Recently, researchers from the Institute of Oceanology, Chinese Academy of Sciences, have made significant progress in the genomics of the silver croaker, a valuable economic fish species in China. They have released, for the first time, a high-quality chromosomal-level reference genome of the silver croaker. The research findings were published online in the journal "Scientific Data," a subsidiary of "Nature."
The silver croaker, belonging to the suborder Sparoidei, family Sciaenidae, and genus Pennahia, is widely distributed in the nearshore waters of the northwest Pacific Ocean, ranging from the northern South China Sea to coastal areas of Japan, Korea, and Russia. With delicate flesh and rich oils, the silver croaker holds significant economic value and is an important species in Chinese fisheries industry.
The global distribution of seven valid species in the genus Pagrus, as depicted by the Ocean Research Institute.
The supply of Pagrus pagrus is highly dependent on fisheries, with China's marine fishing intensity increasing since the 1980s. In recent years, the annual catch of Pagrus species, mainly Pagrus pagrus, has exceeded 300,000 tons, posing a significant risk to the wild resources of Pagrus pagrus.
Currently, breakthroughs have been made in artificial breeding and aquaculture techniques for Pagrus pagrus in China, which are of great significance for the conservation and recovery of its wild resources. However, Pagrus pagrus is extremely sensitive to environmental changes and prone to stress-induced mortality during transportation and aquaculture, limiting the development of the Pagrus pagrus aquaculture industry. Additionally, Pagrus pagrus is morphologically specialized, with a highly compressed body, no pelvic fins, and a special esophageal diverticulum structure in the anterior part of the esophagus, which is a key evolutionary characteristic unique to the Sparidae, and is an important trait for Pagrus pagrus to adapt to feeding on small crustaceans and jellyfish.
Previously, based on global mitochondrial genome data of the genus Pagrus and morphological and distribution characteristics, Dr. Liu Jing's team at the Ocean Research Institute first clarified the diversity and geographical distribution patterns of Pagrus species worldwide, as well as their evolutionary history. The research results indicate that there are currently seven valid species in the genus Pagrus worldwide, namely: Pagrus pagrus, Pagrus sinensis, Pagrus auriga, Pagrus liui, Pagrus chrysophrys, Pagrus lini, and Pagrus unicolor. The previously reported species, Pagrus major, is considered a synonym of Pagrus pagrus.
The genome characteristics of the Japanese seabass at the chromosome level - Image provided by the Institute of Oceanography
Building upon previous research, the research team comprehensively employed relevant sequencing technologies to deeply sequence and assemble the genome of the Japanese seabass. For the first time internationally, they obtained a high-quality chromosome-level reference genome of the Japanese seabass, revealing precisely 24 chromosomes with a genome size of 518.06 megabase pairs. The assembled genome has a Contig N50 length of 20.47 megabase pairs and a Scaffold N50 length of 22.86 megabase pairs, indicating extremely high genome integrity at the chromosome level. Repeat sequences constitute 13.45% of the genome. Moreover, they identified 24,696 protein-coding genes, with a BUSCO assessment value for genome completeness reaching 98.90%.
These research findings provide a high-quality reference genome basis for in-depth analysis of evolutionary traits such as esophageal diverticulum and absence of pelvic fins in the Japanese seabass, as well as for genetic resource assessment, breeding of stress-resistant varieties, and sustainable utilization of Japanese seabass fisheries resources.
This research received funding from the National Natural Science Foundation of China and the Strategic Priority Research Program of the Chinese Academy of Sciences (Type B).
Related Paper Information: https://doi.org/10.1038/s41597-024-03070-0
