Genomic diversifications of five Gossypium allopolyploid species and their impact on cotton improvement.,Nature Genetics

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Genomic diversifications of five Gossypium allopolyploid species and their impact on cotton improvement.
Nature Genetics ( IF 31.7 ) Pub Date : 2020-04-20 , DOI: 10.1038/s41588-020-0614-5
Z Jeffrey Chen _{1,

2} , Avinash Sreedasyam ₃ , Atsumi Ando ₁ , Qingxin Song _{1,

2} , Luis M De Santiago ₄ , Amanda M Hulse-Kemp ₅ , Mingquan Ding _{1,

6} , Wenxue Ye ₂ , Ryan C Kirkbride ₁ , Jerry Jenkins ₃ , Christopher Plott ₃ , John Lovell ₃ , Yu-Ming Lin ₄ , Robert Vaughn ₄ , Bo Liu ₄ , Sheron Simpson ₇ , Brian E Scheffler ₇ , Li Wen ₈ , Christopher A Saski ₈ , Corrinne E Grover ₉ , Guanjing Hu ₉ , Justin L Conover ₉ , Joseph W Carlson ₁₀ , Shengqiang Shu ₁₀ , Lori B Boston ₃ , Melissa Williams ₃ , Daniel G Peterson ₁₁ , Keith McGee ₁₂ , Don C Jones ₁₃ , Jonathan F Wendel ₉ , David M Stelly ₄ , Jane Grimwood ₃ , Jeremy Schmutz _{3,

10}

Affiliation

Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA.
State Key Laboratory for Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, China.
HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA.
Department of Soil and Crop Sciences, Texas A&M University System, College Station, TX, USA.
US Department of Agriculture-Agricultural Research Service, Genomics and Bioinformatics Research Unit, Raleigh, NC, USA.
College of Agriculture and Food Science, Zhejiang A&F University, Lin'an, China.
US Department of Agriculture-Agricultural Research Service, Genomics and Bioinformatics Research Unit, Stoneville, MS, USA.
Department of Plant and Environmental Sciences, Clemson University, Clemson, SC, USA.
Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA, USA.
The US Department of Energy Joint Genome Institute, Walnut Creek, CA, USA.
Institute for Genomics, Biocomputing and Biotechnology and Department of Plant and Soil Sciences, Mississippi State University, Mississippi State, MS, USA.
School of Agriculture and Applied Sciences, Alcorn State University, Lorman, MS, USA.
Agriculture and Environmental Research, Cotton Incorporated, Cary, NC, USA.

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 N6-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.

中文翻译：

五种棉同种多倍体物种的基因组多样化及其对棉花改良的影响。

多倍体是许多动物和所有开花植物的进化创新，但其对选择和驯化的影响仍然难以捉摸。在这里，我们分析了所有五种多倍体棉种的基因组进化和多样化，包括具有经济意义的陆地棉和皮马棉。尽管这些多倍体基因组在基因含量和同义性上是保守的，但它们已通过亚基因组转座子交换而多样化，从而平衡了基因组的大小，进化速率的异质性以及沿袭和沿袭同源物之间的正向选择。这些不同的进化轨迹伴随着多倍体谱系之间的基因家族多样化和同源表达差异。选择和驯化驱动两种栽培棉纤维中平行基因表达的相似性，涉及共表达网络和N6-甲基腺苷RNA修饰。此外，多倍体诱导重组抑制，这与改变的表观遗传环境相关，可以通过野生渗入克服。这些基因组见解将使人们有能力进行基因重组，修饰表观遗传景观和目标基因以改善作物。

更新日期：2020-04-24

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