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Title: 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. Furthermore, 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,more » 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.« less
Authors:
 [1] ;  [1] ;  [2] ;  [3] ;  [2] ;  [1]
  1. Vanderbilt Univ., Nashville, TN (United States)
  2. Univ. of Wisconsin, Madison, WI (United States)
  3. U.S. Dept. of Agriculture, Peoria, IL (United States)
Publication Date:
Grant/Contract Number:
FC02-07ER64494
Type:
Accepted Manuscript
Journal Name:
G3
Additional Journal Information:
Journal Volume: 6; Journal Issue: 12; Journal ID: ISSN 2160-1836
Publisher:
Genetics Society of America
Research Org:
Univ. of Wisconsin-Madison, Madison, WI (United States)
Sponsoring Org:
USDOE Office of Science (SC), Biological and Environmental Research (BER) (SC-23)
Country of Publication:
United States
Language:
English
Subject:
60 APPLIED LIFE SCIENCES; 59 BASIC BIOLOGICAL SCIENCES; phylogenomics; maximum likelihood; incongruence; genome completeness; nuclear markers
OSTI Identifier:
1361388

Shen, Xing -Xing, Zhou, Xiaofan, Kominek, Jacek, Kurtzman, Cletus P., Hittinger, Chris Todd, and Rokas, Antonis. Reconstructing the backbone of the Saccharomycotina yeast phylogeny using genome-scale data. United States: N. p., Web. doi:10.1534/g3.116.034744.
Shen, Xing -Xing, Zhou, Xiaofan, Kominek, Jacek, Kurtzman, Cletus P., Hittinger, Chris Todd, & Rokas, Antonis. Reconstructing the backbone of the Saccharomycotina yeast phylogeny using genome-scale data. United States. doi:10.1534/g3.116.034744.
Shen, Xing -Xing, Zhou, Xiaofan, Kominek, Jacek, Kurtzman, Cletus P., Hittinger, Chris Todd, and Rokas, Antonis. 2016. "Reconstructing the backbone of the Saccharomycotina yeast phylogeny using genome-scale data". United States. doi:10.1534/g3.116.034744. https://www.osti.gov/servlets/purl/1361388.
@article{osti_1361388,
title = {Reconstructing the backbone of the Saccharomycotina yeast phylogeny using genome-scale data},
author = {Shen, Xing -Xing and Zhou, Xiaofan and Kominek, Jacek and Kurtzman, Cletus P. and Hittinger, Chris Todd and Rokas, Antonis},
abstractNote = {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. Furthermore, 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.},
doi = {10.1534/g3.116.034744},
journal = {G3},
number = 12,
volume = 6,
place = {United States},
year = {2016},
month = {9}
}