Identify yeasts by ribosomal barcode sequencing of ITS and partial 26S regions.

Most of the yeasts were isolated before 1999 (the oldest from 1893) and were thus identified by traditional phenotype tests. Since 2000, when ribosomal sequencing became affordable, we have re-identified over 80% of the yeast strains by barcode sequencing of ITS and partial 26S regions. The DNA sequences of hundreds of yeast strains, approximately 200 different species, did not match known species when they were analyzed. These yeasts are currently assigned a provisional species name such as “Komagataella aff. phaffii”, indicating that it is a new species similar to (affinis) to the named species. The DNA sequences of a few of these new species have been deposited into GenBank. Public availability of these DNA sequences has enabled other researchers at other institutions with additional strains of the same novel species to include Phaff collection yeasts in new species descriptions, including recently described Komagataella mondaviorum and Rasporomyces dianae. In our R. dianae publication, we were able to add additional strains, and an additional co-author from South Africa, because their DNA sequence in GenBank of a yeast from South Africa matched the DNA sequence of our yeast strain from California. Because the ribosomal sequences of most novel yeast species in the Phaff collection are only in the in-house database, and not yet deposited in GenBank, this “dark data” prevents other taxonomists from including Phaff collection yeast strains in their new species descriptions. Yeast species descriptions are considered more meaningful if they include a larger number of strains to represent to geographic and host habitat diversity of the species.