title: Transcriptome sequencing, and rapid development and application of SNP markers for the legume pod borer Maruca vitrata (Lepidoptera: Crambidae).
abstract: 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.
authors.affiliation: Department of Entomology, Purdue University, West Lafayette, Indiana, United States of America.
authors.forename: Venu M
authors.initials: VM
authors.lastname: Margam
authors.forename: Brad S
authors.initials: BS
authors.lastname: Coates
authors.forename: Darrell O
authors.initials: DO
authors.lastname: Bayles
authors.forename: Richard L
authors.initials: RL
authors.lastname: Hellmich
authors.forename: Tolulope
authors.initials: T
authors.lastname: Agunbiade
authors.forename: Manfredo J
authors.initials: MJ
authors.lastname: Seufferheld
authors.forename: Weilin
authors.initials: W
authors.lastname: Sun
authors.forename: Jeremy A
authors.initials: JA
authors.lastname: Kroemer
authors.forename: Malick N
authors.initials: MN
authors.lastname: Ba
authors.forename: Clementine L
authors.initials: CL
authors.lastname: Binso-Dabire
authors.forename: Ibrahim
authors.initials: I
authors.lastname: Baoua
authors.forename: Mohammad F
authors.initials: MF
authors.lastname: Ishiyaku
authors.forename: Fernando G
authors.initials: FG
authors.lastname: Covas
authors.forename: Ramasamy
authors.initials: R
authors.lastname: Srinivasan
authors.forename: Joel
authors.initials: J
authors.lastname: Armstrong
authors.forename: Larry L
authors.initials: LL
authors.lastname: Murdock
authors.forename: Barry R
authors.initials: BR
authors.lastname: Pittendrigh
mesh_terms: D000349:Africa; D000818:Animals; D018076:DNA, Complementary / Q000235:genetics; D030541:Databases, Genetic; D004064:Digestive System / Q000378:metabolism; D020224:Expressed Sequence Tags; D005638:Fruit / Q000469:parasitology*; D020869:Gene Expression Profiling / Q000379:methods*; D017344:Genes, Insect / Q000235:genetics; D005819:Genetic Markers; D005828:Genetics, Population; D005838:Genotype; D005843:Geography; D007814:Larva / Q000235:genetics; D007915:Lepidoptera / Q000235:genetics*; D058977:Molecular Sequence Annotation; D008969:Molecular Sequence Data; D010802:Phylogeny; D020641:Polymorphism, Single Nucleotide / Q000235:genetics*; D012044:Regression Analysis; D012469:Salivary Glands / Q000378:metabolism; D017422:Sequence Analysis, DNA / Q000379:methods*; D012689:Sequence Homology, Nucleic Acid; D012984:Software
chemical_list: D018076:DNA, Complementary; D005819:Genetic Markers