ArticleGenome research2008
Revisiting the Saccharomyces cerevisiae predicted ORFeome.
Article in Genome research, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
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Who cites it
15 citing papers in PubMed.
- Discovering the hidden function in fungal genomes.Nature communications · 2024Review
- Origins, evolution, and physiological implications of de novo genes in yeast.Yeast (Chichester, England) · 2022Review
- Article
- Synteny-based analyses indicate that sequence divergence is not the main source of orphan genes.eLife · 2020Article
- A Comprehensive Analysis of Transcript-Supported De Novo Genes in Saccharomyces sensu stricto Yeasts.Molecular biology and evolution · 2017Article
- iSeq: A New Double-Barcode Method for Detecting Dynamic Genetic Interactions in Yeast.G3 (Bethesda, Md.) · 2017Article
- Article
- Re-annotation of protein-coding genes in the genome of saccharomyces cerevisiae based on support vector machines.PloS one · 2013Article
- Proto-genes and de novo gene birth.Nature · 2012Article
- Searching in microbial genomes for encoded small proteins.Microbial biotechnology · 2011Article
- Undetected antisense tRNAs in mitochondrial genomes?Biology direct · 2010Article
- Novel genes exhibit distinct patterns of function acquisition and network integration.Genome biology · 2010Article
- Gene Ontology and the annotation of pathogen genomes: the case of Candida albicans.Trends in microbiology · 2009Review
- Novel low abundance and transient RNAs in yeast revealed by tiling microarrays and ultra high-throughput sequencing are not conserved across closely related yeast species.PLoS genetics · 2008Article
- Differentiating protein-coding and noncoding RNA: challenges and ambiguities.PLoS computational biology · 2008Review
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Authors and funding
16 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Accurately defining the coding potential of an organism, i.e., all protein-encoding open reading frames (ORFs) or "ORFeome," is a prerequisite to fully understand its biology. ORFeome annotation involves iterative computational predictions from genome sequences combined with experimental verifications. Here we reexamine a set of Saccharomyces cerevisiae "orphan" ORFs recently removed from the original ORFeome annotation due to lack of conservation across evolutionarily related yeast species. We show that many orphan ORFs produce detectable transcripts and/or translated products in various functional genomics and proteomics experiments. By combining a naïve Bayes model that predicts the likelihood of an ORF to encode a functional product with experimental verification of strand-specific transcripts, we argue that orphan ORFs should still remain candidates for functional ORFs. In support of this model, interstrain intraspecies genome sequence variation is lower across orphan ORFs than in intergenic regions, indicating that orphan ORFs endure functional constraints and resist deleterious mutations. We conclude that ORFs should be evaluated based on multiple levels of evidence and not be removed from ORFeome annotation solely based on low sequence conservation in other species. Rather, such ORFs might be important for micro-evolutionary divergence between species.
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