Universität zu Köln

Willemsen, Anouk ORCID: 0000-0002-8511-3244, Zwart, Mark P., Higueras, Pablo, Sardanyes, Josep and Elena, Santiago F. ORCID: 0000-0001-8249-5593 (2016). Predicting the Stability of Homologous Gene Duplications in a Plant RNA Virus. Genome Biol. Evol., 8 (9). S. 3065 - 3083. OXFORD: OXFORD UNIV PRESS. ISSN 1759-6653

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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.

Item Type:	Journal Article
Creators:	Creators Email ORCID ORCID Put Code Willemsen, Anouk UNSPECIFIED orcid.org/0000-0002-8511-3244 UNSPECIFIED Zwart, Mark P. UNSPECIFIED UNSPECIFIED UNSPECIFIED Higueras, Pablo UNSPECIFIED UNSPECIFIED UNSPECIFIED Sardanyes, Josep UNSPECIFIED UNSPECIFIED UNSPECIFIED Elena, Santiago F. UNSPECIFIED orcid.org/0000-0001-8249-5593 UNSPECIFIED
URN:	urn:nbn:de:hbz:38-265568
DOI:	10.1093/gbe/evw219
Journal or Publication Title:	Genome Biol. Evol.
Volume:	8
Number:	9
Page Range:	S. 3065 - 3083
Date:	2016
Publisher:	OXFORD UNIV PRESS
Place of Publication:	OXFORD
ISSN:	1759-6653
Language:	English
Faculty:	Unspecified
Divisions:	Unspecified
Subjects:	no entry
Uncontrolled Keywords:	Keywords Language TOBACCO-ETCH-VIRUS; NUCLEOTIDE-SEQUENCE; EVOLUTION; GENOME; ACCUMULATION; MUTATION; IDENTIFICATION; RECOMBINATION; RETROVIRUSES; RHABDOVIRUS Multiple languages Evolutionary Biology; Genetics & Heredity Multiple languages
Refereed:	Yes
URI:	http://kups.ub.uni-koeln.de/id/eprint/26556