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Transcriptome sequencing and estimation of DNA methylation level in the subsocial wood-feeding cockroach Cryptocercus punctulatus (Blattodea: Cryptocercidae)

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Abstract

The wood-feeding cockroach genus Cryptocercus is a subsocial and sister group of the eusocial cockroaches, i.e., termites. Although Cryptocercus is a key taxon for understanding the evolution of eusociality in the Blattodea (cockroaches and termites), few genetic resources are available for comparative genetic analyses. In this study, we conducted transcriptome sequencing of Cryptocercus punctulatus Scudder using next-generation sequencing technology to generate a massive genetic resource. By transcriptome sequencing and subsequent de novo transcriptome assembly, we obtained 132,191 contigs. The assembled transcriptome contained almost all of the conserved core eukaryote or insect genes. Furthermore, juvenile hormone- and DNA methylation-related genes that are considered to be key genes for the caste polyphenism in eusocial insects, were identified from the transcriptome assembly. In addition, the ratio of the observed (O) cytosine-phosphate-guanine (CpG) content to the expected (E) one (CpG O/E), which is a proxy for the DNA methylation level, was calculated for coding regions extracted from the assembly. The CpG O/E values were less than 1 in most of the coding regions, and the frequency distribution of the CpG O/E values was bimodal rather than unimodal. These results indicate that most C. punctulatus genes are involved in DNA methylation.

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References

  • Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 25:3389–3402

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Bell WJ, Roth LM, Nalepa CA (2007) Cockroaches: ecology, behavior, and natural history. Johns Hopkins University Press, Baltimore

    Google Scholar 

  • Bewick AJ, Vogel KJ, Moore AJ, Schmitz RJ (2017) Evolution of DNA methylation across insects. Mol Biol Evol 34:654–665

    PubMed  Google Scholar 

  • Bird AP (1980) DNA methylation and the frequency of CpG in animal DNA. Nucleic Acids Res 8:1499–1504

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Conesa A, Gotz S, Garcia-Gomez JM, Terol J, Talon M, Robles M (2005) Blast2GO: a universal tool for annotation, visualization and analysis in functional genomics research. Bioinformatics 21:3674–3676

    Article  CAS  PubMed  Google Scholar 

  • Coulondre C, Miller JH, Farabaugh PJ, Gilbert W (1978) Molecular basis of base substitution hotspots in Escherichia coli. Nature 274:775–780

    Article  CAS  PubMed  Google Scholar 

  • Dedeine F, Weinert LA, Bigot D, Josse T, Ballenghien M, Cahais V, Galtier N, Gayral P (2015) Comparative analysis of transcriptomes from secondary reproductives of three Reticulitermes termite species. PLoS One 10:e0145596

    Article  PubMed  PubMed Central  Google Scholar 

  • Duncan BK, Miller JH (1980) Mutagenic deamination of cytosine residues in DNA. Nature 287:560–561

    Article  CAS  PubMed  Google Scholar 

  • Elango N, Yi SV (2008) DNA methylation and structural and functional bimodality of vertebrate promoters. Mol Biol Evol 25:1602–1608

    Article  CAS  PubMed  Google Scholar 

  • Elango N, Hunt BG, Goodisman MAD, Yi SV (2009) DNA methylation is widespread and associated with differential gene expression in castes of the honeybee, Apis mellifera. Proc Natl Acad Sci USA 106:11206–11211

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Ewing B, Green P (1998) Base-calling of automated sequencer traces using Phred. II. Error probabilities. Genome Res 8:186–194

    Article  CAS  PubMed  Google Scholar 

  • Glastad KM, Hunt BG, Yi SV, Goodisman MA (2011) DNA methylation in insects: on the brink of the epigenomic era. Insect Mol Biol 20:553–565

    Article  CAS  PubMed  Google Scholar 

  • Glastad KM, Hunt BG, Goodisman MA (2013) Evidence of a conserved functional role for DNA methylation in termites. Insect Mol Biol 22:143–154

    Article  CAS  PubMed  Google Scholar 

  • Grabherr MG, Haas BJ, Yassour M et al (2011) Full-length transcriptome assembly from RNA-Seq data without a reference genome. Nat Biotechnol 29:644–652

