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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oai:doaj.org-article:a698bebd763548788397660d54829c1c2021-11-18T06:50:43ZTranscriptome sequencing, and rapid development and application of SNP markers for the legume pod borer Maruca vitrata (Lepidoptera: Crambidae).1932-620310.1371/journal.pone.0021388https://doaj.org/article/a698bebd763548788397660d54829c1c2011-01-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/21754987/pdf/?tool=EBIhttps://doaj.org/toc/1932-6203The 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.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 PittendrighPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 6, Iss 7, p e21388 (2011) |
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Medicine R Science Q 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). |
| 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. |
| format |
article |
| 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 |
| 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) |
| publishDate |
2011 |
| url |
https://doaj.org/article/a698bebd763548788397660d54829c1c |
| work_keys_str_mv |
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