SPPADBASE: the first on-line searchable database of PCR primers for phytopathogenic fungi

The fast and unambiguous identification of microbial pathogens affecting plants or plant products is an essential prerequisite for obtaining high-quality and safe production. Ecologically friendly practice of the modern agriculture requires the adoption of diagnostic techniques able to detect minimum inoculum levels of pathogens in soil, seeds, transplants or crops, to limit the raise of epidemics and to address the adoption of rational and efficient control means. Moreover, there is an increasing public and official awareness of the potential threat of bio-terrorism directed against food and agriculture (Monke, 2004). Rapid detection techniques for bioweapon agents are a critical need for the first-responder community. Among the nucleic acid-based diagnostic techniques, those involving the Polymerase Chain Reaction (PCR; Mullis and Faloona, 1987) are the most suited for early detection of phytopathogenic agents, due to their high sensitivity and the potential for automation. Many sequence source types could be selected and used as target for specific primer design. These may include, for instance, Random Amplified Polymorphic DNAs (Williams et al., 1990; Welsh and McClelland, 1990), internal transcribed spacer (ITS) regions of the ribosomal RNA genes (White et al., 1990) or other specific gene sequences. Primer sets can be designed to target specificity at the genus, species, or physiological race level, to distinguish a particular pathogen from closely related organisms. A common and tedious task for researchers and technicians is to search for and retrieve bibliographic references of published and validated specific primer sets for a given pathogen querying the Internet, abstract collections and monthly journals’ tables of contents. Very few examples of specific primer set collections for phytopathogenic agents have been released: a summary of primers for the diagnostic characterization of phytopathogenic bacteria seems to be the only one printed so far (Louws et al., 1999). Moreover, among 719 molecular biology databases publicly available recorded by Galperin (2006) or among the 2470 BMC biomedical databases catalog available at http://databases.biomedcentral.com/, no online repository of primer sets of this kind is accessible. To overcome this lack of information, we released the first online searchable database of primer sets useful for the detection and identification of plant pathogenic fungi.