Widespread Incomplete Lineage Sorting and Introgression Shaped Adaptive Radiation in the Gossypium genus

作者：棉花生物育种与综合利用全国重点实验室 日期：2023-10-24 访问量：

Yanchao Xu, Yangyang Wei, Zhongli Zhou, Xiaoyan Cai, Scott Boden, Muhammad Jawad Umer, Luqman Bin Safdar, Yuling Liu, Dingsha Jin, Yuqing Hou, Yuhong Wang, Sarah Brooke Wall, Kunbo Wang, Shuxun Yu , Baohong Zhang, Renhai Peng , Fang Liu

Plant Communication

Doi:10.1016/j.xplc.2023.100728

Abstract:

Cotton (Gossypium) stands as a crucial economic crop, serving as the primary source of natural fiber for the textile sector. However, the evolutionary mechanisms driving speciation within the Gossypium genus remain unresolved. In this investigation, we leveraged 25 Gossypium genomes and introduced four novel assemblies – G. harknessii (Ghar), G. Gossypioides (Ggos), G. trilobum (Gtri), and G. klotzschianum (Gklo) – to delve into the speciation history of this genus. Notably, we encountered intricate phylogenies potentially stemming from introgression. These complexities are further compounded by incomplete lineage sorting (ILS), a factor likely instrumental in shaping the swift diversification of cotton. Our focus subsequently shifted to the rapid radiation episode during a concise period in Gossypium evolution. For a recently diverged lineage comprising G. davidsonii (Gdav), Gklo, and G. raimondii (Grai), we constructed a finely detailed ILS map. Intriguingly, this analysis revealed the non-random distribution of ILS regions across the reference Gklo genome. Moreover, we identified signs of robust natural selection influencing specific ILS regions. Noteworthy variations pertaining to speciation emerged between the closely akin sister species Gklo and Gdav. Approximately 15.74% of speciation structural genes (SSV) and 12.04% of speciation-associated genes (SAGs) were estimated to intersect with ILS signatures. These findings contribute to an enriched comprehension of ILS's role in adaptive radiation, thereby shedding fresh light on the intricate speciation history of the Gossypium genus.