RNA Sequencing, De novo assembly, functional annotation and SSR analysis of the endangered diving beetle Cybister chinensis (= Cybister japonicus) using the Illumina platform
Hee-Ju Hwang
Department of Life Science and Biotechnology, College of Natural Sciences, Soonchunhyang University, Asan, Chungcheongnam-do, South Korea
These authors contributed equally to this work.Search for more papers by this authorBharat Bhusan Patnaik
Trident School of Biotech Sciences, Trident Academy of Creative Technology (TACT), Chandaka Industrial Estate, Bhubaneswar, Odisha, India
These authors contributed equally to this work.Search for more papers by this authorSe Won Kang
Biological Resource Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Jeongeup-Si, Jeollabuk-do, South Korea
Search for more papers by this authorSo Young Park
Nakdonggang National Institute of Biological Resources, Biodiversity Conservation and Change Research Division, Sangju-si, Gyeongsangbuk-do, South Korea
Search for more papers by this authorJong Min Chung
Department of Life Science and Biotechnology, College of Natural Sciences, Soonchunhyang University, Asan, Chungcheongnam-do, South Korea
Search for more papers by this authorMin Kyu Sang
Department of Life Science and Biotechnology, College of Natural Sciences, Soonchunhyang University, Asan, Chungcheongnam-do, South Korea
Search for more papers by this authorJie Eun Park
Department of Life Science and Biotechnology, College of Natural Sciences, Soonchunhyang University, Asan, Chungcheongnam-do, South Korea
Search for more papers by this authorHye Rin Min
Department of Life Science and Biotechnology, College of Natural Sciences, Soonchunhyang University, Asan, Chungcheongnam-do, South Korea
Search for more papers by this authorJiyeon Seong
Genomic Informatics center, Hankyong National University, Anseong-si, Kyonggi-do, South Korea
Search for more papers by this authorYong Hun Jo
Division of Plant Biotechnology, Institute of Environmentally-Friendly Agriculture (IEFA), College of Agriculture and Life Sciences, Chonnam National University, Gwangju, Republic of Korea
Search for more papers by this authorMi Young Noh
Division of Plant Biotechnology, Institute of Environmentally-Friendly Agriculture (IEFA), College of Agriculture and Life Sciences, Chonnam National University, Gwangju, Republic of Korea
Search for more papers by this authorJong Dae Lee
Department of Environmental Health Science, College of Natural Sciences, Soonchunhyang University, Asan, Chungcheongnam-do, South Korea
Search for more papers by this authorKi Yoon Jung
Department of Life Science and Biotechnology, College of Natural Sciences, Soonchunhyang University, Asan, Chungcheongnam-do, South Korea
Search for more papers by this authorHong Seog Park
Research Institute, GnC BIO Co., LTD, Daejeon, South Korea
Search for more papers by this authorHeon Cheon Jeong
Hampyeong county Insect Institute, Hampyeong County Agricultural Technology Centerm 90, Jeollanam-do, South Korea
Search for more papers by this authorCorresponding Author
Yong Seok Lee
Department of Life Science and Biotechnology, College of Natural Sciences, Soonchunhyang University, Asan, Chungcheongnam-do, South Korea
Correspondence
Yong Seok Lee, Department of Life Science and Biotechnology, College of Natural Sciences, Soonchunhyang University, 22 Soonchunhyangro, Shinchang-myeon, Asan, Chungcheongnam-do 31538, Korea.
