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Identification of xenobiotic biodegradation and metabolism-related genes in the copepod Tigriopus japonicus whole transcriptome analysis
- Kim, Hui-Su, Lee, Bo-Young, Won, Eun-Ji, Han, Jeonghoon, Hwang, Dae-Sik, Park, Heum Gi, Lee, Jae-Seong
- Marine genomics 2015 v.24 pp. 207-208
- Tigriopus japonicus, biodegradation, biomarkers, ecotoxicology, genes, heat shock proteins, high-throughput nucleotide sequencing, metabolism, peroxidases, superoxide dismutase, transcriptome, transcriptomics
- In this study, the whole transcriptome of Tigriopus japonicus was sequenced using next generation sequencing technology. De novo assembly was performed using Trinity, which assembled 140,130 contigs. Transdecoder found 54,761 candidate coding contigs, 39,507 of which showed homology to other species covering 15,310 genes by BLAST analysis. Functional gene annotation was performed by Gene Ontology, InterProScan, and KEGG pathway analyses. In addition to various metabolism-related pathways, xenobiotic biodegradation and metabolism were other interesting pathways in T. japonicus. Transcripts encoding various enzymes (e.g. superoxide dismutase, heat shock protein, and peroxidases) in response to a variety of stimuli were identified, which might be useful candidate biomarkers for ecotoxicology studies.