Molecular evolution of the plastid genome during diversification of the cotton genus.

•Gossypium chloroplasts genome size attributable to indels occurred in the LSC region.•IR-single copy region junctions are both variable and homoplasious among species.•Phylogenetic analysis revealed new information on intrageneric relationships.•The D-genome inferred indicated the earliest lineages of the D-genome are extinct.•Early radiation of all major clades within the genus indicative of extinctions.