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Hartfelder K (2000) Insect juvenile hormone: from “status quo” to high society. Braz J Med Biol Res 33:157–177

    Article  CAS  PubMed  Google Scholar 

  • Hartfelder K, Emlen DJ (2005) Endocrine control of insect polyphenism. In: Gilbert LI, Iatrou K, Gill SS (eds) Comprehensive molecular insect science, vol 3. Elsevier, Oxford, pp 651–703

    Chapter  Google Scholar 

  • Hayashi Y, Shigenobu S, Watanabe D et al (2013) Construction and characterization of normalized cDNA libraries by 454 pyrosequencing and estimation of DNA methylation levels in three distantly related termite species. PLoS One 8:e76678

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Hojo M, Maekawa K, Saitoh S, Shigenobu S, Miura T, Hayashi Y, Tokuda G, Maekawa H (2012) Exploration and characterization of genes involved in the synthesis of diterpene defence secretion in nasute termite soldiers. Insect Mol Biol 21:545–557

    Article  CAS  PubMed  Google Scholar 

  • Hunt BG, Brisson JA, Yi SV, Goodisman MAD (2010) Functional conservation of DNA methylation in the pea aphid and the honeybee. Genome Biol Evol 2:719–728

    PubMed  PubMed Central  Google Scholar 

  • Inward D, Beccaloni G, Eggleton P (2007) Death of an order: a comprehensive molecular phylogenetic study confirms that termites are eusocial cockroaches. Biol Lett 3:331–335

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Ishikawa A, Ogawa K, Gotoh H et al (2012) Juvenile hormone titre and related gene expression during the change of reproductive modes in the pea aphid. Insect Mol Biol 21:49–60

    Article  CAS  PubMed  Google Scholar 

  • Klass KD, Nalepa CA, Lo N (2008) Wood-feeding cockroaches as models for termite evolution (Insecta: Dictyoptera): Cryptocercus vs. Parasphaeria boleiriana. Mol Phylogenet Evol 46:809–817

    Article  PubMed  Google Scholar 

  • Kucharski R, Maleszka J, Foret S, Maleszka R (2008) Nutritional control of reproductive status in honeybees via DNA methylation. Science 319:1827–1830

    Article  CAS  PubMed  Google Scholar 

  • Langmead B, Trapnell C, Pop M, Salzberg SL (2009) Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol 10:R25

    Article  PubMed  PubMed Central  Google Scholar 

  • Lo N, Li B, Ujvari B (2012) DNA methylation in the termite Coptotermes lacteus. Insect Soc 59:257–261

    Article  Google Scholar 

  • Lohse M, Bolger AM, Nagel A, Fernie AR, Lunn JE, Stitt M, Usadel B (2012) RobiNA: a user-friendly, integrated software solution for RNA-Seq-based transcriptomics. Nucleic Acids Res 40:W622–W627

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Maekawa K, Hayashi Y, Lee T, Lo N (2014) Presoldier differentiation of Australian termite species induced by juvenile hormone analogs. Aust J Entomol 53:138–143

    Article  Google Scholar 

  • Min XJ, Butler G, Storms R, Tsang A (2005) OrfPredictor: predicting protein-coding regions in EST-derived sequences. Nucleic Acids Res 33:W677–W680

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Misof B, Liu S, Meusemann K et al (2014) Phylogenomics resolves the timing and pattern of insect evolution. Science 346:763–767

    Article  CAS  PubMed  Google Scholar 

  • Mitaka Y, Kobayashi K, Mikheyev A, Tin MM, Watanabe Y, Matsuura K (2016) Caste-specific and sex-specific expression of chemoreceptor genes in a termite. PLoS One 11:e0146125

    Article  PubMed  PubMed Central  Google Scholar 

  • Miura T, Scharf ME (2011) Molecular basis underlying caste differentiation in termites. In: Bignell DE, Roisin Y, Lo N (eds) Biology of termites: a modern synthesis. Springer, Dordrecht, pp 211–253

    Google Scholar 

  • Moczek AP, Snell-Rood EC (2008) The basis of bee-ing different: the role of gene silencing in plasticity. Evol Dev 10:511–513

