Beyond the shape: molecular systematics and phytopathological diagnostic

Crop protection can be implemented by several strategies, among them prophylaxis guarantees profitable productions and a slight environmental impact. Diagnosis of pathogens exploited different strategies, according to the organisms to be detected. Historically, fungi have been identified by morphological characters, bacteria by physiological tests and viruses by symptoms on indexing plants. Immunological assays (devised to detect bacteria and viruses) at first, and nucleic acid based assays (available for all biotic pathogens) later, reduced strategy discrepancies. The fast evolution in regulation and techniques that we are living nowadays, deeply changed the terms. It is, now,possible to identify all the pathogens affecting a crop in a single sample (multiplexing) and to examine a high number of samples at a time.We can state that there is no pathogen that cannot be identified through assays that guarantee the sensitivity and the specificity required by certification schemes, eradication procedures and quarantine protocols. The same fast technical evolution renders the exploitation of the new sophisticate and powerful tools more and more cheap and simple. At the present stage, a deeper knowledge of the biology and the epidemiology of plant pathogens changes the problem from technical to conceptual. Conventional fungal taxonomy is no more apt to depict frameworks to house the biological complexity of fungal pathogens; molecular phylogeny opened new horizons and posed new questions. Molecular systematics can bring into harmony systematic schemes, biological complexity and phytopathological aspects. To explain concepts, examples including toxigenic Fusarium and Diaporthe helianthi, as a quarantine pathogen, will be discussed.