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Frequent birth of de novo genes in the compact yeast genome

https://doi.org/10.1101/575837
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What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

inferredcites →https://doi.org/10.1016/j.celrep.2016.05.043openalex-snapshot
Protein Abundance Control by Non-coding Antisense Transcription
inferredcites →https://doi.org/10.1016/j.jmb.2009.11.053openalex-snapshot
Identifying and Quantifying Orphan Protein Sequences in Fungi
inferredcites →https://doi.org/10.1016/j.sbi.2014.05.006openalex-snapshot
Orphans and new gene origination, a structural and evolutionary perspective
inferredcites →https://doi.org/10.1016/j.tig.2014.08.004openalex-snapshot
Volatile evolution of long noncoding RNA repertoires: mechanisms and biological implications
inferredcites →https://doi.org/10.1016/j.tplants.2014.07.003openalex-snapshot
Coming of age: orphan genes in plants
inferredcites →https://doi.org/10.1038/cr.2010.31openalex-snapshot
A de novo originated gene depresses budding yeast mating pathway and is repressed by the protein encoded by its antisense strand
inferredcites →https://doi.org/10.1038/nature02579openalex-snapshot
Genome evolution in yeasts
inferredcites →https://doi.org/10.1038/nature07728openalex-snapshot
Bidirectional promoters generate pervasive transcription in yeast
inferredcites →https://doi.org/10.1038/nature11184openalex-snapshot
Proto-genes and de novo gene birth
inferredcites →https://doi.org/10.1038/nbt.1883openalex-snapshot
Full-length transcriptome assembly from RNA-Seq data without a reference genome
inferredcites →https://doi.org/10.1038/nchembio.1120openalex-snapshot
Peptidomic discovery of short open reading frame–encoded peptides in human cells
inferredcites →https://doi.org/10.1038/nmeth.1923openalex-snapshot
Fast gapped-read alignment with Bowtie 2
inferredcites →https://doi.org/10.1038/nprot.2012.016openalex-snapshot
Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks
inferredcites →https://doi.org/10.1038/nprot.2012.086openalex-snapshot
The ribosome profiling strategy for monitoring translation in vivo by deep sequencing of ribosome-protected mRNA fragments
inferredcites →https://doi.org/10.1038/nrg3053openalex-snapshot
The evolutionary origin of orphan genes
inferredcites →https://doi.org/10.1038/nrg3521openalex-snapshot
New genes as drivers of phenotypic evolution
inferredcites →https://doi.org/10.1038/s41467-018-04026-wopenalex-snapshot
Random sequences rapidly evolve into de novo promoters
inferredcites →https://doi.org/10.1038/s41559-017-0146openalex-snapshot
Young genes are highly disordered as predicted by the preadaptation hypothesis of de novo gene birth
inferredcites →https://doi.org/10.1038/s41559-018-0506-6openalex-snapshot
Translation of neutrally evolving peptides provides a basis for de novo gene evolution
inferredcites →https://doi.org/10.1038/s41559-018-0639-7openalex-snapshot
Incipient de novo genes can evolve from frozen accidents that escaped rapid transcript turnover
inferredcites →https://doi.org/10.1038/s41586-018-0030-5openalex-snapshot
Genome evolution across 1,011 Saccharomyces cerevisiae isolates
inferredcites →https://doi.org/10.1073/pnas.0509809103openalex-snapshot
Novel genes derived from noncoding DNA in Drosophila melanogaster are frequently X-linked and exhibit testis-biased expression
inferredcites →https://doi.org/10.1073/pnas.1514670112openalex-snapshot
QQS orphan gene regulates carbon and nitrogen partitioning across species via NF-YC interactions
inferredcites →https://doi.org/10.1073/pnas.1817138116openalex-snapshot
Molecular mechanism and history of non-sense to sense evolution of antifreeze glycoprotein gene in northern gadids
inferredcites →https://doi.org/10.1073/pnas.89.20.9489openalex-snapshot
Origins of genes: "big bang" or continuous creation?
inferredcites →https://doi.org/10.1091/mbc.11.12.4241openalex-snapshot
Genomic Expression Programs in the Response of Yeast Cells to Environmental Changes
inferredcites →https://doi.org/10.1093/bioinformatics/bti310openalex-snapshot
GMAP: a genomic mapping and alignment program for mRNA and EST sequences
inferredcites →https://doi.org/10.1093/bioinformatics/btu170openalex-snapshot
Trimmomatic: a flexible trimmer for Illumina sequence data
inferredcites →https://doi.org/10.1093/gbe/evr099openalex-snapshot
Putatively Noncoding Transcripts Show Extensive Association with Ribosomes
inferredcites →https://doi.org/10.1093/gbe/evw074openalex-snapshot
De Novo Genes Arise at a Slow but Steady Rate along the Primate Lineage and Have Been Subject to Incomplete Lineage Sorting
inferredcites →https://doi.org/10.1093/gbe/evw164openalex-snapshot
On the Origin of De Novo Genes inArabidopsis thalianaPopulations
inferredcites →https://doi.org/10.1093/gbe/evx136openalex-snapshot
New Genes and Functional Innovation in Mammals
inferredcites →https://doi.org/10.1093/gbe/evy231openalex-snapshot
From de novo to ‘de nono’: The majority of novel protein coding genes identified with phylostratigraphy are old genes or recent duplicates
inferredcites →https://doi.org/10.1093/molbev/msi045openalex-snapshot
Inverse Relationship Between Evolutionary Rate and Age of Mammalian Genes
