Transcriptome characterisation of the ant Formica exsecta with new insights into the evolution of desaturase genes in social hymenoptera.

<h4>Background</h4>Despite the recent sequencing of seven ant genomes, no genomic data are available for the genus Formica, an important group for the study of eusocial traits. We sequenced the transcriptome of the ant Formica exsecta with the 454 FLX Titanium technology from a pooled sa...

Descripción completa

Guardado en:

Detalles Bibliográficos
Autores principales:	Hélène Badouin, Khalid Belkhir, Emma Gregson, Juan Galindo, Liselotte Sundström, Stephen J Martin, Roger K Butlin, Carole M Smadja
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2013
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/84e63f9db0d144cfab19ecae838c4180
Etiquetas:	Agregar Etiqueta Sin Etiquetas, Sea el primero en etiquetar este registro!

id	oai:doaj.org-article:84e63f9db0d144cfab19ecae838c4180
record_format	dspace
spelling	oai:doaj.org-article:84e63f9db0d144cfab19ecae838c41802021-11-18T07:37:45ZTranscriptome characterisation of the ant Formica exsecta with new insights into the evolution of desaturase genes in social hymenoptera.1932-620310.1371/journal.pone.0068200https://doaj.org/article/84e63f9db0d144cfab19ecae838c41802013-01-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/23874539/pdf/?tool=EBIhttps://doaj.org/toc/1932-6203<h4>Background</h4>Despite the recent sequencing of seven ant genomes, no genomic data are available for the genus Formica, an important group for the study of eusocial traits. We sequenced the transcriptome of the ant Formica exsecta with the 454 FLX Titanium technology from a pooled sample of workers from 70 Finnish colonies.<h4>Results</h4>About 1,000,000 reads were obtained from a normalised cDNA library. We compared the assemblers MIRA3.0 and Newbler2.6 and showed that the latter performed better on this dataset due to a new option which is dedicated to improve contig formation in low depth portions of the assemblies. The 29,579 contigs represent 27 Mb. 50% showed similarity with known proteins and 25% could be assigned a category of gene ontology. We found more than 13,000 high-quality single nucleotide polymorphisms. The Δ9 desaturase gene family is an important multigene family involved in chemical communication in insects. We found six Δ9 desaturases in this Formica exsecta transcriptome dataset that were used to reconstruct a maximum-likelihood phylogeny of insect desaturases and to test for signatures of positive selection in this multigene family in ant lineages. We found differences with previous phylogenies of this gene family in ants, and found two clades potentially under positive selection.<h4>Conclusion</h4>This first transcriptome reference sequence of Formica exsecta provided sequence and polymorphism data that will allow researchers working on Formica ants to develop studies to tackle the genetic basis of eusocial phenotypes. In addition, this study provided some general guidelines for de novo transcriptome assembly that should be useful for future transcriptome sequencing projects. Finally, we found potential signatures of positive selection in some clades of the Δ9 desaturase gene family in ants, which suggest the potential role of sequence divergence and adaptive evolution in shaping the large diversity of chemical cues in social insects.Hélène BadouinKhalid BelkhirEmma GregsonJuan GalindoLiselotte SundströmStephen J MartinRoger K ButlinCarole M SmadjaPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 8, Iss 7, p e68200 (2013)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Hélène Badouin Khalid Belkhir Emma Gregson Juan Galindo Liselotte Sundström Stephen J Martin Roger K Butlin Carole M Smadja Transcriptome characterisation of the ant Formica exsecta with new insights into the evolution of desaturase genes in social hymenoptera.
