1
|
Margam VM, Coates BS, Bayles DO, Hellmich RL, Agunbiade T, Seufferheld MJ, Sun W, Kroemer JA, Ba MN, Binso-Dabire CL, Baoua I, Ishiyaku MF, Covas FG, Srinivasan R, Armstrong J, Murdock LL, Pittendrigh BR. Transcriptome sequencing, and rapid development and application of SNP markers for the legume pod borer Maruca vitrata (Lepidoptera: Crambidae). PLoS One 2011; 6:e21388. [PMID: 21754987 PMCID: PMC3130784 DOI: 10.1371/journal.pone.0021388] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2011] [Accepted: 05/26/2011] [Indexed: 01/31/2023] Open
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.
Collapse
Affiliation(s)
- Venu M. Margam
- Department of Entomology, Purdue University, West Lafayette, Indiana, United States of America
| | - Brad S. Coates
- United States Department of Agriculture – Agricultural Research Service, Corn Insect and Crop Genetics Research Unit, Genetics Laboratory, Iowa State University, Ames, Iowa, United States of America
| | - Darrell O. Bayles
- United States Department of Agriculture – Agricultural Research Service, Corn Insect and Crop Genetics Research Unit, Genetics Laboratory, Iowa State University, Ames, Iowa, United States of America
| | - Richard L. Hellmich
- United States Department of Agriculture – Agricultural Research Service, Corn Insect and Crop Genetics Research Unit, Genetics Laboratory, Iowa State University, Ames, Iowa, United States of America
| | - Tolulope Agunbiade
- Department of Entomology, University of Illinois at Urbana-Champaign, Champaign, Illinois, United States of America
| | - Manfredo J. Seufferheld
- Department of Crop Sciences, University of Illinois at Urbana-Champaign, Champaign, Illinois, United States of America
| | - Weilin Sun
- Department of Entomology, University of Illinois at Urbana-Champaign, Champaign, Illinois, United States of America
| | - Jeremy A. Kroemer
- United States Department of Agriculture – Agricultural Research Service, Corn Insect and Crop Genetics Research Unit, Genetics Laboratory, Iowa State University, Ames, Iowa, United States of America
| | - Malick N. Ba
- Institut de l'Environnement et de Recherches Agricoles (INERA), Station de Kamboinsé, Ouagadougou, Burkina Faso
| | - Clementine L. Binso-Dabire
- Institut de l'Environnement et de Recherches Agricoles (INERA), Station de Kamboinsé, Ouagadougou, Burkina Faso
| | - Ibrahim Baoua
- Institut National de Recherche Agronomique du Niger, Maradi, Niger
| | - Mohammad F. Ishiyaku
- Department of Plant Science, Institute for Agricultural Research, Ahmadu Bello University, Zaria, Nigeria
| | | | | | - Joel Armstrong
- Ecosystem Sciences, The Commonwealth Scientific and Industrial Research Organization, Black Mountain, Australian Capital Territory, Australia
| | - Larry L. Murdock
- Department of Entomology, Purdue University, West Lafayette, Indiana, United States of America
| | - Barry R. Pittendrigh
- Department of Entomology, University of Illinois at Urbana-Champaign, Champaign, Illinois, United States of America
| |
Collapse
|
2
|
Margam VM, Coates BS, Hellmich RL, Agunbiade T, Seufferheld MJ, Sun W, Ba MN, Sanon A, Binso-Dabire CL, Baoua I, Ishiyaku MF, Covas FG, Srinivasan R, Armstrong J, Murdock LL, Pittendrigh BR. Mitochondrial genome sequence and expression profiling for the legume pod borer Maruca vitrata (Lepidoptera: Crambidae). PLoS One 2011; 6:e16444. [PMID: 21311752 PMCID: PMC3032770 DOI: 10.1371/journal.pone.0016444] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2010] [Accepted: 12/20/2010] [Indexed: 11/18/2022] Open
Abstract
