Campus Units

Ecology, Evolution and Organismal Biology

Document Type

Article

Publication Version

Published Version

Publication Date

2016

Journal or Book Title

PloS one

Volume

11

Issue

6

First Page

e0157183

DOI

10.1371/journal.pone.0157183

Abstract

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.

Comments

This article is published as Chen, Zhiwen, Kun Feng, Corrinne E. Grover, Pengbo Li, Fang Liu, Yumei Wang, Qin Xu et al. "Chloroplast DNA structural variation, phylogeny, and age of divergence among diploid cotton species." PloS one 11, no. 6 (2016): e0157183. 10.1371/journal.pone.0157183. Posted with permission.

Creative Commons License

Creative Commons Attribution 4.0 License
This work is licensed under a Creative Commons Attribution 4.0 License.

Copyright Owner

Chen et al.

Language

en

File Format

application/pdf

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