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.
Highlights
Cotton is the most important fiber crop plant in the world
Gossypium chloroplast genomes from six diploid species were newly sequenced for this study, representing four of the eight cotton diploid genome groups (G. robinsonii C2, G. incanum E4, G. somalense E2, G. capitis-viridis B3, G. areysianum E3, G. populifolium K; GenBank accessions JN019791 to JN019795 and KP221924, respectively)
These cp genomes (Table 1) show high identity and similarity in gene content and genome organization with each other and with previously published cotton cp genomes [20], with only minor differences in genome size and composition. The length of these six genomes range in size by only 521 bp, from the largest (G. robinsonii, C2, 159,726 bp) to the smallest (G. incanum, E4, 159,205 bp), with most of the size differences occurring in the large single-copy (LSC) region (Table 1 and Fig 1)
Summary
Cotton is the most important fiber crop plant in the world. Four species were domesticated and remain under cultivation today, the New World allopolyploids G. hirsutum and G. barbadense (2n = 52), and the Old World diploids G. arboreum and G. herbaceum (2n = 26) [1,2]. The primary cultivated species is Upland cotton (G. hirsutum L.), which accounts for more than 90% of global cotton fiber output. PLOS ONE | DOI:10.1371/journal.pone.0157183 June 16, 2016
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