inferredcites →https://doi.org/10.1093/molbev/msn281openalex-snapshot
Origin of Primate Orphan Genes: A Comparative Genomics Approach
inferredcites →https://doi.org/10.1093/molbev/msx057openalex-snapshot
The goddard and saturn genes are essential for Drosophila male fertility and may have arisen de novo
inferredcites →https://doi.org/10.1093/molbev/msx210openalex-snapshot
A Comprehensive Analysis of Transcript-Supported De Novo Genes in Saccharomyces sensu stricto Yeasts
inferredcites →https://doi.org/10.1093/molbev/msx311openalex-snapshot
De Novo Gene Evolution of Antifreeze Glycoproteins in Codfishes Revealed by Whole Genome Sequence Data
inferredcites →https://doi.org/10.1093/molbev/msx315openalex-snapshot
A Molecular Portrait of De Novo Genes in Yeasts
inferredcites →https://doi.org/10.1098/rstb.2014.0332openalex-snapshot
New genes from non-coding sequence: the role of de novo protein-coding genes in eukaryotic evolutionary innovation
inferredcites →https://doi.org/10.1101/329730openalex-snapshot
The high turnover of ribosome-associated transcripts from de novo ORFs produces gene-like characteristics available for de novo gene emergence in wild yeast populations
inferredcites →https://doi.org/10.1101/510214openalex-snapshot
Studying the dawn of de novo gene emergence in mice reveals fast integration of new genes into functional networks
inferredcites →https://doi.org/10.1101/gr.076588.108openalex-snapshot
On the origin of new genes in Drosophila
inferredcites →https://doi.org/10.1101/gr.095026.109openalex-snapshot
Recent de novo origin of human protein-coding genes
inferredcites →https://doi.org/10.1101/gr.164996.113openalex-snapshot
Ribosome profiling reveals post-transcriptional buffering of divergent gene expression in yeast
inferredcites →https://doi.org/10.1101/gr.190546.115openalex-snapshot
The frequent evolutionary birth and death of functional promoters in mouse and human
inferredcites →https://doi.org/10.1101/gr.196469.115openalex-snapshot
TransRate: reference-free quality assessment of de novo transcriptome assemblies
inferredcites →https://doi.org/10.1101/gr.239822.118openalex-snapshot
Turnover of ribosome-associated transcripts from de novo ORFs produces gene-like characteristics available for de novo gene emergence in wild yeast populations
inferredcites →https://doi.org/10.1101/gr.3567505openalex-snapshot
Estimating the tempo and mode of gene family evolution from comparative genomic data
inferredcites →https://doi.org/10.1126/science.1168978openalex-snapshot
Genome-Wide Analysis in Vivo of Translation with Nucleotide Resolution Using Ribosome Profiling
inferredcites →https://doi.org/10.1126/science.1248286openalex-snapshot
Origin and Spread of de Novo Genes in Drosophila melanogaster Populations
inferredcites →https://doi.org/10.1128/mbio.01024-18openalex-snapshot
Tracing the De Novo Origin of Protein-Coding Genes in Yeast
inferredcites →https://doi.org/10.1186/1471-2105-7-433openalex-snapshot
M-GCAT: interactively and efficiently constructing large-scale multiple genome comparison frameworks in closely related species
inferredcites →https://doi.org/10.1186/1471-2164-14-117openalex-snapshot
Phylogenetic patterns of emergence of new genes support a model of frequent de novo evolution
inferredcites →https://doi.org/10.1186/1471-2164-6-150openalex-snapshot
Proposed methods for testing and selecting the ERCC external RNA controls
inferredcites →https://doi.org/10.1371/journal.pbio.1000414openalex-snapshot
The Role of Nucleosome Positioning in the Evolution of Gene Regulation
inferredcites →https://doi.org/10.1371/journal.pgen.1002379openalex-snapshot
De Novo Origin of Human Protein-Coding Genes
inferredcites →https://doi.org/10.1371/journal.pgen.1005199openalex-snapshot
Beyond Glycolysis: GAPDHs Are Multi-functional Enzymes Involved in Regulation of ROS, Autophagy, and Plant Immune Responses
inferredcites →https://doi.org/10.1371/journal.pgen.1005721openalex-snapshot
Origins of De Novo Genes in Human and Chimpanzee
inferredcites →https://doi.org/10.1534/genetics.106.069245openalex-snapshot
Evidence for de Novo Evolution of Testis-Expressed Genes in the Drosophila yakuba / Drosophila erecta Clade
inferredcites →https://doi.org/10.1534/genetics.107.084491openalex-snapshot
De Novo Origination of a New Protein-Coding Gene in Saccharomyces cerevisiae
inferredcites →https://doi.org/10.7554/elife.01311openalex-snapshot
The life cycle of Drosophila orphan genes
inferredcites →https://doi.org/10.7554/elife.03523openalex-snapshot
Long non-coding RNAs as a source of new peptides
inferredcites →https://doi.org/10.7554/elife.03671openalex-snapshot
Quantitative analysis of mammalian GIRK2 channel regulation by G proteins, the signaling lipid PIP2 and Na+ in a reconstituted system
inferredcites →https://doi.org/10.7554/elife.06633openalex-snapshot
Ventromedial hypothalamic neurons control a defensive emotion state
inferredcites →https://doi.org/10.7554/elife.08890openalex-snapshot
Many lncRNAs, 5’UTRs, and pseudogenes are translated and some are likely to express functional proteins
inferredcites →https://doi.org/10.7554/elife.09977openalex-snapshot
Fast turnover of genome transcription across evolutionary time exposes entire non-coding DNA to de novo gene emergence

