Chromosome-level genome of Poropuntius huangchuchieni provides a diploid progenitor-like reference genome for the allotetraploid Cyprinus carpio
Chromosome-level genome of Poropuntius huangchuchieni provides a diploid progenitor-like reference genome for the allotetraploid Cyprinus carpio
复制标题
黄楚池孔雀的染色体水平基因组为异源四倍体鲤鱼提供了二倍体祖先样参考基因组
DOI：
10.1111/1755-0998.13365
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发表时间：
2021-03-04
影响因子：
7.7
通讯作者：
Xu, Peng
中科院分区：
文献类型：
--
作者：
Chen, Lin;Li, Bijun;Xu, Peng
分布于湄公河和红河流域的鲤科二倍体黄楚鱼是异源四倍体鲤鱼中亲缘关系最近的二倍体祖先物种之一。因此，该基因组对于研究鲤科鱼类的多倍体进化是必不可少的。在这里，我们报告了一个染色体水平的基因组组装，通过整合牛津纳米孔和Hi-C技术。重组基因组大小为1021.38 Mb，其中895.66 Mb定位在25条染色体上，N50为32.93Mb。该基因组包含486.28个Mb重复元件和24,099个蛋白质编码基因。大约95.9%的完整BUSCO被检测到，这表明基因组的完整性很高。进化分析表明，约12Mya时，黄楚鱼与鲤鱼发生了分化。黄楚鱼与鲤鱼B亚组的基因组比较为研究异源四倍体物种形成过程中的染色体重排提供了新的思路。有了完整的基因集，在黄楚竹和鲤鱼之间鉴定出17,474个同源基因，为异源四倍体基因组中的基因成分提供了广泛的视角，这对未来的基因组和遗传分析至关重要。该高质量基因组数据集为异源四倍体鲤鱼的进化和适应提供了一个类似二倍体祖先的参考。
The diploid Poropuntius huangchuchieni in the cyprinid family, which is distributed in the Mekong and Red River basins, is one of the most closely related diploid progenitor-like species of allotetraploid common carp. Therefore, the P. huangchuchieni genome is essential for polyploidy evolution studies in Cyprinidae. Here, we report a chromosome-level genome assembly of P. huangchuchieni by integrating Oxford Nanopore and Hi-C technology. The assembled genome size was 1021.38 Mb, 895.66 Mb of which was anchored onto 25 chromosomes with a N50 of 32.93 Mb. The genome contained 486.28 Mb repetitive elements and 24,099 protein-coding genes. Approximately 95.9% of the complete BUSCOs were detected, suggesting a high completeness of the genome. Evolutionary analysis revealed that P. huangchuchieni diverged from Cyprinus carpio at approximately 12 Mya. Genome comparison between P. huangchuchieni and the B subgenome of C. carpio provided insights into chromosomal rearrangements during the allotetraploid speciation. With the complete gene set, 17,474 orthologous genes were identified between P. huangchuchieni and C. carpio, providing a broad view of the gene component in the allotetraploid genome, which is critical for future genomic and genetic analyses. The high-quality genomic dataset created for P. huangchuchieni provides a diploid progenitor-like reference for the evolution and adaptation of allotetraploid carps.