ArticleMolecular biology and evolution2014
Experimental evolution of pseudogenization and gene loss in a plant RNA virus.
Article in Molecular biology and evolution, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers.
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Who cites it
20 citing papers in PubMed, 44 citations in OpenAlex.
- Hidden evolutionary constraints dictate the retention of coronavirus accessory genes.Current biology : CB · 2024Article
- Increased Frequency of Indels in Hypervariable Regions of SARS-CoV-2 Proteins-A Possible Signature of Adaptive Selection.Frontiers in genetics · 2022Article
- P1 ofJournal of virology · 2021Article
- Poorly Conserved P15 Proteins of Cileviruses Retain Elements of Common Ancestry and Putative Functionality: A Theoretical Assessment on the Evolution of Cilevirus Genomes.Frontiers in plant science · 2021Article
- Modeling multipartite virus evolution: the genome formula facilitates rapid adaptation to heterogeneous environmentsVirus evolution · 2020Article
- On the stability of sequences inserted into viral genomes.Virus evolution · 2019Review
- Article
- Engineered Functional Redundancy Relaxes Selective Constraints upon Endogenous Genes in Viral RNA Genomes.Genome biology and evolution · 2018Article
- Emergency Services of Viral RNAs: Repair and Remodeling.Microbiology and molecular biology reviews : MMBR · 2018Review
- Maize chlorotic mottle virus exhibits low divergence between differentiated regional sub-populations.Scientific reports · 2018Article
- 2b or Not 2b: Experimental Evolution of Functional Exogenous Sequences in a Plant RNA Virus.Genome biology and evolution · 2017Article
- High virulence does not necessarily impede viral adaptation to a new host: a case study using a plant RNA virus.BMC evolutionary biology · 2017Article
- Different Evolutionary Paths to Complexity for Small and Large Populations of Digital Organisms.PLoS computational biology · 2016Article
- Predicting the Stability of Homologous Gene Duplications in a Plant RNA Virus.Genome biology and evolution · 2016Article
- Evolutionary transitions during RNA virus experimental evolution.Philosophical transactions of the Royal Society of London. Series B, Biological sciences · 2016Review
- Evolution of Genome Size in Asexual Digital Organisms.Scientific reports · 2016Article
- Multiple Barriers to the Evolution of Alternative Gene Orders in a Positive-Strand RNA Virus.Genetics · 2016Article
- Development of a Mild Viral Expression System for Gain-Of-Function Study of Phytoplasma Effector In Planta.PloS one · 2015Article
- Shrinkage of genome size in a plant RNA virus upon transfer of an essential viral gene into the host genome.Genome biology and evolution · 2014Article
- Within-host spatiotemporal dynamics of plant virus infection at the cellular level.PLoS genetics · 2014Article
Corrections and comments
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Authors and funding
4 authors at 2 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Viruses have evolved highly streamlined genomes and a variety of mechanisms to compress them, suggesting that genome size is under strong selection. Horizontal gene transfer has, on the other hand, played an important role in virus evolution. However, evolution cannot integrate initially nonfunctional sequences into the viral genome if they are rapidly purged by selection. Here we report on the experimental evolution of pseudogenization in virus genomes using a plant RNA virus expressing a heterologous gene. When long 9-week passages were performed, the added gene was lost in all lineages, whereas viruses with large genomic deletions were fixed in only two out of ten 3-week lineages and none in 1-week lineages. Illumina next-generation sequencing revealed considerable convergent evolution in the 9- and 3-week lineages with genomic deletions. Genome size was correlated to within-host competitive fitness, although there was no correlation with virus accumulation or virulence. Within-host competitive fitness of the 3-week virus lineages without genomic deletions was higher than for the 1-week lineages. Our results show that the strength of selection for a reduced genome size and the rate of pseudogenization depend on demographic conditions. Moreover, for the 3-week passage condition, we observed increases in within-host fitness, whereas selection was not strong enough to quickly remove the nonfunctional heterologous gene. These results suggest a demographically determined "sweet spot" might exist, where heterologous insertions are not immediately lost while evolution can act to integrate them into the viral genome.
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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.