Genomic diversifications of five Gossypium allopolyploid species and their impact on cotton improvement
Genomic diversifications of five Gossypium allopolyploid species and their impact on cotton improvement
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DOI：
10.1038/s41588-020-0614-5
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发表时间：
2020-04-20
期刊：
影响因子：
30.8
通讯作者：
Schmutz, Jeremy
中科院分区：
文献类型：
--
作者：
Chen, Z. Jeffrey;Sreedasyam, Avinash;Schmutz, Jeremy
5个异源多倍体棉种的测序和基因组多样性为深入了解多倍体基因组进化和棉花改良提供了表观遗传图景。多倍体对许多动物和所有开花植物来说是一种进化创新，但它对选择和驯化的影响仍然难以捉摸。在这里，我们分析了所有五个异源多倍体棉花物种的基因组进化和多样性，包括经济上重要的陆地棉和皮马棉。虽然这些多倍体基因组在基因含量和同源性上是保守的，但它们已经通过亚基因组转座子交换而多样化，这种交换平衡了基因组大小、进化速度异质性和谱系内和谱系之间同源基因之间的正选择。这些不同的进化轨迹伴随着基因家族的多样化和多倍体谱系之间同源基因表达的差异。选择和驯化推动了两个栽培棉纤维中平行基因表达的相似性，包括共表达网络和N-6-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景观相关，可以通过野生导入来克服。这些基因组洞察力将使操纵基因重组、修改表观遗传景观和针对作物改良的基因的努力成为可能。
Sequencing and genomic diversification of five allopolyploid cotton species provide insights into polyploid genome evolution and epigenetic landscapes for cotton improvement.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.