Article

Genomic diversifications of five Gossypium allopolyploid species and their impact on cotton improvement

Z. Jeffrey ChenDepartment of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USAAvinash SreedasyamHudsonAlpha Institute for Biotechnology, Huntsville, AL, USAAtsumi AndoDepartment of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USAQingxin SongDepartment of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USALuis M. De SantiagoDepartment of Soil and Crop Sciences, Texas A&M University System, College Station, TX, USAAmanda M. Hulse‐KempUS Department of Agriculture-Agricultural Research Service, Genomics and Bioinformatics Research Unit, Raleigh, NC, USAMingquan DingCollege of Agriculture and Food Science, Zhejiang A&F University, Lin'an, ChinaWenxue YeState Key Laboratory for Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, ChinaRyan C. KirkbrideDepartment of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USAJerry JenkinsHudsonAlpha Institute for Biotechnology, Huntsville, AL, USAChristopher PlottHudsonAlpha Institute for Biotechnology, Huntsville, AL, USAJohn T. LovellHudsonAlpha Institute for Biotechnology, Huntsville, AL, USALin Yu-MingDepartment of Soil and Crop Sciences, Texas A&M University System, College Station, TX, USARobert N. VaughnDepartment of Soil and Crop Sciences, Texas A&M University System, College Station, TX, USABo LiuDepartment of Soil and Crop Sciences, Texas A&M University System, College Station, TX, USASheron SimpsonUS Department of Agriculture-Agricultural Research Service, Genomics and Bioinformatics Research Unit, Stoneville, MS, USABrian E. SchefflerUS Department of Agriculture-Agricultural Research Service, Genomics and Bioinformatics Research Unit, Stoneville, MS, USAWen LiDepartment of Plant and Environmental Sciences, Clemson University, Clemson, SC, USAChristopher SaskiDepartment of Plant and Environmental Sciences, Clemson University, Clemson, SC, USACorrinne E. GroverDepartment of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA, USAGuanjing HuDepartment of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA, USAJustin L. ConoverDepartment of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA, USAJoseph W. CarlsonThe US Department of Energy Joint Genome Institute, Walnut Creek, CA, USAShengqiang ShuThe US Department of Energy Joint Genome Institute, Walnut Creek, CA, USALori Beth BostonHudsonAlpha Institute for Biotechnology, Huntsville, AL, USAMelissa WilliamsHudsonAlpha Institute for Biotechnology, Huntsville, AL, USADaniel G. PetersonInstitute for Genomics, Biocomputing and Biotechnology and Department of Plant and Soil Sciences, Mississippi State University, Mississippi State, MS, USAKeith McGeeSchool of Agriculture and Applied Sciences, Alcorn State University, Lorman, MS, USADon C. JonesAgriculture and Environmental Research, Cotton Incorporated, Cary, NC, USAJonathan F. WendelDepartment of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA, USADavid M. StellyDepartment of Soil and Crop Sciences, Texas A&M University System, College Station, TX, USAJane GrimwoodHudsonAlpha Institute for Biotechnology, Huntsville, AL, USAJeremy SchmutzHudsonAlpha Institute for Biotechnology, Huntsville, AL, USA

2020en

ABI

Abstract

Abstract Polyploidy is an evolutionary innovation for many animals and all flowering plants, but its impact on selection and domestication remains elusive. Here we analyze genome evolution and diversification for all five allopolyploid cotton species, including economically important Upland and Pima cottons. Although these polyploid genomes are conserved in gene content and synteny, they have diversified by subgenomic transposon exchanges that equilibrate genome size, evolutionary rate heterogeneities and positive selection between homoeologs within and among lineages. These differential evolutionary trajectories are accompanied by gene-family diversification and homoeolog expression divergence among polyploid lineages. Selection and domestication drive parallel gene expression similarities in fibers of two cultivated cottons, involving coexpression networks and N 6 -methyladenosine RNA modifications. Furthermore, polyploidy induces recombination suppression, which correlates with altered epigenetic landscapes and can be overcome by wild introgression. These genomic insights will empower efforts to manipulate genetic recombination and modify epigenetic landscapes and target genes for crop improvement.

Identifiers

DOI: 10.1038/s41588-020-0614-5

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