ArticleScientific reports2015
Differential gene retention as an evolutionary mechanism to generate biodiversity and adaptation in yeasts.
Article in Scientific reports, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 31 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
31 citing papers in PubMed, 66 citations in OpenAlex.
- A Cross-Domain Framework for the Dual Nature of Geotrichum and Magnusiomyces Across Plant, Food, and Clinical Systems.Current microbiology · 2026Review
- Genomic and transcriptomic insights into Trichomonascus vanleenenianus, a xylan-degrading yeast isolated from saproxylic insect larvae.BMC genomics · 2026Article
- Architecture and function of yeast phosphatidate phosphatase Pah1 domains/regions.Biochimica et biophysica acta. Molecular and cell biology of lipids · 2024Review
- Reduction of Ribosomal Expansion Segments in Yeast Species of the Magnusiomyces/Saprochaete Clade.Genome biology and evolution · 2024Article
- Genomic factors shape carbon and nitrogen metabolic niche breadth across Saccharomycotina yeasts.Science (New York, N.Y.) · 2024Article
- Characterization and phylogenetic analysis of the complete mitochondrial genome ofMitochondrial DNA. Part B, Resources · 2024Article
- Functional mapping of N-terminal residues in the yeast proteome uncovers novel determinants for mitochondrial protein import.PLoS genetics · 2023Article
- Uncovering the Biotechnological Importance ofFoods (Basel, Switzerland) · 2023Review
- Yca1 metacaspase: diverse functions determine how yeast live and let die.FEMS yeast research · 2023Article
- Gene Recruitments and Dismissals in the Argonaut Genome Provide Insights into Pelagic Lifestyle Adaptation and Shell-like Eggcase Reacquisition.Genome biology and evolution · 2022Article
- Whole-Genome Sequences of Two Kazachstania barnettii Strains Isolated from Anthropic Environments.Genome biology and evolution · 2022Article
- PhylomeDB V5: an expanding repository for genome-wide catalogues of annotated gene phylogenies.Nucleic acids research · 2022Article
- Molecular Genetic Analysis with Microsatellite-like Loci Reveals Specific Dairy-Associated and Environmental Populations of the YeastMicroorganisms · 2022Article
- CAZyme prediction in ascomycetous yeast genomes guides discovery of novel xylanolytic species with diverse capacities for hemicellulose hydrolysis.Biotechnology for biofuels · 2021Article
- Phenotypic and Genetic Characterization of the Cheese Ripening YeastFrontiers in microbiology · 2020Article
- Purification, Characterization and Thermodynamic Assessment of an Alkaline Protease byIranian journal of biotechnology · 2019Article
- Genome sequence of the opportunistic human pathogen Magnusiomyces capitatus.Current genetics · 2019Article
- A gene graveyard in the genome of the fungus Podospora comata.Molecular genetics and genomics : MGG · 2019Article
- Exon junction complex components Y14 and Mago still play a role in budding yeast.Scientific reports · 2019Article
- Geotrichum candidum gene expression and metabolite accumulation inside the cells reflect the strain oxidative stress sensitivity and ability to produce flavour compounds.FEMS yeast research · 2019Article
Corrections and comments
- Erratum issued
Authors and funding
19 authors at 7 institutions in 3 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The evolutionary history of the characters underlying the adaptation of microorganisms to food and biotechnological uses is poorly understood. We undertook comparative genomics to investigate evolutionary relationships of the dairy yeast Geotrichum candidum within Saccharomycotina. Surprisingly, a remarkable proportion of genes showed discordant phylogenies, clustering with the filamentous fungus subphylum (Pezizomycotina), rather than the yeast subphylum (Saccharomycotina), of the Ascomycota. These genes appear not to be the result of Horizontal Gene Transfer (HGT), but to have been specifically retained by G. candidum after the filamentous fungi-yeasts split concomitant with the yeasts' genome contraction. We refer to these genes as SRAGs (Specifically Retained Ancestral Genes), having been lost by all or nearly all other yeasts, and thus contributing to the phenotypic specificity of lineages. SRAG functions include lipases consistent with a role in cheese making and novel endoglucanases associated with degradation of plant material. Similar gene retention was observed in three other distantly related yeasts representative of this ecologically diverse subphylum. The phenomenon thus appears to be widespread in the Saccharomycotina and argues that, alongside neo-functionalization following gene duplication and HGT, specific gene retention must be recognized as an important mechanism for generation of biodiversity and adaptation in yeasts.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.