What points at this work

Incoming claims: where this work appears in other papers’ reference lists and arguments.

inferred← citeshttps://doi.org/10.1007/s00438-023-02090-6openalex-snapshot
Four classic “de novo” genes all have plausible homologs and likely evolved from retro-duplicated or pseudogenic sequences
inferred← citeshttps://doi.org/10.1093/molbev/msaa046openalex-snapshot
Readthrough Errors Purge Deleterious Cryptic Sequences, Facilitating the Birth of Coding Sequences
inferred← citeshttps://doi.org/10.1101/2023.05.28.542624openalex-snapshot
Four classic “de novo” genes all have plausible homologs and likely evolved from retro-duplicated or pseudogenic sequences
inferred← citeshttps://doi.org/10.1186/s13059-019-1884-zopenalex-snapshot
ReorientExpress: reference-free orientation of nanopore cDNA reads with deep learning
inferred← citeshttps://doi.org/10.1186/s13104-019-4286-0openalex-snapshot
Transcriptomics data of 11 species of yeast identically grown in rich media and oxidative stress conditions
inferred← citeshttps://doi.org/10.21203/rs.3.rs-2996044/v1openalex-snapshot
Four classic “de novo” genes all have plausible homologs and likely evolved from retro-duplicated or pseudogenic sequences
inferred← citeshttps://doi.org/10.21203/rs.3.rs-2996044/v2openalex-snapshot
Four classic “de novo” genes all have plausible homologs and likely evolved from retro-duplicated or pseudogenic sequences
inferred← citeshttps://doi.org/10.3389/fgene.2021.722981openalex-snapshot
Landscape of the Dark Transcriptome Revealed Through Re-mining Massive RNA-Seq Data
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