Maternal dominance contributes to subgenome differentiation in allopolyploid fishes.
Maternal dominance contributes to subgenome differentiation in allopolyploid fishes.
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异源多倍体鱼类亚基因组分化的母体优势。
DOI：
10.1038/s41467-023-43740-y
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发表时间：
2023-12-15
影响因子：
16.6
通讯作者：
Zhang, Hua-Hao
中科院分区：
文献类型：
--
作者：
Xu, Min-Rui-Xuan;Liao, Zhen-Yang;Brock, Jordan R.;Du, Kang;Li, Guo-Yin;Chen, Zhi-Qiang;Wang, Ying-Hao;Gao, Zhong-Nan;Agarwal, Gaurav;Wei, Kevin H-C;Shao, Feng;Pang, Shuai;Platts, Adrian E.;van de Velde, Jozefien;Lin, Hong-Min;Teresi, Scott J.;Bird, Kevin;Niederhuth, Chad E.;Xu, Jin-Gen;Yu, Guo-Hua;Yang, Jian-Yuan;Dai, Si-Fa;Nelson, Andrew;Braasch, Ingo;Zhang, Xiao-Gu;Schartl, Manfred;Edger, Patrick P.;Han, Min-Jin;Zhang, Hua-Hao
硬骨鱼是现存脊椎动物中最大、最多样化的类群，具有丰富的古代和现代多倍体历史。先前对异源四倍体鲤鱼和金鱼（鲤鱼）的研究报道了一个显性亚基因组，该亚基因组表达量更高，并表现出有偏差的基因保留。然而，导致观察到的“亚基因组优势”的潜在机制仍然知之甚少。在这里，我们报告了二十一个鲤鱼的高质量基因组，以研究三个独立的异源多倍体事件后的起源和随后的亚基因组进化模式。我们鉴定了二倍体祖先物种现存最接近的亲属，研究了亚基因组之间的遗传和表观遗传差异，并得出结论，观察到的亚基因组优势模式可能是由于每个多倍体中母本优势和转座元件密度的组合。这些发现为理解硬骨鱼中观察到的亚基因组优势模式以及最终多倍体在促进进化创新中的作用提供了重要基础。由于过去的重复，鲤科鱼类含有多个亚基因组。在这里，徐等人。报告了 21 种鲤鱼的新基因组，并得出结论，观察到的亚基因组优势模式可能是由于母体优势和每个多倍体中的转座元件密度所致。
Teleost fishes, which are the largest and most diverse group of living vertebrates, have a rich history of ancient and recent polyploidy. Previous studies of allotetraploid common carp and goldfish (cyprinids) reported a dominant subgenome, which is more expressed and exhibits biased gene retention. However, the underlying mechanisms contributing to observed ‘subgenome dominance’ remains poorly understood. Here we report high-quality genomes of twenty-one cyprinids to investigate the origin and subsequent subgenome evolution patterns following three independent allopolyploidy events. We identify the closest extant relatives of the diploid progenitor species, investigate genetic and epigenetic differences among subgenomes, and conclude that observed subgenome dominance patterns are likely due to a combination of maternal dominance and transposable element densities in each polyploid. These findings provide an important foundation to understanding subgenome dominance patterns observed in teleost fishes, and ultimately the role of polyploidy in contributing to evolutionary innovations. Cyprinids fish species contain multiple subgenomes as a result of past duplications. Here, Xu et al. report new genomes of 21 cyprinid fish and conclude that observed subgenome dominance patterns are likely due to both maternal dominance and transposable element densities in each polyploid.
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