An improved genome assembly and annotation of the Antarctic copepod Tigriopus kingsejongensis and comparison of fatty acid metabolism between T. kingsejongensis and the temperate copepod T. japonicus

• Published in: Comparative biochemistry and physiology. Part D, Genomics & proteomics Genomics & proteomics, 2020-09, Vol.35, p.100703-100703, Article 100703
• Main Authors: Lee, Min-Chul, Choi, Beom-Soon, Kim, Min-Sub, Yoon, Deok-Seo, Park, Jun Chul, Kim, Sanghee, Lee, Jae-Seong
• Format: Article
• Language: English
• Subjects: Animals; Antarctic Regions; Arthropod Proteins - genetics; Arthropod Proteins - metabolism; Copepod; Copepoda - genetics; Copepoda - metabolism; Elovl; Fad; Fatty acid; Fatty Acids - genetics; Fatty Acids - metabolism; Genome; Molecular Sequence Annotation; Tigriopus kingsejongensis
• ISSN: 1744-117X; 1878-0407
• DOI: 10.1016/j.cbd.2020.100703

Copepods in the genus Tigriopus are widely distributed in the intertidal zone worldwide. To assess differences in fatty acid (FA) metabolism among congeneric species in this genus inhabiting polar and temperate environments, we analyzed and compared FA profiles of the Antarctic copepod Tigriopus kingsejongensis and the temperate copepod T. japonicus. Higher amounts of total FAs were found in the Antarctic copepod T. kingsejongensis than the temperate copepod T. japonicus under administration of the identical amount of Tetraselmis suecica. To determine the genomic basis for this, we identified fatty acid metabolism-related genes in an improved genome of T. kingsejongensis. The total length of the assembled genome was approximately 338 Mb with N50 = 1.473 Mb, 938 scaffolds, and a complete Benchmarking Universal Single-Copy Orthologs value of 95.8%. A total of 25,470 genes were annotated using newly established pipeline. We identified eight elongation of very long-chain fatty acid protein (Elovl) genes and nine fatty acid desaturase (Fad) genes in the genome of T. kingsejongensis. In addition, fatty acid profiling suggested that the duplicated Δ5/6 desaturase gene in T. kingsejongensis is likely to play an essential role in synthesis of different FAs in T. kingsejongensis to those in T. japonicus. However, further experimental research is required to validate our in silico findings. This study provides a better understanding of fatty acid metabolism in the Antarctic copepod T. kingsejongensis. [Display omitted] •The Antarctic copepod showed higher amount of total fatty acid and the proportion of monounsaturated fatty acid.•Under the same food administration, the types of single fatty acids were different among the two copepods.•The Antarctic copepod has a larger genome than temperate copepod, but the number of a predicted gene was similar.•Further duplicated Δ5/6 Fad genes possibly contribute to the difference in the type of fatty acids.