Reconstructing the backbone of the Saccharomycotina yeast phylogeny using genome-scale data

Shen, Xing -Xing; Zhou, Xiaofan; Kominek, Jacek; Kurtzman, Cletus P.; Hittinger, Chris Todd; Rokas, Antonis

doi:10.1534/g3.116.034744

Title: Reconstructing the backbone of the Saccharomycotina yeast phylogeny using genome-scale data

Journal Article · Mon Sep 26 00:00:00 EDT 2016 · G3

DOI:https://doi.org/10.1534/g3.116.034744· OSTI ID:1361388

Shen, Xing -Xing ^[1]; Zhou, Xiaofan ^[1]; Kominek, Jacek ^[2]; Kurtzman, Cletus P. ^[3]; Hittinger, Chris Todd ^[2]; Rokas, Antonis ^[1]

Vanderbilt Univ., Nashville, TN (United States)
Univ. of Wisconsin, Madison, WI (United States)
U.S. Dept. of Agriculture, Peoria, IL (United States)

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.

View Accepted Manuscript (DOE)

Cite

Export

Save

Research Organization:: Univ. of Wisconsin, Madison, WI (United States)

Sponsoring Organization:: USDOE Office of Science (SC), Biological and Environmental Research (BER)

Grant/Contract Number:: FC02-07ER64494

OSTI ID:: 1361388

Journal Information:: G3, Vol. 6, Issue 12; ISSN 2160-1836

Publisher:: Genetics Society of AmericaCopyright Statement

Country of Publication:: United States

Language:: English

Citation Metrics:

Cited by: 135 works

Citation information provided by
Web of Science

References (99)