description	<h4>Background</h4>Despite the recent sequencing of seven ant genomes, no genomic data are available for the genus Formica, an important group for the study of eusocial traits. We sequenced the transcriptome of the ant Formica exsecta with the 454 FLX Titanium technology from a pooled sample of workers from 70 Finnish colonies.<h4>Results</h4>About 1,000,000 reads were obtained from a normalised cDNA library. We compared the assemblers MIRA3.0 and Newbler2.6 and showed that the latter performed better on this dataset due to a new option which is dedicated to improve contig formation in low depth portions of the assemblies. The 29,579 contigs represent 27 Mb. 50% showed similarity with known proteins and 25% could be assigned a category of gene ontology. We found more than 13,000 high-quality single nucleotide polymorphisms. The Δ9 desaturase gene family is an important multigene family involved in chemical communication in insects. We found six Δ9 desaturases in this Formica exsecta transcriptome dataset that were used to reconstruct a maximum-likelihood phylogeny of insect desaturases and to test for signatures of positive selection in this multigene family in ant lineages. We found differences with previous phylogenies of this gene family in ants, and found two clades potentially under positive selection.<h4>Conclusion</h4>This first transcriptome reference sequence of Formica exsecta provided sequence and polymorphism data that will allow researchers working on Formica ants to develop studies to tackle the genetic basis of eusocial phenotypes. In addition, this study provided some general guidelines for de novo transcriptome assembly that should be useful for future transcriptome sequencing projects. Finally, we found potential signatures of positive selection in some clades of the Δ9 desaturase gene family in ants, which suggest the potential role of sequence divergence and adaptive evolution in shaping the large diversity of chemical cues in social insects.
format	article
author	Hélène Badouin Khalid Belkhir Emma Gregson Juan Galindo Liselotte Sundström Stephen J Martin Roger K Butlin Carole M Smadja
author_facet	Hélène Badouin Khalid Belkhir Emma Gregson Juan Galindo Liselotte Sundström Stephen J Martin Roger K Butlin Carole M Smadja
author_sort	Hélène Badouin
title	Transcriptome characterisation of the ant Formica exsecta with new insights into the evolution of desaturase genes in social hymenoptera.
title_short	Transcriptome characterisation of the ant Formica exsecta with new insights into the evolution of desaturase genes in social hymenoptera.
title_full	Transcriptome characterisation of the ant Formica exsecta with new insights into the evolution of desaturase genes in social hymenoptera.
title_fullStr	Transcriptome characterisation of the ant Formica exsecta with new insights into the evolution of desaturase genes in social hymenoptera.
title_full_unstemmed	Transcriptome characterisation of the ant Formica exsecta with new insights into the evolution of desaturase genes in social hymenoptera.
title_sort	transcriptome characterisation of the ant formica exsecta with new insights into the evolution of desaturase genes in social hymenoptera.
publisher	Public Library of Science (PLoS)
publishDate	2013
url	https://doaj.org/article/84e63f9db0d144cfab19ecae838c4180
work_keys_str_mv	AT helenebadouin transcriptomecharacterisationoftheantformicaexsectawithnewinsightsintotheevolutionofdesaturasegenesinsocialhymenoptera AT khalidbelkhir transcriptomecharacterisationoftheantformicaexsectawithnewinsightsintotheevolutionofdesaturasegenesinsocialhymenoptera AT emmagregson transcriptomecharacterisationoftheantformicaexsectawithnewinsightsintotheevolutionofdesaturasegenesinsocialhymenoptera AT juangalindo transcriptomecharacterisationoftheantformicaexsectawithnewinsightsintotheevolutionofdesaturasegenesinsocialhymenoptera AT liselottesundstrom transcriptomecharacterisationoftheantformicaexsectawithnewinsightsintotheevolutionofdesaturasegenesinsocialhymenoptera AT stephenjmartin transcriptomecharacterisationoftheantformicaexsectawithnewinsightsintotheevolutionofdesaturasegenesinsocialhymenoptera AT rogerkbutlin transcriptomecharacterisationoftheantformicaexsectawithnewinsightsintotheevolutionofdesaturasegenesinsocialhymenoptera AT carolemsmadja transcriptomecharacterisationoftheantformicaexsectawithnewinsightsintotheevolutionofdesaturasegenesinsocialhymenoptera
_version_	1718423172721672192

Transcriptome characterisation of the ant Formica exsecta with new insights into the evolution of desaturase genes in social hymenoptera.

Ejemplares similares