Evolution of genome size and complexity in the Rhabdoviridae

Walker, Peter J., Firth, Cadhla, Widen, Steven G., Blasdell, Kim R., Guzman, Hilda, Wood, Thomas G., Paradkar, Prasad N., Holmes, Edward C., Tesh, Robert B., and Vasilakis, Nikos (2015) Evolution of genome size and complexity in the Rhabdoviridae. PLoS Pathogens, 11 (2). e1004664.

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Abstract

RNA viruses exhibit substantial structural, ecological and genomic diversity. However, genome size in RNA viruses is likely limited by a high mutation rate, resulting in the evolution of various mechanisms to increase complexity while minimising genome expansion. Here we conduct a large-scale analysis of the genome sequences of 99 animal rhabdoviruses, including 45 genomes which we determined de novo, to identify patterns of genome expansion and the evolution of genome complexity. All but seven of the rhabdoviruses clustered into 17 well-supported monophyletic groups, of which eight corresponded to established genera, seven were assigned as new genera, and two were taxonomically ambiguous. We show that the acquisition and loss of new genes appears to have been a central theme of rhabdovirus evolution, and has been associated with the appearance of alternative, overlapping and consecutive ORFs within the major structural protein genes, and the insertion and loss of additional ORFs in each gene junction in a clade-specific manner. Changes in the lengths of gene junctions accounted for as much as 48.5% of the variation in genome size from the smallest to the largest genome, and the frequency with which new ORFs were observed increased in the 3’ to 5’ direction along the genome. We also identify several new families of accessory genes encoded in these regions, and show that non-canonical expression strategies involving TURBS-like termination-reinitiation, ribosomal frame-shifts and leaky ribosomal scanning appear to be common. We conclude that rhabdoviruses have an unusual capacity for genomic plasticity that may be linked to their discontinuous transcription strategy from the negative-sense single-stranded RNA genome, and propose a model that accounts for the regular occurrence of genome expansion and contraction throughout the evolution of the Rhabdoviridae

Item ID: 59904
Item Type: Article (Research - C1)
ISSN: 1553-7374
Copyright Information: © 2015 Walker et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
Funders: Institute for Human Infections and Immunity, National Institutes of Health (NIH)
Projects and Grants: NIH HHSN272201000040I/HHSN27200004/D04
Date Deposited: 03 Sep 2019 01:18
FoR Codes: 06 BIOLOGICAL SCIENCES > 0604 Genetics > 060409 Molecular Evolution @ 70%
06 BIOLOGICAL SCIENCES > 0605 Microbiology > 060506 Virology @ 30%
SEO Codes: 97 EXPANDING KNOWLEDGE > 970106 Expanding Knowledge in the Biological Sciences @ 100%
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