Email: [email protected]
Search for more papers by this authorHee-Ju Hwang
Department of Life Science and Biotechnology, College of Natural Sciences, Soonchunhyang University, Asan, Chungcheongnam-do, South Korea
These authors contributed equally to this work.Search for more papers by this authorBharat Bhusan Patnaik
Trident School of Biotech Sciences, Trident Academy of Creative Technology (TACT), Chandaka Industrial Estate, Bhubaneswar, Odisha, India
These authors contributed equally to this work.Search for more papers by this authorSe Won Kang
Biological Resource Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Jeongeup-Si, Jeollabuk-do, South Korea
Search for more papers by this authorSo Young Park
Nakdonggang National Institute of Biological Resources, Biodiversity Conservation and Change Research Division, Sangju-si, Gyeongsangbuk-do, South Korea
Search for more papers by this authorJong Min Chung
Department of Life Science and Biotechnology, College of Natural Sciences, Soonchunhyang University, Asan, Chungcheongnam-do, South Korea
Search for more papers by this authorMin Kyu Sang
Department of Life Science and Biotechnology, College of Natural Sciences, Soonchunhyang University, Asan, Chungcheongnam-do, South Korea
Search for more papers by this authorJie Eun Park
Department of Life Science and Biotechnology, College of Natural Sciences, Soonchunhyang University, Asan, Chungcheongnam-do, South Korea
Search for more papers by this authorHye Rin Min
Department of Life Science and Biotechnology, College of Natural Sciences, Soonchunhyang University, Asan, Chungcheongnam-do, South Korea
Search for more papers by this authorJiyeon Seong
Genomic Informatics center, Hankyong National University, Anseong-si, Kyonggi-do, South Korea
Search for more papers by this authorYong Hun Jo
Division of Plant Biotechnology, Institute of Environmentally-Friendly Agriculture (IEFA), College of Agriculture and Life Sciences, Chonnam National University, Gwangju, Republic of Korea
Search for more papers by this authorMi Young Noh
Division of Plant Biotechnology, Institute of Environmentally-Friendly Agriculture (IEFA), College of Agriculture and Life Sciences, Chonnam National University, Gwangju, Republic of Korea
Search for more papers by this authorJong Dae Lee
Department of Environmental Health Science, College of Natural Sciences, Soonchunhyang University, Asan, Chungcheongnam-do, South Korea
Search for more papers by this authorKi Yoon Jung
Department of Life Science and Biotechnology, College of Natural Sciences, Soonchunhyang University, Asan, Chungcheongnam-do, South Korea
Search for more papers by this authorHong Seog Park
Research Institute, GnC BIO Co., LTD, Daejeon, South Korea
Search for more papers by this authorHeon Cheon Jeong
Hampyeong county Insect Institute, Hampyeong County Agricultural Technology Centerm 90, Jeollanam-do, South Korea
Search for more papers by this authorCorresponding Author
Yong Seok Lee
Department of Life Science and Biotechnology, College of Natural Sciences, Soonchunhyang University, Asan, Chungcheongnam-do, South Korea
Correspondence
Yong Seok Lee, Department of Life Science and Biotechnology, College of Natural Sciences, Soonchunhyang University, 22 Soonchunhyangro, Shinchang-myeon, Asan, Chungcheongnam-do 31538, Korea.
Email: [email protected]
Search for more papers by this authorAbstract
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 from C. japonicus till 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.
Supporting Information
| Filename | Description |
|---|---|
| enr12292-sup-0001-Table_S1.docxWord 2007 document , 12.4 KB |
Table S1 Pre-processing of raw reads of Cybister japonicus transcriptome obtained from Illumina sequencer. |
| enr12292-sup-0002-Table_S2.docxWord 2007 document , 13.4 KB | Table S2 KEGG Orthology (KO) classifications of Cybister japonicus unigenes mapped to four categories; Environmental Information Processing, Genetic Information Processing, Metabolism, and Organismal Systems. |
| enr12292-sup-0003-Table_S3.docxWord 2007 document , 18.6 KB | Table S3 Detailed analysis of KEGG pathways and the sequences of enzymes in the pathway |
| enr12292-sup-0004-Table_S4.docxWord 2007 document , 12.1 KB | Table S4 Features of the SSR types identified in the unigenes of Cybister japonicus |
Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
References
- Akira S, Uematsu STakeuchi O (2006) Pathogen recognition and innate immunity. Cell 124: 783–801.
- Altincicek B, Elashry A, Guz N et al. (2013) Next-generation sequencing based transcriptome analysis of septic-injury responsive genes in the beetle Tribolium castaneum. PLoS One 8: e52004.
- Ashburner M, Ball CA, Blake JA et al. (2000) Gene ontology: tool for the unification of biology. Nature Genetics 25: 25–29.
- Brayer KJ, Segal DJ (2008) Keep your fingers off my DNA: protein-protein interactions mediated by the C2H2 zinc finger domains. Cellular Biochemistry and Biophysics 50: 111–131.
- Conesa A, Gotz S, Garcia-Gomez JM et al. (2005) Blast2GO: a universal tool for annotation, visualization and analysis in functional genomics research. Bioinformatics 21: 3674–3676.
- DeLay B, Mamidala P, Wijeratne A et al. (2012) Transcriptome analysis of the salivary glands of potato leafhopper, Empoasca fabae. Journal of Insect Physiology 58: 1626–1634. https://doi.org/10.1016/jinsphys.2012.10.002.
- Duan Y, Gong ZJ, Wu RH et al. (2017) Transcriptome analysis of molecular mechanisms responsible for light-stress response in Mythimna separate (Walker). Scientific Reports 7: 45188.
- Ewing B, Green P (1998) Base-calling of automated sequencer traces using phred. II. Error probabilities. Genome Research 8(3): 186–194.
- Firmino AAP, de Assis Fonseca FC, de Macedo LLP et al. (2013) Transcriptome analysis in cotton boll weevil (Anthomonas grandis) and RNA interference in Insect Pests. PLoS One 8: e85079.
