Genomic diversity and evolution of the Hawaiian Islands endemic Kokia (Malvaceae)

Authors: KAYAL, EHSAN - Iowa State University; ARICK II, MARK - Mississippi State University; HSU, CHAN-YU - Mississippi State University; THRASH, ADAM - Mississippi State University; YORKSTON, MITSUKO - University Of Hawaii; MORDEN, CLIFFORD - University Of Hawaii; WENDEL, JONATHAN - Iowa State University; PETERSON, DANIEL - Mississippi State University; GROVER, CORRINNE - Iowa State University

Submitted to: G3: Genes, genomics, genetics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 7/8/2024
Publication Date: 8/6/2024
Citation: Kayal, E., Arick Ii, M.A., Hsu, C., Thrash, A., Yorkston, M., Morden, C.W., Wendel, J.F., Peterson, D.G., Grover, C.E. 2024. Genomic diversity and evolution of the Hawaiian Islands endemic Kokia (Malvaceae). G3: Genes, genomics, genetics. https://doi.org/10.1093/g3journal/jkae180.
DOI: https://doi.org/10.1093/g3journal/jkae180

Interpretive Summary: Island species are highly vulnerable due to habitat destruction and their often small population sizes with reduced genetic diversity. The Hawaiian Islands constitute the most isolated archipelago on the planet, harboring many endemic species. Kokia is an endangered flowering plant genus endemic to these islands, encompassing 3 extant and 1 extinct species. Recent studies provided evidence of unexpected genetic diversity within Kokia. Here, we provide high-quality genome assemblies for all 3 extant Kokia species, including an improved genome for Kokia drynarioides. All 3 Kokia genomes contain 12 chromosomes exhibiting high synteny within and between Kokia and the sister taxon Gossypioides kirkii. Gene content analysis revealed a net loss of genes in K. cookei compared to other species, whereas the gene complement in K. drynarioides remains stable and that of Kokia kauaiensis displays a net gain. A dated phylogeny estimates the divergence time from the last common ancestor for the 3 Kokia species at ~1.2 million years ago (mya), with the sister taxa (K. cookei + K. drynarioides) diverging ~0.8 mya. Kokia appears to have followed a stepping-stone pattern of colonization and diversification of the Hawaiian archipelago, likely starting on low or now submerged older islands. The genetic resources provided may benefit conservation efforts of this endangered endemic genus.

Technical Abstract: Island species are highly vulnerable due to habitat destruction and their often small population sizes with reduced genetic diversity. The Hawaiian Islands constitute the most isolated archipelago on the planet, harboring many endemic species. Kokia is an endangered flowering plant genus endemic to these islands, encompassing 3 extant and 1 extinct species. Recent studies provided evidence of unexpected genetic diversity within Kokia. Here, we provide high-quality genome assemblies for all 3 extant Kokia species, including an improved genome for Kokia drynarioides. All 3 Kokia genomes contain 12 chromosomes exhibiting high synteny within and between Kokia and the sister taxon Gossypioides kirkii. Gene content analysis revealed a net loss of genes in K. cookei compared to other species, whereas the gene complement in K. drynarioides remains stable and that of Kokia kauaiensis displays a net gain. A dated phylogeny estimates the divergence time from the last common ancestor for the 3 Kokia species at ~1.2 million years ago (mya), with the sister taxa (K. cookei + K. drynarioides) diverging ~0.8 mya. Kokia appears to have followed a stepping-stone pattern of colonization and diversification of the Hawaiian archipelago, likely starting on low or now submerged older islands. The genetic resources provided may benefit conservation efforts of this endangered endemic genus.