Reconstructing the Backbone of the Saccharomycotina Yeast Phylogeny Using Genome-Scale Data.
Understanding the phylogenetic relationships among the yeasts of the subphylum Saccharomycotina is a prerequisite for understanding the evolution of their metabolisms and ecological lifestyles. In the last two decades, the use of rDNA and multilocus data sets has greatly advanced our understanding of the yeast phylogeny, but many deep relationships remain unsupported. In contrast, phylogenomic analyses have involved relatively few taxa and lineages that were often selected with limited considerations for covering the breadth of yeast biodiversity. Here we used genome sequence data from 86 publicly available yeast genomes representing nine of the 11 known major lineages and 10 nonyeast fungal outgroups to generate a 1233-gene, 96-taxon data matrix. Species phylogenies reconstructed using two different methods (concatenation and coalescence) and two data matrices (amino acids or the first two codon positions) yielded identical and highly supported relationships between the nine major lineages. Aside from the lineage comprised by the family Pichiaceae, all other lineages were monophyletic. Most interrelationships among yeast species were robust across the two methods and data matrices. However, eight of the 93 internodes conflicted between analyses or data sets, including the placements of: the clade defined by species that have reassigned the CUG codon to encode serine, instead of leucine; the clade defined by a whole genome duplication; and the species Ascoidea rubescens These phylogenomic analyses provide a robust roadmap for future comparative work across the yeast subphylum in the disciplines of taxonomy, molecular genetics, evolutionary biology, ecology, and biotechnology. To further this end, we have also provided a BLAST server to query the 86 Saccharomycotina genomes, which can be found at http://y1000plus.org/blast.
Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee 37235.
Xing-Xing
XX
Shen
Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee 37235.
Xiaofan
0000-0002-2879-6317
X
Zhou
Laboratory of Genetics, Genome Center of Wisconsin, DOE Great Lakes Bioenergy Research Center, Wisconsin Energy Institute, J. F. Crow Institute for the Study of Evolution, University of Wisconsin-Madison, Madison, Wisconsin 53706.
Jacek
0000-0002-1916-0122
J
Kominek
Mycotoxin Prevention and Applied Microbiology Research Unit, National Center for Agricultural Utilization Research, Agricultural Research Service, U.S. Department of Agriculture, Peoria, Illinois 61604 antonis.rokas@vanderbilt.edu.
Cletus P
CP
Kurtzman
Laboratory of Genetics, Genome Center of Wisconsin, DOE Great Lakes Bioenergy Research Center, Wisconsin Energy Institute, J. F. Crow Institute for the Study of Evolution, University of Wisconsin-Madison, Madison, Wisconsin 53706 antonis.rokas@vanderbilt.edu.
Chris Todd
0000-0001-5088-7461
CT
Hittinger
Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee 37235 antonis.rokas@vanderbilt.edu.
Antonis
0000-0002-7248-6551
A
Rokas
D001203:Ascomycota / Q000145:classification* / Q000235:genetics*; D019295:Computational Biology / Q000379:methods; D005819:Genetic Markers; D016681:Genome, Fungal; D023281:Genomics / Q000379:methods; D010802:Phylogeny; D057188:Workflow
D005819:Genetic Markers
genome completeness; incongruence; maximum likelihood; nuclear markers; phylogenomics
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