Data from: Divergent subgenome evolution after allopolyploidization in African clawed frogs (Xenopus)

Whole genome duplication (WGD), the doubling of the nuclear DNA of a species, contributes to biological innovation by creating genetic redundancy. One mode of WGD is allopolyploidization, wherein each genome from two ancestral species becomes a 'subgenom' of a polyploid descendant species. The evolutionary trajectory of a duplicated gene that arises from WGD is influenced both by natural selection, creating new or partitioning functions, and by gene silencing (pseudogenization). Here, we explored how these two phenomena varied over time and within allopolyploid genomes in several allotetraploid clawed frog species (Xenopus). Our analysis demonstrates that, across these polyploid genomes, purifying selection was greatly relaxed compared to a diploid outgroup, was asymmetric between each subgenome, and that coding regions are shorter in the subgenome with more relaxed purifying selection. As well, we found that the rate of gene loss was higher in the subgenome under weaker purifying selection and has remained relatively consistent over time after WGD. Our findings provide perspective from vertebrates on the evolutionary forces that likely shape allopolyploid genomes on other branches of the tree of life.

全基因组复制（Whole genome duplication, WGD）指物种核DNA发生加倍，通过产生遗传冗余推动生物创新。异源多倍化（allopolyploidization）是WGD的一类模式，即两个祖先物种的每套基因组分别成为多倍体后代物种的一套‘亚基因组（subgenome）’。由WGD产生的重复基因的进化轨迹，同时受自然选择与基因沉默（假基因化，pseudogenization）的影响：前者可催生新功能或实现功能分化，后者则会使基因失活。
本研究以数种异源四倍体爪蟾属（Xenopus）物种为研究对象，探究了这两种现象随时间推移以及在异源多倍体基因组内的变化规律。分析结果表明，相较于二倍体外类群（outgroup），这些多倍体基因组所受的纯化选择（purifying selection）显著放松；且两套亚基因组间的纯化选择强度存在不对称性，纯化选择更宽松的亚基因组中编码区长度更短。此外，研究发现纯化选择较弱的亚基因组发生基因丢失的速率更高，且该速率在WGD事件后长期保持相对稳定。
本研究为理解生命之树其他分支上塑造异源多倍体基因组的进化力量，提供了来自脊椎动物的研究视角。