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Open Access Research article

Survey and analysis of microsatellites from transcript sequences in Phytophthora species: frequency, distribution, and potential as markers for the genus

Diana P Garnica1, Andrés M Pinzón12, Lina M Quesada-Ocampo1, Adriana J Bernal1, Emiliano Barreto2, Niklaus J Grünwald3 and Silvia Restrepo1*

Author Affiliations

1 Laboratorio de Micología y Fitopatología Uniandes (LAMFU), Universidad de Los Andes. Bogotá, Colombia

2 Centro de Bioinformática-Instituto de Biotecnología (IBUN), Universidad Nacional de Colombia. Bogotá, Colombia

3 Horticultural Crops Research Laboratory, USDA ARS, Corvallis, OR, 97330, USA

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BMC Genomics 2006, 7:245  doi:10.1186/1471-2164-7-245

Published: 28 September 2006

Abstract

Background

Members of the genus Phytophthora are notorious pathogens with world-wide distribution. The most devastating species include P. infestans, P. ramorum and P. sojae. In order to develop molecular methods for routinely characterizing their populations and to gain a better insight into the organization and evolution of their genomes, we used an in silico approach to survey and compare simple sequence repeats (SSRs) in transcript sequences from these three species. We compared the occurrence, relative abundance, relative density and cross-species transferability of the SSRs in these oomycetes.

Results

The number of SSRs in oomycetes transcribed sequences is low and long SSRs are rare. The in silico transferability of SSRs among the Phytophthora species was analyzed for all sets generated, and primers were selected on the basis of similarity as possible candidates for transferability to other Phytophthora species. Sequences encoding putative pathogenicity factors from all three Phytophthora species were also surveyed for presence of SSRs. However, no correlation between gene function and SSR abundance was observed. The SSR survey results, and the primer pairs designed for all SSRs from the three species, were deposited in a public database.

Conclusion

In all cases the most common SSRs were trinucleotide repeat units with low repeat numbers. A proportion (7.5%) of primers could be transferred with 90% similarity between at least two species of Phytophthora. This information represents a valuable source of molecular markers for use in population genetics, genetic mapping and strain fingerprinting studies of oomycetes, and illustrates how genomic databases can be exploited to generate data-mining filters for SSRs before experimental validation.