title: RNA-seq based whole transcriptome analysis of the cyclopoid copepod Paracyclopina nana focusing on xenobiotics metabolism.
abstract: Copepods are among the most abundant taxa in marine invertebrates, and cyclopoid copepods include more than 1500 species and subspecies. In marine ecosystems, planktonic copepods play a significant role as food resources in the food web and sensitively respond to environmental changes. The copepod Paracylopina nana is one of the planktonic brackish water copepods and considered as a promising model species in ecotoxicology. We sequenced the whole transcriptome of P. nana using RNA-seq technology. De novo sequence assembly by Trinity integrated with TransDecoder produced 67,179 contigs including putative alternative spliced variants. A total of 12,474 genes were identified based on BLAST analysis, and gene sequences were most similar to the sequences of the branchiopod Daphnia. Gene Ontology and KEGG pathway analysis showed that most transcripts annotated were involved in pathways of various metabolisms, immune system, signal transduction, and translation. Considering numbers of sequences and enzymes involved in the pathways, particularly attention was paid to genes potentially involved in xenobiotics biodegradation and metabolism. With regard to xenobiotics metabolism, various xenobiotic metabolizing enzymes such as oxidases, dehydrogenases, and transferases were obtained from the annotated transcripts. The whole transcriptome analysis of P. nana provides valuable resources for future studies of xenobiotics-related metabolism in this marine copepod species.
authors.affiliation: Department of Biological Science, College of Science, Sungkyunkwan University, Suwon 440-746, South Korea.
authors.forename: Bo-Young
authors.initials: BY
authors.lastname: Lee
authors.affiliation: Department of Biological Science, College of Science, Sungkyunkwan University, Suwon 440-746, South Korea.
authors.forename: Hui-Su
authors.initials: HS
authors.lastname: Kim
authors.affiliation: National Instrumentation Center for Environmental Management (NICEM), College of Agriculture and Life Sciences, Seoul National University, Seoul 151-921, South Korea.
authors.forename: Beom-Soon
authors.initials: BS
authors.lastname: Choi
authors.affiliation: Department of Biological Science, College of Science, Sungkyunkwan University, Suwon 440-746, South Korea.
authors.forename: Dae-Sik
authors.initials: DS
authors.lastname: Hwang
authors.affiliation: National Instrumentation Center for Environmental Management (NICEM), College of Agriculture and Life Sciences, Seoul National University, Seoul 151-921, South Korea.
authors.forename: Ah Young
authors.initials: AY
authors.lastname: Choi
authors.affiliation: Department of Biological Science, College of Science, Sungkyunkwan University, Suwon 440-746, South Korea.
authors.forename: Jeonghoon
authors.initials: J
authors.lastname: Han
authors.affiliation: Department of Biological Science, College of Science, Sungkyunkwan University, Suwon 440-746, South Korea.
authors.forename: Eun-Ji
authors.initials: EJ
authors.lastname: Won
authors.affiliation: National Instrumentation Center for Environmental Management (NICEM), College of Agriculture and Life Sciences, Seoul National University, Seoul 151-921, South Korea.
authors.forename: Ik-Young
authors.initials: IY
authors.lastname: Choi
authors.affiliation: Department of Food and Nutrition, College of Health Science, Honam University, Gwang ju 506-714, South Korea; Department of Food and Nutrition, College of Human Ecology, Hanyang University, Seoul 133-791, South Korea.
authors.forename: Seung-Hwi
authors.initials: SH
authors.lastname: Lee
authors.affiliation: Department of Food and Nutrition, College of Human Ecology, Hanyang University, Seoul 133-791, South Korea.
authors.forename: Ae-Son
authors.initials: AS
authors.lastname: Om
authors.affiliation: Department of Marine Resource Development, College of Life Sciences, Gangneung-Wonju National University, Gangneung 210-702, South Korea.
authors.forename: Heum Gi
authors.initials: HG
authors.lastname: Park
authors.affiliation: Department of Biological Science, College of Science, Sungkyunkwan University, Suwon 440-746, South Korea. Electronic address: jslee2@skku.edu.
authors.forename: Jae-Seong
authors.initials: JS
authors.lastname: Lee
mesh_terms: D000818:Animals; D033342:Copepoda / Q000235:genetics*; D020869:Gene Expression Profiling / Q000379:methods*; D012313:RNA / Q000235:genetics; D059467:Transcriptome / Q000235:genetics; D015262:Xenobiotics / Q000378:metabolism*
chemical_list: D015262:Xenobiotics; D012313:RNA
keywords: Cyclopoid copepod; Paracyclopina nana; RNA-seq; Transcriptome; Xenobiotics metabolism