ArticleMolecular biology and evolution2017
A Comprehensive Analysis of Transcript-Supported De Novo Genes in Saccharomyces sensu stricto Yeasts.
Article in Molecular biology and evolution, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.
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Who cites it
18 citing papers in PubMed, 32 citations in OpenAlex.
- Orphan and de novo Genes in Fungi and Animals: Identification, Origins and Functions.Genome biology and evolution · 2025Review
- Comprehensive profiling of ribo-seq detected small sequences in yeast reveals robust conservation patterns and their potential mechanisms of origin.BMC genomics · 2025Article
- A putative scenario of how de novo protein-coding genes originate in the Saccharomyces cerevisiae lineage.BMC genomics · 2024Article
- Large-scale long terminal repeat insertions produced a significant set of novel transcripts in cotton.Science China. Life sciences · 2023Article
- Origins, evolution, and physiological implications of de novo genes in yeast.Yeast (Chichester, England) · 2022Review
- IntraspecificNAR genomics and bioinformatics · 2022Article
- Pervasive translation ineLife · 2022Article
- Frequent lineage-specific substitution rate changes support an episodic model for protein evolution.G3 (Bethesda, Md.) · 2021Article
- Intergenic ORFs as elementary structural modules of de novo gene birth and protein evolution.Genome research · 2021Article
- A putative de novo evolved gene required for spermatid chromatin condensation in Drosophila melanogaster.PLoS genetics · 2021Article
- Uncovering de novo gene birth in yeast using deep transcriptomics.Nature communications · 2021Article
- Landscape of the Dark Transcriptome Revealed Through Re-mining Massive RNA-Seq Data.Frontiers in genetics · 2021Article
- Overlapping protein-coding genes in human genome and their coincidental expression in tissues.Scientific reports · 2019Article
- Differences Between the Raw Material and the Products ofGenetics · 2019Article
- Turnover of ribosome-associated transcripts from de novo ORFs produces gene-like characteristics available for de novo gene emergence in wild yeast populations.Genome research · 2019Article
- De novo gene birth.PLoS genetics · 2019Article
- From De Novo to "De Nono": The Majority of Novel Protein-Coding Genes Identified with Phylostratigraphy Are Old Genes or Recent Duplicates.Genome biology and evolution · 2018Article
- Tracing themBio · 2018Article
Corrections and comments
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Authors and funding
3 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Novel genes arising from random DNA sequences (de novo genes) have been suggested to be widespread in the genomes of different organisms. However, our knowledge about the origin and evolution of de novo genes is still limited. To systematically understand the general features of de novo genes, we established a robust pipeline to analyze >20,000 transcript-supported coding sequences (CDSs) from the budding yeast Saccharomyces cerevisiae. Our analysis pipeline combined phylogeny, synteny, and sequence alignment information to identify possible orthologs across 20 Saccharomycetaceae yeasts and discovered 4,340 S. cerevisiae-specific de novo genes and 8,871 S. sensu stricto-specific de novo genes. We further combine information on CDS positions and transcript structures to show that >65% of de novo genes arose from transcript isoforms of ancient genes, especially in the upstream and internal regions of ancient genes. Fourteen identified de novo genes with high transcript levels were chosen to verify their protein expressions. Ten of them, including eight transcript isoform-associated CDSs, showed translation signals and five proteins exhibited specific cytosolic localizations. Our results suggest that de novo genes frequently arise in the S. sensu stricto complex and have the potential to be quickly integrated into ancient cellular network.
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