Kokia, Gossypioides, and Their Sister, Gossypium

Kokia and Gossypioides are sister genera to Gossypium. Kokia is limited to the Hawaiian Islands while Gossypioides is found only in Madagascar and East Africa. Recently, we sequenced the genome of Kokia drynarioides and annotated the K. drynarioides and existing Gossypioidies kirkii draft genomes. Comparison of these two genomes with each other and that of Gossypium raimondii allowed us to generate estimates of divergence based on 13,000 gene orthologs. Our analysis indicates that the Kokia/Gossypioides lineage diverged from Gossypium roughly 10 MYA, while Kokia and Gossypioides diverged about 5 MYA after a 17,500 km transoceanic dispersal event delivered a Kokia ancestor to Hawaii. Study of the gene contents of the three species indicates that both Kokia and Gossypioides have experienced significant net gene losses (30% or about 10,000 genes) since their divergence from Gossypium raimondii. As the vast majority of gene deletions are common to both G. kirkii and K. drynarioides, it is likely that most gene deletion events occurred prior to the Gossypioides/Kokia split. With regard to repeat sequences, Kokia and Gossypioides have statistically indistinguishable repeat sequence contents and distributions despite representing different genera. In contrast, G. raimondii has a greatly reduced repeat content compared to G. herbaceum and G. arboreum. Not surprisingly, the major repeat sequence differences between Gossypioides kirkii, K. drynarioides, G. ramondii, and the A-genome cottons is a reflection of the relative abundance of LTR/Gypsy retrotransposons. The genome sequences of Kokia and Gossypioides are of interest not only as outgroups to Gossypium, but because their high levels of gene deletion make them interesting subjects for studying gene reduction in non-parasitic plants.