Monday, August 26, 2013

Barcoding P.A.T.H.S.

A group of Italian researchers made their sequences of type and historical material publicly available through a new database, called “Barcoding P.A.T.H.S.” (Plant & Algal Type & Historical Specimens). It represents a library of reference sequences, easy to update, and against which putative new species or other plant material can be compared (they use a BLAST tool on the site). As the acronym P.A.T.H.S suggests, specimens comprise water, and land plants and algae, interpreted sensu lato to include not only microalgae and seaweeds, but also cyanobacteria. 

Most importantly, the project focuses solely on reference specimens and includes type specimens and historical material. The intention is to tackle the problem of frequent misidentifications, e.g. for sequences available in public databases obtained from incorrectly identified specimens or with a number of superfluous and synonymised species entities recorded for some taxa. It has been stated very often that the ideal approach to DNA Barcoding would be to sequence type specimens and historical material wherever possible. This new initiative is a great example. I'll try to find more for this week's blog posts as we are long past the stage of having just great ideas.

The Italian group is now reaching out to the community through a small paper published in Taxon. Here a small excerpt:
Our project has just begun and our group is willing to establish  collaborations with other research groups, museums, and botanical  gardens involved in similar DNA barcoding studies. Such collaborations would increase the molecular data regarding type and  historical specimens and make them accessible to everyone. In the  P.A.T.H.S. database each sample that represents the type strain of a  newly described species (supported by publication on ISI journals)  can be included. In addition, it is possible for collaborators to add  unpublished sequences so they are available for comparison with  BLAST, but not visible or downloadable by other users, this would  facilitate the rapid sharing of data. However, the sequences have to be submitted to one of the public databases, like GenBank.

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