Phylogenetics of Saccharomycetales, the ascomycete yeasts

Abstract

Ascomycete yeasts (phylum Ascomycota: subphylum Saccharomycotina: class Saccharomycetes: order Saccharomycetales) comprise a monophyletic lineage with a single order of about 1000 known species. These yeasts live as saprobes, often in association with plants, animals and their interfaces. A few species account for most human mycotic infections, and fewer than 10 species are plant pathogens. Yeasts are responsible for important industrial and biotechnological processes, including baking, brewing and synthesis of recombinant proteins. Species such as Saccharomyces cerevisiae are model organisms in research, some of which led to a Nobel Prize. Yeasts usually reproduce asexually by budding, and their sexual states are not enclosed in a fruiting body. The group also is well defined by synapomorphies visible at the ultrastructural level. Yeast identification and classification changed dramatically with the availability of DNA sequencing. Species identification now benefits from a constantly updated sequence database and no longer relies on ambiguous growth tests. A phylogeny based on single gene analyses has shown the order to be remarkably divergent despite morphological similarities among members. The limits of many previously described genera are not supported by sequence comparisons, and multigene phylogenetic studies are under way to provide a stable circumscription of genera, families and orders. One recent multigene study has resolved species of the Saccharomycetaceae into genera that differ markedly from those defined by analysis of morphology and growth responses, and similar changes are likely to occur in other branches of the yeast tree as additional sequences become available.

• Hemiascomycetes
• rDNA
• systematics

We thank Nhu H. Nguyen for his constructive review of the manuscript before submission. We also thank Dr Conrad Schoch for providing unpublished sequence data used in the analyses. MB and S-OS acknowledge support from the National Science Foundation (DEB-0417180, DBI-0400797). M-AL acknowledges a Discovery Grant from the Natural Science and Engineering Research Council of Canada. We all are grateful for the use ofPUBLIC resources, including the GenBank, CBS, and NRRL databases and culture collections. This work was greatly encouraged by the Deep Hypha project financed ed by NSF: Research Coordination Networks in Biological Sciences: A Phylogeny for Kingdom Fungi (NSF-0090301).