We report the assembly of the 14,054 bp near complete sequencing of the mitochondrial genome of the legume pod borer (LPB), Maruca vitrata (Lepidoptera: Crambidae), which we subsequently used to estimate divergence and relationships within the lepidopteran lineage. The arrangement and orientation of the 13 protein-coding, 2 rRNA, and 19 tRNA genes sequenced was typical of insect mitochondrial DNA sequences described to date. The sequence contained a high A+T content of 80.1% and a bias for the use of codons with A or T nucleotides in the 3rd position. Transcript mapping with midgut and salivary gland ESTs for mitochondrial genome annotation showed that translation from protein-coding genes initiates and terminates at standard mitochondrial codons, except for the coxI gene, which may start from an arginine CGA codon. The genomic copy of coxII terminates at a T nucleotide, and a proposed polyadenylation mechanism for completion of the TAA stop codon was confirmed by comparisons to EST data. EST contig data further showed that mature M. vitrata mitochondrial transcripts are monocistronic, except for bicistronic transcripts for overlapping genes nd4/nd4L and nd6/cytb, and a tricistronic transcript for atp8/atp6/coxIII. This processing of polycistronic mitochondrial transcripts adheres to the tRNA punctuated cleavage mechanism, whereby mature transcripts are cleaved only at intervening tRNA gene sequences. In contrast, the tricistronic atp8/atp6/coxIII in Drosophila is present as separate atp8/atp6 and coxIII transcripts despite the lack of an intervening tRNA. Our results indicate that mitochondrial processing mechanisms vary between arthropod species, and that it is crucial to use transcriptional information to obtain full annotation of mitochondrial genomes.
Collapse
Affiliation(s)
- Venu M. Margam
- Department of Entomology, Purdue University, West Lafayette, Indiana, United States of America
| | - Brad S. Coates
- United States Department of Agriculture – Agricultural Research Service, Corn Insect and Crop Genetics Research Unit, Genetics Laboratory, Iowa State University, Ames, Iowa, United States of America
| | - Richard L. Hellmich
- United States Department of Agriculture – Agricultural Research Service, Corn Insect and Crop Genetics Research Unit, Genetics Laboratory, Iowa State University, Ames, Iowa, United States of America
| | - Tolulope Agunbiade
- Department of Entomology, University of Illinois at Urbana-Champaign, Champaign, Illinois, United States of America
| | - Manfredo J. Seufferheld
- Department of Crop Sciences, University of Illinois at Urbana-Champaign, Champaign, Illinois, United States of America
| | - Weilin Sun
- Department of Entomology, University of Illinois at Urbana-Champaign, Champaign, Illinois, United States of America
| | - Malick N. Ba
- Station de Kamboinsé,Institut de l'Environnement et de Recherches Agricoles (INERA), Ouagadougou, Burkina Faso
| | - Antoine Sanon
- Station de Kamboinsé,Institut de l'Environnement et de Recherches Agricoles (INERA), Ouagadougou, Burkina Faso
| | - Clementine L. Binso-Dabire
- Station de Kamboinsé,Institut de l'Environnement et de Recherches Agricoles (INERA), Ouagadougou, Burkina Faso
| | - Ibrahim Baoua
- Institut National de Recherche Agronomique du Niger, Maradi, Niger
| | - Mohammad F. Ishiyaku
- Department of Plant Science, Institute for Agricultural Research, Ahmadu Bello University, Zaria, Nigeria
| | - Fernando G. Covas
- University of Puerto Rico, Mayaguez, Puerto Rico, United States of America
| | | | - Joel Armstrong
- Entomology, The Commonweatlth of Scientific and Industrial Research Organization, Black Mountain, Australian Capital Territory, Australia
| | - Larry L. Murdock
- Department of Entomology, Purdue University, West Lafayette, Indiana, United States of America
| | - Barry R. Pittendrigh
- Department of Entomology, University of Illinois at Urbana-Champaign, Champaign, Illinois, United States of America
| |
Collapse
|