A database to support plant pest diagnostic activities

Molecular Decision Scheme

The regulated species listed below have been successfully identified using the mentioned protocols. It is very likely that other fungi species can successfully be identified using these protocols, but validation data has not been generated to support this. Protocols in blue are published in PM7/129.


How to identify a fungal species with Q-bank (in construction)

To perform an identification of a fungal species with no knowledge of the fungal genus to which the species could belong, start with a "Blast against all Q-bank (fungal) sequences" from the ID menu on the main or the fungal Q-bank page. The sequence(s) should not contain any alignment gap characters (often indicated by "-") or other non-standard symbols. Click on the first hyperlink in the hits retrieved from the search to open the page containing the detailed information on that entry. At the top of this page is an item called "Organism group". This item identifies the fungal organism group to which the species of interest belongs. With the knowledge of which organism group, a focussed multilocus search can be performed in that specific group under the menu item "ID" and then the corresponding "organism group" multilocus identification under "Multilocus sequence ID per group". Under the first tab (1. Description) you can enter a title or description under "Item name" for the analysis you are about to perform. In the second tab (2. Sequences) you can paste the sequence(s) into the corresponding locus blocks. Click on the "Start identification" button at the bottom of the page. The results can be viewed as a phylogenetic tree ("Draw tree" item at the top of the page) or as a percentage similarity.

For example, you have performed a blast against all Q-bank (fungal) sequences using a fungal internal transcribed spacers of the nrDNA operon (ITS) sequence, for example that of Mycosphaerella gibsonii. The highest identity should be that of a strain of Mycosphaerella gibsonii, by now clicking on the first hyperlink of that entry (in this case the CBS culture number) a new page with information on that strain opens.  Under "Organism group" it states that this species belongs to "Mycosphaerella" and under "Quarantine status" its EU and EPPO status values are displayed as well as information on the "Diagnostic locus for identification in Q-bank". Under the diagnostic locus section for this species it is mentioned that ITS must be combined with beta-tubulin (TUB2) following the Molecular Decision Scheme above. Therefore a multilocus identification for this species using at least ITS and TUB2 is required.  This can then be performed by pasting these sequences into the appropriate locus blocks in the section "2. Sequences" of the "Multilocus sequence ID per group" item for "Mycosphaerella".