Primers for fourteen protein-coding genes and the deep phylogeny of the true yeasts

Abstract

The Saccharomycetales or ‘true yeasts’ consist of more than 800 described species, including many of scientific, medical and commercial importance. Considerable progress has been made in determining the phylogenetic relationships of these species, largely based on rDNA sequences, but many nodes for early-diverging lineages cannot be resolved with rDNA alone. rDNA is also not ideal for delineating recently diverged species. From published full-genome sequence data, we have identified 14 regions of protein-coding genes that can be PCR-amplified in a large proportion of a diverse collection of 25 yeast species using degenerate primers. Phylogenetic analysis of the sequences thus obtained reveals a well-resolved phylogeny of the Saccharomycetales with many branches having high bootstrap support. Analysis of published sequences from the Saccharomyces paradoxus species complex shows that these protein-coding gene fragments are also informative about genealogical relationships amongst closely related strains. Our set of protein-coding gene fragments is therefore suitable for analysing both ancient and recent evolutionary relationships amongst yeasts.

Selection of Orthologous Genes for Construction of a Highly Resolved Phylogenetic Tree and Clarification of the Phylogeny of Trichosporonales Species

“…The later addition of RPB1 and RPB2 improved the resolution for the Saccharomycetales yeast species [ 15 ]. Recently, Koufopanou et al [ 37 ] reported primer sets for 14 genes to clarify the topology of basal species among the Saccharomycetales. Of our 30 genes, glutamate synthase and adenosyl homocysteinase were used for multiple gene analysis by Koufopanou et al [ 37 ], and CDC19 was selected as a candidate during the first screening stage but was not used in the published analysis.…”

“…Recently, Koufopanou et al [ 37 ] reported primer sets for 14 genes to clarify the topology of basal species among the Saccharomycetales. Of our 30 genes, glutamate synthase and adenosyl homocysteinase were used for multiple gene analysis by Koufopanou et al [ 37 ], and CDC19 was selected as a candidate during the first screening stage but was not used in the published analysis. Gene duplication in the Tor pathway was also reported in some fungi by Shertz et al [ 38 ].…”

A Gondwanan imprint on global diversity and domestication of wine and cider yeast Saccharomyces uvarum

“…We deployed a recent multi-locus sequence approach 63 to examine the evolutionary relationships among the species and known populations of the genus Saccharomyces , including the new Australasian population of S. uvarum described here. Complete coding sequences for the fourteen genes were extracted from the available annotations of six Saccharomyces species 51,64 , ( Saccharomyces Genome Database).…”