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.本数据集收录的酵母菌绝大多数分离于1999年之前（最古老菌株可追溯至1893年），均通过传统表型测试完成鉴定。自2000年核糖体测序成本降至可接受区间以来，我们已通过内转录间隔区（ITS）与部分26S区域的条形码测序，重新鉴定了80%以上的酵母菌株。对数百株酵母菌（涵盖约200个不同物种）开展序列分析后发现，其序列无法匹配任何已知物种。此类酵母菌目前被授予暂定种名，例如“Komagataella aff. phaffii”，其中“aff.”为“近缘的（affinis）”缩写，表明该菌株与已命名物种亲缘关系相近。其中部分新种的DNA序列已提交至基因库（GenBank）。这些序列的公开获取，使得其他机构的研究人员可借助同一新种的额外菌株，将菲夫收藏（Phaff collection）酵母菌纳入新物种描述工作——例如近年正式发表的Komagataella mondaviorum与Rasporomyces dianae。在我们发表的关于R. dianae的研究论文中，得益于南非一株酵母菌的GenBank序列与我们来自加利福尼亚的酵母菌株序列完全匹配，我们得以补充收录更多菌株，并新增了一名来自南非的共同作者。由于菲夫收藏中绝大多数新发现酵母菌的核糖体序列仅存于内部数据库，尚未提交至GenBank，这类“暗数据”阻碍了其他分类学家将菲夫收藏酵母菌株纳入其新种描述工作。若物种描述涵盖更多菌株以体现其地理分布与宿主生境多样性，则被认为更具学术价值。