Cnidoscolus mild mosaic virus: a new bipartite begomovirus isolated from Cnidoscolus urens in Brazil.

A novel bipartite begomovirus infecting Cnidoscolus urens (Euphorbiaceae) from Pernambuco State, Brazil, has been characterized. The complete DNA-A (2657 nt) and DNA-B (2622 nt) components of the viral isolates show the typical genome organization of New World bipartite begomoviruses. DNA-A of the isolates had the highest percentage of nucleotide sequence identity (88.6-88.9%) to cnidoscolus mosaic leaf deformation virus. Based on the current classification criteria for the genus Begomovirus, the virus infecting C. urens should be considered a new member of the genus, and the name "cnidoscolus mild mosaic virus" is proposed for the virus, and the name "Begomovirus caboniensis" is proposed for its species.

High molecular diversity and divergent subpopulations of the begomovirus cnidoscolus mosaic leaf deformation virus associated with Cnidoscolus urens.

Begomoviruses have circular, single-stranded DNA genomes encapsidated into twinned quasi-icosahedral particles and are transmitted by whiteflies of the Bemisia tabaci sibling group. Begomoviruses infect cultivated and non-cultivated plants, causing great losses in economically important crops worldwide. To better understand the genetic diversity of begomoviruses infecting the non-cultivated host Cnidoscolus urens, leaf samples exhibiting virus-like symptoms were collected in different localities in the state of Alagoas, Brazil, during 2015 and 2016. Forty-two complete DNA-A sequences were cloned and sequenced by the Sanger method. Based on nucleotide sequence comparisons, the 42 new isolates were identified as the bipartite begomovirus cnidoscolus mosaic leaf deformation virus (CnMLDV). The CnMLDV isolates were clustered in two phylogenetic groups (clusters I and II) corresponding to their sampling areas, and the high value of Wright's F fixation index observed for the DNA-A sequences suggests population structuring. At least seven independent intraspecies recombination events were predicted among CnMLDV isolates, with recombination breakpoints located in the common region (CR) and in the CP and Rep genes. Also, a high per site nucleotide diversity (π) was observed for CnMLDV isolates, with CP being significantly more variable than Rep. Despite the high genetic variability, strong negative or purifying selection was identified as the main selective force acting upon CP and Rep.

Cnidoscolus mosaic leaf deformation virus: a novel begomovirus infecting euphorbiaceous plants in Brazil.

Begomoviruses have been detected infecting the weed Cnidoscolus urens (family Euphorbiaceae) since 2004, but the viral species to which these viruses belonged was not known. Here, we report for the first time the complete genome sequence of a bipartite begomovirus obtained from C. urens collected in the state of Alagoas, Brazil. This isolate met the criteria to be classified as a member of a new begomovirus species, and the tentative name cnidoscolus mosaic leaf deformation virus (CnMLDV) is proposed. Pairwise sequence comparisons and phylogenetic analysis showed that the DNA-A genomic component of CnMLDV is most closely related to that of passionfruit severe leaf distortion virus, with 86.3 % nucleotide sequence identity.

Complete nucleotide sequence of a new begomovirus infecting a malvaceous weed in Brazil.

Begomoviruses are single-strand DNA plant viruses that infect economically important crops worldwide, exhibiting high genetic variability and species diversity. Based on the current taxonomic criteria established for the genus Begomovirus, a new member of this genus infecting a malvaceous weed is reported here. The name triumfetta yellow mosaic virus is proposed. At least one recombination event was detected in this new begomovirus, with putative parents being begomoviruses from tomato and Centrosema.

Synonymous site variation due to recombination explains higher genetic variability in begomovirus populations infecting non-cultivated hosts.

Begomoviruses are ssDNA plant viruses that cause serious epidemics in economically important crops worldwide. Non-cultivated plants also harbour many begomoviruses, and it is believed that these hosts may act as reservoirs and as mixing vessels where recombination may occur. Begomoviruses are notoriously recombination-prone, and also display nucleotide substitution rates equivalent to those of RNA viruses. In Brazil, several indigenous begomoviruses have been described infecting tomatoes following the introduction of a novel biotype of the whitefly vector in the mid-1990s. More recently, a number of viruses from non-cultivated hosts have also been described. Previous work has suggested that viruses infecting non-cultivated hosts have a higher degree of genetic variability compared with crop-infecting viruses. We intensively sampled cultivated and non-cultivated plants in similarly sized geographical areas known to harbour either the weed-infecting Macroptilium yellow spot virus (MaYSV) or the crop-infecting Tomato severe rugose virus (ToSRV), and compared the molecular evolution and population genetics of these two distantly related begomoviruses. The results reinforce the assertion that infection of non-cultivated plant species leads to higher levels of standing genetic variability, and indicate that recombination, not adaptive selection, explains the higher begomovirus variability in non-cultivated hosts.

High genetic variability and recombination in a begomovirus population infecting the ubiquitous weed Cleome affinis in northeastern Brazil.

Diseases caused by begomoviruses are a serious constraint to crop production in many tropical and subtropical areas of the world, including Brazil. Begomoviruses are whitefly-transmitted, single-stranded DNA viruses that are often associated with weed plants, which may act as natural reservoirs of viruses that cause epidemics in crop plants. Cleome affinis (family Capparaceae) is an annual weed that is frequently associated with leguminous crops in Brazil. Samples of C. affinis were collected in four states in the northeast of Brazil. Analysis of 14 full-length DNA-A components revealed that only one begomovirus was present, with 91-96% identity to cleome leaf crumple virus (ClLCrV). In a phylogenetic tree, ClLCrV forms a basal group relative to all other Brazilian begomoviruses. Evidence of multiple recombination events was detected among the ClLCrV isolates, which also display a high degree of genetic variability. Despite ClLCrV being the only begomovirus found, its phylogenetic placement, high genetic variability and recombinant nature suggest that C. affinis may act as a source of novel viruses for crop plants. Alternatively, ClLCrV could be a genetically isolated begomovirus. Further studies on the biological properties of ClLCrV should help to clarify the role of C. affinis in the epidemiological scenario of Brazilian begomoviruses.