Nomenclatural issues concerning cultured yeasts and other fungi: why it is important to avoid unneeded name changes

The unambiguous application of fungal names is important to communicate scientific findings. Names are critical for (clinical) diagnostics, legal compliance, and regulatory controls, such as biosafety, food security, quarantine regulations, and industrial applications. Consequently, the stability of the taxonomic system and the traceability of nomenclatural changes is crucial for a broad range of users and taxonomists. The unambiguous application of names is assured by the preservation of nomenclatural history and the physical organisms representing a name. Fungi are extremely diverse in terms of ecology, lifestyle, and methods of study. Predominantly unicellular fungi known as yeasts are usually investigated as living cultures. Methods to characterize yeasts include physiological (growth) tests and experiments to induce a sexual morph; both methods require viable cultures. Thus, the preservation and availability of viable reference cultures are important, and cultures representing reference material are cited in species descriptions. Historical surveys revealed drawbacks and inconsistencies between past practices and modern requirements as stated in the International Code of Nomenclature for Algae, Fungi, and Plants (ICNafp). Improper typification of yeasts is a common problem, resulting in a large number invalid yeast species names. With this opinion letter, we address the problem that culturable microorganisms, notably some fungi and algae, require specific provisions under the ICNafp. We use yeasts as a prominent example of fungi known from cultures. But viable type material is important not only for yeasts, but also for other cultivable Fungi that are characterized by particular morphological structures (a specific type of spores), growth properties, and secondary metabolites. We summarize potential proposals which, in our opinion, will improve the stability of fungal names, in particular by protecting those names for which the reference material can be traced back to the original isolate

Into the wild: new yeast genomes from natural environments and new tools for their analysis

This is a pre-copyedited, author-produced version of an article accepted for publication in FEMS Yeast Research following peer review. The version of record "D Libkind, D Peris, F A Cubillos, J L Steenwyk, D A Opulente, Q K Langdon, A Rokas, C T Hittinger, Into the wild: new yeast genomes from natural environments and new tools for their analysis, FEMS Yeast Research, Volume 20, Issue 2, March 2020, foaa008" is available online at: https://doi.org/10.1093/femsyr/foaa008Genomic studies of yeasts from the wild have increased considerably in the past few years. This revolution has been fueled by advances in high-throughput sequencing technologies and a better understanding of yeast ecology and phylogeography, especially for biotechnologically important species. The present review aims to first introduce new bioinformatic tools available for the generation and analysis of yeast genomes. We also assess the accumulated genomic data of wild isolates of industrially relevant species, such as Saccharomyces spp., which provide unique opportunities to further investigate the domestication processes associated with the fermentation industry and opportunistic pathogenesis. The availability of genome sequences of other less conventional yeasts obtained from the wild has also increased substantially, including representatives of the phyla Ascomycota (e.g. Hanseniaspora) and Basidiomycota (e.g. Phaffia). Here, we review salient examples of both fundamental and applied research that demonstrate the importance of continuing to sequence and analyze genomes of wild yeasts.DL has been funded through CONICET (PIP11220130100392CO) and Universidad Nacional del Comahue (B199). Research in AR's lab has been funded through a National Science Foundation grant (DEB-1442113); JLS and AR have also received funding by the Howard Hughes Medical Institute through the James H. Gilliam Fellowships for Advanced Study program. CTH has been funded through the National Science Foundation (DEB-1442148), USDA National Institute of Food and Agriculture (Hatch Project 1020204), and DOE Great Lakes Bioenergy Research Center (DE-SC0018409). CTH is a Pew Scholar in the Biomedical Sciences and a H. I. Romnes Faculty Fellow, supported by the Pew Charitable Trusts and Office of the Vice Chancellor for Research and Graduate Education with funding from the Wisconsin Alumni Research Foundation, respectively. DP is a Marie Sklodowska-Curie fellow of the European Union’s Horizon 2020 research and innovation program (Grant Agreement No. 747775).Peer reviewe