Peng, RenhaiXu, YanchaoTian, ShilinUnver, TurgayLiu, ZhenZhou, ZhongliCai, XiaoyanWang, KunboWei, YangyangLiu, YulingWang, HengHu, GuanjingZhang, ZhongrenGrover, Corrinne E.Hou, YuqingWang, YuhongLi, PengtaoWang, TaoLu, QuanweWang, YuanyuanGhazal, HassanZhang, BaohongVan Montagu, MarcVan de Peer, YvesWendel, Jonathan F.Liu, Fang2023-10-122023-10-122022-09-19Peng, R., Xu, Y., Tian, S. et al. 2022, 'Evolutionary divergence of duplicated genomes in newly described allotetraploid cottons', Proceedings of the National Academy of Sciences of the United States of America, vol. 119, no. 39, pp. 1-11. DOI : 10.1073/pnas.2208496119.0027-8424 (print)1091-6490 (online)10.1073/pnas.2208496119http://hdl.handle.net/2263/92854DATA, MATERIALS AND SOFTWARE AVAILABILITY : Raw sequencing and transcriptome data for the three newly assembled cotton genomes have been deposited in the National Center for Biotechnology Information (NCBI) Sequence Read Archive, https://www.ncbi.nlm.nih.gov/sra (BioProject accession no. PRJNA739494) (115). The genome sequence information is available under accession nos. JAHRBX 000000000, JAHRHL000000000, and JAHRHM000000000 (116, 117, 118). The genome assembly raw data and the transcriptomic data are available under accession nos. SRR15018757–SRR15111907 (119, 120) and SRR14970131– SRR14970150 (121, 122), respectively. All other study data are included in the main text and supporting information.SUPPLEMENTARY MATERIALS : SUPPLEMENTARY FILE 1. pnas.2208496119.sapp.pdf (2.6M) GUID: D25CC3F8-FF90-4D6F-B54F-0A0B4CC4F93D SUPPLEMENTARY FILE 2. pnas.2208496119.sd01.xlsx (1.2M) GUID: B44CFC56-4825-4A18-9934-FB836193F045 SUPPLEMENTARY FILE 3. pnas.2208496119.sd02.xlsx (17K) GUID: 21D0A0AF-8FC3-45E3-80D3-13C98D0C12F4Allotetraploid cotton (Gossypium) species represents a model system for the study of plant polyploidy, molecular evolution, and domestication. Here, chromosome-scale genome sequences were obtained and assembled for two recently described wild species of tetraploid cotton, Gossypium ekmanianum [(AD)6, Ge] and Gossypium stephensii [(AD)7, Gs], and one early form of domesticated Gossypium hirsutum, race punctatum [(AD)1, Ghp]. Based on phylogenomic analysis, we provide a dated whole-genome level perspective for the evolution of the tetraploid Gossypium clade and resolved the evolutionary relationships of Gs, Ge, and domesticated G. hirsutum. We describe genomic structural variation that arose during Gossypium evolution and describe its correlates— including phenotypic differentiation, genetic isolation, and genetic convergence— that contributed to cotton biodiversity and cotton domestication. Presence/absence variation is prominent in causing cotton genomic structural variations. A presence/ absence variation-derived gene encoding a phosphopeptide-binding protein is implicated in increasing fiber length during cotton domestication. The relatively unimproved Ghp offers the potential for gene discovery related to adaptation to environmental challenges. Expanded gene families enoyl-CoA δ isomerase 3 and RAP2-7 may have contributed to abiotic stress tolerance, possibly by targeting plant hormone-associated biochemical pathways. Our results generate a genomic context for a better understanding of cotton evolution and for agriculture.en© 2022 the Author(s). Published by PNAS. This open access article is distributed under Creative Commons Attribution-NonCommercial-NoDerivatives License 4.0 (CC BY-NC-ND).Tetraploid cottonPolyploid dynamicsStructure variationsAdaptive evolutionAllotetraploid cotton (Gossypium)Article