Construction and Characterization of Normalized cDNA Libraries by 454 Pyrosequencing and Estimation of DNA Methylation Levels in Three Distantly Related Termite Species

Yoshinobu Hayashi, Shuji Shigenobu, Dai Watanabe, Kouhei Toga, Ryota Saiki, Keisuke Shimada, Thomas Bourguignon, Nathan Lo, Masaru Hojo, Kiyoto Maekawa, Toru Miura

Research output: Contribution to journalArticle

10 Citations (Scopus)

Abstract

In termites, division of labor among castes, categories of individuals that perform specialized tasks, increases colony-level productivity and is the key to their ecological success. Although molecular studies on caste polymorphism have been performed in termites, we are far from a comprehensive understanding of the molecular basis of this phenomenon. To facilitate future molecular studies, we aimed to construct expressed sequence tag (EST) libraries covering wide ranges of gene repertoires in three representative termite species, Hodotermopsis sjostedti, Reticulitermes speratus and Nasutitermes takasagoensis. We generated normalized cDNA libraries from whole bodies, except for guts containing microbes, of almost all castes, sexes and developmental stages and sequenced them with the 454 GS FLX titanium system. We obtained >1.2 million quality-filtered reads yielding >400 million bases for each of the three species. Isotigs, which are analogous to individual transcripts, and singletons were produced by assembling the reads and annotated using public databases. Genes related to juvenile hormone, which plays crucial roles in caste differentiation of termites, were identified from the EST libraries by BLAST search. To explore the potential for DNA methylation, which plays an important role in caste differentiation of honeybees, tBLASTn searches for DNA methyltransferases (dnmt1, dnmt2 and dnmt3) and methyl-CpG binding domain (mbd) were performed against the EST libraries. All four of these genes were found in the H. sjostedti library, while all except dnmt3 were found in R. speratus and N. takasagoensis. The ratio of the observed to the expected CpG content (CpG O/E), which is a proxy for DNA methylation level, was calculated for the coding sequences predicted from the isotigs and singletons. In all of the three species, the majority of coding sequences showed depletion of CpG O/E (less than 1), and the distributions of CpG O/E were bimodal, suggesting the presence of DNA methylation.

Original languageEnglish
Article numbere76678
JournalPLoS One
Volume8
Issue number9
DOIs
Publication statusPublished - 2013 Sep 30
Externally publishedYes

Fingerprint

Isoptera
DNA methylation
DNA Methylation
Gene Library
Social Class
cDNA libraries
Hodotermopsis sjostedti
Nasutitermes takasagoensis
Expressed Sequence Tags
expressed sequence tags
Reticulitermes speratus
caste determination
Genes
Juvenile Hormones
polyethism
titanium
genes
methyltransferases
Methyltransferases
juvenile hormones

ASJC Scopus subject areas

  • Biochemistry, Genetics and Molecular Biology(all)
  • Agricultural and Biological Sciences(all)

Cite this

Construction and Characterization of Normalized cDNA Libraries by 454 Pyrosequencing and Estimation of DNA Methylation Levels in Three Distantly Related Termite Species. / Hayashi, Yoshinobu; Shigenobu, Shuji; Watanabe, Dai; Toga, Kouhei; Saiki, Ryota; Shimada, Keisuke; Bourguignon, Thomas; Lo, Nathan; Hojo, Masaru; Maekawa, Kiyoto; Miura, Toru.

In: PLoS One, Vol. 8, No. 9, e76678, 30.09.2013.

Research output: Contribution to journalArticle

Hayashi, Yoshinobu ; Shigenobu, Shuji ; Watanabe, Dai ; Toga, Kouhei ; Saiki, Ryota ; Shimada, Keisuke ; Bourguignon, Thomas ; Lo, Nathan ; Hojo, Masaru ; Maekawa, Kiyoto ; Miura, Toru. / Construction and Characterization of Normalized cDNA Libraries by 454 Pyrosequencing and Estimation of DNA Methylation Levels in Three Distantly Related Termite Species. In: PLoS One. 2013 ; Vol. 8, No. 9.
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