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

A dehydration-inducible gene in the truffle Tuber borchii identifies a novel group of dehydrins

BACKGROUND: The expressed sequence tag M6G10 was originally isolated from a screening for differentially expressed transcripts during the reproductive stage of the white truffle Tuber borchii. mRNA levels for M6G10 increased dramatically during fruiting body maturation compared to the vegetative mycelial stage. RESULTS: Bioinformatics tools, phylogenetic analysis and expression studies were used to support the hypothesis that this sequence, named TbDHN1, is the first dehydrin (DHN)-like coding gene isolated in fungi. Homologs of this gene, all defined as "coding for hypothetical proteins" in public databases, were exclusively found in ascomycetous fungi and in plants. Although complete (or almost complete) fungal genomes and EST collections of some Basidiomycota and Glomeromycota are already available, DHN-like proteins appear to be represented only in Ascomycota. A new and previously uncharacterized conserved signature pattern was identified and proposed to Uniprot database as the main distinguishing feature of this new group of DHNs. Expression studies provide experimental evidence of a transcript induction of TbDHN1 during cellular dehydration. CONCLUSION: Expression pattern and sequence similarities to known plant DHNs indicate that TbDHN1 is the first characterized DHN-like protein in fungi. The high similarity of TbDHN1 with homolog coding sequences implies the existence of a novel fungal/plant group of LEA Class II proteins characterized by a previously undescribed signature pattern

Identification of Fusarium oxysporum f. sp. basilici isolated from soil, basil seed, and plants by RAPD analysis

Fifty-two isolates of Fusarium oxysporum, obtained from infected basil plants, seed, flower residues, and soil from different growing areas in Italy and Israel, were analyzed by random amplified polymorphic DNA-polymerase chain reaction (RAPD-PCR), coupled to a DNA extraction protocol from colonies grown on Fusarium-selective medium. In a pathogenicity assay, 35 isolates caused 32 to 92% disease on seedlings of the highly susceptible basil cultivar Fine verde, while 17 isolates were nonpathogenic on basil. Thirty of the F. oxysporum f. sp. basilici isolates obtained from soil or wilted plants gave identical amplification patterns using 31 different random primers. All tested primers allowed clear differentiation of F. oxysporum f. sp. basilici from representatives of other formae speciales and from nonpathogenic strains of F. oxysporum. RAPD profiles obtained from DNA of isolates extracted directly from cultures grown on Fusarium selective medium were identical to those obtained from DNA extracted from lyophilized myceli