- Fujimaki K, Fujisawa T, Yazawa S, Nishimura O, Sota T (2014) Comparative transcriptomic analysis of two closely related ground beetle species with marked genetic divergence using pyrosequencing. Zoological Science 31: 587–592.
- Gamsjaeger R, Liew CK, Loughlin FE, Crossley M, Mackay JP (2007) Sticky fingers: zinc-fingers as protein-recognition motifs. Trends Biochemical Science 32: 63–70.
- Hill DP, Smith B, Mc-Andrews Hill MS, Blake JA (2008) Gene ontology annotations: what they mean and where they come from. BMC Bioinformatics 9: S2.
- Holliday AE, Mattingly TM, Holliday NJ (2015) Defensive secretions of larvae of a carabid beetle. Physiological Entomology 40: 131–137.
- Kanehisa M, Goto S, Sato Y, Furumichi MTanabe M (2012) KEGG for integration and interpretation of large-scale molecular data sets. Nucleic Acids Research 40: D109–D114.
- Kang SW, Park SY, Patnaik BB et al. (2015) Construction of PANM database (Protostome DB) for rapid annotation of NGS data in mollusks. Korean Journal of Malacology 31: 243–247.
10.9710/kjm.2015.31.3.243 Google Scholar
- Kang SW, Patnaik BB, Hwang HJ et al. (2016a) Sequencing and de novo assembly of visceral mass transcriptome of the critically endangered land snail Satsuma myomphala: annotation and SSR discovery. Comparative Biochemistry and Physiology Part D: Genomics and Proteomics 21: 77–89.
- Kang SW, Park SY, Patnaik BB et al. (2016b) The protostome database (PANM-DB): version 2.0 release with updated sequences. Korean Journal of Malacology 32: 185–188.
- Karaiskou N, Buggiotti L, Leder E, Primmer CR (2008) High degree of transferability of 86 newly developed zebra finch EST-linked microsatellite markers in 8 bird species. J Hered 99(6): 688–693.
10.1093/jhered/esn052 Google Scholar
- Kumar A, Congiu L, Lindstrom L et al. (2014) Sequencing, de novo assembly and annotation of the Colorado potato beetle, Leptinotarsa decemlineata, Transcriptome. PLoS One 9: e86012.
- Liu Z-K, Wen JB (2016) Transcriptomic analysis of Eucryptorrhynchus chinensis (Coleoptera: Curculionidae) using 454 pyrosequencing technology. Journal of Insect Science 82: 1–6.
- Miller KB, Bergsten J, Whiting MF (2007) Phylogeny and classification of diving beetles in the tribe Cybistrini (Coleoptera, Dytiscidae, Dytiscinae). Zoologica Scripta 36: 41–59.
- Mitchell A, Chang HY, Daugherty L et al. (2015) The InterPro families database: the classification resource after 15 years. Nucleic Acids Research 43: D213–D221.
- Morozova O, Marra MA (2008) Applications of next-generation sequencing technologies in functional genomics. Genomics 92: 255–264.
- Morris K, Lorenzen M, Hiromasa Y et al. (2009) Tribolium castaneum larval gut transcriptome and proteome: a resource for the study of the coleopteran gut. Journal of Proteome Research 8: 3889–3898.
- Ohba S-y (2009a) Feeding habits of the diving beetle larvae, Cybister brevis Aube (Coleoptera: Dytiscidae) in Japanese wetlands. Applied Entomological Science 44: 447–453.
- Ohba S-y (2009b) Ontogenetic dietary shift in the larvae of Cybister japonicus (Coleoptera: Dytiscidae) in Japanese rice fields. Environmental Entomology 38: 856–860.
- Ohba S-y, Inatani Y (2012) Feeding preferences of the endangered diving beetle Cybister tripunctatus orientalis Gschwendtner (Coleoptera: Dytiscidae). Psyche. https://doi.org/10.1155/2012/139714.
- Ohba S-y, Takagi M (2010) Predatory ability of adult diving beetles on the Japanese encephalitis vector Culex tritaeniorhynchus. Journal of American Mosquito Control Association 26: 32–36.
- Oppenheim SJ, Baker RH, Simon S, DeSalle R (2015) We can't be all supermodels: the value of comparative transcriptomics to the study of non-model insects. Insect Molecular Biology 24: 139–154.
- Palmer WJ, Duarte A, Schrader M et al. (2016) A gene associated with social immunity in the burying beetle Nicrophorus vespilloides. Proceedings of the Royal Society B. Biological Sciences 283: 20152733.
- Pankewitz F, Hilker M (2008) Polyketides in insects: ecological role of these widespread chemicals and evolutionary aspects of their biogenesis. Biological Reviews of the Cambridge Philosophical Society 83: 209–226.
