The copepod Tigriopus japonicus genomic DNA information (574 Mb) and molecular anatomy Jae-Seong Lee a, * , Jae-Sung Rhee b , Ryeo-Ok Kim a , Dae-Sik Hwang b , Jeonghoon Han b , Beom-Soon Choi b , Gyung Soo Park c , Il-Chan Kim d , Heum Gi Park e , Young-Mi Lee f, * a Department of Chemistry, College of Natural Sciences, Hanyang University, Seoul 133-791, South Korea b Department of Molecular and Environmental Bioscience, Graduate School, Hanyang University, Seoul 133-791, South Korea c Department of Marine Biotechnology, College of Liberal Arts and Sciences, Anyang University, Ganghwa 417-833, South Korea d Polar BioCenter, Korea Polar Research Institute, Korea Ocean Research and Development Institute, Incheon 406-840, South Korea e Faculty of Marine Bioscience and Technology, College of Life Sciences, Kangnung-Wonju National University, Gangneung 210-702, South Korea f Department of Life Science, College of Natural Sciences, Sangmyung University, Seoul 110-743, South Korea article info Keywords: Copepod Tigriopus japonicus GS-FLX GS-FLX-Titanium Genomic DNA Unigene abstract The intertidal copepod, Tigriopus japonicus, has been recognized as a promising model species for marine environmental genomics. To obtain extensive genomic DNA sequences from this species, we sequenced genomic DNA from adult copepods using genomic sequencers GS-FLX and GS-FLX-Titanium and attained 1,914,995 reads (average read length 299.8 bp) including 574.2 Mb of genomic DNA information. After subjecting them to assembly, we acquired 193,642 contigs (total contigs length 129.7 Mb), and finally were able to obtain 10,894 unigenes (E-value > 0.1; length > 200 bp) containing 33,081,455 bp after a nonredundant (NR) blast search. In this paper, we summarize the genomic DNA sequences of T. japonicus and discuss its potential use in environmental genomics and ecotoxicological studies for uncovering mechanisms of environmental stresses and chemical toxicities to marine crustaceans. Ó 2009 Elsevier Ltd. All rights reserved. The information on genomic DNA sequences is increasingly important, especially in non-model organisms. Recently, several genome sequencers (e.g. GS-FLX, GS-FLX-Titanium, and SOLEXA) are available for rapid DNA sequencing, and enable us to obtain extensive DNA or cDNA sequence information in a short period of time (Margulies et al., 2005). To date, several research groups have used sequencers to obtain massive sequence information from Daphnia, salmon louse, and others (Eichner et al., 2008; Qi et al., 2009; Quinn et al., 2008), while the total genomes of some model species (e.g. Drosophila etc.) were completely sequenced. The copepod Tigriopus japonicus is one of the most promising marine model organisms for environmental genomics and ecotox- icological studies (Raisuddin et al., 2007), because it has a short generation time (2–3 weeks), is hardy and easy to maintain in the laboratory for experimentation, and is sensitive to various environmental contaminants. Therefore, their genomic DNA se- quence information would be highly beneficial for revealing the molecular mechanisms of toxic actions of chemical contaminants to marine crustaceans. To obtain extensive genomic DNA sequence information from T. japonicus, we employed GS-FLX and GS-FLX-Titanium sequencers using genomic DNA as template. In this paper, we reported the genomic DNA sequence information obtained from the GS-FLX se- quencer with BLAST data and discussed the usefulness of GS-FLX and GS-FLX-Titanium sequencers for genomic DNA sequencing and acquiring gene pools from non-model marine organisms such as the copepod. T. japonicus were collected with a mesh from laboratory cul- tures, and the samples were stored at À20 °C until DNA extraction. Total genomic DNA of T. japonicus was isolated from the stored samples using the DNeasy tissue Kit (Qiagen, Valencia, CA) accord- ing to the manufacturer’s instructions. To develop the GS-FLX and GS-FLX-Titanium shotgun library, we sheared the genomic DNA of T. japonicus mechanically into fragments, and made the blunt end ligation to adaptors. The adaptors contained the amplification and sequencing primers necessary to the GS-FLX and GS-FLX-Tita- nium sequencing process. After adaptor ligation, the fragments were denatured and clonally amplified via emulsion PCR, thereby generating millions of copies of template per bead. The DNA beads were then distributed into picolitre-sized wells on a fibre-optic slide (PicoTiter-Plate™) (Margulies et al., 2005), along with a mix- ture of smaller beads coated with the enzymes required for the pyrosequencing reaction, including the firefly enzyme luciferase. The four DNA nucleotides were then flushed sequentially over the plate. Light signals released upon base incorporation were captured by a CCD camera, and the sequence of bases incorporated 0141-1136/$ - see front matter Ó 2009 Elsevier Ltd. All rights reserved. doi:10.1016/j.marenvres.2009.12.003 * Corresponding authors. Tel.: +82 2 2220 0769; fax: +82 2 2299 9450. E-mail addresses: jslee2@hanyang.ac.kr (J.-S. Lee), ymlee70@smu.ac.kr (Y.-M. Lee). Marine Environmental Research 69 (2010) S21–S23 Contents lists available at ScienceDirect Marine Environmental Research journal homepage: www.elsevier.com/locate/marenvrev