Tue - February 8, 2005

Mushroom DNA sequences online at NCBI


For the modern biologist who happens to be interested in mushrooms: There's a treasure trove of taxonomic and DNA sequence data online. Almost every species that has been described has had at least a few genes sequenced.

The results are online and freely available at NCBI, where you can also find out about the full classification system by using the "taxonomy" search option. Just another one of the things that PubMed makes possible.

One day as I lamented the challenges of unambiguous identification of closely related or morphologically similar species, I wondered whether one could use DNA sequence to make an authoritative ID.

Of course, this would take a lot of legwork. First, one would have to choose a sequence that was similar enough across all mushrooms that it would be straightforward to sequence it. Fortunately, this is already solved: ribosomal RNAs are the industry standard for this kind of cross-species comparison).

More importantly, one would have to sequence these genes in pre-identified samples, in order to create a reference. This requires the samples themselves and an unambiguous identification, presumably performed by someone else. Hence, I reasoned, this wasn't ultimately a useful approach.

Unless someone else would, you know, go ahead and sequence every mushroom for me.

I was thrilled to learn that this has been done.

Taxonomy searching at NCBI ((choose "Taxonomy" on the pulldown menu) allows a search by full scientific name, genus alone, or indeed any higher-level taxonomic category. Hits are linked to all sequences recorded for the species of interest. So far I haven't found a single species that isn't described.

This is a valuable tool, not just for difficult identifications, but for educating the amateur mycologist about the relationships between various mushroom species.

Also, in the unlikely event that one finds a previously undescribed fungus, a DNA sequence will serve as an important part both of the proof of novelty and in the initial characterization and classification of the species.

P.S.: OK, granted that this requires one to have access to DNA sequencing facilities, but I'm guessing that among those who read this blog, I'm not the only biologist.

Posted at 10:00 AM    

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