Advertisement

Applied Entomology and Zoology

, Volume 52, Issue 4, pp 643–651 | Cite as

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

  • Yoshinobu Hayashi
  • Kiyoto Maekawa
  • Christine A. Nalepa
  • Toru Miura
  • Shuji Shigenobu
Original Research Paper

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.

Keywords

DNA methyltransferase De novo transcriptome assembly Gene repertoire Juvenile hormone 

Notes

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).

Compliance with ethical standards

Conflict of interest

The authors declare that they have no conflict of interest.

Supplementary material

13355_2017_519_MOESM1_ESM.fa (159.7 mb)
Supplementary material 1 (FA 163561 kb)
13355_2017_519_MOESM2_ESM.fa (72.4 mb)
Supplementary material 2 (FA 74129 kb)
13355_2017_519_MOESM3_ESM.fa (27.1 mb)
Supplementary material 3 (FA 27780 kb)

References

  1. 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 25:3389–3402CrossRefPubMedPubMedCentralGoogle Scholar
  2. Bell WJ, Roth LM, Nalepa CA (2007) Cockroaches: ecology, behavior, and natural history. Johns Hopkins University Press, BaltimoreGoogle Scholar
  3. Bewick AJ, Vogel KJ, Moore AJ, Schmitz RJ (2017) Evolution of DNA methylation across insects. Mol Biol Evol 34:654–665PubMedGoogle Scholar
  4. Bird AP (1980) DNA methylation and the frequency of CpG in animal DNA. Nucleic Acids Res 8:1499–1504CrossRefPubMedPubMedCentralGoogle Scholar
  5. 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 21:3674–3676CrossRefPubMedGoogle Scholar
  6. Coulondre C, Miller JH, Farabaugh PJ, Gilbert W (1978) Molecular basis of base substitution hotspots in Escherichia coli. Nature 274:775–780CrossRefPubMedGoogle Scholar
  7. 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:e0145596CrossRefPubMedPubMedCentralGoogle Scholar
  8. Duncan BK, Miller JH (1980) Mutagenic deamination of cytosine residues in DNA. Nature 287:560–561CrossRefPubMedGoogle Scholar
  9. Elango N, Yi SV (2008) DNA methylation and structural and functional bimodality of vertebrate promoters. Mol Biol Evol 25:1602–1608CrossRefPubMedGoogle Scholar
  10. 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 106:11206–11211CrossRefPubMedPubMedCentralGoogle Scholar
  11. Ewing B, Green P (1998) Base-calling of automated sequencer traces using Phred. II. Error probabilities. Genome Res 8:186–194CrossRefPubMedGoogle Scholar
  12. Glastad KM, Hunt BG, Yi SV, Goodisman MA (2011) DNA methylation in insects: on the brink of the epigenomic era. Insect Mol Biol 20:553–565CrossRefPubMedGoogle Scholar
  13. Glastad KM, Hunt BG, Goodisman MA (2013) Evidence of a conserved functional role for DNA methylation in termites. Insect Mol Biol 22:143–154CrossRefPubMedGoogle Scholar
  14. Grabherr MG, Haas BJ, Yassour M et al (2011) Full-length transcriptome assembly from RNA-Seq data without a reference genome. Nat Biotechnol 29:644–652CrossRefPubMedPubMedCentralGoogle Scholar
  15. Hartfelder K (2000) Insect juvenile hormone: from “status quo” to high society. Braz J Med Biol Res 33:157–177CrossRefPubMedGoogle Scholar
  16. 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 651–703CrossRefGoogle Scholar
  17. 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:e76678CrossRefPubMedPubMedCentralGoogle Scholar
  18. 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 21:545–557CrossRefPubMedGoogle Scholar
  19. Hunt BG, Brisson JA, Yi SV, Goodisman MAD (2010) Functional conservation of DNA methylation in the pea aphid and the honeybee. Genome Biol Evol 2:719–728PubMedPubMedCentralGoogle Scholar
