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ARS Home » Pacific West Area » Parlier, California » San Joaquin Valley Agricultural Sciences Center » Crop Diseases, Pests and Genetics Research » Research » Publications at this Location » Publication #230377
Title: PrimerSNP: a web tool for whole-genome selection of allele-specific and common primers of phylogenetically-related bacterial genomic sequences

Author
item YAO, JIQIANG - CRB
item Lin, Hong
item VANDEYNE, ALLEN - UC DAVIS
item DODDAPANENI, HARSHAVARDHAN - UC DAVIS
item FRANCIS, MARTHA - UNIV FLORIDA
item MACEDO LEMOS, ELIANA G. - BRAZIL
item Civerolo, Edwin

Submitted to: BMC Microbiology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 9/18/2008
Publication Date: 10/20/2008
Citation: Yao, J., Lin, H., Vandeyne, A., Doddapaneni, H., Francis, M., Macedo Lemos, E., Civerolo, E.L. 2008. PrimerSNP: a web tool for whole-genome selection of allele-specific and common primers of phylogenetically-related bacterial genomic sequences. BMC Microbiology, 8:185doi:10.1186/1471-2180-8-185.

Interpretive Summary: The increasing number of genomic sequences of bacteria makes it possible to select unique sequence variations of a particular strain/species at the whole genome level and thus to develop a detection tool to identify these differences. The high similarity of genomic sequences among genetically-related bacteria requires the identification of the few locations in the genome that can be represented as unique markers for strain differentiation. PrimerSNP developed in this study is application software that can be used to identify and design strain specific markers. PrimerSNP is an online tool that can be used to design primers based on strain specific SNPs for multiple strains/species of microorganisms at the whole genome level. Additionally, PrimerSNP also provides a feature for design common primers that can amplify all the homologous sequences from multiple strains/species of microorganisms. Experimental validation shows that this software has a successful prediction rate of 80.4 - 100% for strain specific primer design. PrimerSNP is freely available at http://cropdisease.ars.usda.gov/~primer.

Technical Abstract: The increasing number of genomic sequences of bacteria makes it possible to select unique SNPs of a particular strain/species at the whole genome level and thus design specific primers based on the SNPs. The high similarity of genomic sequences among phylogenetically-related bacteria requires the identification of the few loci in the genome that can serve as unique markers for strain differentiation. PrimerSNP attempts to identify reliable strain specific markers, on which specific primers are designed for pathogen detection purpose. PrimerSNP is an online tool to design primers based on strain specific SNPs for multiple strains/species of microorganisms at the whole genome level. The allele-specific primers could distinguish query sequences of one strain from other homologous sequences by standard PCR reaction. Additionally, PrimerSNP provides a feature for design common primers that can amplify all the homologous sequences of multiple strains/species of microorganisms. PrimerSNP is freely available at http://cropdisease.ars.usda.gov/~primer. PrimerSNP is a high-throughput specific primer generation tool for the differentiation of phylogenetically-related strains/species. Experimental validation shows that this software has a successful prediction rate of 80.4 - 100% for strain specific primer design.