Key Laboratory of Aquatic Genomics, Ministry of Agriculture, Chinese Academy of Fishery Sciences, Fengtai, Beijing, 100141, China.
State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, 361102, China.
Nat Commun. 2019 Oct 11;10(1):4625. doi: 10.1038/s41467-019-12644-1.
Common carp (Cyprinus carpio) is an allotetraploid species derived from recent whole genome duplication and provides a model to study polyploid genome evolution in vertebrates. Here, we generate three chromosome-level reference genomes of C. carpio and compare to related diploid Cyprinid genomes. We identify a Barbinae lineage as potential diploid progenitor of C. carpio and then divide the allotetraploid genome into two subgenomes marked by a distinct genome similarity to the diploid progenitor. We estimate that the two diploid progenitors diverged around 23 Mya and merged around 12.4 Mya based on the divergence rates of homoeologous genes and transposable elements in two subgenomes. No extensive gene losses are observed in either subgenome. Instead, we find gene expression bias across surveyed tissues such that subgenome B is more dominant in homoeologous expression. CG methylation in promoter regions may play an important role in altering gene expression in allotetraploid C. carpio.
鲤鱼（Cyprinus carpio）是一种异源四倍体物种，源自最近的全基因组复制，为研究脊椎动物多倍体基因组进化提供了模型。在这里，我们生成了三种鲤鱼的染色体水平参考基因组，并与相关的二倍体鲤科基因组进行了比较。我们确定了一个 Barbinae 谱系作为鲤鱼的潜在二倍体祖先是，然后将异源四倍体基因组分为两个亚基因组，这两个亚基因组与二倍体祖先是显著相似的。根据两个亚基因组中同源基因和转座元件的分化速率，我们估计两个二倍体祖先是在大约 2300 万年前分化的，大约在 1240 万年前合并的。在这两个亚基因组中都没有观察到广泛的基因丢失。相反，我们在检测到的组织中发现了基因表达的偏倚，使得亚基因组 B 在同源表达中更为主导。CG 甲基化在启动子区域可能在改变异源四倍体鲤鱼的基因表达中发挥了重要作用。
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