    Article  CAS  PubMed  Google Scholar 

  • Nalepa CA (1984) Colony composition, protozoan transfer and some life-history characteristics of the woodroach Cryptocercus punctulatus Scudder (Dictyoptera, Cryptocercidae). Behav Ecol Sociobiol 14:273–279

    Article  Google Scholar 

  • Nalepa CA (2010) Altricial development in subsocial cockroach ancestors: foundation for the evolution of phenotypic plasticity in termites. Evol Dev 12:95–105

    Article  PubMed  Google Scholar 

  • Nalepa CA (2011) Altricial development in wood-feeding cockroaches: the key antecedent of termite eusociality. In: Bignell DE, Roisin Y, Lo N (eds) Biology of termites: a modern synthesis. Springer, Dordrecht, pp 69–95

    Google Scholar 

  • Nijhout HF (1994) Insect hormones. Princeton University Press, Princeton

    Google Scholar 

  • Nijhout HF, Reed MC (2008) A mathematical model for the regulation of juvenile hormone titers. J Insect Physiol 54:255–264

    Article  CAS  PubMed  Google Scholar 

  • Nijhout HF, Wheeler DE (1982) Juvenile-hormone and the physiological-basis of insect polymorphisms. Q Rev Biol 57:109–133

    Article  CAS  Google Scholar 

  • Ohkuma M, Brune A (2011) Diversity, structure, and evolution of the termite gut microbial community. In: Bignell DE, Roisin Y, Lo N (eds) Biology of termites: a modern synthesis. Springer, Dordrecht, pp 413–438

    Google Scholar 

  • Ott J (1979) Detection of rare major genes in lipid levels. Hum Genet 51:79–91

    Article  CAS  PubMed  Google Scholar 

  • Park YC, Choe JC (2003) Morphological differences of immature stages between males and females in a Korean wood feeding cockroach (Cryptocercus kyebangensis). Korean J Biol Sci 7:105–109

    Article  Google Scholar 

  • Park J, Peng Z, Zeng J et al (2011) Comparative analyses of DNA methylation and sequence evolution using Nasonia genomes. Mol Biol Evol 28:3345–3354

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Parra G, Bradnam K, Korf I (2007) CEGMA: a pipeline to accurately annotate core genes in eukaryotic genomes. Bioinformatics 23:1061–1067

    Article  CAS  PubMed  Google Scholar 

  • Poulsen M, Hu H, Li C et al (2014) Complementary symbiont contributions to plant decomposition in a fungus-farming termite. Proc Natl Acad Sci USA 111:14500–14505

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Roberts A, Pachter L (2013) Streaming fragment assignment for real-time analysis of sequencing experiments. Nat Methods 10:71–73

    Article  CAS  PubMed  Google Scholar 

  • Sacchi L, Nalepa CA, Bigliardi E, Corona S, Grigolo A, Laudani U, Bandi C (1998) Ultrastructural studies of the fat body and bacterial endosymbionts of Cryptocercus punctulatus Scudder (Blattaria: Cryptocercidae). Symbiosis 25:251–269

    Google Scholar 

  • Sarda S, Zeng J, Hunt BG, Yi SV (2012) The evolution of invertebrate gene body methylation. Mol Biol Evol 29:1907–1916

    Article  CAS  PubMed  Google Scholar 

  • Scharf ME, Ratliff CR, Hoteling JT, Pittendrigh BR, Bennett GW (2003) Caste differentiation responses of two sympatric Reticulitermes termite species to juvenile hormone homologs and synthetic juvenoids. Insect Soc 50:346–354

    Article  Google Scholar 

  • Seelinger G, Seelinger U (1983) On the social-organization, alarm and fighting in the primitive cockroach Cryptocercus punctulatus Scudder. J Comp Ethol 61:315–333

    Google Scholar 

  • Suzuki MM, Bird A (2008) DNA methylation landscapes: provocative insights from epigenomics. Nat Rev Genet 9:465–476

    Article  CAS  PubMed  Google Scholar 

  • Suzuki MM, Kerr AR, De Sousa D, Bird A (2007) CpG methylation is targeted to transcription units in an invertebrate genome. Genome Res 17:625–631

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • R Core Team (2014) R: a language and environment for statistical computing. R Foundation for Statistical Computing, Vienna. http://www.R-project.org/

