Genomics/Technical resources Identification of xenobiotic biodegradation and metabolism-related genes in the copepod Tigriopus japonicus whole transcriptome analysis Hui-Su Kim a,1 , Bo-Young Lee a,1 , Eun-Ji Won a , Jeonghoon Han a , Dae-Sik Hwang a , Heum Gi Park b , Jae-Seong Lee a, ⁎ a Department of Biological Science, College of Science, Sungkyunkwan University, Suwon 440-746, South Korea b Department of Marine Resource Development, College of Life Sciences, Gangneung-Wonju National University, Gangneung 210-702, South Korea abstract article info Article history: Received 11 May 2015 Received in revised form 15 May 2015 Accepted 15 May 2015 Available online xxxx Keywords: Whole transcriptome analysis Environmental stimulus Copepod Tigriopus japonicus In this study, the whole transcriptome of Tigriopus japonicus was sequenced using next generation sequencing tech- nology. 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. © 2015 Elsevier B.V. All rights reserved. 1. Introduction Currently, the Arthropod Genomic Consortium has launched the i5k project, which will sequence the genomes of 5000 arthropod species including copepods (https://i5k.nal.usda.gov/). Copepod is one of the targeted taxa that have been ranked as a model species for this project. In fact, copepod is the second largest taxa of crustacean and is dominant in aquatic zooplankton communities accounting for about 70% of the biomass of marine zooplankton (Wells, 1984). The intertidal benthic copepod Tigriopus japonicus inhabits rock pools and is distributed along the coasts of the Western Pacific with wide ranges of adaptability for salinity and temperature (Kwok and Leung, 2005). Their benthic life habit means this species meets the requirement for monitoring the sediment-water interface (Raisuddin et al., 2007). Thus, ecology, phylogeography, and behavior studies have been conducted for monitoring the environmental stressors and pollution in diverse marine environments in the genus Tigriopus (Kwok and Leung, 2005). Toxicity tests using different chemicals, including trace metals, endocrine- disrupting chemicals (EDC), and engineered nanomaterials have been performed in T. japonicus (Lee et al., 2007). To date, fragmentary knowledge on molecular defense mechanisms has been increasingly reported from the genus Tigriopus, and T. japonicus is considered a promising new model species for ecotoxicol- ogy (Raisuddin et al., 2007). Genome and transcriptome sequences of Tigriopus califonicus are now available via the i5k project (https://i5k. nal.usda.gov/Tigriopus_californicus), increasing the usefulness of T. japonicus in view of parallel studies. Through parallel studies of the genus Tigriopus, valuable comparative information will be provided that can be used to examine molecular mechanisms and the evolution of sister species within the genus Tigriopus. 2. Data description 2.1. Sequence assembly and gene annotation After sequencing, sequence reads with a Q-score below 30 and a length shorter than 90 bp were removed for quality control, and the remaining sequences were used for further analysis. The large contigs of the sequence reads, filtered by the quality control, were constructed using the de novo assembler Trinity (Grabherr et al., 2011). TransDecoder (http://transdecoder.sourceforge.net/) was used to identify candidate coding regions from the assembled transcripts and/ or contigs; the candidate coding regions were used for BLAST analysis against the NCBI non-redundant (nr) protein database. The presence of conserved domains in the assembled transcripts was identified and Marine Genomics xxx (2015) xxx–xxx ⁎ Corresponding author. Tel.: +82 31 290 7011. E-mail address: jslee2@skku.edu (J.-S. Lee). 1 These authors contributed equally to this work. MARGEN-00333; No of Pages 2 http://dx.doi.org/10.1016/j.margen.2015.05.011 1874-7787/© 2015 Elsevier B.V. All rights reserved. Contents lists available at ScienceDirect Marine Genomics journal homepage: www.elsevier.com/locate/margen Please cite this article as: Kim, H.-S., et al., Identification of xenobiotic biodegradation and metabolism-related genes in the copepod Tigriopus japonicus whole transcriptome analysis, Mar. Genomics (2015), http://dx.doi.org/10.1016/j.margen.2015.05.011