Wednesday, August 28, 2013

Italian fungi

As promised earlier here another example for ongoing and past efforts to barcode existing collections. 

Over the last couple of years the University of California, Berkeley and the Venice Museum of Natural History in Italy were collaborating to extensively catalog a museum collection using DNA Barcoding. The Venice Museum hosts the largest and best preserved fungal collection in Italy with more than 25,000 samples, representing approximately 6,000 species of fungi including many rare specimens. A diverse representation of the Venice collection was sampled and sent to Berkeley, where the fungal DNA Barcode region (ITS) was sequenced.

The Venice collection is one of the first ones in the world to be used for building an extensive DNA Barcode library. The collection is unique as it is entirely generated and curated by volunteers, and in fact it is the outlet of the largest amateur mycological association in the world, the Associazione Micologica Bresadola, which currently has about 13,000 active members.

The results of this work have been published this spring and they are indeed promising:
Our goals were to investigate issues related to large sequencing projects, develop heuristic methods for assessing the overall performance of such a project, and evaluate the prospects of such efforts to reduce the current gap in fungal biodiversity knowledge. The effort generated 1107 sequences submitted to GenBank, including 416 previously unrepresented taxa and 398 sequences exhibiting a best BLAST match to an unidentified environmental sequence. Specimen age and taxon affected sequencing success, and subsequent work on failed specimens showed that an ITS1 mini-barcode greatly increased sequencing success without greatly reducing the discriminating power of the barcode. 

An interactive map showing the geographic location of all sequenced accessions, linked to collection data and searchable by taxon, is available for viewing (see image above). The researchers made the DNA Barcodes avaiable in an organized fashion (e.g. by genera) on their project website and they explicitly invite researchers to use the sequences in their analyses and provide feedback that could be useful for refining the taxonomic identifications attached to the data.

No comments:

Post a Comment