Chloroplast DNA Structural Variation, Phylogeny, and Age of Divergence among Diploid Cotton Species.
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.
Department of Plant Genetics and Breeding/Key Laboratory of Crop Heterosis and Utilization of Ministry of Education/Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China.
Zhiwen
Z
Chen
State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, Henan, China.
Kun
K
Feng
Department of Ecology, Evolution and Organismal Biology, Iowa State University, Ames, IA 50011, United States of America.
Corrinne E
CE
Grover
Department of Plant Genetics and Breeding/Key Laboratory of Crop Heterosis and Utilization of Ministry of Education/Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China.
Pengbo
P
Li
State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, Henan, China.
Fang
F
Liu
Department of Plant Genetics and Breeding/Key Laboratory of Crop Heterosis and Utilization of Ministry of Education/Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China.
Yumei
Y
Wang
Department of Plant Genetics and Breeding/Key Laboratory of Crop Heterosis and Utilization of Ministry of Education/Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China.
Qin
Q
Xu
State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, Henan, China.
Mingzhao
M
Shang
State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, Henan, China.
Zhongli
Z
Zhou
State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, Henan, China.
Xiaoyan
X
Cai
State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, Henan, China.
Xingxing
X
Wang
Department of Ecology, Evolution and Organismal Biology, Iowa State University, Ames, IA 50011, United States of America.
Jonathan F
JF
Wendel
State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, Henan, China.
Kunbo
K
Wang
Department of Plant Genetics and Breeding/Key Laboratory of Crop Heterosis and Utilization of Ministry of Education/Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China.
Jinping
http://orcid.org/0000-0002-4110-8179
J
Hua
D002736:Chloroplasts / Q000235:genetics*; D056915:DNA Copy Number Variations; D018742:DNA, Chloroplast / Q000235:genetics*; D004171:Diploidy; D049810:Genetic Speciation; D054628:Genome, Chloroplast; D003368:Gossypium / Q000145:classification / Q000235:genetics*; D054643:INDEL Mutation; D016366:Open Reading Frames; D010802:Phylogeny; D017422:Sequence Analysis, DNA; D057891:Tetraploidy
D018742:DNA, Chloroplast