Abstract
Cotton is one of the most economically important fiber crop plants worldwide. The genus Gossypium contains a single allotetraploid group (AD) and eight diploid genome groups (A–G and K). However, the evolution of repeat sequences in the chloroplast genomes and the phylogenetic relationships of Gossypium species are unclear. Thus, we determined the variations in the repeat sequences and the evolutionary relationships of 40 cotton chloroplast genomes, which represented the most diverse in the genus, including five newly sequenced diploid species, i.e., G. nandewarense (C1-n), G. armourianum (D2-1), G. lobatum (D7), G. trilobum (D8), and G. schwendimanii (D11), and an important semi-wild race of upland cotton, G. hirsutum race latifolium (AD1). The genome structure, gene order, and GC content of cotton species were similar to those of other higher plant plastid genomes. In total, 2860 long sequence repeats (>10 bp in length) were identified, where the F-genome species had the largest number of repeats (G. longicalyx F1: 108) and E-genome species had the lowest (G. stocksii E1: 53). Large-scale repeat sequences possibly enrich the genetic information and maintain genome stability in cotton species. We also identified 10 divergence hotspot regions, i.e., rpl33-rps18, psbZ-trnG (GCC), rps4-trnT (UGU), trnL (UAG)-rpl32, trnE (UUC)-trnT (GGU), atpE, ndhI, rps2, ycf1, and ndhF, which could be useful molecular genetic markers for future population genetics and phylogenetic studies. Site-specific selection analysis showed that some of the coding sites of 10 chloroplast genes (atpB, atpE, rps2, rps3, petB, petD, ccsA, cemA, ycf1, and rbcL) were under protein sequence evolution. Phylogenetic analysis based on the whole plastomes suggested that the Gossypium species grouped into six previously identified genetic clades. Interestingly, all 13 D-genome species clustered into a strong monophyletic clade. Unexpectedly, the cotton species with C, G, and K-genomes were admixed and nested in a large clade, which could have been due to their recent radiation, incomplete lineage sorting, and introgression hybridization among different cotton lineages. In conclusion, the results of this study provide new insights into the evolution of repeat sequences in chloroplast genomes and interspecific relationships in the genus Gossypium.
Highlights
Cotton is one of the most economically important fiber crop plants throughout the world (Wendel, 1989; Ruan et al, 2003)
The coding sequence lengths of the six Gossypium chloroplast genomes ranged from 78,528 bp (G. hirsutum race latifolium) to 78,696 bp (G. lobatum)
The SSC and IR sizes ranged from 20,233 bp (G. trilobum) to 20,318 bp (G. schwendimanii) and from 25,550 bp (G. lobatum)
Summary
Cotton is one of the most economically important fiber crop plants throughout the world (Wendel, 1989; Ruan et al, 2003). The ancestor of cotton diversified into ∼46 diploid species (divided into eight genome groups designated as A–G and K) and 7 allotetraploid species designated as the AD genome (Senchina et al, 2003; Wendel et al, 2010; Grover et al, 2015; Wendel and Grover, 2015; Chen et al, 2017a,b). It is considered that the polyploid clade originated circa 1–2 million years ago, possibly due to transoceanic dispersal events involving an African-Asian A-genome species that subsequently hybridized with a New World D-genome species (Wendel, 1989; Adams and Wendel, 2004; Wendel and Grover, 2015; Chen et al, 2016, 2017a,b)
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