ArticlePLoS genetics2008
A catalog of neutral and deleterious polymorphism in yeast.
Article in PLoS genetics, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 140 papers.
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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.
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Who cites it
140 citing papers in PubMed, 262 citations in OpenAlex.
- A comprehensive in silico investigation into the deleterious nonsynonymous single nucleotide polymorphisms of the human transcription factor EB (TFEB) gene and their predicted association with cancer.Journal, genetic engineering & biotechnology · 2026Article
- Estimating the distribution of fitness effects of loss of heterozygosity (LOH) events using an engineered library of Saccharomyces cerevisiae.PLoS genetics · 2026Article
- Computational Prediction of Deleterious SNPs in the GALNS Gene Implicated in Morquio A Syndrome (MPS IVA).ACS omega · 2026Article
- From one genome to thousands, and beyond.FEMS yeast research · 2026Review
- Pathogenic KRAS variants disrupt structure and dynamics: Insights from integrated computational analyses.PloS one · 2026Article
- Functional and structural analysis of missense variants in the humanJournal of public health in Africa · 2025Article
- Initiating-clone analysis in patients with acute myeloid leukemia secondary to essential thrombocythemia.Scientific reports · 2024Article
- From beer to breadboards: yeast as a force for biological innovation.Genome biology · 2024Review
- A comprehensive in silico investigation into the pathogenic SNPs in the RTEL1 gene and their biological consequences.PloS one · 2024Article
- Application of whole exome sequencing in the diagnosis of muscular disorders: a study of Taiwanese pediatric patients.Frontiers in genetics · 2024Article
- Gene-by-environment interactions influence the fitness cost of gene copy-number variation in yeast.G3 (Bethesda, Md.) · 2023Article
- Genome-wide probing of eukaryotic nascent RNA structure elucidates cotranscriptional folding and its antimutagenic effect.Nature communications · 2023Article
- Identification genetic variations in some heat shock protein genes of Tali goat breed and study their structural and functional effects on relevant proteins.Veterinary medicine and science · 2023Article
- Gene-by-environment interactions influence the fitness cost of gene copy-number variation in yeast.bioRxiv : the preprint server for biology · 2023Article
- In-silico assessment of high-risk non-synonymous SNPs in ADAMTS3 gene associated with Hennekam syndrome and their impact on protein stability and function.BMC bioinformatics · 2023Article
- Article
- UGDR: a generic pipeline to detect recombined regions in polyploid and complex hybrid yeast genomes.BMC bioinformatics · 2022Article
- Diagnosis of a Single-Nucleotide Variant in Whole-Exome Sequencing Data for Patients With Inherited Diseases: Machine Learning Study Using Artificial Intelligence Variant Prioritization.JMIR bioinformatics and biotechnology · 2022Article
- Gene loss and compensatory evolution promotes the emergence of morphological novelties in budding yeast.Nature ecology & evolution · 2022Article
- Idiosyncratic epistasis leads to global fitness-correlated trends.Science (New York, N.Y.) · 2022Article
80 more citing papers are in PubMed but not listed here.
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PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
7 authors at 2 institutions in 1 country.
Funding
Abstract
The abundance and identity of functional variation segregating in natural populations is paramount to dissecting the molecular basis of quantitative traits as well as human genetic diseases. Genome sequencing of multiple organisms of the same species provides an efficient means of cataloging rearrangements, insertion, or deletion polymorphisms (InDels) and single-nucleotide polymorphisms (SNPs). While inbreeding depression and heterosis imply that a substantial amount of polymorphism is deleterious, distinguishing deleterious from neutral polymorphism remains a significant challenge. To identify deleterious and neutral DNA sequence variation within Saccharomyces cerevisiae, we sequenced the genome of a vineyard and oak tree strain and compared them to a reference genome. Among these three strains, 6% of the genome is variable, mostly attributable to variation in genome content that results from large InDels. Out of the 88,000 polymorphisms identified, 93% are SNPs and a small but significant fraction can be attributed to recent interspecific introgression and ectopic gene conversion. In comparison to the reference genome, there is substantial evidence for functional variation in gene content and structure that results from large InDels, frame-shifts, and polymorphic start and stop codons. Comparison of polymorphism to divergence reveals scant evidence for positive selection but an abundance of evidence for deleterious SNPs. We estimate that 12% of coding and 7% of noncoding SNPs are deleterious. Based on divergence among 11 yeast species, we identified 1,666 nonsynonymous SNPs that disrupt conserved amino acids and 1,863 noncoding SNPs that disrupt conserved noncoding motifs. The deleterious coding SNPs include those known to affect quantitative traits, and a subset of the deleterious noncoding SNPs occurs in the promoters of genes that show allele-specific expression, implying that some cis-regulatory SNPs are deleterious. Our results show that the genome sequences of both closely and distantly related species provide a means of identifying deleterious polymorphisms that disrupt functionally conserved coding and noncoding sequences.
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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.