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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

https://doi.org/10.1101/329730
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What this work says

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

inferredcites →https://doi.org/10.1002/mbo3.773openalex-snapshot
A collection of barcoded natural isolates of Saccharomyces paradoxus to study microbial evolutionary ecology
inferredcites →https://doi.org/10.1007/978-1-4939-3079-1_7openalex-snapshot
Translation Analysis at the Genome Scale by Ribosome Profiling
inferredcites →https://doi.org/10.1016/j.cell.2016.02.066openalex-snapshot
Ribosome Footprint Profiling of Translation throughout the Genome
inferredcites →https://doi.org/10.1016/j.sbi.2015.02.017openalex-snapshot
Found in translation: functions and evolution of a recently discovered alternative proteome
inferredcites →https://doi.org/10.1016/j.tig.2015.02.007openalex-snapshot
Genes from scratch – the evolutionary fate of de novo genes
inferredcites →https://doi.org/10.1016/j.tig.2017.12.009openalex-snapshot
The Definition of Open Reading Frame Revisited
inferredcites →https://doi.org/10.1038/nature01644openalex-snapshot
Sequencing and comparison of yeast species to identify genes and regulatory elements
inferredcites →https://doi.org/10.1038/nature07743openalex-snapshot
Population genomics of domestic and wild yeasts
inferredcites →https://doi.org/10.1038/nature11184openalex-snapshot
Proto-genes and de novo gene birth
inferredcites →https://doi.org/10.1038/nature12121openalex-snapshot
Extensive transcriptional heterogeneity revealed by isoform profiling
inferredcites →https://doi.org/10.1038/ng.363openalex-snapshot
Human mutation rate associated with DNA replication timing
inferredcites →https://doi.org/10.1038/nmeth.3688openalex-snapshot
Detecting actively translated open reading frames in ribosome profiling data
inferredcites →https://doi.org/10.1038/nmicrobiol.2015.3openalex-snapshot
Speciation driven by hybridization and chromosomal plasticity in a wild yeast
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/nrg.2016.78openalex-snapshot
Open questions in the study of de novo genes: what, how and why
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/s41559-017-0127openalex-snapshot
Random sequences are an abundant source of bioactive RNAs or peptides
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/s41586-018-0030-5openalex-snapshot
Genome evolution across 1,011 Saccharomyces cerevisiae isolates
inferredcites →https://doi.org/10.1038/s41588-018-0243-4openalex-snapshot
Genetic dissection of interspecific differences in yeast thermotolerance
inferredcites →https://doi.org/10.1039/c2mb25265aopenalex-snapshot
qPCA: a scalable assay to measure the perturbation of protein–protein interactions in living cells
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.0601091103openalex-snapshot
A high-resolution map of transcription in the yeast genome
inferredcites →https://doi.org/10.1073/pnas.0803466105openalex-snapshot
A genome-wide view of the spectrum of spontaneous mutations in yeast
inferredcites →https://doi.org/10.1073/pnas.0901808106openalex-snapshot
The universal distribution of evolutionary rates of genes and distinct characteristics of eukaryotic genes of different apparent ages
inferredcites →https://doi.org/10.1093/bioinformatics/bti541openalex-snapshot
IUPred: web server for the prediction of intrinsically unstructured regions of proteins based on estimated energy content
inferredcites →https://doi.org/10.1093/bioinformatics/btn013openalex-snapshot
Using native and syntenically mapped cDNA alignments to improve de novo gene finding
inferredcites →https://doi.org/10.1093/bioinformatics/btp347openalex-snapshot
ABACAS: algorithm-based automatic contiguation of assembled sequences
inferredcites →https://doi.org/10.1093/bioinformatics/btq033openalex-snapshot
BEDTools: a flexible suite of utilities for comparing genomic features
inferredcites →https://doi.org/10.1093/bioinformatics/bts174openalex-snapshot
IDBA-UD: a de novo assembler for single-cell and metagenomic sequencing data with highly uneven depth
inferredcites →https://doi.org/10.1093/bioinformatics/btw791openalex-snapshot
Historian: accurate reconstruction of ancestral sequences and evolutionary rates
inferredcites →https://doi.org/10.1093/gbe/evr054openalex-snapshot
Mutation Rates across Budding Yeast Chromosome VI Are Correlated with Replication Timing
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/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/msm088openalex-snapshot
PAML 4: Phylogenetic Analysis by Maximum Likelihood
inferredcites →https://doi.org/10.1093/molbev/msr280openalex-snapshot
The Mutational Profile of the Yeast Genome Is Shaped by Replication
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/msx139openalex-snapshot
