Department of Molecular and Cell, University of California, Berkeley, CA, 94720, USA.
US Department of Energy Joint Genome Institute, 1 Cyclotron Road, Berkeley, CA, 94720, USA.
Nat Commun. 2023 Jun 1;14(1):3180. doi: 10.1038/s41467-023-38560-z.
Hybridization brings together chromosome sets from two or more distinct progenitor species. Genome duplication associated with hybridization, or allopolyploidy, allows these chromosome sets to persist as distinct subgenomes during subsequent meioses. Here, we present a general method for identifying the subgenomes of a polyploid based on shared ancestry as revealed by the genomic distribution of repetitive elements that were active in the progenitors. This subgenome-enriched transposable element signal is intrinsic to the polyploid, allowing broader applicability than other approaches that depend on the availability of sequenced diploid relatives. We develop the statistical basis of the method, demonstrate its applicability in the well-studied cases of tobacco, cotton, and Brassica napus, and apply it to several cases: allotetraploid cyprinids, allohexaploid false flax, and allooctoploid strawberry. These analyses provide insight into the origins of these polyploids, revise the subgenome identities of strawberry, and provide perspective on subgenome dominance in higher polyploids.
杂交将来自两个或更多不同祖先物种的染色体组结合在一起。与杂交相关的基因组复制，即异源多倍体，允许这些染色体组在随后的减数分裂中作为不同的亚基因组持续存在。在这里，我们提出了一种基于重复元件基因组分布的鉴定多倍体亚基因组的通用方法，这些重复元件在祖先中是活跃的。这种亚基因组富集的转座元件信号是多倍体固有的，其适用性比其他依赖于已测序的二倍体亲缘关系的方法更广泛。我们开发了该方法的统计基础，证明了它在烟草、棉花和油菜等研究充分的情况下的适用性，并将其应用于几个案例：异源四倍体鲤科鱼类、异源六倍体假亚麻和同源八倍体草莓。这些分析提供了对这些多倍体起源的深入了解，修正了草莓的亚基因组身份，并为高等多倍体中亚基因组优势提供了视角。
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