Abstract
Multipartite viruses contain more than one distinctive genome component, and the origin of multipartite viruses has been suggested to evolve from a non-segmented wild-type virus. To explore whether recombination also plays a role in the evolution of the genomes of multipartite viruses, we developed a systematic approach that employs motif-finding tools to detect conserved motifs from divergent genomic regions and applies statistical approaches to select high-confidence motifs. The information that this approach provides helps us understand the evolution of viruses. In this study, we compared our motif-based strategy with current alignment-based recombination-detecting methods and applied our methods to the analysis of multipartite single-stranded plant DNA viruses, including bipartite begomoviruses, Banana bunchy top virus (BBTV) (consisting of 6 genome components) and Faba bean necrotic yellows virus (FBNYV) (consisting of 8 genome components). Our analysis revealed that recombination occurred between genome components in some begomoviruses, BBTV and FBNYV. Our data also show that several unusual recombination events have contributed to the evolution of BBTV genome components. We believe that similar approaches can be applied to resolve the evolutionary history of other viruses.
Highlights
Multipartite viruses contain more than one genome component, and for a multipartite virus to initiate a successful infection, all of the genome components must infect the same host cell and simultaneously replicate within the cell
Multiple Em for Motif Elicitation (MEME) detected identical motif locations in each genome and was unable to detect any recombination event. This indicated that when analyzing genome sequences that are similar and well aligned, alignment-based methods are better than motif-based methods in detecting recombination events
To further evaluate the motifs that were detected in the begomovirus genomes, we introduced another value, the mean pairwise distance Dh, which described the compactness of a set of motifs more precisely
Summary
Multipartite viruses contain more than one genome component (or segment), and for a multipartite virus to initiate a successful infection, all of the genome components must infect the same host cell and simultaneously replicate within the cell. Because the genome components of a multipartite virus can utilize the same protein(s) for replication and encapsidation, conserved sequences can be observed within these genome components. Aside from the small conserved region, the nucleotide sequences of the remaining genome components are usually quite different from each other. It has been suggested that multipartite viruses evolved from a nonsegmented wild-type virus, different factors favoring the generation of segmented genomes have been proposed [1,2]. Recombination events have been found between genome components in a variety of multipartite viruses [3,4,5,6,7,8,9]. Viruses evolved to have a fast replication cycle, and some studies have indicated that recombination events occur frequently [10,11,12,13,14]. If recombination accumulated during the long evolution process in the small genome of a virus, the sequence of the recombined genome could be shuffled, and we would not be able to align it well
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