Construction and characterization of normalized cDNA libraries by 454 pyrosequencing and estimation of DNA methylation levels in three distantly related termite species.

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 und...

Descripción completa

Guardado en:

Detalles Bibliográficos
Autores principales:	Yoshinobu Hayashi, Shuji Shigenobu, Dai Watanabe, Kouhei Toga, Ryota Saiki, Keisuke Shimada, Thomas Bourguignon, Nathan Lo, Masaru Hojo, Kiyoto Maekawa, Toru Miura
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2013
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/51d3ac5654744760853a13646e9a9e01
Etiquetas:	Agregar Etiqueta Sin Etiquetas, Sea el primero en etiquetar este registro!

id	oai:doaj.org-article:51d3ac5654744760853a13646e9a9e01
record_format	dspace
spelling	oai:doaj.org-article:51d3ac5654744760853a13646e9a9e012021-11-18T08:53:20ZConstruction and characterization of normalized cDNA libraries by 454 pyrosequencing and estimation of DNA methylation levels in three distantly related termite species.1932-620310.1371/journal.pone.0076678https://doaj.org/article/51d3ac5654744760853a13646e9a9e012013-01-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/24098800/?tool=EBIhttps://doaj.org/toc/1932-6203In 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.Yoshinobu HayashiShuji ShigenobuDai WatanabeKouhei TogaRyota SaikiKeisuke ShimadaThomas BourguignonNathan LoMasaru HojoKiyoto MaekawaToru MiuraPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 8, Iss 9, p e76678 (2013)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Yoshinobu Hayashi Shuji Shigenobu Dai Watanabe Kouhei Toga Ryota Saiki Keisuke Shimada Thomas Bourguignon Nathan Lo Masaru Hojo Kiyoto Maekawa Toru Miura Construction and characterization of normalized cDNA libraries by 454 pyrosequencing and estimation of DNA methylation levels in three distantly related termite species.
description	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.
format	article
author	Yoshinobu Hayashi Shuji Shigenobu Dai Watanabe Kouhei Toga Ryota Saiki Keisuke Shimada Thomas Bourguignon Nathan Lo Masaru Hojo Kiyoto Maekawa Toru Miura
author_facet	Yoshinobu Hayashi Shuji Shigenobu Dai Watanabe Kouhei Toga Ryota Saiki Keisuke Shimada Thomas Bourguignon Nathan Lo Masaru Hojo Kiyoto Maekawa Toru Miura
author_sort	Yoshinobu Hayashi
title	Construction and characterization of normalized cDNA libraries by 454 pyrosequencing and estimation of DNA methylation levels in three distantly related termite species.
title_short	Construction and characterization of normalized cDNA libraries by 454 pyrosequencing and estimation of DNA methylation levels in three distantly related termite species.
title_full	Construction and characterization of normalized cDNA libraries by 454 pyrosequencing and estimation of DNA methylation levels in three distantly related termite species.
title_fullStr	Construction and characterization of normalized cDNA libraries by 454 pyrosequencing and estimation of DNA methylation levels in three distantly related termite species.
title_full_unstemmed	Construction and characterization of normalized cDNA libraries by 454 pyrosequencing and estimation of DNA methylation levels in three distantly related termite species.
title_sort	construction and characterization of normalized cdna libraries by 454 pyrosequencing and estimation of dna methylation levels in three distantly related termite species.
publisher	Public Library of Science (PLoS)
publishDate	2013
url	https://doaj.org/article/51d3ac5654744760853a13646e9a9e01
work_keys_str_mv	AT yoshinobuhayashi constructionandcharacterizationofnormalizedcdnalibrariesby454pyrosequencingandestimationofdnamethylationlevelsinthreedistantlyrelatedtermitespecies AT shujishigenobu constructionandcharacterizationofnormalizedcdnalibrariesby454pyrosequencingandestimationofdnamethylationlevelsinthreedistantlyrelatedtermitespecies AT daiwatanabe constructionandcharacterizationofnormalizedcdnalibrariesby454pyrosequencingandestimationofdnamethylationlevelsinthreedistantlyrelatedtermitespecies AT kouheitoga constructionandcharacterizationofnormalizedcdnalibrariesby454pyrosequencingandestimationofdnamethylationlevelsinthreedistantlyrelatedtermitespecies AT ryotasaiki constructionandcharacterizationofnormalizedcdnalibrariesby454pyrosequencingandestimationofdnamethylationlevelsinthreedistantlyrelatedtermitespecies AT keisukeshimada constructionandcharacterizationofnormalizedcdnalibrariesby454pyrosequencingandestimationofdnamethylationlevelsinthreedistantlyrelatedtermitespecies AT thomasbourguignon constructionandcharacterizationofnormalizedcdnalibrariesby454pyrosequencingandestimationofdnamethylationlevelsinthreedistantlyrelatedtermitespecies AT nathanlo constructionandcharacterizationofnormalizedcdnalibrariesby454pyrosequencingandestimationofdnamethylationlevelsinthreedistantlyrelatedtermitespecies AT masaruhojo constructionandcharacterizationofnormalizedcdnalibrariesby454pyrosequencingandestimationofdnamethylationlevelsinthreedistantlyrelatedtermitespecies AT kiyotomaekawa constructionandcharacterizationofnormalizedcdnalibrariesby454pyrosequencingandestimationofdnamethylationlevelsinthreedistantlyrelatedtermitespecies AT torumiura constructionandcharacterizationofnormalizedcdnalibrariesby454pyrosequencingandestimationofdnamethylationlevelsinthreedistantlyrelatedtermitespecies
_version_	1718421200234872832

Construction and characterization of normalized cDNA libraries by 454 pyrosequencing and estimation of DNA methylation levels in three distantly related termite species.

Ejemplares similares