Phylogenomics Philippe, Hervé; Delsuc, Frédéric; Brinkmann, Henner Annual Review of Ecology, Evolution, and Systematics, Vol. 36, Issue 1 https://doi.org/10.1146/annurev.ecolsys.35.112202.130205	journal	December 2005
Phylotranscriptomic analysis of the origin and early diversification of land plants Wickett, Norman J.; Mirarab, Siavash; Nguyen, Nam Proceedings of the National Academy of Sciences, Vol. 111, Issue 45 https://doi.org/10.1073/pnas.1323926111	journal	October 2014
Yeast evolutionary genomics Dujon, Bernard Nature Reviews Genetics, Vol. 11, Issue 7 https://doi.org/10.1038/nrg2811	journal	July 2010
Coalescent versus Concatenation Methods and the Placement of Amborella as Sister to Water Lilies Xi, Zhenxiang; Liu, Liang; Rest, Joshua S. Systematic Biology, Vol. 63, Issue 6 https://doi.org/10.1093/sysbio/syu055	journal	July 2014
Resolving conflict in eutherian mammal phylogeny using phylogenomics and the multispecies coalescent model Song, S.; Liu, L.; Edwards, S. V. Proceedings of the National Academy of Sciences, Vol. 109, Issue 37 https://doi.org/10.1073/pnas.1211733109	journal	August 2012
The Impact of Missing Data on Species Tree Estimation Xi, Zhenxiang; Liu, Liang; Davis, Charles C. Molecular Biology and Evolution, Vol. 33, Issue 3 https://doi.org/10.1093/molbev/msv266	journal	November 2015
ASTRAL: genome-scale coalescent-based species tree estimation Mirarab, S.; Reaz, R.; Bayzid, Md. S. Bioinformatics, Vol. 30, Issue 17 https://doi.org/10.1093/bioinformatics/btu462	journal	August 2014
Novel Information Theory-Based Measures for Quantifying Incongruence among Phylogenetic Trees Salichos, Leonidas; Stamatakis, Alexandros; Rokas, Antonis Molecular Biology and Evolution, Vol. 31, Issue 5 https://doi.org/10.1093/molbev/msu061	journal	February 2014
A Genome-Scale Investigation of How Sequence, Function, and Tree-Based Gene Properties Influence Phylogenetic Inference Shen, Xing-Xing; Salichos, Leonidas; Rokas, Antonis Genome Biology and Evolution, Vol. 8, Issue 8 https://doi.org/10.1093/gbe/evw179	journal	August 2016
Evaluating Rare Amino Acid Substitutions (RGC_CAMs) in a Yeast Model Clade Polzin, Kenneth; Rokas, Antonis PLoS ONE, Vol. 9, Issue 3 https://doi.org/10.1371/journal.pone.0092213	journal	March 2014
Molecular Phylogeny of Sequenced Saccharomycetes Reveals Polyphyly of the Alternative Yeast Codon Usage Mühlhausen, Stefanie; Kollmar, Martin Genome Biology and Evolution, Vol. 6, Issue 12 https://doi.org/10.1093/gbe/evu152	journal	July 2014
The gene tree delusion Springer, Mark S.; Gatesy, John Molecular Phylogenetics and Evolution, Vol. 94 https://doi.org/10.1016/j.ympev.2015.07.018	journal	January 2016
Inferring ancient divergences requires genes with strong phylogenetic signals Salichos, Leonidas; Rokas, Antonis Nature, Vol. 497, Issue 7449 https://doi.org/10.1038/nature12130	journal	May 2013
Sequenceserver: a modern graphical user interface for custom BLAST databases Priyam, Anurag; Woodcroft, Ben J.; Rai, Vivek Molecular Biology and Evolution https://doi.org/10.1101/033142	journal	November 2015
Increased Taxon Sampling Greatly Reduces Phylogenetic Error Zwickl, Derrick J.; Hillis, David M. Systematic Biology, Vol. 51, Issue 4 https://doi.org/10.1080/10635150290102339	journal	July 2002
The genome sequence of the wine yeast VIN7 reveals an allotriploid hybrid genome with Saccharomyces cerevisiae and Saccharomyces kudriavzevii origins Borneman, Anthony R.; Desany, Brian A.; Riches, David FEMS Yeast Research, Vol. 12, Issue 1 https://doi.org/10.1111/j.1567-1364.2011.00773.x	journal	December 2011
MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability Katoh, K.; Standley, D. M. Molecular Biology and Evolution, Vol. 30, Issue 4 https://doi.org/10.1093/molbev/mst010	journal	January 2013
The Reacquisition of Biotin Prototrophy in Saccharomyces cerevisiae Involved Horizontal Gene Transfer, Gene Duplication and Gene Clustering Hall, Charles; Dietrich, Fred S. Genetics, Vol. 177, Issue 4 https://doi.org/10.1534/genetics.107.074963	journal	December 2007
Genome-scale approaches to resolving incongruence in molecular phylogenies Rokas, Antonis; Williams, Barry L.; King, Nicole Nature, Vol. 425, Issue 6960 https://doi.org/10.1038/nature02053	journal	October 2003
Pichia sorbitophila , an Interspecies Yeast Hybrid, Reveals Early Steps of Genome Resolution After Polyploidization Louis, Véronique Leh; Despons, Laurence; Friedrich, Anne G3: Genes\|Genomes\|Genetics, Vol. 2, Issue 2 https://doi.org/10.1534/g3.111.000745	journal	February 2012
Draft Genome Sequence of Geotrichum candidum Strain 3C Polev, D. E.; Bobrov, K. S.; Eneyskaya, E. V. Genome Announcements, Vol. 2, Issue 5 https://doi.org/10.1128/genomeA.00956-14	journal	September 2014
Comparative genomics of biotechnologically important yeasts Riley, Robert; Haridas, Sajeet; Wolfe, Kenneth H. Proceedings of the National Academy of Sciences, Vol. 113, Issue 35 https://doi.org/10.1073/pnas.1603941113	journal	August 2016
RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies Stamatakis, Alexandros Bioinformatics, Vol. 30, Issue 9 https://doi.org/10.1093/bioinformatics/btu033	journal	January 2014
High quality de novo sequencing and assembly of the Saccharomyces arboricolus genome Liti, Gianni; Ba, Alex N. Nguyen; Blythe, Martin BMC Genomics, Vol. 14, Issue 1 https://doi.org/10.1186/1471-2164-14-69	journal	January 2013
Is a new and General Theory of Molecular Systematics Emerging? Edwards, Scott V. Evolution, Vol. 63, Issue 1 https://doi.org/10.1111/j.1558-5646.2008.00549.x	journal	January 2009
Differential gene retention as an evolutionary mechanism to generate biodiversity and adaptation in yeasts Morel, Guillaume; Sterck, Lieven; Swennen, Dominique Scientific Reports, Vol. 5, Issue 1 https://doi.org/10.1038/srep11571	journal	June 2015
Gene prediction with a hidden Markov model and a new intron submodel Stanke, M.; Waack, S. Bioinformatics, Vol. 19, Issue Suppl 2 https://doi.org/10.1093/bioinformatics/btg1080	journal	September 2003
Morphological and ecological similarities: wood-boring beetles associated with novel xylose-fermenting yeasts, Spathaspora passalidarum gen. sp. nov. and Candida jeffriesii sp. nov. Nguyen, Nhu H.; Suh, Sung-Oui; Marshall, Christopher J. Mycological Research, Vol. 110, Issue 10, p. 1232-1241 https://doi.org/10.1016/j.mycres.2006.07.002	journal	October 2006
Maximum likelihood phylogenetic estimation from DNA sequences with variable rates over sites: Approximate methods Yang, Ziheng Journal of Molecular Evolution, Vol. 39, Issue 3 https://doi.org/10.1007/BF00160154	journal	September 1994
Reconstructing the Fungal Tree of Life Using Phylogenomics and a Preliminary Investigation of the Distribution of Yeast Prion-Like Proteins in the Fungal Kingdom Medina, Edgar M.; Jones, Gary W.; Fitzpatrick, David A. Journal of Molecular Evolution, Vol. 73, Issue 3-4 https://doi.org/10.1007/s00239-011-9461-4	journal	September 2011
Calculating Bootstrap Probabilities of Phylogeny Using Multilocus Sequence Data Seo, T. -K. Molecular Biology and Evolution, Vol. 25, Issue 5 https://doi.org/10.1093/molbev/msn043	journal	February 2008
The Awesome Power of Yeast Evolutionary Genetics: New Genome Sequences and Strain Resources for the Saccharomyces sensu stricto Genus Scannell, Devin R.; Zill, Oliver A.; Rokas, Antonis G3: Genes\|Genomes\|Genetics, Vol. 1, Issue 1 https://doi.org/10.1534/g3.111.000273	journal	June 2011
