Yang Yang, Wang Tong, Chen Jingfang, Wu Lina, Wu Xi, Zhang Weiwei, Luo Jian, Xia Junhong, Meng Zining, Liu Xiaochun
State Key Laboratory of Biocontrol, Life Sciences School, Sun Yat-sen University, Guangzhou, China.
State Key Laboratory of Marine Resource Utilization in South China Sea, Key Laboratory of Tropical Biological Resources of Education, Marine Sciences College of Hainan University, Haikou, China.
Mol Ecol Resour. 2022 Feb;22(2):711-723. doi: 10.1111/1755-0998.13494. Epub 2021 Sep 14.
The brown-marbled grouper (Epinephelus fuscoguttatus) is an important species of fish in the coral reef ecosystem and marine aquaculture industry. In this study, a high-quality chromosome-level genome of brown-marbled grouper was assembled using Oxford Nanopore technology and Hi-C technology. The GC content and heterozygosity were approximately 42% and 0.35%, respectively. A total of 230 contigs with a total length of 1047 Mb and contig N50 of 13.8 Mb were assembled, and 228 contigs (99.13%) were anchored into 24 chromosomes. A total of 24,005 protein-coding genes were predicted, among which 23,862 (99.4%) predicted genes were annotated. Phylogenetic analysis showed that brown-marbled grouper and humpback grouper were clustered into one clade that separated approximately 11-23 million years ago. Collinearity analyses showed that there was no obvious duplication of large fragments between chromosomes in the brown-marbled grouper. Genomes of the humpback grouper and giant grouper showed a high collinearity with that of the brown-marbled grouper. A total of 305 expanded gene families were detected in the brown-marbled grouper genome, which is mainly involved in disease resistance. In addition, a genetic linkage map with 3061.88 cM was constructed. Based on the physical and genetic map, one growth-related quantitative trait loci was detected in 32,332,447 bp of chromosome 20, and meox1 and etv4 were considered candidate growth-related genes. This study provides pivotal genetic resources for further evolutionary analyses and artificial breeding of groupers.
棕点石斑鱼（Epinephelus fuscoguttatus）是珊瑚礁生态系统和海水养殖业中的重要鱼类品种。在本研究中，利用牛津纳米孔技术和Hi-C技术组装了高质量的棕点石斑鱼染色体水平基因组。其GC含量和杂合度分别约为42%和0.35%。共组装出230个重叠群，总长度为1047 Mb，重叠群N50为13.8 Mb，其中228个重叠群（99.13%）被锚定到24条染色体上。共预测出24,005个蛋白质编码基因，其中23,862个（99.4%）预测基因得到注释。系统发育分析表明，棕点石斑鱼和驼背鲈聚为一个分支，该分支大约在1100 - 2300万年前分化。共线性分析表明，棕点石斑鱼染色体之间没有明显的大片段重复。驼背鲈和鞍带石斑鱼的基因组与棕点石斑鱼的基因组具有高度共线性。在棕点石斑鱼基因组中检测到305个扩张基因家族，主要参与抗病性。此外，构建了一张长度为3,061.88 cM的遗传连锁图谱。基于物理图谱和遗传图谱，在20号染色体32,332,447 bp区域检测到一个与生长相关的数量性状位点，meox1和etv4被认为是与生长相关的候选基因。本研究为石斑鱼进一步的进化分析和人工育种提供了关键的遗传资源。