  • Terrapon N, Li C, Robertson HM et al (2014) Molecular traces of alternative social organization in a termite genome. Nat Commun 5:3636

    Article  CAS  PubMed  Google Scholar 

  • The International Aphid Genomics Consortium (2010) Genome sequence of the pea aphid Acyrthosiphon pisum. PLoS Biol 8:e1000313

    Article  PubMed Central  Google Scholar 

  • Watanabe D, Gotoh H, Miura T, Maekawa K (2011) Soldier presence suppresses presoldier differentiation through a rapid decrease of JH in the termite Reticulitermes speratus. J Insect Physiol 57:791–795

    Article  CAS  PubMed  Google Scholar 

  • Watanabe D, Gotoh H, Miura T, Maekawa K (2014) Social interactions affecting caste development through physiological actions in termites. Front Physiol 5:127

    Article  PubMed  PubMed Central  Google Scholar 

  • Waterhouse RM, Tegenfeldt F, Li J, Zdobnov EM, Kriventseva EV (2013) OrthoDB: a hierarchical catalog of animal, fungal and bacterial orthologs. Nucleic Acids Res 41:D358–D365

    Article  CAS  PubMed  Google Scholar 

  • Yanai I, Benjamin H, Shmoish M et al (2005) Genome-wide midrange transcription profiles reveal expression level relationships in human tissue specification. Bioinformatics 21:650–659

    Article  CAS  PubMed  Google Scholar 

  • Yi SV, Goodisman MAD (2009) Computational approaches for understanding the evolution of DNA methylation in animals. Epigenetics 4:551–556

    Article  CAS  PubMed  Google Scholar 

  • Zdobnov EM, Apweiler R (2001) InterProScan- an integration platform for the signature-recognition methods in InterPro. Bioinformatics 17:847–848

    Article  CAS  PubMed  Google Scholar 

  • Zemach A, McDaniel IE, Silva P, Zilberman D (2010) Genome-wide evolutionary analysis of eukaryotic DNA methylation. Science 328:916–919

    Article  CAS  PubMed  Google Scholar 

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Acknowledgements

We thank Dr. K. Yamaguchi for technical support with the Illumina sequencing, and are grateful to the director and staff of Mountain Lake Biological Station for permission to work on their grounds. We also thank two anonymous reviewers for their helpful comments on earlier drafts of this article. Computational resources were provided by the Data Integration and Analysis Facility, NIBB. This study was conducted as part of the Model Organism Development Collaborative Research Projects of NIBB, and was supported by a Grant for Basic Science Research Projects from the Sumitomo Foundation (no. 150189 to Y. H.) and Japan Society for the Promotion of Science KAKENHI (Grant Nos. JP16K18591 and 25251041 to Y. H. and T. M., respectively).

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Authors and Affiliations

  1. Graduate School of Environmental Science, Hokkaido University, Sapporo, Hokkaido, 060-0810, Japan

    Yoshinobu Hayashi & Toru Miura

  2. Department of Biology, Keio University, Yokohama, Kanagawa, 223-8521, Japan

    Yoshinobu Hayashi

  3. Graduate School of Science and Engineering, University of Toyama, Toyama, Toyama, 930-8555, Japan

    Kiyoto Maekawa

  4. Department of Entomology, North Carolina State University, Raleigh, NC, 27695-7613, USA

    Christine A. Nalepa

  5. Misaki Marine Biological Station, Graduate School of Science, University of Tokyo, Miura, Kanagawa, 238-0225, Japan

    Toru Miura

  6. Core Research Facilities, National Institute for Basic Biology, National Institutes of Natural Sciences, Okazaki, Aichi, 444-8585, Japan

    Shuji Shigenobu

  7. Department of Basic Biology, School of Life Science, Graduate University for Advanced Studies, Okazaki, Aichi, 444-8585, Japan

    Shuji Shigenobu

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  1. Yoshinobu Hayashi
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Correspondence to Yoshinobu Hayashi.

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Hayashi, Y., Maekawa, K., Nalepa, C.A. et al. Transcriptome sequencing and estimation of DNA methylation level in the subsocial wood-feeding cockroach Cryptocercus punctulatus (Blattodea: Cryptocercidae). Appl Entomol Zool 52, 643–651 (2017). https://doi.org/10.1007/s13355-017-0519-7

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