  20. Inward D, Beccaloni G, Eggleton P (2007) Death of an order: a comprehensive molecular phylogenetic study confirms that termites are eusocial cockroaches. Biol Lett 3:331–335CrossRefPubMedPubMedCentralGoogle Scholar
  21. 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 21:49–60CrossRefPubMedGoogle Scholar
  22. Klass KD, Nalepa CA, Lo N (2008) Wood-feeding cockroaches as models for termite evolution (Insecta: Dictyoptera): Cryptocercus vs. Parasphaeria boleiriana. Mol Phylogenet Evol 46:809–817CrossRefPubMedGoogle Scholar
  23. Kucharski R, Maleszka J, Foret S, Maleszka R (2008) Nutritional control of reproductive status in honeybees via DNA methylation. Science 319:1827–1830CrossRefPubMedGoogle Scholar
  24. 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:R25CrossRefPubMedPubMedCentralGoogle Scholar
  25. Lo N, Li B, Ujvari B (2012) DNA methylation in the termite Coptotermes lacteus. Insect Soc 59:257–261CrossRefGoogle Scholar
  26. 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–W627CrossRefPubMedPubMedCentralGoogle Scholar
  27. Maekawa K, Hayashi Y, Lee T, Lo N (2014) Presoldier differentiation of Australian termite species induced by juvenile hormone analogs. Aust J Entomol 53:138–143CrossRefGoogle Scholar
  28. Min XJ, Butler G, Storms R, Tsang A (2005) OrfPredictor: predicting protein-coding regions in EST-derived sequences. Nucleic Acids Res 33:W677–W680CrossRefPubMedPubMedCentralGoogle Scholar
  29. Misof B, Liu S, Meusemann K et al (2014) Phylogenomics resolves the timing and pattern of insect evolution. Science 346:763–767CrossRefPubMedGoogle Scholar
  30. 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:e0146125CrossRefPubMedPubMedCentralGoogle Scholar
  31. 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 211–253Google Scholar
  32. Moczek AP, Snell-Rood EC (2008) The basis of bee-ing different: the role of gene silencing in plasticity. Evol Dev 10:511–513CrossRefPubMedGoogle Scholar
  33. Nalepa CA (1984) Colony composition, protozoan transfer and some life-history characteristics of the woodroach Cryptocercus punctulatus Scudder (Dictyoptera, Cryptocercidae). Behav Ecol Sociobiol 14:273–279CrossRefGoogle Scholar
  34. Nalepa CA (2010) Altricial development in subsocial cockroach ancestors: foundation for the evolution of phenotypic plasticity in termites. Evol Dev 12:95–105CrossRefPubMedGoogle Scholar
  35. 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 69–95Google Scholar
  36. Nijhout HF (1994) Insect hormones. Princeton University Press, PrincetonGoogle Scholar
  37. Nijhout HF, Reed MC (2008) A mathematical model for the regulation of juvenile hormone titers. J Insect Physiol 54:255–264CrossRefPubMedGoogle Scholar
  38. Nijhout HF, Wheeler DE (1982) Juvenile-hormone and the physiological-basis of insect polymorphisms. Q Rev Biol 57:109–133CrossRefGoogle Scholar
  39. 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 413–438Google Scholar
  40. Ott J (1979) Detection of rare major genes in lipid levels. Hum Genet 51:79–91CrossRefPubMedGoogle Scholar
  41. 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 7:105–109CrossRefGoogle Scholar
  42. Park J, Peng Z, Zeng J et al (2011) Comparative analyses of DNA methylation and sequence evolution using Nasonia genomes. Mol Biol Evol 28:3345–3354CrossRefPubMedPubMedCentralGoogle Scholar
  43. Parra G, Bradnam K, Korf I (2007) CEGMA: a pipeline to accurately annotate core genes in eukaryotic genomes. Bioinformatics 23:1061–1067CrossRefPubMedGoogle Scholar
  44. 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 111:14500–14505CrossRefPubMedPubMedCentralGoogle Scholar