Mitochondrial Recombination and Introgression during Speciation by Hybridization
inferredcites →https://doi.org/10.1093/molbev/msx149openalex-snapshot
SMS: Smart Model Selection in PhyML
inferredcites →https://doi.org/10.1093/molbev/msx153openalex-snapshot
The Rapid Evolution of an Ohnolog Contributes to the Ecological Specialization of Incipient Yeast Species
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/10.1093/nar/gkh340openalex-snapshot
MUSCLE: multiple sequence alignment with high accuracy and high throughput
inferredcites →https://doi.org/10.1093/nar/gkt878openalex-snapshot
The dynamics of genome replication using deep sequencing
inferredcites →https://doi.org/10.1093/nar/gkv1189openalex-snapshot
Reference sequence (RefSeq) database at NCBI: current status, taxonomic expansion, and functional annotation
inferredcites →https://doi.org/10.1093/nar/gkx1098openalex-snapshot
Ensembl 2018
inferredcites →https://doi.org/10.1093/nar/gky179openalex-snapshot
De novo annotation and characterization of the translatome with ribosome profiling data
inferredcites →https://doi.org/10.1093/sysbio/syq010openalex-snapshot
New Algorithms and Methods to Estimate Maximum-Likelihood Phylogenies: Assessing the Performance of PhyML 3.0
inferredcites →https://doi.org/10.1098/rsbl.2006.0534openalex-snapshot
Mate choice assays and mating propensity differences in natural yeast populations
inferredcites →https://doi.org/10.1101/289330openalex-snapshot
Differences between the de novo proteome and its non-functional precursor can result from neutral constraints on its birth process, not necessarily from natural selection alone
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/10.1111/j.1567-1364.2002.tb00048.xopenalex-snapshot
Saccharomyces cerevisiaeandSaccharomyces paradoxuscoexist in a natural woodland site in North America and display different levels of reproductive isolation from European conspecifics
inferredcites →https://doi.org/10.1111/mec.12864openalex-snapshot
Chromosomal variation segregates within incipient species and correlates with reproductive isolation
inferredcites →https://doi.org/10.1111/nyas.12460openalex-snapshot
Effects of new mutations on fitness: insights from models and data
inferredcites →https://doi.org/10.1126/science.1153878openalex-snapshot
An in Vivo Map of the Yeast Protein Interactome
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/10.1126/science.860134openalex-snapshot
Evolution and Tinkering
inferredcites →https://doi.org/10.1186/1471-2105-12-116openalex-snapshot
Ultra-fast sequence clustering from similarity networks with SiLiX
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/gb-2009-10-3-r25openalex-snapshot
Ultrafast and memory-efficient alignment of short DNA sequences to the human genome
inferredcites →https://doi.org/10.1186/s12864-016-3278-xopenalex-snapshot
Plastid: nucleotide-resolution analysis of next-generation sequencing and genomics data
inferredcites →https://doi.org/10.1186/s13059-014-0550-8openalex-snapshot
Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2
inferredcites →https://doi.org/10.1371/journal.pbio.0020029openalex-snapshot
Functional Bias and Spatial Organization of Genes in Mutational Hot and Cold Regions in the Human Genome
inferredcites →https://doi.org/10.1371/journal.pcbi.1000734openalex-snapshot
A Human-Specific De Novo Protein-Coding Gene Associated with Human Brain Functions
inferredcites →https://doi.org/10.1371/journal.pgen.1002942openalex-snapshot
Hominoid-Specific De Novo Protein-Coding Genes Originating from Long Non-Coding RNAs
inferredcites →https://doi.org/10.1371/journal.pgen.1005751openalex-snapshot
Dissecting the Genetic Basis of a Complex cis-Regulatory Adaptation
inferredcites →https://doi.org/10.1371/journal.pone.0092621openalex-snapshot
SynChro: A Fast and Easy Tool to Reconstruct and Visualize Synteny Blocks along Eukaryotic Chromosomes
inferredcites →https://doi.org/10.14806/ej.17.1.200openalex-snapshot
Cutadapt removes adapter sequences from high-throughput sequencing reads
inferredcites →https://doi.org/10.1534/g3.111.000273openalex-snapshot
The Awesome Power of Yeast Evolutionary Genetics: New Genome Sequences and Strain Resources for theSaccharomyces sensu strictoGenus
inferredcites →https://doi.org/10.1534/genetics.105.050336openalex-snapshot
Recently Evolved Genes Identified From Drosophila yakuba and D. erecta Accessory Gland Expressed Sequence Tags
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.03523openalex-snapshot
Long non-coding RNAs as a source of new peptides
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

What points at this work

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

inferred← citeshttps://doi.org/10.1101/575837openalex-snapshot
Frequent birth of de novo genes in the compact yeast genome
inferred← citeshttps://doi.org/10.1371/journal.pgen.1008160openalex-snapshot
De novo gene birth
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