Orders and Families of Ascosporogenous Yeasts and Yeast-Like Taxa Compared from Ribosomal RNA Sequence Similarities Kurtzman, C. P.; Robnett, C. J. Ascomycete Systematics https://doi.org/10.1007/978-1-4757-9290-4_22	book	January 1994
Multiple rounds of speciation associated with reciprocal gene loss in polyploid yeasts Scannell, Devin R.; Byrne, Kevin P.; Gordon, Jonathan L. Nature, Vol. 440, Issue 7082 https://doi.org/10.1038/nature04562	journal	March 2006
A beginner's guide to eukaryotic genome annotation Yandell, Mark; Ence, Daniel Nature Reviews Genetics, Vol. 13, Issue 5 https://doi.org/10.1038/nrg3174	journal	April 2012
Among-site rate variation and its impact on phylogenetic analyses Yang, Ziheng Trends in Ecology & Evolution, Vol. 11, Issue 9 https://doi.org/10.1016/0169-5347(96)10041-0	journal	September 1996
A Rapid Bootstrap Algorithm for the RAxML Web Servers Stamatakis, Alexandros; Hoover, Paul; Rougemont, Jacques Systematic Biology, Vol. 57, Issue 5 https://doi.org/10.1080/10635150802429642	journal	October 2008
Dating divergences in the Fungal Tree of Life: review and new analyses Taylor, J. W.; Berbee, M. L. Mycologia, Vol. 98, Issue 6 https://doi.org/10.3852/mycologia.98.6.838	journal	November 2006
Phylogenetic relationships among yeasts of the ? complex? determined from multigene sequence analyses Kurtzman, C.; Robnett, C. FEMS Yeast Research, Vol. 3, Issue 4 https://doi.org/10.1016/S1567-1356(03)00012-6	journal	June 2003
Estimating the Dimension of a Model Schwarz, Gideon The Annals of Statistics, Vol. 6, Issue 2 https://doi.org/10.1214/aos/1176344136	journal	March 1978
OrthoDB: a hierarchical catalog of animal, fungal and bacterial orthologs Waterhouse, Robert M.; Tegenfeldt, Fredrik; Li, Jia Nucleic Acids Research, Vol. 41, Issue D1 https://doi.org/10.1093/nar/gks1116	journal	November 2012
Multigene phylogenetic analysis of the Trichomonascus, Wickerhamiella and Zygoascus yeast clades, and the proposal of Sugiyamaella gen. nov. and 14 new species combinations: Multigene phylogenetic analysis of yeast clades Kurtzman, Cletus P.; Robnett, Christie J. FEMS Yeast Research, Vol. 7, Issue 1 https://doi.org/10.1111/j.1567-1364.2006.00157.x	journal	January 2007
A Bayesian Mixture Model for Across-Site Heterogeneities in the Amino-Acid Replacement Process Lartillot, Nicolas; Philippe, Hervé Molecular Biology and Evolution, Vol. 21, Issue 6 https://doi.org/10.1093/molbev/msh112	journal	June 2004
Beyond the Whole-Genome Duplication: Phylogenetic Evidence for an Ancient Interspecies Hybridization in the Baker's Yeast Lineage Marcet-Houben, Marina; Gabaldón, Toni PLOS Biology, Vol. 13, Issue 8 https://doi.org/10.1371/journal.pbio.1002220	journal	August 2015
PhyloBayes 3: a Bayesian software package for phylogenetic reconstruction and molecular dating Lartillot, Nicolas; Lepage, Thomas; Blanquart, Samuel Bioinformatics, Vol. 25, Issue 17 https://doi.org/10.1093/bioinformatics/btp368	journal	June 2009
An Improved General Amino Acid Replacement Matrix Le, S. Q.; Gascuel, O. Molecular Biology and Evolution, Vol. 25, Issue 7 https://doi.org/10.1093/molbev/msn067	journal	April 2008
Phylogenomic Analyses Support the Monophyly of Taphrinomycotina, including Schizosaccharomyces Fission Yeasts Liu, Y.; Leigh, J. W.; Brinkmann, H. Molecular Biology and Evolution, Vol. 26, Issue 1 https://doi.org/10.1093/molbev/msn221	journal	October 2008
Evolution of pathogenicity and sexual reproduction in eight Candida genomes Butler, Geraldine; Rasmussen, Matthew D.; Lin, Michael F. Nature, Vol. 459, Issue 7247 https://doi.org/10.1038/nature08064	journal	May 2009
Avoiding Missing Data Biases in Phylogenomic Inference: An Empirical Study in the Landfowl (Aves: Galliformes) Hosner, Peter A.; Faircloth, Brant C.; Glenn, Travis C. Molecular Biology and Evolution, Vol. 33, Issue 4 https://doi.org/10.1093/molbev/msv347	journal	December 2015
Bulk Segregant Analysis by High-Throughput Sequencing Reveals a Novel Xylose Utilization Gene from Saccharomyces cerevisiae Wenger, Jared W.; Schwartz, Katja; Sherlock, Gavin PLoS Genetics, Vol. 6, Issue 5 https://doi.org/10.1371/journal.pgen.1000942	journal	May 2010
Multiple GAL pathway gene clusters evolved independently and by different mechanisms in fungi Slot, J. C.; Rokas, A. Proceedings of the National Academy of Sciences, Vol. 107, Issue 22 https://doi.org/10.1073/pnas.0914418107	journal	May 2010
Reconstructing the early evolution of Fungi using a six-gene phylogeny James, Timothy Y.; Kauff, Frank; Schoch, Conrad L. Nature, Vol. 443, Issue 7113 https://doi.org/10.1038/nature05110	journal	October 2006
Basic Local Alignment Search Tool Altschul, S. Journal of Molecular Biology, Vol. 215, Issue 3 https://doi.org/10.1006/jmbi.1990.9999	journal	October 1990
Computing the Internode Certainty and Related Measures from Partial Gene Trees Kobert, Kassian; Salichos, Leonidas; Rokas, Antonis Molecular Biology and Evolution, Vol. 33, Issue 6 https://doi.org/10.1093/molbev/msw040	journal	February 2016
Relationships among genera of the Saccharomycotina ( Ascomycota ) from multigene phylogenetic analysis of type species Kurtzman, Cletus P.; Robnett, Christie J. FEMS Yeast Research, Vol. 13, Issue 1 https://doi.org/10.1111/1567-1364.12006	journal	February 2013
BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs Simão, Felipe A.; Waterhouse, Robert M.; Ioannidis, Panagiotis Bioinformatics, Vol. 31, Issue 19 https://doi.org/10.1093/bioinformatics/btv351	journal	June 2015
Estimating phylogenetic trees from genome-scale data: Phylogenies and the multispecies coalecsent model Liu, Liang; Xi, Zhenxiang; Wu, Shaoyuan Annals of the New York Academy of Sciences, Vol. 1360, Issue 1 https://doi.org/10.1111/nyas.12747	journal	April 2015
Saccharomyces diversity and evolution: a budding model genus Hittinger, Chris Todd Trends in Genetics, Vol. 29, Issue 5 https://doi.org/10.1016/j.tig.2013.01.002	journal	May 2013
Application of Phylogenetic Networks in Evolutionary Studies Huson, Daniel H.; Bryant, David Molecular Biology and Evolution, Vol. 23, Issue 2 https://doi.org/10.1093/molbev/msj030	journal	October 2005
Expansion of Hexose Transporter Genes Was Associated with the Evolution of Aerobic Fermentation in Yeasts Lin, Z.; Li, W. -H. Molecular Biology and Evolution, Vol. 28, Issue 1 https://doi.org/10.1093/molbev/msq184	journal	July 2010
Bushes in the Tree of Life Rokas, Antonis; Carroll, Sean B. PLoS Biology, Vol. 4, Issue 11 https://doi.org/10.1371/journal.pbio.0040352	journal	November 2006
Effects of missing data on species tree estimation under the coalescent Hovmöller, Rasmus; Lacey Knowles, L.; Kubatko, Laura S. Molecular Phylogenetics and Evolution, Vol. 69, Issue 3 https://doi.org/10.1016/j.ympev.2013.06.004	journal	December 2013
ProtTest 3: fast selection of best-fit models of protein evolution Darriba, Diego; Taboada, Guillermo L.; Doallo, Ramón Bioinformatics, Vol. 27, Issue 8 https://doi.org/10.1093/bioinformatics/btr088	journal	February 2011
Evolutionary trees from DNA sequences: A maximum likelihood approach Felsenstein, Joseph Journal of Molecular Evolution, Vol. 17, Issue 6 https://doi.org/10.1007/BF01734359	journal	November 1981
Life with 6000 Genes Goffeau, A.; Barrell, B. G.; Bussey, H. Science, Vol. 274, Issue 5287 https://doi.org/10.1126/science.274.5287.546	journal	October 1996
Parallel inactivation of multiple GAL pathway genes and ecological diversification in yeasts Hittinger, C. T.; Rokas, A.; Carroll, S. B. Proceedings of the National Academy of Sciences, Vol. 101, Issue 39 https://doi.org/10.1073/pnas.0404319101	journal	September 2004
