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De novo assembly and annotation of the Antarctic copepod (Tigriopus kingsejongensis) transcriptome

Cited 5 time in scopus
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Title
De novo assembly and annotation of the Antarctic copepod (Tigriopus kingsejongensis) transcriptome
Authors
Kim, Hui-Su
Lee, Bo-Young
Han, Jeong
hoon
Lee, Young Hwan
Min, Gi-Sik
Kim, Sanghee
Lee, Jae-Seong
Subject
Genetics & Heredity; Marine & Freshwater Biology
Keywords
Transcriptome; RNA-seq; Antarctic; Copepod; Tigriopus kingsejongensis; Lipid metabolism
Issue Date
2016
Citation
Kim, Hui-Su, et al. 2016. "De novo assembly and annotation of the Antarctic copepod (Tigriopus kingsejongensis) transcriptome". Marine Genomics, 28: 37-39.
Abstract
The whole transcriptome of the Antarctic copepod (Tigriopus kingsejongensis) was sequenced using Illumina RNA-seq. De novo assembly was performed with 64,785,098 raw reads using Trinity, which assembled into 81,653 contigs. TransDecoder found 38,250 candidate coding contigs which showed homology to other species by BLAST analysis. Functional gene annotation was performed by Gene Ontology (GO), InterProScan, and KEGG pathway analyses. Finally, we identified a number of expressed gene catalog for T. kingsejongensis that is a useful model animal for gene information-based polar research to uncover molecular mechanisms of environmental adaptation on harsh environments. In particular, we observed highly developing lipid metabolism in T. kingsejongensis directly compared to those of the Far East Pacific coast copepod Tigriopus japonicus at the transcriptome level.
DOI
http://dx.doi.org/10.1016/j.margen.2016.04.009
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