Database construction and comparative genomics analysis of genes involved in nutritional metabolic diseases in fish

• Published in: Comparative biochemistry and physiology. Part D, Genomics & proteomics Vol. 50; p. 101241
• Main Authors: Zhang, Yuru, Zhang, Junmei, Fan, Haiying, Lu, Ronghua, Nie, Guoxing
• Format: Journal Article
• Language: English
• Published: Netherlands Elsevier Inc 01.06.2024
• Subjects: Animals; Comparative systems biology; Databases, Genetic; Fish Diseases - genetics; Fish genome database; Fishes - genetics; Genomics; KEGG; Metabolic Diseases - genetics; NCBI; Nutritional metabolic diseases; OMIM; Zebrafish - genetics; Nutritional metabolic diseases; Comparative systems biology; NCBI; Fish genome database; KEGG; OMIM
• ISSN: 1744-117X; 1878-0407; 1878-0407
• DOI: 10.1016/j.cbd.2024.101241

Nutritional metabolic diseases in fish frequently arise in the setting of intensive aquaculture. The etiology and pathogenesis of these conditions involve energy metabolic disorders influenced by both internal genetic factors and external environmental conditions. The exploration of genes associated with nutritional and metabolic disorder has sparked considerable interest within both the aquaculture scientific community and the industry. High-throughput sequencing technology offers researchers extensive genetic information. Effectively mining, analyzing, and securely storing this data is crucial, especially for advancing disease prevention and treatment strategies. Presently, the exploration and application of gene databases concerning nutritional and metabolic disorders in fish are at a nascent stag. Therefore, this study focused on the model organism zebrafish and five primary economic fish species as the subjects of investigation. Using information from KEGG, OMIM, and existing literature, a novel gene database associated with nutritional metabolic diseases in fish was meticulously constructed. This database encompassed 4583 genes for Danio rerio, 6287 for Cyprinus carpio, 3289 for Takifugu rubripes, 3548 for Larimichthys crocea, 3816 for Oreochromis niloticus, and 5708 for Oncorhynchus mykiss. Through a comparative systems biology approach, we discerned a relatively high conservation of genes linked to nutritional metabolic diseases across these fish species, with over 54.9 % of genes being conserved throughout all six species. Additionally, the analysis pinpointed the existence of 13 species-specific genes within the genomes of large yellow croaker, tilapia, and rainbow trout. These genes exhibit the potential to serve as novel candidate targets for addressing nutritional metabolic diseases. [Display omitted] •Utilizing data from KEGG, OMIM, and literature, we crafted a novel gene database linked to nutritional metabolic diseases in six primary fish species.•Through comparative systems biology approach, a significant conservation of genes (54.9 %) associated with nutritional metabolic diseases was identified across all six species.•This study also identified 13 species-specific genes within the genomes of large yellow croaker, tilapia, and rainbow trout, showcasing their potential as novel candidate targets for addressing nutritional metabolic diseases.