A Genome-Scale Investigation of Incongruence in Culicidae Mosquitoes Wang, Yuyu; Zhou, Xiaofan; Yang, Ding Genome Biology and Evolution, Vol. 7, Issue 12 https://doi.org/10.1093/gbe/evv235	journal	November 2015
Response to Comment on "Statistical binning enables an accurate coalescent-based estimation of the avian tree" Mirarab, S.; Bayzid, M. S.; Boussau, B. Science, Vol. 350, Issue 6257 https://doi.org/10.1126/science.aaa7719	journal	October 2015
Molecular evidence for an ancient duplication of the entire yeast genome Wolfe, Kenneth H.; Shields, Denis C. Nature, Vol. 387, Issue 6634 https://doi.org/10.1038/42711	journal	June 1997
Accelerated Profile HMM Searches Eddy, Sean R. PLoS Computational Biology, Vol. 7, Issue 10 https://doi.org/10.1371/journal.pcbi.1002195	journal	October 2011
trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses Capella-Gutierrez, S.; Silla-Martinez, J. M.; Gabaldon, T. Bioinformatics, Vol. 25, Issue 15 https://doi.org/10.1093/bioinformatics/btp348	journal	June 2009
Combining data in phylogenetic analysis Huelsenbeck, John P.; Bull, J. J.; Cunningham, Clifford W. Trends in Ecology & Evolution, Vol. 11, Issue 4 https://doi.org/10.1016/0169-5347(96)10006-9	journal	April 1996
Microbe domestication and the identification of the wild genetic stock of lager-brewing yeast Libkind, D.; Hittinger, C. T.; Valerio, E. Proceedings of the National Academy of Sciences, Vol. 108, Issue 35 https://doi.org/10.1073/pnas.1105430108	journal	August 2011
Cytoscape: A Software Environment for Integrated Models of Biomolecular Interaction Networks Shannon, P. Genome Research, Vol. 13, Issue 11 https://doi.org/10.1101/gr.1239303	journal	November 2003
BLAST+: architecture and applications Camacho, Christiam; Coulouris, George; Avagyan, Vahram BMC Bioinformatics, Vol. 10, Issue 1 https://doi.org/10.1186/1471-2105-10-421	journal	January 2009
Phylogenetic relationships among species of Pichia, Issatchenkia and Williopsis determined from multigene sequence analysis, and the proposal of Barnettozyma gen. nov., Lindnera gen. nov. and Wickerhamomyces gen. nov. Kurtzman, Cletus P.; Robnett, Christie J.; Basehoar-Powers, Eleanor FEMS Yeast Research, Vol. 8, Issue 6 https://doi.org/10.1111/j.1567-1364.2008.00419.x	journal	September 2008
Genomics and the making of yeast biodiversity Hittinger, Chris Todd; Rokas, Antonis; Bai, Feng-Yan Current Opinion in Genetics & Development, Vol. 35 https://doi.org/10.1016/j.gde.2015.10.008	journal	December 2015
Error, signal, and the placement of Ctenophora sister to all other animals Whelan, Nathan V.; Kocot, Kevin M.; Moroz, Leonid L. Proceedings of the National Academy of Sciences, Vol. 112, Issue 18 https://doi.org/10.1073/pnas.1503453112	journal	April 2015
One Thousand Two Hundred Ninety Nuclear Genes from a Genome-Wide Survey Support Lungfishes as the Sister Group of Tetrapods Liang, Dan; Shen, Xing Xing; Zhang, Peng Molecular Biology and Evolution, Vol. 30, Issue 8 https://doi.org/10.1093/molbev/mst072	journal	May 2013
BiNGO: a Cytoscape plugin to assess overrepresentation of Gene Ontology categories in Biological Networks Maere, S.; Heymans, K.; Kuiper, M. Bioinformatics, Vol. 21, Issue 16 https://doi.org/10.1093/bioinformatics/bti551	journal	June 2005
Early diverging Ascomycota: phylogenetic divergence and related evolutionary enigmas Sugiyama, J.; Hosaka, K.; Suh, S. -O. Mycologia, Vol. 98, Issue 6 https://doi.org/10.3852/mycologia.98.6.996	journal	November 2006
Clade- and species-specific features of genome evolution in the Saccharomycetaceae Wolfe, Kenneth H.; Armisén, David; Proux-Wera, Estelle FEMS Yeast Research, Vol. 15, Issue 5 https://doi.org/10.1093/femsyr/fov035	journal	June 2015
Identification and phylogeny of ascomycetous yeasts from analysis of nuclear large subunit (26S) ribosomal DNA partial sequences Kurtzman, Cletus P.; Robnett, Christie J. Antonie van Leeuwenhoek, Vol. 73, Issue 4, p. 331-371 https://doi.org/10.1023/A:1001761008817	journal	January 1998
Basic local alignment search tool Altschul, Stephen F.; Gish, Warren; Miller, Webb Journal of Molecular Biology, Vol. 215, Issue 3, p. 403-410 https://doi.org/10.1016/S0022-2836(05)80360-2	journal	October 1990
Phylogenetic analysis of ascomycete yeasts that form coenzyme Q-9 and the proposal of the new genera Babjeviella, Meyerozyma, Millerozyma, Priceomyces, and Scheffersomyces Kurtzman, Cletus P.; Suzuki, Motofumi Mycoscience, Vol. 51, Issue 1 https://doi.org/10.1007/S10267-009-0011-5	journal	January 2010
Early diverging Ascomycota: phylogenetic divergence and related evolutionary enigmas Sugiyama, Junta; Hosaka, Kentaro; Suh, Sung-Oui Mycologia, Vol. 98, Issue 6 https://doi.org/10.1080/15572536.2006.11832628	journal	November 2006
Dating divergences in the Fungal Tree of Life: review and new analyses Taylor, John W.; Berbee, Mary L. Mycologia, Vol. 98, Issue 6 https://doi.org/10.1080/15572536.2006.11832614	journal	November 2006
Systematic discovery of pseudomonad genetic factors involved in sensitivity to tailocins Carim, Sean; Azadeh, Ashley L.; Kazakov, Alexey E. The ISME Journal, Vol. 15, Issue 8 https://doi.org/10.1038/s41396-021-00921-1	journal	March 2021
Coriander Genomics Database: a genomic, transcriptomic, and metabolic database for coriander Song, Xiaoming; Nie, Fulei; Chen, Wei Horticulture Research, Vol. 7, Issue 1 https://doi.org/10.1038/s41438-020-0261-0	journal	April 2020
Friendship stability in adolescence is associated with ventral striatum responses to vicarious rewards Schreuders, Elisabeth; Braams, Barbara R.; Crone, Eveline A. Nature Communications, Vol. 12, Issue 1 https://doi.org/10.1038/s41467-020-20042-1	journal	January 2021
Retracted: Molecular Phylogeny of Sequenced Saccharomycetes Reveals Polyphyly of the Alternative Yeast Codon Usage Mühlhausen, Stefanie; Kollmar, Martin Genome Biology and Evolution, Vol. 6, Issue 5 https://doi.org/10.1093/gbe/evu093	journal	May 2014
Error, signal, and the placement of Ctenophora sister to all other animals Whelan, Nathan; Kocot, Kevin M.; Moroz, Leonid L. figshare https://doi.org/10.6084/m9.figshare.1334306.v1	dataset	January 2015
Rare genomic changes as a tool for phylogenetics Rokas, Antonis; Holland, Peter W. H. Trends in Ecology & Evolution, Vol. 15, Issue 11 https://doi.org/10.1016/s0169-5347(00)01967-4	journal	November 2000
Funding Sequencing Efforts Bond, Enriqueta; Austin, M. J. Finley Science, Vol. 275, Issue 5303 https://doi.org/10.1126/science.275.5303.1049f	journal	February 1997
Retraction for Polev et al., “Draft Genome Sequence of Geotrichum candidum Strain 3C” Polev, Dmitrii E.; Bobrov, Kirill S.; Eneyskaya, Elena V. Microbiology Resource Announcements, Vol. 8, Issue 24 https://doi.org/10.1128/mra.00561-19	journal	June 2019
RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies Stamatakis, A. Karlsruhe https://doi.org/10.5445/ir/1000045818	text	January 2014
Error, signal, and the placement of Ctenophora sister to all other animals Whelan, Nathan; Kocot, Kevin M.; Moroz, Leonid L. figshare https://doi.org/10.6084/m9.figshare.1334306.v3	dataset	January 2016
A genome-scale investigation of incongruence in Culicidae mosquitoes Wang, Yuyu; Zhou, Xiaofan; Rokas, Antonis figshare https://doi.org/10.6084/m9.figshare.1566851	dataset	January 2015
Reconstructing the backbone of the Saccharomycotina yeast phylogeny using genome-scale data Shen, Xing-Xing figshare https://doi.org/10.6084/m9.figshare.3370675.v1	dataset	January 2016

