with the 26 previously released cpDNA sequences, we performed comparative phylogenetic analyses of 34 Gossypium chloroplast genomes that collectively represent most of the diversity in the genus. Gossypium chloroplasts span a small range in size that is mostly attributable to indels that occur in the large single copy (LSC) region of the genome. Phylogenetic analysis using a concatenation of all genes provides robust support for six major Gossypium clades, largely supporting earlier inferences but also revealing new information on intrageneric relationships. Using Theobroma cacao as an outgroup, diversification of the genus was dated, yielding results that are in accord with previous estimates of divergence times, but also offering new perspectives on the basal, early radiation of all major clades within the genus as well as gaps in the record indicative of extinctions. Like most higher-plant chloroplast genomes, all cotton species exhibit a conserved quadripartite structure, i.e., two large inverted repeats (IR) containing most of the ribosomal RNA genes, and two unique regions, LSC (large single sequence) and SSC (small single sequence). Within Gossypium, the IR-single copy region junctions are both variable and homoplasious among species. Two genes, accD and psaJ, exhibited greater rates of synonymous and non-synonymous substitutions than did other genes. Most genes exhibited Ka/Ks ratios suggestive of neutral evolution, with 8 exceptions distributed among one to several species. This research provides an overview of the molecular evolution of a single, large non-recombining molecular during the diversification of this important genus.

KEYWORDS:

Chloroplast genomes; Divergence time; Gossypium; Ka and Ks; Phylogenetic analysis

PMID:
28414099
DOI:
10.1016/j.ympev.2017.04.014
[Indexed for MEDLINE]

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