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Draft genome sequence and tissue expression panel of Pacific saury (Cololabis saira).

ABSTRACT: 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.

SUBMITTER: Nakamura Y

PROVIDER: S-EPMC11077904 | biostudies-literature | 2024 Jun

REPOSITORIES: biostudies-literature

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Draft genome sequence and tissue expression panel of Pacific saury (Cololabis saira).

Nakamura Yoji Y Yasuike Motoshige M Fuji Taiki T Suyama Satoshi S Mekuchi Miyuki M

DNA research : an international journal for rapid publication of reports on genes and genomes 20240601 3

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/posterio ...[more]

PMID: 38566577

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Project description:ObjectivesThis study aimed to assess the effects of storage temperature on the lipidomics profile change in Pacific saury (Cololabis saira).MethodsIn this paper, C. saira underwent frozen storage at two different temperatures, T1 (-18 °C) and T2 (-25 °C), for a duration of three months. Chemical and lipidomic methods were used to determine the changes in lipids during the storage process.ResultsResults showed that the content of triglyceride and phospholipid decreased significantly (p < 0.05), and free fatty acid increased significantly (p < 0.05), while the content of total cholesterol remained relatively constant across different storage temperatures. Additionally, an increasing trend in AV, POV, and TBARS contents was observed after the freezing process, with lipid oxidation being significantly higher in the -18 °C group compared to the -25 °C group (p < 0.05). A comprehensive analysis identified 4854 lipid molecules in the muscles of C. saira, categorized into 46 lipid subclasses, predominantly including triglycerides (TG), phosphatidylcholine (PC), phosphatidylethanolamine (PE), phosphatidylinositol (PI), phosphatidylglycerol (PG), and diglycerides (DG). Among them, TG was the most abundant lipid, followed by PC. Using orthogonal partial least squares discriminant analysis (OPLS-DA) with a variable importance in projection (VIP) score > 1 and p value < 0.05 as criteria, 338, 271, and 103 highly significantly differentiated lipids were detected in the comparison groups CK vs. T1, CK vs. T2, and T1 vs. T2, respectively. The results indicated that storage at -18 °C had a more pronounced effect than storage at -25 °C. During the freezing process, TG expression was significantly down-regulated, and TG(18:4_14:0_20:5), TG(20:5_13:0_22:6), TG(22:6_14:1_22:6), and TG(18:4_13:0_22:6) were the most predominant individuals. The CK group was initially present in C. saira before storage. Differential lipid molecules in the CK vs. T1 and CK vs. T2 groups were screened using a fold change (FC) > 2 or FC < 0.5. In the CK vs. T2 group, 102 highly significant differential lipid molecules were identified, with 55 being down-regulated across seven subclasses. In contrast, the CK vs. T1 group revealed 254 highly significant differential lipid molecules, with 85 down-regulated across 13 subclasses. The results showed that more PCs and PEs were down-regulated, with a higher differential abundance of PE and PC in the -25 °C group compared to the -18 °C group. The differential metabolites were primarily enriched in 17 metabolic pathways, with glycerophospholipid metabolism being the most prominent, followed by sphingolipid metabolism during the frozen storage.ConclusionsOverall, -25 °C storage in production was more favorable for maintaining the lipid stability of C. saira. This work could provide useful information for aquatic product processing and lipidomics.

Dataset Information

Draft genome sequence and tissue expression panel of Pacific saury (Cololabis saira).

Publications

Draft genome sequence and tissue expression panel of Pacific saury (Cololabis saira).

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