ArticleG3 (Bethesda, Md.)2016
Reconstructing the Backbone of the Saccharomycotina Yeast Phylogeny Using Genome-Scale Data.
Article in G3 (Bethesda, Md.), 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 115 papers.
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Who cites it
115 citing papers in PubMed.
- Inhibitors of spore germination act against diverse human fungal pathogens.bioRxiv : the preprint server for biology · 2026Article
- Mitochondrial retrograde control of transcription evolves with respiratory stress, metabolic adaptation, and virulence in budding yeasts.Molecular biology and evolution · 2026Article
- Uncovering the hidden yeast diversity in fermented coffee: Insights from a shotgun metagenomic approach.PloS one · 2026Article
- MyESL: A Software for Evolutionary Sparse Learning in Molecular Phylogenetics and Genomics.Molecular biology and evolution · 2025Article
- Accurate, scalable, and fully automated inference of species trees from raw genome assemblies using ROADIES.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Species evolution: cryptic species and phenotypic noise with a particular focus on fungal systematics.Frontiers in cellular and infection microbiology · 2025Review
- Chemical and Electrophysiological Characterisation of Headspace Volatiles from Yeasts Attractive to Drosophila suzukii.Journal of chemical ecology · 2024Article
- The genus Cortinarius should not (yet) be split.IMA fungus · 2024Article
- Discovering Fragile Clades and Causal Sequences in Phylogenomics by Evolutionary Sparse Learning.Molecular biology and evolution · 2024Article
- The promise and pitfalls of synteny in phylogenomics.PLoS biology · 2024Article
- Macroevolutionary dynamics of gene family gain and loss along multicellular eukaryotic lineages.Nature communications · 2024Article
- Intrinsically disordered regions of the Msn2 transcription factor encode multiple functions using interwoven sequence grammars.Nucleic acids research · 2024Article
- The metabolic domestication syndrome of budding yeast.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
- Phylogenomic analysis and molecular identification of true fruit flies.Frontiers in genetics · 2024Article
- Incongruence in the phylogenomics era.Nature reviews. Genetics · 2023Review
- Article
- Next-generation fungal identification using target enrichment and Nanopore sequencing.BMC genomics · 2023Article
- A genome-informed higher rank classification of the biotechnologically important fungal subphylumStudies in mycology · 2023Article
- A global phylogenomic analysis of the shiitake genusProceedings of the National Academy of Sciences of the United States of America · 2023Article
- Macroevolutionary diversity of traits and genomes in the model yeast genus Saccharomyces.Nature communications · 2023Article
55 more citing papers are in PubMed but not listed here.
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Authors and funding
6 authors.
Funding
Abstract
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.
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