Comparative Genomics of an Unusual Biogeographic Disjunction in the Cotton Tribe (Gossypieae) Yields Insights into Genome Downsizing

Abstract

Long-distance insular dispersal is associated with divergence and speciation because of founder effects and strong genetic drift. The cotton tribe (Gossypieae) has experienced multiple transoceanic dispersals, generating an aggregate geographic range that encompasses much of the tropics and subtropics worldwide. Two genera in the Gossypieae, Kokia and Gossypioides, exhibit a remarkable geographic disjunction, being restricted to the Hawaiian Islands and Madagascar/East Africa, respectively. We assembled and use de novo genome sequences to address questions regarding the divergence of these two genera from each other and from their sister-group, Gossypium. In addition, we explore processes underlying the genome downsizing that characterizes Kokia and Gossypioides relative to other genera in the tribe. Using 13,000 gene orthologs and synonymous substitution rates, we show that the two disjuncts last shared a common ancestor ∼5 Ma, or half as long ago as their divergence from Gossypium. We report relative stasis in the transposable element fraction. In comparison to Gossypium, there is loss of ∼30% of the gene content in the two disjunct genera and a history of genome-wide accumulation of deletions. In both genera, there is a genome-wide bias toward deletions over insertions, and the number of gene losses exceeds the number of gains by ∼2- to 4-fold. The genomic analyses presented here elucidate genomic consequences of the demographic and biogeographic history of these closest relatives of Gossypium, and enhance their value as phylogenetic outgroups.

Insights into the Evolution of the New World Diploid Cottons (Gossypium, SubgenusHouzingenia) Based on Genome Sequencing

“…A similar conclusion was reached for the two A-genome (subgenus Gossypium ) species, whose small change in genome size (∼1.05×) masks differences in TE accumulation (Renny-Byfield et al. 2016; Grover et al. 2017).…”

“…Species divergence time estimates were calculated via chronos from {ape} (Paradis et al. 2004), using the divergence estimates previously calculated for the Malvaceae (Grover et al. 2017) and penalized likelihood (Sanderson 2002; Kim and Sanderson 2008) and maximum likelihood.…”

“…2017). Furthermore, research comparing the two sister genera to cotton [i.e., Kokia and Gossypioides ; {Grover et al. 2017}] reveals that their equivalent genome sizes belies a more dynamic scenario of repetitive sequence gain and loss.…”

The genomic landscape of molecular responses to natural drought stress in Panicum hallii

“…The majority of PAV genes were private to either HAL2 or FIL2 and never had orthologous sequences in any outgroups (Table 1 , Supplementary Data 5 ). Other studies find that such private genes are generally of low quality 18 and may not represent novel derived CDS, but instead are simply due to weak gene evidence that only survives thresholding in a single genome 19 . Indeed, private genes were 9.6x more likely to be low confidence, with low homology or transcript support, than 1:1 orthogroup genes.…”

Genome sequencing of the Australian wild diploid species Gossypium australe highlights disease resistance and delayed gland morphogenesis

“…A Markov Chain Monte Carlo analysis was run for 1 000 000 generations using a burn‐in of 100 000 iterations. Divergence time for the root node of Malvaceae obtained from the fossil estimate (Carvalho et al ., ; Grover et al ., ) and TimeTree database ( http://www.timetree.org/) was used as the calibration point.…”