An improved transcriptome annotation reveals asymmetric expression and distinct regulation patterns in allotetraploid common carp

文献类型： 外文期刊

第一作者： Wang, Qi

作者： Wang, Qi;Huang Yang, Meidi;Yu, Shuangting;Chen, Yingjie;Wang, Kaikuo;Zhang, Yan;Zhao, Ran;Li, Jiongtang;Wang, Qi;Huang Yang, Meidi;Yu, Shuangting;Chen, Yingjie;Wang, Kaikuo;Zhang, Yan;Zhao, Ran;Li, Jiongtang

作者机构：

期刊名称：COMMUNICATIONS BIOLOGY （ 影响因子：5.1； 五年影响因子：5.8 ）

ISSN：

年卷期： 2024 年 7 卷 1 期

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收录情况： SCI

摘要： In allotetraploid common carp, protein-coding homoeologs presented divergent expression levels between the two subgenomes. However, whether subgenome dominance occurs in other transcriptional and post-transcriptional events remains unknown. Using Illumina RNA sequencing and PacBio full-length sequencing, we refined the common carp transcriptome annotation and explored differences in four transcriptional and post-transcriptional events between the two subgenomes. The results revealed that the B subgenome presented more alternative splicing events, as did lncRNAs and circRNAs. However, the expression levels, tissue specificity, sequence features, and functions of lncRNAs and circRNAs did not significantly differ between the two subgenomes, suggesting a common regulatory mechanism shared by the two subgenomes. Furthermore, both the number and base substitution frequency of RNA editing events were greater in the B subgenome. Functional analyses of these transcriptional events also revealed subgenome bias. Genes that undergo alternative splicing in the A subgenome participate in more biological processes, and lncRNA targets show a preference between subgenomes. CircRNA host genes in the B subgenome were associated with more biological functions, and RNA editing preferentially occurred in noncoding regions or led to nonsynonymous mutations in the B subgenome. Taken together, the refined transcriptome annotation revealed complicated and imbalanced expression strategies in allotetraploid common carp. Comprehensive transcriptomic analysis revealed distinct patterns in expression, regulation, and function of alternative splicing, lncRNA, circRNA,and RNA editing events between the two subgenomes of allotetraploid common carp.

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