ArticleGenome research2007
The evolution of genome compression and genomic novelty in RNA viruses.
Article in Genome research, 2007. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 106 papers, 1 of them a synthesis that pooled it.
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Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
106 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Pooled it
- Widespread genomic islands are hotspots of genome variations and mosaicism in giant viruses.Nature communications · 2026Article
- SARS-CoV-2 nucleocapsid protein variants have differential RNA chaperone activity.The FEBS journal · 2026Article
- Lessons from oncology: Can cancer lead the way in resistance management?Evolution, medicine, and public health · 2026Article
- Article
- Article
- A chimeric viral platform for directed evolution in mammalian cells.Nature communications · 2025Article
- Review
- Evaluation of metatranscriptomic sequencing protocols to obtain full-length RNA virus genomes from mammalian tissues.PloS one · 2025Article
- Hidden evolutionary constraints dictate the retention of coronavirus accessory genes.Current biology : CB · 2024Article
- The application of single-molecule optical tweezers to study disease-related structural dynamics in RNA.Biochemical Society transactions · 2024Review
- Insights into the genetic variability and evolutionary dynamics of tomato spotted wilt orthotospovirus in China.BMC genomics · 2024Article
- Adaptation of turnip mosaic virus toVirus evolution · 2024Article
- Bacteriophage Φ21's receptor-binding protein evolves new functions through destabilizing mutations that generate non-genetic phenotypic heterogeneity.Virus evolution · 2024Article
- Innovation in viruses: fitness valley crossing, neutral landscapes, or just duplications?Virus evolution · 2024Article
- Overlaps Between CDS Regions of Protein-Coding Genes in the Human Genome: A Case Study on the NR1D1-THRA Gene Pair.Journal of molecular evolution · 2023Article
- Raman Fingerprints of SARS-CoV-2 Omicron Subvariants: Molecular Roots of Virological Characteristics and Evolutionary Directions.ACS infectious diseases · 2023Article
- The panzootic potential of SARS-CoV-2.Bioscience · 2023Article
- A conserved Y-shaped RNA structure in the 3'UTR of chikungunya virus genome as a host-specialized element that modulates viral replication and evolution.PLoS pathogens · 2023Article
- Review
46 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
3 authors.
Funding
Abstract
The genomes of RNA viruses are characterized by their extremely small size and extremely high mutation rates (typically 10 kb and 10(-4)/base/replication cycle, respectively), traits that are thought to be causally linked. One aspect of their small size is the genome compression caused by the use of overlapping genes (where some nucleotides code for two genes). Using a comparative analysis of all known RNA viral species, we show that viruses with larger genomes tend to have less gene overlap. We provide a numerical model to show how a high mutation rate could lead to gene overlap, and we discuss the factors that might explain the observed relationship between gene overlap and genome size. We also propose a model for the evolution of gene overlap based on the co-opting of previously unused ORFs, which gives rise to two types of overlap: (1) the creation of novel genes inside older genes, predominantly via +1 frameshifts, and (2) the incremental increase in overlap between originally contiguous genes, with no frameshift preference. Both types of overlap are viewed as the creation of genomic novelty under pressure for genome compression. Simulations based on our model generate the empirical size distributions of overlaps and explain the observed frameshift preferences. We suggest that RNA viruses are a good model system for the investigation of general evolutionary relationship between genome attributes such as mutational robustness, mutation rate, and size.
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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.