Zhao Xiang, Liu Yaxian, Du Xueqing, Ma Siyu, Song Na, Zhao Linlin
The Key Laboratory of Mariculture, Ocean University of China, Ministry of Education, Qingdao 266003, China.
Yantai Laishan Marine Fisheries Supervision and Monitoring Brigade, Yantai 264000, China.
Animals (Basel). 2022 Jul 27;12(15):1914. doi: 10.3390/ani12151914.
The shimofuri goby () is a small and highly adaptable goby, distributed along the coasts of China, the Sea of Japan, and the west coastal and estuarine areas of the Northwest Pacific. Next-generation sequencing was used to generate genome-wide survey data to provide essential characterization of the shimofuri goby genome and for the further mining of genomic information. The genome size of the shimofuri goby was estimated to be approximately 887.60 Mb through K-mer analysis, with a heterozygosity ratio and repeat sequence ratio of 0.47% and 32.60%, respectively. The assembled genome was used to identify microsatellite motifs (Simple Sequence Repeats, SSRs), extract single-copy homologous genes and assemble the mitochondrial genome. A total of 288,730 SSRs were identified. The most frequent SSRs were dinucleotide repeats (with a frequency of 61.15%), followed by trinucleotide (29.87%), tetranucleotide (6.19%), pentanucleotide (1.13%), and hexanucleotide repeats (1.66%). The results of the phylogenetic analysis based on single-copy homologous genes showed that the shimofuri goby and can be clustered into one branch. The shimofuri goby was originally thought to be the same as the chameleon goby () due to their close morphological resemblance. However, a complete mitochondrial genome was assembled and the results of the phylogenetic analysis support the inclusion of the shimofuri goby as a separate species. PSMC analysis indicated that the shimofuri goby experienced a bottleneck event during the Pleistocene Glacial Epoch, in which its population size decreased massively, and then it began to recover gradually after the Last Glacial Maximum. This study provides a reference for the further assembly of the complete genome map of the shimofuri goby, and is a valuable genomic resource for the study of its evolutionary biology.
细纹鳚虎鱼（）是一种小型且适应性很强的鳚虎鱼，分布于中国沿海、日本海以及西北太平洋西部沿海和河口地区。利用二代测序技术生成全基因组调查数据，以对细纹鳚虎鱼基因组进行基本特征描述，并进一步挖掘基因组信息。通过K-mer分析估计细纹鳚虎鱼的基因组大小约为887.60 Mb，杂合度率和重复序列率分别为0.47%和32.60%。组装后的基因组用于鉴定微卫星基序（简单序列重复，SSRs）、提取单拷贝同源基因并组装线粒体基因组。共鉴定出288,730个SSRs。最常见的SSRs是二核苷酸重复（频率为61.15%），其次是三核苷酸（29.87%）、四核苷酸（6.19%）、五核苷酸（1.13%）和六核苷酸重复（1.66%）。基于单拷贝同源基因的系统发育分析结果表明，细纹鳚虎鱼和可以聚为一个分支。由于形态上非常相似，细纹鳚虎鱼最初被认为与变色鳚虎鱼（）是同一物种。然而，组装了完整的线粒体基因组，系统发育分析结果支持将细纹鳚虎鱼作为一个独立物种。PSMC分析表明，细纹鳚虎鱼在更新世冰期经历了一次瓶颈事件，其种群数量大幅减少，然后在末次盛冰期后开始逐渐恢复。本研究为进一步组装细纹鳚虎鱼的完整基因组图谱提供了参考，是研究其进化生物学的宝贵基因组资源。