Cited By (73)

Dynamic Changes in Yeast Phosphatase Families Allow for Specialization in Phosphate and Thiamine Starvation Nahas, John V.; Iosue, Christine L.; Shaik, Noor F. G3: Genes\|Genomes\|Genetics, Vol. 8, Issue 7 https://doi.org/10.1534/g3.118.200303	journal	May 2018
YeasTSS: an integrative web database of yeast transcription start sites McMillan, Jonathan; Lu, Zhaolian; Rodriguez, Judith S. Database, Vol. 2019 https://doi.org/10.1093/database/baz048	journal	January 2019
Evolution of protein kinase substrate recognition at the active site Bradley, David; Beltrao, Pedro PLOS Biology, Vol. 17, Issue 6 https://doi.org/10.1371/journal.pbio.3000341	journal	June 2019
Phylogenetic conflicts, combinability, and deep phylogenomics in plants Smith, Stephen A.; Walker-Hale, Nathanael; Walker, Joseph F. Systematic Biology https://doi.org/10.1101/371930	posted_content	October 2019
The analysis of the polyamine oxidase genes in the methylotrophic yeast Komagataella phaffii Ivanova, Alina V.; Sidorin, Anton V.; Sambuk, Elena V. Ecological genetics, Vol. 17, Issue 4 https://doi.org/10.17816/ecogen17447-55	journal	December 2019
Characterization of a Maltase from an Early-Diverged Non-Conventional Yeast Blastobotrys adeninivorans Visnapuu, Triinu; Meldre, Aivar; Põšnograjeva, Kristina International Journal of Molecular Sciences, Vol. 21, Issue 1 https://doi.org/10.3390/ijms21010297	journal	December 2019
Factors driving metabolic diversity in the budding yeast subphylum Opulente, Dana A.; Rollinson, Emily J.; Bernick-Roehr, Cleome BMC Biology, Vol. 16, Issue 1 https://doi.org/10.1186/s12915-018-0498-3	journal	March 2018
Genome Mining of Non-Conventional Yeasts: Search and Analysis of MAL Clusters and Proteins Viigand, Katrin; Põšnograjeva, Kristina; Visnapuu, Triinu Genes, Vol. 9, Issue 7 https://doi.org/10.3390/genes9070354	journal	July 2018
Evolutionary instability of CUG-Leu in the genetic code of budding yeasts Krassowski, Tadeusz; Coughlan, Aisling Y.; Shen, Xing-Xing Nature Communications, Vol. 9, Issue 1 https://doi.org/10.1038/s41467-018-04374-7	journal	May 2018
Evolution of protein kinase substrate recognition at the active site Bradley, David; Beltrao, Pedro https://doi.org/10.1101/443945	posted_content	October 2018
Additional Layer of Regulation via Convergent Gene Orientation in Yeasts Gilet, Jules; Conte, Romain; Torchet, Claire Molecular Biology and Evolution, Vol. 37, Issue 2 https://doi.org/10.1093/molbev/msz221	journal	October 2019
Treehouse: a user-friendly application to obtain subtrees from large phylogenies Steenwyk, Jacob L.; Rokas, Antonis BMC Research Notes, Vol. 12, Issue 1 https://doi.org/10.1186/s13104-019-4577-5	journal	August 2019
Gene editing in clinical isolates of Candida parapsilosis using CRISPR/Cas9 Lombardi, Lisa; Turner, Siobhán A.; Zhao, Fang Scientific Reports, Vol. 7, Issue 1 https://doi.org/10.1038/s41598-017-08500-1	journal	August 2017
Genome sequence of the opportunistic human pathogen Magnusiomyces capitatus Brejová, Bronislava; Lichancová, Hana; Brázdovič, Filip Current Genetics, Vol. 65, Issue 2 https://doi.org/10.1007/s00294-018-0904-y	journal	November 2018
A Phylogenomic Supertree of Birds Kimball, Rebecca T.; Oliveros, Carl H.; Wang, Ning Diversity, Vol. 11, Issue 7 https://doi.org/10.3390/d11070109	journal	July 2019
Phylogenomics from low‐coverage whole‐genome sequencing Zhang, Feng; Ding, Yinhuan; Zhu, Chao‐Dong Methods in Ecology and Evolution, Vol. 10, Issue 4 https://doi.org/10.1111/2041-210x.13145	journal	January 2019
TPP riboswitch-dependent regulation of an ancient thiamin transporter in Candida Donovan, Paul D.; Holland, Linda M.; Lombardi, Lisa PLOS Genetics, Vol. 14, Issue 5 https://doi.org/10.1371/journal.pgen.1007429	journal	May 2018
Gene Selection and Evolutionary Modeling Affect Phylogenomic Inference of Neuropterida Based on Transcriptome Data Wang, Yuyu; Zhou, Xiaofan; Wang, Liming International Journal of Molecular Sciences, Vol. 20, Issue 5 https://doi.org/10.3390/ijms20051072	journal	March 2019
Quartet-Based Computations of Internode Certainty Provide Robust Measures of Phylogenetic Incongruence Zhou, Xiaofan; Lutteropp, Sarah; Czech, Lucas Systematic Biology, Vol. 69, Issue 2 https://doi.org/10.1093/sysbio/syz058	journal	August 2019
Misidentification of genome assemblies in public databases: The case of Naumovozyma dairenensis and proposal of a protocol to correct misidentifications Stavrou, Aimilia A.; Mixão, Verónica; Boekhout, Teun Yeast, Vol. 35, Issue 6 https://doi.org/10.1002/yea.3303	journal	February 2018
Evolutionary Conservation of the Components in the TOR Signaling Pathways Tatebe, Hisashi; Shiozaki, Kazuhiro Biomolecules, Vol. 7, Issue 4 https://doi.org/10.3390/biom7040077	journal	November 2017
Genomic features and evolution of the conditionally dispensable chromosome in the tangerine pathotype of Alternaria alternata Wang, Mingshuang; Fu, Huilan; Shen, Xing‐Xing Molecular Plant Pathology, Vol. 20, Issue 10 https://doi.org/10.1111/mpp.12848	journal	July 2019
Physiologically Relevant Alternative Carbon Sources Modulate Biofilm Formation, Cell Wall Architecture, and the Stress and Antifungal Resistance of Candida glabrata Chew, Shu Yih; Ho, Kok Lian; Cheah, Yoke Kqueen International Journal of Molecular Sciences, Vol. 20, Issue 13 https://doi.org/10.3390/ijms20133172	journal	June 2019
Functional and evolutionary characterization of a secondary metabolite gene cluster in budding yeasts Krause, David J.; Kominek, Jacek; Opulente, Dana A. Proceedings of the National Academy of Sciences, Vol. 115, Issue 43 https://doi.org/10.1073/pnas.1806268115	journal	October 2018
