Predicting the Stability of Homologous Gene Duplications in a Plant RNA Virus

Abstract : One of the striking features of many eukaryotes is the apparent amount of redundancy in coding and non-coding elements of their genomes. Despite the possible evolutionary advantages, there are fewer examples of redundant sequences in viral genomes, particularly those with RNA genomes. The factors constraining the maintenance of redundant sequences in present-day RNA virus genomes are not well known. Here, we use Tobacco etch virus, a plant RNA virus, to investigate the stability of genetically redundant sequences by generating viruses with potentially beneficial gene duplications. Subsequently, we tested the viability of these viruses and performed experimental evolution. We found that all gene duplication events resulted in a loss of viability or in a significant reduction in viral fitness. Moreover, upon analyzing the genomes of the evolved viruses, we always observed the deletion of the duplicated gene copy and maintenance of the ancestral copy. Interestingly, there were clear differences in the deletion dynamics of the duplicated gene associated with the passage duration and the size and position of the duplicated copy. Based on the experimental data, we developed a mathematical model to characterize the stability of genetically redundant sequences, and showed that fitness effects are not enough to predict genomic stability. A context-dependent recombination rate is also required, with the context being the duplicated gene and its position. Our results therefore demonstrate experimentally the deleterious nature of gene duplications in RNA viruses. Beside previously described constraints on genome size, we identified additional factors that reduce the likelihood of the maintenance of duplicated genes.
Liste complète des métadonnées

Littérature citée [52 références]  Voir  Masquer  Télécharger

https://hal.umontpellier.fr/hal-02004240
Contributeur : Philip Agnew <>
Soumis le : vendredi 1 février 2019 - 16:12:37
Dernière modification le : mercredi 29 mai 2019 - 10:56:23
Document(s) archivé(s) le : jeudi 2 mai 2019 - 22:12:23

Fichier

evw219.pdf
Fichiers éditeurs autorisés sur une archive ouverte

Identifiants

Collections

Citation

Anouk Willemsen, Mark Zwart, Pablo Higueras, Josep Sardanyés, Santiago Elena. Predicting the Stability of Homologous Gene Duplications in a Plant RNA Virus. Genome Biology and Evolution, Society for Molecular Biology and Evolution, 2016, 8 (9), pp.3065-3082. ⟨10.1093/gbe/evw219⟩. ⟨hal-02004240⟩

Partager

Métriques

Consultations de la notice

68

Téléchargements de fichiers

136