Analysis of Complete Nucleotide Sequences of 12 <em>Gossypium</em> Chloroplast Genomes: Origin and Evolution of Allotetraploids

<div><h3>Background</h3><p>Cotton (<em>Gossypium</em> spp.) is a model system for the analysis of polyploidization. Although ascertaining the donor species of allotetraploid cotton has been intensively studied, sequence comparison of <em>Gossypium</em> chloroplast genomes is still of interest to understand the mechanisms underlining the evolution of <em>Gossypium</em> allotetraploids, while it is generally accepted that the parents were A- and D-genome containing species. Here we performed a comparative analysis of 13 <em>Gossypium</em> chloroplast genomes, twelve of which are presented here for the first time.</p> <h3>Methodology/Principal Findings</h3><p>The size of 12 chloroplast genomes under study varied from 159,959 bp to 160,433 bp. The chromosomes were highly similar having >98% sequence identity. They encoded the same set of 112 unique genes which occurred in a uniform order with only slightly different boundary junctions. Divergence due to indels as well as substitutions was examined separately for genome, coding and noncoding sequences. The genome divergence was estimated as 0.374% to 0.583% between allotetraploid species and A-genome, and 0.159% to 0.454% within allotetraploids. Forty protein-coding genes were completely identical at the protein level, and 20 intergenic sequences were completely conserved. The 9 allotetraploids shared 5 insertions and 9 deletions in whole genome, and 7-bp substitutions in protein-coding genes. The phylogenetic tree confirmed a close relationship between allotetraploids and the ancestor of A-genome, and the allotetraploids were divided into four separate groups. Progenitor allotetraploid cotton originated 0.43–0.68 million years ago (MYA).</p> <h3>Conclusion</h3><p>Despite high degree of conservation between the <em>Gossypium</em> chloroplast genomes, sequence variations among species could still be detected. <em>Gossypium</em> chloroplast genomes preferred for 5-bp indels and 1–3-bp indels are mainly attributed to the SSR polymorphisms. This study supports that the common ancestor of diploid A-genome species in <em>Gossypium</em> is the maternal source of extant allotetraploid species and allotetraploids have a monophyletic origin. <em>G. hirsutum</em> AD1 lineages have experienced more sequence variations than other allotetraploids in intergenic regions. The available complete nucleotide sequences of 12 <em>Gossypium</em> chloroplast genomes should facilitate studies to uncover the molecular mechanisms of compartmental co-evolution and speciation of <em>Gossypium</em> allotetraploids.</p>