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: Venu M Margam, Brad S Coates, Darrell O Bayles, Richard L Hellmich, Tolulope Agunbiade, Manfredo J Seufferheld, Weilin Sun, Jeremy A Kroemer, Malick N Ba, Clementine L Binso-Dabire, Ibrahim Baoua, Mohammad F Ishiyaku, Fernando G Covas, Ramasamy Srinivasan, Joel Armstrong, Larry L Murdock, Barry R Pittendrigh
Format: Article
Language:English
Published: Public Library of Science (PLoS) 2011-01-01
Series:PLoS ONE
Online Access:https://www.ncbi.nlm.nih.gov/pmc/articles/pmid/21754987/pdf/?tool=EBI
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spelling doaj-a698bebd763548788397660d54829c1c2021-03-03T19:52:59ZengPublic Library of Science (PLoS)PLoS ONE1932-62032011-01-0167e2138810.1371/journal.pone.0021388Transcriptome sequencing, and rapid development and application of SNP markers for the legume pod borer Maruca vitrata (Lepidoptera: Crambidae).Venu M MargamBrad S CoatesDarrell O BaylesRichard L HellmichTolulope AgunbiadeManfredo J SeufferheldWeilin SunJeremy A KroemerMalick N BaClementine L Binso-DabireIbrahim BaouaMohammad F IshiyakuFernando G CovasRamasamy SrinivasanJoel ArmstrongLarry L MurdockBarry R PittendrighThe 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.https://www.ncbi.nlm.nih.gov/pmc/articles/pmid/21754987/pdf/?tool=EBI
collection DOAJ
language English
format Article
sources DOAJ
author Venu M Margam
Brad S Coates
Darrell O Bayles
Richard L Hellmich
Tolulope Agunbiade
Manfredo J Seufferheld
Weilin Sun
Jeremy A Kroemer
Malick N Ba
Clementine L Binso-Dabire
Ibrahim Baoua
Mohammad F Ishiyaku
Fernando G Covas
Ramasamy Srinivasan
Joel Armstrong
Larry L Murdock
Barry R Pittendrigh
spellingShingle Venu M Margam
Brad S Coates
Darrell O Bayles
Richard L Hellmich
Tolulope Agunbiade
Manfredo J Seufferheld
Weilin Sun
Jeremy A Kroemer
Malick N Ba
Clementine L Binso-Dabire
Ibrahim Baoua
Mohammad F Ishiyaku
Fernando G Covas
Ramasamy Srinivasan
Joel Armstrong
Larry L Murdock
Barry R Pittendrigh
Transcriptome sequencing, and rapid development and application of SNP markers for the legume pod borer Maruca vitrata (Lepidoptera: Crambidae).
PLoS ONE
author_facet Venu M Margam
Brad S Coates
Darrell O Bayles
Richard L Hellmich
Tolulope Agunbiade
Manfredo J Seufferheld
Weilin Sun
Jeremy A Kroemer
Malick N Ba
Clementine L Binso-Dabire
Ibrahim Baoua
Mohammad F Ishiyaku
Fernando G Covas
Ramasamy Srinivasan
Joel Armstrong
Larry L Murdock
Barry R Pittendrigh
author_sort Venu M Margam
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).
publisher Public Library of Science (PLoS)
series PLoS ONE
issn 1932-6203
publishDate 2011-01-01
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.
url https://www.ncbi.nlm.nih.gov/pmc/articles/pmid/21754987/pdf/?tool=EBI
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