The ever increasing diversity of begomoviruses infecting non‐cultivated hosts: new species from Sida spp. and Leonurus sibiricus, plus two New World alphasatellites

Abstract

Begomoviruses (whitefly-transmitted, single-stranded DNA plant viruses) are among the most damaging pathogens causing epidemics in economically important crops worldwide. Besides cultivated plants, many weed and wild hosts act as virus reservoirs where recombination may occur, resulting in new species. The aim of this study was to further characterise the diversity of begomoviruses infecting two major weed genera, Sida and Leonurus. Total DNA was extracted from samples collected in the states of Rio Grande do Sul, Paraná and Mato Grosso do Sul during the years 2009-2011. Viral genomes were enriched by rolling circle amplification (RCA), linearised into unit length genomes using various restriction enzymes, cloned and sequenced. A total of 78 clones were obtained: 37 clones from Sida spp. plants and 41 clones from Leonurus sibiricus plants. Sequence analysis indicated the presence of six bipartite begomovirus species and two alphasatellites. In Sida spp. plants we found Sida micrantha mosaic virus (SiMMV), Euphorbia yellow mosaic virus (EuYMV), and three isolates that represent new species, for which the following names are proposed: Sida chlorotic mottle virus (SiCMoV), Sida bright yellow mosaic virus (SiBYMV) and Sida golden yellow spot virus (SiGYSV), an Old World-like begomovirus. L. sibiricus plants had a lower diversity of begomoviruses compared to Sida spp., with only Tomato yellow spot virus (ToYSV) and EuYMV (for the first time detected infecting plants of the genus Leonurus) detected. Two satellite DNA molecules were found: Euphorbia yellow mosaic alphasatellite, for the first time detected infecting plants of the genus Sida, and a new alphasatellite associated with ToYSV in L. sibiricus. These results constitute further evidence of the high species diversity of begomoviruses in non-cultivated hosts, particularly Sida spp.

Reconstruction and Characterization of Full-Length Begomovirus and Alphasatellite Genomes Infecting Pepper through Metagenomics

“…We used these RCA-RFLP comparisons to assess the potential problem of generating chimeric begomovirus genomes that could derive from the assembly of sequences belonging to different species in a mixed infection sample. There are several reports about the occurrence of mixed infection in the field, caused by the transmission of the viruses by the same vector [12,55,63,71]. However, in this work, we only detected single infections in pepper.…”

“…This was the first record of an alphasatellite infecting pepper and the first alphasatellite reported in Argentina. ToYSA 2 is phylogenetically related to alphasatellites associated with new world begomoviruses in non-cultivated plants, like euphorbia yellow mosaic alphasatellite (EuYMA) identified in Euphorbia heterophylla and Sida spp., cleome leaf crumple alphasatellite (ClLCrA) in Cleome affinis, and tomato yellow spot alphasatellite (ToYSA) in Leonurus sibiricus (synonym L. japonicus) [68,71,72]. We found ToYSA 2 associated with ToYSV in L. japonicus and pepper, showing that it could be transferred from weed to crop or vice versa.…”

Alphasatellitidae: a new family with two subfamilies for the classification of geminivirus- and nanovirus-associated alphasatellites

“…In the New World where monopartite begomoviruses are very rare, betasatellites have not been identified and alphasatellites have only ever been reported to occur in association with bipartite Begomovirus infections [10,32,37].…”

Ecology and diversity of plant viruses, and epidemiology of plant virus‐induced diseases

“…Ferro et al . () used rolling circle amplification, a powerful technique for detection and amplification of circular DNA molecules, to characterise begomoviruses infecting wild hosts from two plant genera, Sida and Leonorus , in Brazil. After sequencing 78 DNA clones, the authors identified isolates not only from four known begomoviral species, but also belonging to three new begomoviral species, as well as a new alphasatellite (Ferro et al ., ).…”

“…() used rolling circle amplification, a powerful technique for detection and amplification of circular DNA molecules, to characterise begomoviruses infecting wild hosts from two plant genera, Sida and Leonorus , in Brazil. After sequencing 78 DNA clones, the authors identified isolates not only from four known begomoviral species, but also belonging to three new begomoviral species, as well as a new alphasatellite (Ferro et al ., ). Cataloguing the viral diversity in wild species is highly significant and interesting, as wild species may constitute a diversity reservoir for viruses which may jump from wild to cultivated hosts resulting in emerging diseases in crops (Woolhouse et al ., ), and these may have potentially devastating consequences.…”