  45. Roberts A, Pachter L (2013) Streaming fragment assignment for real-time analysis of sequencing experiments. Nat Methods 10:71–73CrossRefPubMedGoogle Scholar
  46. 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 25:251–269Google Scholar
  47. Sarda S, Zeng J, Hunt BG, Yi SV (2012) The evolution of invertebrate gene body methylation. Mol Biol Evol 29:1907–1916CrossRefPubMedGoogle Scholar
  48. 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 50:346–354CrossRefGoogle Scholar
  49. Seelinger G, Seelinger U (1983) On the social-organization, alarm and fighting in the primitive cockroach Cryptocercus punctulatus Scudder. J Comp Ethol 61:315–333Google Scholar
  50. Suzuki MM, Bird A (2008) DNA methylation landscapes: provocative insights from epigenomics. Nat Rev Genet 9:465–476CrossRefPubMedGoogle Scholar
  51. Suzuki MM, Kerr AR, De Sousa D, Bird A (2007) CpG methylation is targeted to transcription units in an invertebrate genome. Genome Res 17:625–631CrossRefPubMedPubMedCentralGoogle Scholar
  52. R Core Team (2014) R: a language and environment for statistical computing. R Foundation for Statistical Computing, Vienna. http://www.R-project.org/
  53. Terrapon N, Li C, Robertson HM et al (2014) Molecular traces of alternative social organization in a termite genome. Nat Commun 5:3636CrossRefPubMedGoogle Scholar
  54. The International Aphid Genomics Consortium (2010) Genome sequence of the pea aphid Acyrthosiphon pisum. PLoS Biol 8:e1000313CrossRefPubMedCentralGoogle Scholar
  55. 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 57:791–795CrossRefPubMedGoogle Scholar
  56. Watanabe D, Gotoh H, Miura T, Maekawa K (2014) Social interactions affecting caste development through physiological actions in termites. Front Physiol 5:127CrossRefPubMedPubMedCentralGoogle Scholar
  57. 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–D365CrossRefPubMedGoogle Scholar
  58. Yanai I, Benjamin H, Shmoish M et al (2005) Genome-wide midrange transcription profiles reveal expression level relationships in human tissue specification. Bioinformatics 21:650–659CrossRefPubMedGoogle Scholar
  59. Yi SV, Goodisman MAD (2009) Computational approaches for understanding the evolution of DNA methylation in animals. Epigenetics 4:551–556CrossRefPubMedGoogle Scholar
  60. Zdobnov EM, Apweiler R (2001) InterProScan- an integration platform for the signature-recognition methods in InterPro. Bioinformatics 17:847–848CrossRefPubMedGoogle Scholar
  61. Zemach A, McDaniel IE, Silva P, Zilberman D (2010) Genome-wide evolutionary analysis of eukaryotic DNA methylation. Science 328:916–919CrossRefPubMedGoogle Scholar

Copyright information

© The Japanese Society of Applied Entomology and Zoology 2017

Authors and Affiliations

  • Yoshinobu Hayashi
    • 1
    • 2
  • Kiyoto Maekawa
    • 3
  • Christine A. Nalepa
    • 4
  • Toru Miura
    • 1
    • 5
  • Shuji Shigenobu
    • 6
    • 7
  1. 1.Graduate School of Environmental ScienceHokkaido UniversitySapporoJapan
  2. 2.Department of BiologyKeio UniversityYokohamaJapan
  3. 3.Graduate School of Science and EngineeringUniversity of ToyamaToyamaJapan
  4. 4.Department of EntomologyNorth Carolina State UniversityRaleighUSA
  5. 5.Misaki Marine Biological Station, Graduate School of ScienceUniversity of TokyoMiuraJapan
  6. 6.Core Research Facilities, National Institute for Basic BiologyNational Institutes of Natural SciencesOkazakiJapan
  7. 7.Department of Basic Biology, School of Life ScienceGraduate University for Advanced StudiesOkazakiJapan

Personalised recommendations