Comparative Transcriptomics Highlights New Features of the Iron Starvation Response in the Human Pathogen Candida glabrata Benchouaia, Médine; Ripoche, Hugues; Sissoko, Mariam Frontiers in Microbiology, Vol. 9 https://doi.org/10.3389/fmicb.2018.02689	journal	November 2018
A genomic survey of nitrogen assimilation pathways in budding yeasts (sub-phylum Saccharomycotina) Linder, Tomas Yeast, Vol. 36, Issue 5 https://doi.org/10.1002/yea.3364	journal	December 2018
Coverage-versus-Length plots, a simple quality control step for de novo yeast genome sequence assemblies Douglass, Alexander P.; O’Brien, Caoimhe E.; Offei, Benjamin G3: Genes\|Genomes\|Genetics https://doi.org/10.1101/421347	journal	September 2018
Aurora kinase Ipl1 facilitates bilobed distribution of clustered kinetochores to ensure error‐free chromosome segregation in Candida albicans Varshney, Neha; Sanyal, Kaustuv Molecular Microbiology, Vol. 112, Issue 2 https://doi.org/10.1111/mmi.14275	journal	May 2019
Evolution from covalent conjugation to non-covalent interaction in the ubiquitin-like ATG12 system Pang, Yu; Yamamoto, Hayashi; Sakamoto, Hirokazu Nature Structural & Molecular Biology, Vol. 26, Issue 4 https://doi.org/10.1038/s41594-019-0204-3	journal	March 2019
Population genomics shows no distinction between pathogenic Candida krusei and environmental Pichia kudriavzevii: One species, four names Douglass, Alexander P.; Offei, Benjamin; Braun-Galleani, Stephanie PLOS Pathogens, Vol. 14, Issue 7 https://doi.org/10.1371/journal.ppat.1007138	journal	July 2018
Evolution of drug resistance in an antifungal-naive chronic Candida lusitaniae infection Demers, Elora G.; Biermann, Amy R.; Masonjones, Sawyer Proceedings of the National Academy of Sciences, Vol. 115, Issue 47 https://doi.org/10.1073/pnas.1807698115	journal	November 2018
Patterns of Conservation and Diversification in the Fungal Polarization Network Diepeveen, Eveline T.; Gehrmann, Thies; Pourquié, Valérie Genome Biology and Evolution, Vol. 10, Issue 7 https://doi.org/10.1093/gbe/evy121	journal	June 2018
Sequenceserver: A Modern Graphical User Interface for Custom BLAST Databases Priyam, Anurag; Woodcroft, Ben J.; Rai, Vivek Molecular Biology and Evolution, Vol. 36, Issue 12 https://doi.org/10.1093/molbev/msz185	journal	August 2019
Phylogenetic Conflicts, Combinability, and Deep Phylogenomics in Plants Smith, Stephen A.; Walker-Hale, Nathanael; Walker, Joseph F. Systematic Biology, Vol. 69, Issue 3 https://doi.org/10.1093/sysbio/syz078	journal	November 2019
Aurora kinase Ipl1 facilitates bilobed distribution of clustered kinetochores to ensure error-free chromosome segregation in Candida albicans Varshney, Neha; Sanyal, Kaustuv Molecular Microbiology https://doi.org/10.1101/542605	journal	February 2019
Independent evolution of polymerization in the Actin ATPase clan regulates hexokinase activity Stoddard, Patrick R.; Lynch, Eric M.; Farrell, Daniel P. BioRxiv https://doi.org/10.1101/686915	posted_content	July 2019
Protein-coding changes preceded cis-regulatory gains in a newly evolved transcription circuit Britton, Candace S.; Sorrells, Trevor R.; Johnson, Alexander D. Science, Vol. 367, Issue 6473 https://doi.org/10.1126/science.aax5217	journal	January 2020
fagin: synteny-based phylostratigraphy and finer classification of young genes Arendsee, Zebulun; Li, Jing; Singh, Urminder BMC Bioinformatics, Vol. 20, Issue 1 https://doi.org/10.1186/s12859-019-3023-y	journal	August 2019
Extensive loss of cell-cycle and DNA repair genes in an ancient lineage of bipolar budding yeasts Steenwyk, Jacob L.; Opulente, Dana A.; Kominek, Jacek PLOS Biology, Vol. 17, Issue 5 https://doi.org/10.1371/journal.pbio.3000255	journal	May 2019
Genomic content of a novel yeast species Hanseniaspora gamundiae sp. nov. from fungal stromata (Cyttaria) associated with a unique fermented beverage in Andean Patagonia, Argentina Čadež, Neža; Bellora, Nicolas; Ulloa, Ricardo PLOS ONE, Vol. 14, Issue 1 https://doi.org/10.1371/journal.pone.0210792	journal	January 2019
Structure and evolution of the 4-helix bundle domain of Zuotin, a J-domain protein co-chaperone of Hsp70 Shrestha, Om Kumar; Sharma, Ruchika; Tomiczek, Bartlomiej PLOS ONE, Vol. 14, Issue 5 https://doi.org/10.1371/journal.pone.0217098	journal	May 2019
Coverage-Versus-Length Plots, a Simple Quality Control Step for de Novo Yeast Genome Sequence Assemblies Douglass, Alexander P.; O’Brien, Caoimhe E.; Offei, Benjamin G3 Genes\|Genomes\|Genetics, Vol. 9, Issue 3 https://doi.org/10.1534/g3.118.200745	journal	March 2019
A Phylogenomic Supertree of Birds Kimball, Rt; Oliveros, Ch; Wang, N. MDPI AG https://doi.org/10.17863/cam.41670	journalarticle	January 2019
TERribly Difficult: Searching for Telomerase RNAs in Saccharomycetes Waldi, Maria; Thiel, Bernhard C.; Ochsenreiter, Roman Genes https://doi.org/10.20944/preprints201805.0234.v1	journal	May 2018
A Trichosporonales genome tree based on 27 haploid and three evolutionarily conserved ‘natural’ hybrid genomes: Trichosporonales genome tree Takashima, Masako; Sriswasdi, Sira; Manabe, Ri-Ichiroh Yeast, Vol. 35, Issue 1 https://doi.org/10.1002/yea.3284	journal	December 2017
Evaluation of the chitin-binding dye Congo red as a selection agent for the isolation, classification, and enumeration of ascomycete yeasts Linder, Tomas Archives of Microbiology, Vol. 200, Issue 4 https://doi.org/10.1007/s00203-018-1498-y	journal	February 2018
Evaluating Fast Maximum Likelihood-Based Phylogenetic Programs Using Empirical Phylogenomic Data Sets Zhou, Xiaofan; Shen, Xing-Xing; Hittinger, Chris Todd Molecular Biology and Evolution, Vol. 35, Issue 2 https://doi.org/10.1093/molbev/msx302	journal	November 2017
BUSCO Applications from Quality Assessments to Gene Prediction and Phylogenomics Waterhouse, Robert M.; Seppey, Mathieu; Simão, Felipe A. Molecular Biology and Evolution, Vol. 35, Issue 3 https://doi.org/10.1093/molbev/msx319	journal	December 2017
