biostudies-literatureUnknown8(8)Wang HIMultipartite 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 begoPloS onee71565https://www.ebi.ac.uk/biostudies/studies/S-EPMC3735576biostudies-literatureApplication of motif-based tools on evolutionary analysis of multipartite single-stranded DNA viruses.PMC3735576Tang CChang CHYeh HHFu HCLin PHWang HIfalseApplication of motif-based tools on evolutionary analysis of multipartite single-stranded DNA viruses.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 bego2013-01-01T00:00:00Z20132026-05-30T09:11:46.544Z2025-07-28T03:04:15.791ZS-EPMC37355762393651710.1371/journal.pone.0071565