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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

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Title
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
Other Titles
남극 요각류와 중온성 요각류 간의 지방산 비교와 단백질 기능분석
Authors
Lee, Min-Chul
Choi, Beom-Soon
Kim, Min-Sub
Yoon, Deok-Seo
Park, Jun Chul
Kim, Sanghee
Lee, Jae-Seong
Subject
Biochemistry & Molecular Biology; Genetics & Heredity
Keywords
Copepod; Fatty acid; Elovl; Fad; Tigriopus kingsejongensis
Issue Date
2020-09
Citation
Lee, Min-Chul, et al. 2020. "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". COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY D-GENOMICS & PROTEOMICS, 35(1): 100703-100713.
Abstract
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 Delta 5/6 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.
URI
https://repository.kopri.re.kr/handle/201206/11806
DOI
http://dx.doi.org/10.1016/j.cbd.2020.100703
Appears in Collections  
2020-2020, Commercialization of new Biomaterials from polar organisms (20-20) / Yim, Joung Han (PE20010)
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