Physicochemical Amino Acid Properties Better Describe Substitution Rates in Large Populations Weber, Claudia C.; Whelan, Simon Molecular Biology and Evolution, Vol. 36, Issue 4 https://doi.org/10.1093/molbev/msz003	journal	January 2019
Patterns of conservation and diversification in the fungal polarization network Diepeveen, Eveline T.; Pourquie, VAlerie; Gehrmann, Thies Genome Biology and Evolution https://doi.org/10.1101/154641	journal	June 2017
Eukaryotic Acquisition of a Bacterial Operon Kominek, Jacek; Doering, Drew T.; Opulente, Dana A. Cell https://doi.org/10.1101/399394	journal	August 2018
Genome Diversity and Evolution in the Budding Yeasts (Saccharomycotina) Dujon, Bernard A.; Louis, Edward J. Genetics, Vol. 206, Issue 2 https://doi.org/10.1534/genetics.116.199216	journal	June 2017
TERribly Difficult: Searching for Telomerase RNAs in Saccharomycetes Waldl, Maria; Thiel, Bernhard C.; Ochsenreiter, Roman Genes https://doi.org/10.1101/323675	journal	May 2018
YeasTSS: An Integrative Web Database of Yeast Transcription Start Sites McMillan, Jonathan; Lu, Zhaolian; Rodriguez, Judith S. Database https://doi.org/10.1101/511477	journal	January 2019
Additional layer of regulation via convergent gene orientation in yeasts Gilet, Jules; Conte, Romain; Torchet, Claire Molecular Biology and Evolution https://doi.org/10.1101/551689	journal	September 2019
Endogenous Stochastic Decoding of the CUG Codon by Competing Ser- and Leu-tRNAs in Ascoidea asiatica Mühlhausen, Stefanie; Schmitt, Hans Dieter; Pan, Kuan-Ting Current Biology, Vol. 28, Issue 13 https://doi.org/10.1016/j.cub.2018.04.085	journal	July 2018
Contentious relationships in phylogenomic studies can be driven by a handful of genes Shen, Xing-Xing; Hittinger, Chris Todd; Rokas, Antonis Nature Ecology & Evolution, Vol. 1, Issue 5 https://doi.org/10.1038/s41559-017-0126	journal	April 2017
Reconstructing Yeasts Phylogenies and Ancestors from Whole Genome Data Feng, Bing; Lin, Yu; Zhou, Lingxi Scientific Reports, Vol. 7, Issue 1 https://doi.org/10.1038/s41598-017-15484-5	journal	November 2017
Pervasive contingency and entrenchment in a billion years of Hsp90 evolution Starr, Tyler N.; Flynn, Julia M.; Mishra, Parul Proceedings of the National Academy of Sciences, Vol. 115, Issue 17 https://doi.org/10.1073/pnas.1718133115	journal	April 2018
Maximum Likelihood Estimation of Species Trees from Gene Trees in the Presence of Ancestral Population Structure Koch, Hillary; DeGiorgio, Michael Genome Biology and Evolution, Vol. 12, Issue 2 https://doi.org/10.1093/gbe/evaa022	journal	February 2020
Signal, Uncertainty, and Conflict in Phylogenomic Data for a Diverse Lineage of Microbial Eukaryotes (Diatoms, Bacillariophyta) Parks, Matthew B.; Wickett, Norman J.; Alverson, Andrew J. Molecular Biology and Evolution, Vol. 35, Issue 1 https://doi.org/10.1093/molbev/msx268	journal	October 2017
Repeated Cis-Regulatory Tuning of a Metabolic Bottleneck Gene during Evolution Kuang, Meihua Christina; Kominek, Jacek; Alexander, William G. Molecular Biology and Evolution, Vol. 35, Issue 8 https://doi.org/10.1093/molbev/msy102	journal	May 2018
A Machine Learning Method for Detecting Autocorrelation of Evolutionary Rates in Large Phylogenies Tao, Qiqing; Tamura, Koichiro; U. Battistuzzi, Fabia Molecular Biology and Evolution, Vol. 36, Issue 4 https://doi.org/10.1093/molbev/msz014	journal	January 2019
Discovery of 17 conserved structural RNAs in fungi Gao, William; Jones, Thomas A.; Rivas, Elena Nucleic Acids Research, Vol. 49, Issue 11 https://doi.org/10.1093/nar/gkab355	journal	June 2021
A new method for detecting autocorrelation of evolutionary rates in large phylogenies Tao, Qiqing; Tamura, Koichiro; Battistuzzi, FAbia Molecular Biology and Evolution https://doi.org/10.1101/346635	journal	October 2018
Identification and in silico analysis of the origin recognition complex in the human fungal pathogen Candida albicans Padmanabhan, Sreedevi; Sanyal, Kaustuv; Dubey, Dharani Dhar BioRxiv https://doi.org/10.1101/430892	journal	September 2018
Phylogenetic reconstruction based on synteny block and gene adjacencies Drillon, Guénola; Champeimont, Raphaël; Oteri, Francesco Molecular Biology and Evolution https://doi.org/10.1101/840942	journal	November 2019
Genome-scale phylogeny and contrasting modes of genome evolution in the fungal phylum Ascomycota Shen, Xing-Xing; Steenwyk, Jacob L.; LaBella, Abigail L. Science Advances, Vol. 6, Issue 45 https://doi.org/10.1126/sciadv.abd0079	journal	November 2020
Inferring duplication episodes from unrooted gene trees Paszek, Jarosław; Górecki, Paweł BMC Genomics, Vol. 19, Issue S5 https://doi.org/10.1186/s12864-018-4623-z	journal	May 2018
Flip/flop mating-type switching in the methylotrophic yeast Ogataea polymorpha is regulated by an Efg1-Rme1-Ste12 pathway Hanson, Sara J.; Byrne, Kevin P.; Wolfe, Kenneth H. PLOS Genetics, Vol. 13, Issue 11 https://doi.org/10.1371/journal.pgen.1007092	journal	November 2017
Noise and biases in genomic data may underlie radically different hypotheses for the position of Iguania within Squamata Mongiardino Koch, Nicolás; Gauthier, Jacques A. PLOS ONE, Vol. 13, Issue 8 https://doi.org/10.1371/journal.pone.0202729	journal	August 2018
An Evolutionary Perspective on Yeast Mating-Type Switching Hanson, Sara J.; Wolfe, Kenneth H. Genetics, Vol. 206, Issue 1 https://doi.org/10.1534/genetics.117.202036	journal	May 2017
Species distribution and susceptibility profiles of Candida species isolated from vulvovaginal candidiasis, emergence of C. lusitaniae Hashemi, Seyed Ebrahim; Shokohi, Tahereh; Abastabar, Mahdi Current Medical Mycology https://doi.org/10.18502/cmm.5.4.2062	journal	December 2019

