Symmetric expression of ohnologs encoding conserved antiviral responses in tetraploid common carp suggest absence of subgenome dominance after whole genome duplication.
Symmetric expression of ohnologs encoding conserved antiviral responses in tetraploid common carp suggest absence of subgenome dominance after whole genome duplication.
复制标题
在四倍体鲤鱼中编码保守抗病毒反应的ohnologs的对称表达表明在全基因组复制后不存在亚基因组优势。
DOI：
10.1016/j.ygeno.2023.110723
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发表时间：
2023
期刊：
影响因子：
4.4
通讯作者：
Blasweiler A
中科院分区：
文献类型：
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作者：
Blasweiler A
异源多倍体通常经历亚基因组显性，其中一个亚基因组显示更高水平的基因表达和更大的基因保留。在这里，我们通过分析在抗病毒免疫防御中至关重要的干扰素刺激基因（ISGs）的功能网络来解决异源四倍体鲤鱼（Cyprinus carpio）的两个亚基因组的功能。作为亚基因组优势的指标，我们研究了保留一组核心的ohningisg。为了便于我们的功能基因组分析，组装了高质量的基因组（WagV4.0）。来自模拟病毒感染的体外实验的转录组数据用于推断ISG表达。转录组分析证实在两个亚基因组上诱导88个ISG同源物。在对照和感染状态下，ISG同源物的平均表达在两个亚基因组之间相当。此外，ohnolog对的最高表达和最可诱导的基因拷贝可以源自任一亚基因组。我们没有发现鲤鱼亚基因组优势的有力证据。
Allopolyploids often experience subgenome dominance, with one subgenome showing higher levels of gene expression and greater gene retention. Here, we address the functionality of both subgenomes of allotetraploid common carp (Cyprinus carpio) by analysing a functional network of interferon-stimulated genes (ISGs) crucial in anti-viral immune defence. As an indicator of subgenome dominance we investigated retainment of a core set of ohnologous ISGs. To facilitate our functional genomic analysis a high quality genome was assembled (WagV4.0). Transcriptome data from an in vitro experiment mimicking a viral infection was used to infer ISG expression. Transcriptome analysis confirmed induction of 88 ISG ohnologs on both subgenomes. In both control and infected states, average expression of ISG ohnologs was comparable between the two subgenomes. Also, the highest expressing and most inducible gene copies of an ohnolog pair could be derived from either subgenome. We found no strong evidence of subgenome dominance for common carp.