ArticleGenome biology and evolution2016
De Novo Genes Arise at a Slow but Steady Rate along the Primate Lineage and Have Been Subject to Incomplete Lineage Sorting.
Article in Genome biology and evolution, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 34 papers.
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Who cites it
34 citing papers in PubMed.
- Orphan and de novo Genes in Fungi and Animals: Identification, Origins and Functions.Genome biology and evolution · 2025Review
- De Novo Genes: Current Status and Future Goals.Genome biology and evolution · 2025Article
- Oncogenic roles of young human de novo genes and their potential as neoantigens in cancer immunotherapy.Cell genomics · 2025Article
- Orphan genes are not a distinct biological entity.BioEssays : news and reviews in molecular, cellular and developmental biology · 2025Review
- A putative scenario of how de novo protein-coding genes originate in the Saccharomyces cerevisiae lineage.BMC genomics · 2024Article
- Diverse Origins of Near-Identical Antifreeze Proteins in Unrelated Fish Lineages Provide Insights Into Evolutionary Mechanisms of New Gene Birth and Protein Sequence Convergence.Molecular biology and evolution · 2024Article
- High-throughput Selection of Human de novo-emerged sORFs with High Folding Potential.Genome biology and evolution · 2024Article
- Selection of a de novo gene that can promote survival of Escherichia coli by modulating protein homeostasis pathways.Nature ecology & evolution · 2023Article
- Gene birth in a model of non-genic adaptation.BMC biology · 2023Article
- Evolution and implications of de novo genes in humans.Nature ecology & evolution · 2023Review
- Hundreds of Out-of-Frame Remodeled Gene Families in the Escherichia coli Pangenome.Molecular biology and evolution · 2022Article
- Pervasive translation of small open reading frames in plant long non-coding RNAs.Frontiers in plant science · 2022Review
- An ancestral genomic sequence that serves as a nucleation site for de novo gene birth.PloS one · 2022Article
- During evolution from the earliest tetrapoda, newly-recruited genes are increasingly paralogues of existing genes and distribute non-randomly among the chromosomes.BMC genomics · 2021Article
- A putative de novo evolved gene required for spermatid chromatin condensation in Drosophila melanogaster.PLoS genetics · 2021Article
- Secondary Structure of HumanFrontiers in oncology · 2021Article
- Stochastic Gain and Loss of Novel Transcribed Open Reading Frames in the Human Lineage.Genome biology and evolution · 2020Article
- Many, but not all, lineage-specific genes can be explained by homology detection failure.PLoS biology · 2020Article
- Only a Single Taxonomically Restricted Gene Family in the Drosophila melanogaster Subgroup Can Be Identified with High Confidence.Genome biology and evolution · 2020Article
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2 authors.
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Abstract
De novo protein-coding gene origination is increasingly recognized as an important evolutionary mechanism. However, there remains a large amount of uncertainty regarding the frequency of these events and the mechanisms and speed of gene establishment. Here, we describe a rigorous search for cases of de novo gene origination in the great apes. We analyzed annotated proteomes as well as full genomic DNA and transcriptional and translational evidence. It is notable that results vary between database updates due to the fluctuating annotation of these genes. Nonetheless we identified 35 de novo genes: 16 human-specific; 5 human and chimpanzee specific; and 14 that originated prior to the divergence of human, chimpanzee, and gorilla and are found in all three genomes. The taxonomically restricted distribution of these genes cannot be explained by loss in other lineages. Each gene is supported by an open reading frame-creating mutation that occurred within the primate lineage, and which is not polymorphic in any species. Similarly to previous studies we find that the de novo genes identified are short and frequently located near pre-existing genes. Also, they may be associated with Alu elements and prior transcription and RNA-splicing at the locus. Additionally, we report the first case of apparent independent lineage sorting of a de novo gene. The gene is present in human and gorilla, whereas chimpanzee has the ancestral noncoding sequence. This indicates a long period of polymorphism prior to fixation and thus supports a model where de novo genes may, at least initially, have a neutral effect on fitness.
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