Parallel subgenome structure and divergent expression evolution of allo-tetraploid common carp and goldfish
| Autor: | Zai-Jie Dong, Qi Wang, Ming-Shu Cui, Hong-Wei Wang, Ju-Hua Yu, Ya-Xin Wang, Jiong-Tang Li, Chen-Ru Yang, Yan Zhang, Ran Zhao, Qing-Song Li, Mei-Di Huang Yang, Zhi-Ying Jia, Yu-Jie Zhao, Xiyin Wang, Xiao-Qing Sun |
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| Rok vydání: | 2021 |
| Předmět: |
Candidate gene
Carps Karyotype Sequence assembly Biology Synteny Article Evolution Molecular Common carp Negative selection Species Specificity Goldfish Genetics Animals Selection Genetic Phylogeny Likelihood Functions Genome Dosage compensation Base Sequence Genetic Variation food and beverages Molecular Sequence Annotation Genomics Genome project Tetraploidy Alternative Splicing Gene Expression Regulation Evolutionary biology Gene expression Ploidy Zoology |
| Zdroj: | Nature Genetics |
| ISSN: | 1546-1718 1061-4036 |
| DOI: | 10.1038/s41588-021-00933-9 |
| Popis: | 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. Genomic analysis of allo-tetraploid common carp and goldfish identifies parallel subgenome structure and divergent expression processes. |
| Databáze: | OpenAIRE |
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