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.

本数据集收录的绝大多数酵母菌分离于1999年之前（最古老的菌株可追溯至1893年），最初均通过传统表型测试（traditional phenotype tests）完成鉴定。自2000年核糖体测序（ribosomal sequencing）成本变得可及以来，我们已通过内转录间隔区（ITS）及26S核糖体RNA部分区域（partial 26S regions）的条形码测序（barcode sequencing），重新鉴定了本库中80%以上的酵母菌菌株。对数百株酵母菌、约200个不同物种进行分析时，发现其DNA序列无法匹配已知物种。目前这类酵母菌被赋予暂定种名（provisional species name），例如"Komagataella aff. phaffii"，其中"aff."表示该菌株与命名物种存在近缘关系（对应拉丁词affinis）。其中部分新种的DNA序列已提交至基因库（GenBank）。这些DNA序列的公开共享，使得其他机构的研究人员可借助同源新菌株，将Phaff保藏库（Phaff collection）的酵母菌纳入新物种描述工作，其中包括近期正式发表的Komagataella mondaviorum与Rasporomyces dianae。在我们关于R. dianae的研究论文中，因南非一株酵母菌的基因库（GenBank）序列与我们保藏的加州酵母菌菌株序列完全匹配，我们得以新增了额外的研究菌株，并吸纳了一名来自南非的共同作者。由于Phaff保藏库（Phaff collection）中多数新发现酵母菌的核糖体序列仅存于内部数据库，尚未提交至基因库（GenBank），这类"暗数据（dark data）"阻碍了其他分类学家（taxonomists）将该保藏库的酵母菌菌株纳入其新物种描述工作。若物种描述纳入更多菌株以体现该物种的地理与宿主生境多样性（geographic and host habitat diversity），则被认为更具学术价值。