Deng Wen-Jian, Li Qian-Qian, Shuai Hao-Nan, Wu Ren-Xie, Niu Su-Fang, Wang Qing-Hua, Miao Ben-Ben
College of Fisheries, Guangdong Ocean University, Zhanjiang 524088, China.
Animals (Basel). 2024 Apr 17;14(8):1202. doi: 10.3390/ani14081202.
is a typical representative of small pelagic fish characterized by fast growth rate, small body size, and high fecundity. It is a high-quality marine commercial fish with high nutritional value. However, the underlying genetics and genomics research focused on is not comprehensive. Herein, a high-quality chromosome-level genome of a male was assembled. The assembled genome length was 716.13 Mb with contig N50 of 19.70 Mb. Notably, we successfully anchored 95.73% contig sequences into 23 chromosomes with a total length of 685.54 Mb and a scaffold N50 of 30.77 Mb. A total of 22,716 protein-coding genes, 274.90 Mb repeat sequences, and 10,060 ncRNAs were predicted, among which 22,037 (97%) genes were successfully functionally annotated. The comparative genome analysis identified 459 unique, 73 expanded, and 52 contracted gene families. Moreover, 2804 genes were identified as candidates for positive selection, of which some that were related to the growth and development of bone, muscle, cardioid, and ovaries, such as some members of the TGF-β superfamily, were likely involved in the evolution of typical biological features in . The study provides an accurate and complete chromosome-level reference genome for further genetic conservation, genomic-assisted breeding, and adaptive evolution research for .
是小型中上层鱼类的典型代表,具有生长速度快、体型小和繁殖力高的特点。它是一种具有高营养价值的优质海洋商业鱼类。然而,针对其的基础遗传学和基因组学研究并不全面。在此,我们组装了一条雄性的高质量染色体水平基因组。组装后的基因组长度为716.13 Mb,重叠群N50为19.70 Mb。值得注意的是,我们成功地将95.73%的重叠群序列锚定到23条染色体上,总长度为685.54 Mb,支架框架,支架N50为30.77 Mb。共预测到22716个蛋白质编码基因、274.90 Mb的重复序列和10060个非编码RNA,其中22037个(97%)基因成功进行了功能注释。比较基因组分析确定了459个独特的、73个扩张的和52个收缩的基因家族。此外,鉴定出2804个正选择候选基因,其中一些与骨骼、肌肉、心脏和卵巢的生长发育相关,如TGF-β超家族的一些成员,可能参与了其典型生物学特征的进化。该研究为进一步开展其遗传保护、基因组辅助育种和适应性进化研究提供了准确完整的染色体水平参考基因组。