Entomological Research

The Entomological Society of Korea (한국곤충학회)
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RNA Sequencing, De novo assembly, functional annotation and SSR analysis of the endangered diving beetle Cybister chinensis (= Cybister japonicus) using the Illumina platform

  • HWANG, Hee-Ju (Department of Life Science and Biotechnology, College of Natural Sciences, Soonchunhyang University) ;
  • PATNAIK, Bharat Bhusan (Trident School of Biotech Sciences, Trident Academy of Creative Technology (TACT), Chandaka Industrial Estate) ;
  • KANG, Se Won (Biological Resource Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB)) ;
  • PARK, So Young (Nakdonggang National Institute of Biological Resources, Biodiversity Conservation and Change Research Division) ;
  • CHUNG, Jong Min (Department of Life Science and Biotechnology, College of Natural Sciences, Soonchunhyang University) ;
  • SANG, Min Kyu (Department of Life Science and Biotechnology, College of Natural Sciences, Soonchunhyang University) ;
  • PARK, Jie Eun (Department of Life Science and Biotechnology, College of Natural Sciences, Soonchunhyang University) ;
  • MIN, Hye Rin (Department of Life Science and Biotechnology, College of Natural Sciences, Soonchunhyang University) ;
  • SEONG, Jiyeon (Genomic Informatics center, Hankyong National University) ;
  • JO, Yong Hun (Division of Plant Biotechnology, Institute of Environmentally-Friendly Agriculture (IEFA), College of Agriculture and Life Sciences, Chonnam National University) ;
  • NOH, Mi Young (Division of Plant Biotechnology, Institute of Environmentally-Friendly Agriculture (IEFA), College of Agriculture and Life Sciences, Chonnam National University) ;
  • LEE, Jong Dae (Department of Environmental Health Science, College of Natural Sciences, Soonchunhyang University) ;
  • JUNG, Ki Yoon (Department of Life Science and Biotechnology, College of Natural Sciences, Soonchunhyang University) ;
  • PARK, Hong Seog (Research Institute, GnC BIO Co., LTD) ;
  • JEONG, Heon Cheon (Hampyeong county Insect Institute, Hampyeong County Agricultural Technology Centerm 90) ;
  • LEE, Yong Seok (Department of Life Science and Biotechnology, College of Natural Sciences, Soonchunhyang University)
  • Received : 2017.10.18
  • Accepted : 2017.12.20
  • Published : 2018.01.29
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Abstract

Cybister chinensis Motschulsky, 1854 (synonym Cybister japonicus Sharp, 1873) is a beetle found in ponds and irrigation canals near rice fields regulating the aquatic faunal community through predation. However, due to loss of natural habitats, use of pesticides, and invasion of alien species the beetle is threatened. With lack of understanding at the trophic ecology and genomics level, the conservation study is hindered to a larger extent. In the present study, Illumina HiSeq 4000 platform has been used to unravel the whole-larval transcriptome of the beetle. A total of 20,129 non-redundant unigenes were assembled from 67,260,666 clean read sequences. About 18,743 unigenes found a homologous match in any one of the databases like PANM, UniGene, Swiss-Prot, Clusters of Orthologous Groups (COG), Gene Ontology (GO), KEGG, and InterProScan. While the zinc finger domains topped the unigene hits, about 660 enzymes (2695 sequences) participating in metabolism, environmental information processing, genetic information processing and organismal system pathways were recorded. Furthermore, the HSP70 class, Toll-like receptors 4, insulin-receptor substrate, and AMP activated protein kinase showed conspicuous presence in the larval transcriptome. Out of a total of 12,491 unigene sequences examined, 1968 SSRs were detected. Majority of them were dinucleotide repeats with six iterations followed by trinucleotide and tetranucleotide repeats with five and four iterations, respectively. This is the first report of cDNA resources fromC. japonicustill date. The data would be crucial for the assessment of the beetle in the wild and making an inventory for utilisation in future genomics and ecological studies.

Keywords

Acknowledgement

Grant : The Genetic and Genomic evaluation of Indigenous Biological Resources, Analysis of genetic characteristics of endangered species

Supported by : National Institute of Biological Resources, National Research Foundation

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