ArticleMolecular biology and evolution2013
The effect of gene overlapping on the rate of RNA virus evolution.
Article in Molecular biology and evolution, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 35 papers, 1 of them a synthesis that pooled it.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
35 citing papers in PubMed, 1 synthesis or guideline pooled it, 52 citations in OpenAlex.
- Pooled it
- Article
- Global identification of mammalian host and nested gene pairs reveal tissue-specific transcriptional interplay.Genome research · 2024Article
- Prolonging genetic circuit stability through adaptive evolution of overlapping genes.Nucleic acids research · 2023Article
- Plasticity, Paralogy, and Pseudogenization: Rhabdoviruses of Freshwater Mussels Elucidate Mechanisms of Viral Genome Diversification and the Evolution of the Finfish-Infecting Rhabdoviral Genera.Journal of virology · 2023Article
- A CRISPR-Cas Cure for HIV/AIDS.International journal of molecular sciences · 2023Review
- Overlapping genes in natural and engineered genomes.Nature reviews. Genetics · 2022Review
- Gene Overlapping as a Modulator ofMicroorganisms · 2022Article
- Genome Sequence Variations of Infectious Bronchitis Virus Serotypes From Commercial Chickens in Mexico.Frontiers in veterinary science · 2022Article
- Detection and genetic characterization of the novel torque teno virus group 6 in Taiwanese general population.Royal Society open science · 2021Article
- Article
- Engineering gene overlaps to sustain genetic constructs in vivo.PLoS computational biology · 2021Article
- Small but mighty: Functional landscape of the versatile geminivirus-encoded C4 protein.PLoS pathogens · 2021Review
- Molecular phylogenetics and evolutionary analysis of a highly recombinant begomovirus, Cotton leaf curl Multan virus, and associated satellites.Virus evolution · 2021Article
- Properties and abundance of overlapping genes in viruses.Virus evolution · 2020Article
- On the stability of sequences inserted into viral genomes.Virus evolution · 2019Review
- Asymmetric evolution in viral overlapping genes is a source of selective protein adaptation.Virology · 2019Article
- A Simple Method to Detect Candidate Overlapping Genes in Viruses Using Single Genome Sequences.Molecular biology and evolution · 2018Article
- Article
- Overlapping genes and the proteins they encode differ significantly in their sequence composition from non-overlapping genes.PloS one · 2018Article
Corrections and comments
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Authors and funding
3 authors at 3 institutions in 4 countries.
Funding
Abstract
Gene overlapping is widely employed by RNA viruses to generate genetic novelty while retaining a small genome size. However, gene overlapping also increases the deleterious effect of mutations as they affect more than one gene, thereby reducing the evolutionary rate of RNA viruses and hence their adaptive capacity. Although there is general agreement on the benefits of gene overlapping as a mechanism of genomic compression for rapidly evolving organisms, its effect on the pace of RNA virus evolution remains a source of debate. To address this issue, we collected sequence data from 117 instances of gene overlapping across 19 families, 30 genera, and 55 species of RNA viruses. On these data, we analyzed how genetic distances, selective pressures, and the distribution of RNA secondary structures and conserved protein functional domains vary between overlapping (OV) and nonoverlapping (NOV) regions. We show that gene overlapping generally results in a decrease in the rate of RNA virus evolution through a reduction in the frequency of synonymous mutations. However, this effect is less pronounced in genes with a terminal rather than an internal gene overlap, which might result from a greater proportion of protein functional conserved domains in NOV than in OV regions, in turn reducing the number of nonsynonymous mutations in the former. Overall, our analyses clarify the role of gene overlapping as a modulator of the evolutionary rates exhibited by RNA viruses and shed light on the factors that shape the genetic diversity of this important group of pathogens.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.