Transcriptome Sequencing, and Rapid Development and Application of SNP Markers for the Legume Pod Borer Maruca vitrata (Lepidoptera: Crambidae)

The legume pod borer, Maruca vitrata (Lepidoptera: Crambidae), is an insect pest species of crops grown by subsistence farmers in tropical regions of Africa. We present the de novo assembly of 3729 contigs from 454- and Sanger-derived sequencing reads for midgut, salivary, and whole adult tissues of...

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Main Authors:	Margam, Venu M., Coates, Brad S., Bayles, Darrell O., Hellmich, Richard L., Agunbiade, Tolulope, Seufferheld, Manfredo J., Sun, Weilin, Kroemer, Jeremy A., Ba, Malick N., Binso-Dabire, Clementine L., Baoua, Ibrahim, Ishiyaku, Mohammad F., Covas, Fernando G., Srinivasan, Ramasamy, Armstrong, Joel, Murdock, Larry L., Pittendrigh, Barry R.
Format:	Online
Language:	English
Published:	Public Library of Science 2011
Online Access:	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3130784/

id	pubmed-3130784
recordtype	oai_dc
spelling	pubmed-31307842011-07-13 Transcriptome Sequencing, and Rapid Development and Application of SNP Markers for the Legume Pod Borer Maruca vitrata (Lepidoptera: Crambidae) Margam, Venu M. Coates, Brad S. Bayles, Darrell O. Hellmich, Richard L. Agunbiade, Tolulope Seufferheld, Manfredo J. Sun, Weilin Kroemer, Jeremy A. Ba, Malick N. Binso-Dabire, Clementine L. Baoua, Ibrahim Ishiyaku, Mohammad F. Covas, Fernando G. Srinivasan, Ramasamy Armstrong, Joel Murdock, Larry L. Pittendrigh, Barry R. Research Article The legume pod borer, Maruca vitrata (Lepidoptera: Crambidae), is an insect pest species of crops grown by subsistence farmers in tropical regions of Africa. We present the de novo assembly of 3729 contigs from 454- and Sanger-derived sequencing reads for midgut, salivary, and whole adult tissues of this non-model species. Functional annotation predicted that 1320 M. vitrata protein coding genes are present, of which 631 have orthologs within the Bombyx mori gene model. A homology-based analysis assigned M. vitrata genes into a group of paralogs, but these were subsequently partitioned into putative orthologs following phylogenetic analyses. Following sequence quality filtering, a total of 1542 putative single nucleotide polymorphisms (SNPs) were predicted within M. vitrata contig assemblies. Seventy one of 1078 designed molecular genetic markers were used to screen M. vitrata samples from five collection sites in West Africa. Population substructure may be present with significant implications in the insect resistance management recommendations pertaining to the release of biological control agents or transgenic cowpea that express Bacillus thuringiensis crystal toxins. Mutation data derived from transcriptome sequencing is an expeditious and economical source for genetic markers that allow evaluation of ecological differentiation. Public Library of Science 2011-07-06 /pmc/articles/PMC3130784/ /pubmed/21754987 http://dx.doi.org/10.1371/journal.pone.0021388 Text en This is an open-access article, free of all copyright, and may be freely reproduced, distributed, transmitted, modified, built upon, or otherwise used by anyone for any lawful purpose. The work is made available under the Creative Commons CC0 public domain dedication. https://creativecommons.org/publicdomain/zero/1.0/ This is an open-access article distributed under the terms of the Creative Commons Public Domain declaration, which stipulates that, once placed in the public domain, this work may be freely reproduced, distributed, transmitted, modified, built upon, or otherwise used by anyone for any lawful purpose.
repository_type	Open Access Journal
institution_category	Foreign Institution
institution	US National Center for Biotechnology Information
building	NCBI PubMed
collection	Online Access
