Widespread incomplete lineage sorting and introgression shaped adaptive radiation in the Gossypium genus  

作　　者：Yanchao Xu Yangyang Wei Zhongli Zhou Xiaoyan Cai Scott ABoden Muhammad Jawad Umer Luqman BSafdar Yuling Liu Dingsha Jin Yuqing Hou Yuhong Wang Sarah Brooke Wall Kunbo Wang Shuxun Yu Baohong Zhang Renhai Peng Fang Liu 

机构地区：[1]National Key Laboratory of Cotton Bio-breeding and Integrated Utilization,Institute of Cotton Research,Chinese Academy of Agricultural Sciences,Anyang 455000,China [2]College of Plant Science and Technology,Huazhong Agricultural University,Wuhan 40070,China [3]College of Biology and Food Engineering,Anyang Institute of Technology,Anyang 455000,China [4]National Nanfan Research Institute(Sanya),Chinese Academy of Agricultural Sciences,Sanya 572024,China [5]School of Agriculture,Food and Wine,University of Adelaide,Adelaide,SA 5005,Australia [6]Sanya Institute,Hainan Academy of Agricultural Sciences,Sanya 572000,China [7]Department of Biology,East Carolina University,Greenville,NC 27858,USA [8]School of Agricultural Sciences,Zhengzhou University,Zhengzhou 450001,China

出　　处：《Plant Communications》2024年第2期185-197,共13页植物通讯（英文）

基　　金：the National Natural Science Foundation of China (32272090,32171994,and 32072023);the Central Plains Science and Technology Innovation Leader Project (214200510029 and 2022C01NY001);the Project of Sanya Yazhou Bay Science and Technology City (SCKY-JYRC-2022-88);the National Key R&D Program of China (2021YFE0101200)for financial support.

摘　　要：Cotton(Gossypium)stands as a crucial economic crop,serving as the primary source of naturalfiber 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 assem-blies—G.harknessii,G.gossypioides,G.trilobum,and G.klotzschianum(Gklo)—to delve into the speciation history of this genus.Notably,we encountered intricate phylogenies potentially stemming from introgres-sion.These complexities are further compounded by incomplete lineage sorting(ILS),a factor likely to have been 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,Gklo,and G.raimondii,we constructed afinely 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 per-taining to speciation emerged between the closely related sister species Gklo and G.davidsonii.Approxi-mately 15.74%of speciation structural variation genes and 12.04%of speciation-associated genes were esti-mated to intersect with ILS signatures.Thesefindings enrich our understanding of the role of ILS in adaptive radiation,shedding fresh light on the intricate speciation history of the Gossypium genus.

关 键 词：cotton speciation Gossypium genus incomplete lineage sorting ILS phylogenetic analysis gene tree resolution 

分 类 号：S562[农业科学—作物学]