RNA-seq based whole transcriptome analysis of the cyclopoid copepod Paracyclopina nana focusing on xenobiotics metabolism Bo-Young Lee a,1 , Hui-Su Kim a,1 , Beom-Soon Choi b , Dae-Sik Hwang a , Ah Young Choi b , Jeonghoon Han a , Eun-Ji Won a , Ik-Young Choi b , Seung-Hwi Lee c,d , Ae-Son Om d , Heum Gi Park e , Jae-Seong Lee a, ⁎ a Department of Biological Science, College of Science, Sungkyunkwan University, Suwon 440-746, South Korea b National Instrumentation Center for Environmental Management (NICEM), College of Agriculture and Life Sciences, Seoul National University, Seoul 151-921, South Korea c Department of Food and Nutrition, College of Health Science, Honam University, Gwang ju 506-714, South Korea d Department of Food and Nutrition, College of Human Ecology, Hanyang University, Seoul 133-791, South Korea e Department of Marine Resource Development, College of Life Sciences, Gangneung-Wonju National University, Gangneung 210-702, South Korea abstract article info Article history: Received 5 December 2014 Received in revised form 16 April 2015 Accepted 30 April 2015 Available online 6 May 2015 Keywords: RNA-seq Transcriptome Xenobiotics metabolism Cyclopoid copepod Paracyclopina nana 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 se- quenced 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. Consid- ering numbers of sequences and enzymes involved in the pathways, particularly attention was paid to genes po- tentially 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. © 2015 Elsevier Inc. All rights reserved. 1. Introduction Among marine invertebrates, copepods represent the most abun- dant taxon, which comprise approximately 11,500 species by estimate of Humes about 20 years ago (Humes, 1994). Cyclopoida, an order of copepod, including more than 1500 species and subspecies, and the tra- ditional systematics of cyclopoid copepods is based on morphological characteristics (Kiefer, 1927; Rylov, 1948; Yeatman, 1959; Dussart, 1969; Monchenko, 1974). In marine ecosystems, copepods play significant roles as food re- sources in the food web and as promising model species in ecotoxicolo- gy (Sun and Fleeger, 1995; Pinto et al., 2001; Raisuddin et al., 2007). Since planktonic copepods have several advantages in their small body size and stress resistance, they have been reported to be attractive candidates for mass culture and good live food resources to substitute or complement conventional live feeds such as rotifers (Brachionus spp.) and brine shrimps (Artemia spp.) (O'Bryen and Lee, 2007; VanderLugt and Lenz, 2008). In addition, copepods respond to environmental changes sensitively and are known to be good indicator species of natu- ral and anthropogenic stressors in aquatic ecosystems. Paracylopina nana (Copepoda, Cyclopoida) is one of the planktonic brackish water co- pepods and widely distributed in estuaries with a wide range of toler- ance to salinity and temperature (Lee et al., 2006). P. nana has similar body shapes and sizes to another cyclopoid copepod Cyclopina kiraensis but a couple of characteristic such as shape of leg 5 and position of the lateral seta of the caudal ramus is distinguishable (Ueda et al., 2001) (Suppl. Fig. S1). P. nana has been recognized as an economically impor- tant food source for higher trophic levels in the estuarine and marine environment and a potential model organism for various environmental researches because of its suitable characteristics such as small size (1 b mm) and short life span (less than 2 weeks) (Ki et al., 2009). In the past decade, the advent of next generation sequencing tech- nology (NGS) has accelerated the massive production of whole genome and transcriptome (RNA-seq) sequences at relatively cheaper costs compared to the conventional Sanger sequencing method. With the aid of new technology, the genomic study of non-model organisms in- cluding copepods becomes more realistic (Lee et al., 2010; Jeong et al., 2014). The massively parallel high-throughput RNA sequencing enables Comparative Biochemistry and Physiology, Part D 15 (2015) 12–19 ⁎ Corresponding author. Tel.: +82 31 290 7011. E-mail address: jslee2@skku.edu (J.-S. Lee). 1 These authors contributed equally to this paper. http://dx.doi.org/10.1016/j.cbd.2015.04.002 1744-117X/© 2015 Elsevier Inc. All rights reserved. Contents lists available at ScienceDirect Comparative Biochemistry and Physiology, Part D journal homepage: www.elsevier.com/locate/cbpd