Bioinformatics and Biosciences Division, Fisheries Stock Assessment Center, Fisheries Resources Institute, Japan Fisheries Research and Education Agency, 2-12-4 Fuku-ura, Kanazawa, Yokohama, Kanagawa 236-8648, Japan.
Highly Migratory Resources Division, Fisheries Stock Assessment Center, Fisheries Resources Institute, Japan Fisheries Research and Education Agency, 2-12-4 Fuku-ura, Kanazawa, Yokohama, Kanagawa 236-8648, Japan.
DNA Res. 2024 Jun 1;31(3). doi: 10.1093/dnares/dsae010.
Pacific saury (Cololabis saira) is an important fish in several countries. Notably, the catch of this fish has markedly decreased recently, which might be due to environmental changes, including feeding habitat changes. However, no clear correlation has been observed. Therefore, the physiological basis of Pacific saury in relation to possible environmental factors must be understood. We sequenced the genome of Pacific saury and extracted RNA from nine tissues (brain, eye, gill, anterior/posterior guts, kidney, liver, muscle, and ovary). In 1.09 Gb assembled genome sequences, a total of 26,775 protein-coding genes were predicted, of which 26,241 genes were similar to known genes in a public database. Transcriptome analysis revealed that 24,254 genes were expressed in at least one of the nine tissues, and 7,495 were highly expressed in specific tissues. Based on the similarity of the expression profiles to those of model organisms, the transcriptome obtained was validated to reflect the characteristics of each tissue. Thus, the present genomic and transcriptomic data serve as useful resources for molecular studies on Pacific saury. In particular, we emphasize that the gene expression data, which serve as the tissue expression panel of this species, can be employed in comparative transcriptomics on marine environmental responses.
太平洋磷沙丁鱼（Cololabis saira）是多个国家的重要鱼类。值得注意的是，这种鱼的捕捞量最近显著减少，这可能是由于环境变化，包括摄食生境的变化。然而，目前还没有观察到明显的相关性。因此，必须了解与可能的环境因素相关的太平洋磷沙丁鱼的生理基础。我们对太平洋磷沙丁鱼进行了基因组测序，并从 9 种组织（脑、眼、鳃、前/后肠、肾、肝、肌肉和卵巢）中提取了 RNA。在组装的 1.09 Gb 基因组序列中，共预测到 26775 个编码蛋白的基因，其中 26241 个基因与公共数据库中的已知基因相似。转录组分析显示，至少有 9 种组织中的 24254 个基因表达，7495 个基因在特定组织中高度表达。基于与模式生物表达谱的相似性，获得的转录组被验证反映了每个组织的特征。因此，本研究的基因组和转录组数据为太平洋磷沙丁鱼的分子研究提供了有用的资源。特别是，我们强调该物种的组织表达谱基因表达数据可用于海洋环境响应的比较转录组学研究。