- Park SY, Patnaik BB, Kang SW et al. (2016) Transcriptomic analysis of the endangered neritid species Clithon retropictus: De novo assembly, functional annotation, and marker discovery. Genes 7: 35.
10.3390/genes7070035 Google Scholar
- Park Y, Aikins J, Wang LJ et al. (2008) Analysis of the transcriptome data in the red flour beetle, Tribolium castaneum. Insect Biochemistry and Molecular Biology 38: 380–386.
- Patnaik BB, Hwang HJ, Kang SW et al. (2015) Transcriptome characterization of non-model endangered lycaenids, Protantigius superans and Spindasis takanosis, using Illumina HiSeq 2500 sequencing. International Journal of Molecular Research 16: 29948–29970.
10.3390/ijms161226213 Google Scholar
- Patnaik BB, Wang TH, Kang SW et al. (2016) Sequencing, de novo assembly, and annotation of the transcriptome of the endangered freshwater pearl bivalve, Cristaria plicata, provides novel insights into functional genes and marker discovery. PLoS One 11: e0148622.
- Pertea G, Huang X, Liang F et al. (2003) TIGR gene indices clustering tool (TGICL): a software system for fast clustering of large EST. Bioinformatics 19: 651–652.
- Ree HI (2005) Studies on Anopheles sinensis, the vector species of vivax malaria in Korea. Korean Journal of Parasitology 43: 75–92.
- Rhee SY, Wood V, Dolinski K, Draghici S (2008) Use and misuse of the gene ontology annotations. Nature Reviews Genetics 9: 509–515.
- Seong J, Kang SW, Patnaik BB et al. (2016) Transcriptome analysis of the tadpole shrimp (Triops longicaudatus) by Illumina paired-end sequencing: assembly, annotation, and marker discovery. Genes 7: 114.
10.3390/genes7120114 Google Scholar
- Song LM, Jiang X, Wang XM et al. (2016) Male tarsi specific odorant-binding proteins in the diving beetle Cybister japonicus sharp. Scientific Reports 6: 31848.
- Song LM, Wang XM, Huang JP et al. (2017) Ultrastructure and morphology of antennal sensilla of the adult diving beetle, Cybister japonicus Sharp. PLoS One 12: e0174643.
- Tatusov RL, Fedorova ND, Jackson JD et al. (2003) The COG database: an updated version includes eukaryotes. BMC Bioinformatics 4: 41.
- Thiel T, Michalek W, Varshney R, Graner AExploting EST (2003) Databases for the development and characterization of gene-derived SSR-markers in barley (Hordeum vulgare L.). Theoretical Applied Genetics 106: 411–422.
- Uliano-Silva M, Americo JA, Brindeiro R Dondero F, Prosdocimi F, Rebelo Mde F (2014) Gene discovery through transcriptome sequencing for the invasive mussel, Limnoperna fortunei. PLoS One 9(7): e102973.
10.1371/journal.pone.0102973 Google Scholar
- Valencia A, Wang H, Soto A et al. (2016) Pyrosequencing of the midgut transcriptome of the Banana weevil Cosmopolites sordidus (Germar) (Coleoptera: Curculionidae) reveals multiple protease-like transcripts. PLoS One 11: e0151001.
10.1371/journal.pone.0151001 Google Scholar
- Vongsangnak W, Chumnanpuen PSriboonlert A (2016) Transcriptome analysis reveals candidate genes involved in luciferin metabolism in Luciola aquatilis (Coleoptera: Lampyridae). PeerJ 4: e2534.
- Wang K, Hong W, Jiao H, Zhao H (2017) Transcriptome sequencing and phylogenetic analysis of four species of luminescent beetles. Scientific Reports 7: 1814.
- Wei HS, Li KB, Zhang S et al. (2017) Identification of candidate chemosensory genes by transcriptome analysis in Loxostege sticticalis Linnaeus. PLoS One 12: e0174036.
- Wheat CW (2010) Rapidly developing functional genomics in ecological model systems via 454 transcriptome sequencing. Genetica 138: 433–451.
- You FM, Huo N, Gu YQ et al. (2008) BatchPrimer 3.0: a high-throughput web application for PCR and sequencing primer design. BMC Bioinformatics 9. https://doi.org/10.1186/1471-2105-9-253.
- Zhang W, Song W, Zhang Z et al. (2014) Transcriptome analysis of dastarcus helophoroides (Coleoptera: Bothridertdae) using Illumina HiSeq Sequencing. PLoS One 9: e100673.
10.1371/journal.pone.0100673 Google Scholar
- Zhu JY, Li Y-H, Yang YS, Li Q-W (2013) De novo assembly and characterization of the global transcriptome for Rhyacionia leptotubula using Illumina paired-end sequencing. PLoS One 8: e81096.
10.1371/journal.pone.0081096 Google Scholar