language	English
format	Online
author	Margam, Venu M. Coates, Brad S. Bayles, Darrell O. Hellmich, Richard L. Agunbiade, Tolulope Seufferheld, Manfredo J. Sun, Weilin Kroemer, Jeremy A. Ba, Malick N. Binso-Dabire, Clementine L. Baoua, Ibrahim Ishiyaku, Mohammad F. Covas, Fernando G. Srinivasan, Ramasamy Armstrong, Joel Murdock, Larry L. Pittendrigh, Barry R.
spellingShingle	Margam, Venu M. Coates, Brad S. Bayles, Darrell O. Hellmich, Richard L. Agunbiade, Tolulope Seufferheld, Manfredo J. Sun, Weilin Kroemer, Jeremy A. Ba, Malick N. Binso-Dabire, Clementine L. Baoua, Ibrahim Ishiyaku, Mohammad F. Covas, Fernando G. Srinivasan, Ramasamy Armstrong, Joel Murdock, Larry L. Pittendrigh, Barry R. Transcriptome Sequencing, and Rapid Development and Application of SNP Markers for the Legume Pod Borer Maruca vitrata (Lepidoptera: Crambidae)
author_facet	Margam, Venu M. Coates, Brad S. Bayles, Darrell O. Hellmich, Richard L. Agunbiade, Tolulope Seufferheld, Manfredo J. Sun, Weilin Kroemer, Jeremy A. Ba, Malick N. Binso-Dabire, Clementine L. Baoua, Ibrahim Ishiyaku, Mohammad F. Covas, Fernando G. Srinivasan, Ramasamy Armstrong, Joel Murdock, Larry L. Pittendrigh, Barry R.
author_sort	Margam, Venu M.
title	Transcriptome Sequencing, and Rapid Development and Application of SNP Markers for the Legume Pod Borer Maruca vitrata (Lepidoptera: Crambidae)
title_short	Transcriptome Sequencing, and Rapid Development and Application of SNP Markers for the Legume Pod Borer Maruca vitrata (Lepidoptera: Crambidae)
title_full	Transcriptome Sequencing, and Rapid Development and Application of SNP Markers for the Legume Pod Borer Maruca vitrata (Lepidoptera: Crambidae)
title_fullStr	Transcriptome Sequencing, and Rapid Development and Application of SNP Markers for the Legume Pod Borer Maruca vitrata (Lepidoptera: Crambidae)
title_full_unstemmed	Transcriptome Sequencing, and Rapid Development and Application of SNP Markers for the Legume Pod Borer Maruca vitrata (Lepidoptera: Crambidae)
title_sort	transcriptome sequencing, and rapid development and application of snp markers for the legume pod borer maruca vitrata (lepidoptera: crambidae)
description	The legume pod borer, Maruca vitrata (Lepidoptera: Crambidae), is an insect pest species of crops grown by subsistence farmers in tropical regions of Africa. We present the de novo assembly of 3729 contigs from 454- and Sanger-derived sequencing reads for midgut, salivary, and whole adult tissues of this non-model species. Functional annotation predicted that 1320 M. vitrata protein coding genes are present, of which 631 have orthologs within the Bombyx mori gene model. A homology-based analysis assigned M. vitrata genes into a group of paralogs, but these were subsequently partitioned into putative orthologs following phylogenetic analyses. Following sequence quality filtering, a total of 1542 putative single nucleotide polymorphisms (SNPs) were predicted within M. vitrata contig assemblies. Seventy one of 1078 designed molecular genetic markers were used to screen M. vitrata samples from five collection sites in West Africa. Population substructure may be present with significant implications in the insect resistance management recommendations pertaining to the release of biological control agents or transgenic cowpea that express Bacillus thuringiensis crystal toxins. Mutation data derived from transcriptome sequencing is an expeditious and economical source for genetic markers that allow evaluation of ecological differentiation.
publisher	Public Library of Science
publishDate	2011
url	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3130784/
_version_	1611464055307894784

Transcriptome Sequencing, and Rapid Development and Application of SNP Markers for the Legume Pod Borer Maruca vitrata (Lepidoptera: Crambidae)

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