National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China.
Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA, USA.
Nat Genet. 2024 Nov;56(11):2562-2573. doi: 10.1038/s41588-024-01964-8. Epub 2024 Oct 29.
Polyploidy is an important driving force in speciation and evolution; however, the genomic basis for parallel selection of a particular trait between polyploids and ancestral diploids remains unexplored. Here we construct graph-based pan-genomes for diploid (A) and allotetraploid (AD) cotton species, enabled by an assembly of 50 genomes of genetically diverse accessions. We delineate a mosaic genome map of tetraploid cultivars that illustrates genomic contributions from semi-wild forms into modern cultivars. Pan-genome comparisons identify syntenic and hyper-divergent regions of continued variation between diploid and tetraploid cottons, and suggest an ongoing process of sequence evolution potentially linked to the contrasting genome size change in two subgenomes. We highlight 43% of genetic regulatory relationships for gene expression in diploid encompassing sequence divergence after polyploidy, and specifically characterize six underexplored convergent genetic loci contributing to parallel selection of fiber quality. This study offers a framework for pan-genomic dissection of genetic regulatory components underlying parallel selection of desirable traits in organisms.
多倍体是物种形成和进化的重要驱动力；然而，多倍体和其祖先二倍体之间特定性状平行选择的基因组基础仍未被探索。在这里，我们通过对 50 个遗传多样性品系的组装，构建了二倍体 (A) 和异源四倍体 (AD) 棉花的基于图的泛基因组。我们描绘了四倍体品种的镶嵌基因组图谱，说明了半野生形式对现代品种的基因组贡献。泛基因组比较鉴定了二倍体和四倍体棉花之间持续变异的同线性和超分化区域，并表明可能与两个亚基因组中基因组大小变化相反的序列进化过程。我们突出显示了涵盖多倍体后序列分歧的二倍体中基因表达的 43%的遗传调控关系，并特别描述了六个未充分探索的趋同遗传基因座，这些基因座对纤维质量的平行选择有贡献。本研究为解析生物体中有利性状平行选择的遗传调控成分提供了一个泛基因组框架。