Similar Records

A genome-informed higher rank classification of the biotechnologically important fungal subphylum Saccharomycotina

Journal Article · Thu May 25 00:00:00 EDT 2023 · Studies in Mycology · OSTI ID:1361388

Groenewald, M.; Hittinger, C. T.; Bensch, K.; +25 more

The cell morphological diversity of Saccharomycotina yeasts

Journal Article · Sat Dec 23 00:00:00 EST 2023 · FEMS Yeast Research · OSTI ID:1361388

Chavez, Christina M.; Groenewald, Marizeth; Hulfachor, Amanda B.; +4 more

Extensive loss of cell-cycle and DNA repair genes in an ancient lineage of bipolar budding yeasts

Journal Article · Tue May 21 00:00:00 EDT 2019 · PLoS Biology (Online) · OSTI ID:1361388

Steenwyk, Jacob L.; Opulente, Dana A.; Kominek, Jacek; +13 more

Related Subjects

60 APPLIED LIFE SCIENCES
59 BASIC BIOLOGICAL SCIENCES
phylogenomics
maximum likelihood
incongruence
genome completeness
nuclear markers

Title: Reconstructing the backbone of the Saccharomycotina yeast phylogeny using genome-scale data

Citation Formats

References (99)

Cited By (73)

Similar Records

Related Subjects