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Parallel subgenome structure and divergent expression evolution of allo-tetraploid common carp and goldfish

文献类型： 外文期刊

作者： Li, Jiong-Tang 1 ; Wang, Qi 1 ; Yang, Mei-Di Huang 1 ; Li, Qing-Song 1 ; Cui, Ming-Shu 1 ; Dong, Zai-Jie 4 ; Wang, Hon 1 ;

作者机构： 1.Chinese Acad Fishery Sci, Key Lab Aquat Genom, Beijing Key Lab Fishery Biotechnol, Minist Agr & Rural Affairs, Beijing, Peoples R China

2.Shanghai Ocean Univ, Coll Fisheries & Life Sci, Shanghai, Peoples R China

3.Chinese Acad Agr Sci, Beijing, Peoples R China

4.Chinese Acad Fishery Sci, Key Lab Freshwater Fisheries & Germplasm Resource, Freshwater Fisheries Res Ctr, Minist Agr & Rural Affairs, Wuxi, Jiangsu, Peoples R China

5.Chinese Acad Fishery Sci, Heilongjiang River Fisheries Res Inst, Harbin, Peoples R China

6.North China Univ Sci & Technol, Tangshan, Peoples R China

期刊名称：NATURE GENETICS （ 影响因子：38.33； 五年影响因子：36.431 ）

ISSN： 1061-4036

年卷期： 2021 年 53 卷 10 期

页码：

收录情况： SCI

摘要： Genomic analysis of allo-tetraploid common carp and goldfish identifies parallel subgenome structure and divergent expression processes. How two subgenomes in allo-tetraploids adapt to coexistence and coordinate through structure and expression evolution requires extensive studies. In the present study, we report an improved genome assembly of allo-tetraploid common carp, an updated genome annotation of allo-tetraploid goldfish and the chromosome-scale assemblies of a progenitor-like diploid Puntius tetrazona and an outgroup diploid Paracanthobrama guichenoti. Parallel subgenome structure evolution in the allo-tetraploids was featured with equivalent chromosome components, higher protein identities, similar transposon divergence and contents, homoeologous exchanges, better synteny level, strong sequence compensation and symmetric purifying selection. Furthermore, we observed subgenome expression divergence processes in the allo-tetraploids, including inter-/intrasubgenome trans-splicing events, expression dominance, decreased expression levels, dosage compensation, stronger expression correlation, dynamic functionalization and balancing of differential expression. The potential disorders introduced by different progenitors in the allo-tetraploids were hypothesized to be alleviated by increasing structural homogeneity and performing versatile expression processes. Resequencing three common carp strains revealed two major ecotypes and uncovered candidate genes relevant to growth and survival rate.

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