Transcriptome sequencing, and rapid development and application of SNP markers for the legume pod borer Maruca vitrata (Lepidoptera: Crambidae)

• Published in: PloS one 2011-07, Vol.6 (7), p.e21388-e21388
• 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: Article
• Language: English
• Subjects: Africa; Agriculture; Animals; Annotations; Anopheles; Aphidoidea; Aphis glycines; Artificial chromosomes; Bicyclus anynana; Biological control; Biological pest control; Biology; Bombyx mori; Borers; Cajanus cajan; Crambidae; Crustaceans; Data processing; Databases, Genetic; Digestive System - metabolism; DNA, Complementary - genetics; Expressed Sequence Tags; Filtration; Fruit - parasitology; Gene expression; Gene Expression Profiling - methods; Gene sequencing; Genes; Genes, Insect - genetics; Genetic engineering; Genetic Markers; Genetics, Population; Genomes; Genomics; Genotype; Geography; Homology; Insecticides; Insects; Laboratories; Larva - genetics; Legumes; Lepidoptera; Lepidoptera - genetics; Markers; Maruca vitrata; Mathematical models; Midgut; Molecular Sequence Annotation; Molecular Sequence Data; Mollusca; Mutation; Pest control; Pesticide resistance; Phylogeny; Plant resistance; Polymorphism, Single Nucleotide - genetics; Population genetics; Regression Analysis; Salivary Glands - metabolism; Sequence Analysis, DNA - methods; Sequence Homology, Nucleic Acid; Single nucleotide polymorphisms; Single-nucleotide polymorphism; Software; Subsistence agriculture; Tissues; Toxins; Transgenic; Tropical environment; Tropical environments; Vigna unguiculata
• ISSN: 1932-6203; 1932-6203
• DOI: 10.1371/journal.pone.0021388

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.