title: Drosophila genomes and the development of affordable molecular markers for species genotyping.
abstract: The recent completion of genome sequencing of 12 species of Drosophila has provided a powerful resource for hypothesis testing, as well as the development of technical tools. Here we take advantage of genome sequence data from two closely related species of Drosophila, Drosophila simulans and Drosophila sechellia, to quickly identify candidate molecular markers for genotyping based on expected insertion or deletion (indel) differences between species. Out of 64 candidate molecular markers selected along the second and third chromosome of Drosophila, 51 molecular markers were validated using PCR and gel electrophoresis. We found that the 20% error rate was due to sequencing errors in the genome data, although we cannot rule out possible indel polymorphisms. The approach has the advantage of being affordable and quick, as it only requires the use of bioinformatics tools for predictions and a PCR and agarose gel based assay for validation. Moreover, the approach could be easily extended to a wide variety of taxa with the only limitation being the availability of complete or partial genome sequence data.
authors.affiliation: Department of Biology, University of Winnipeg, 515 Portage Avenue, Winnipeg, MB R3B 2E9, Canada.
authors.forename: Leigh
authors.initials: L
authors.lastname: Minuk
authors.forename: Alberto
authors.initials: A
authors.lastname: Civetta
mesh_terms: D000818:Animals; D001483:Base Sequence; D004247:DNA / Q000737:chemistry / Q000235:genetics; D004330:Drosophila / Q000145:classification / Q000235:genetics*; D029721:Drosophila Proteins / Q000235:genetics; D004587:Electrophoresis, Agar Gel; D005819:Genetic Markers / Q000235:genetics*; D014644:Genetic Variation; D049750:Genome, Insect / Q000235:genetics*; D005838:Genotype; D008969:Molecular Sequence Data; D058889:Molecular Typing / Q000379:methods*; D016133:Polymerase Chain Reaction; D015203:Reproducibility of Results; D017422:Sequence Analysis, DNA; D012689:Sequence Homology, Nucleic Acid; D013045:Species Specificity
chemical_list: D029721:Drosophila Proteins; D005819:Genetic Markers; D004247:DNA