A new bipartite begomovirus naturally infecting Pyrenacantha sp. in Mozambique.

A begomovirus was isolated from a Pyrenacantha sp. plant with yellow mosaic symptoms collected in a maize production field in Mozambique. The complete DNA-A and DNA-B components have a genomic organization typical of Old World, bipartite begomoviruses. Based on the current ICTV species demarcation criteria for the genus Begomovirus, the virus isolate, named Pyrenacantha yellow mosaic virus (PyYMV), is a member of a new species, for which the name "Begomovirus pyrenacanthae" is proposed. Alignment of their common regions (CR) indicated a 35-nt insertion in the DNA-A CR. The nt sequence identity between the CRs is only 83% but increases to 96% when the 35-nt insertion is removed from the alignment. This is the first report of a begomovirus naturally infecting Pyrenacantha spp.

Evolutionary dynamics of bipartite begomoviruses revealed by complete genome analysis.

Several key evolutionary events marked the evolution of geminiviruses, culminating with the emergence of divided (bipartite) genomes represented by viruses classified in the genus Begomovirus. This genus represents the most abundant group of multipartite viruses, contributing significantly to the observed abundance of multipartite species in the virosphere. Although aspects related to virus-host interactions and evolutionary dynamics have been extensively studied, the bipartite nature of these viruses has been little explored in evolutionary studies. Here, we performed a parallel evolutionary analysis of the DNA-A and DNA-B segments of New World begomoviruses. A total of 239 full-length DNA-B sequences obtained in this study, combined with 292 DNA-A and 76 DNA-B sequences retrieved from GenBank, were analysed. The results indicate that the DNA-A and DNA-B respond differentially to evolutionary processes, with the DNA-B being more permissive to variation and more prone to recombination than the DNA-A. Although a clear geographic segregation was observed for both segments, differences in the genetic structure between DNA-A and DNA-B were also observed, with cognate segments belonging to distinct genetic clusters. DNA-B coding regions evolve under the same selection pressures than DNA-A coding regions. Together, our results indicate an interplay between reassortment and recombination acting at different levels across distinct subpopulations and segments.