Genetic Variation and Possible Mechanisms Driving the Evolution of Worldwide Fig mosaic virus Isolates
Abstract
ABSTRACT Fig mosaic virus (FMV) is a multipartite negative-sense RNA virus infecting fig trees worldwide. FMV is transmitted by vegetative propagation and grafting of plant materials, and by the eriophyid mite Aceria ficus. In this work, the genetic variation and evolutionary mechanisms shaping FMV populations were characterized. Nucleotide sequences from four genomic regions (each within the genomic RNAs 1, 2, 3, and 4) from FMV isolates from different countries were determined and analyzed. FMV genetic variation was low, as is seen for many other plant viruses. Phylogenetic analysis showed some geographically distant FMV isolates which clustered together, suggesting long-distance migration. The extent of migration was limited, although varied, between countries, such that FMV populations of different countries were genetically differentiated. Analysis using several recombination algorithms suggests that genomes of some FMV isolates originated by reassortment of genomic RNAs from different genetically similar isolates. Comparison between nonsynonymous and synonymous substitutions showed selection acting on some amino acids; however, most evolved neutrally. This and neutrality tests together with the limited gene flow suggest that genetic drift plays an important role in shaping FMV populations.
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- "In the current study, sequence analyses of five regions of the CSDaV genome representing almost 42% of the whole genome of 31 isolates, sampled from different hosts/plant tissues, showed a low genetic diversity. It is not a surprising finding because genetic stability has been considered as a rule in natural plant virus populations [23] and similar low genetic diversity was previously reported for many other RNA plant viruses [20,[25][26][27][28][29][30][31]. It has been shown that systemic infections and other events such as host change and transmission can impose bottlenecks, the most common effects of genetic drift, which have been inferred from the low genetic diversity of plant virus populations [32,33] and which might be the reason for the low genetic diversity among the CSDaV isolates. "
[Show abstract] [Hide abstract] ABSTRACT: Citrus sudden death-associated virus (CSDaV) is a monopartite positive-sense single-stranded RNA virus that was suggested to be associated with citrus sudden death (CSD) disease in Brazil. Here, we report the first study of the genetic structure and molecular variability among 31 CSDaV isolates collected from both symptomatic and asymptomatic trees in CSD-affected areas. Analyses of partial nucleotide sequences of five domains of the CSDaV genomic RNA, including those encoding for the methyltransferase, the multi-domain region (MDR), the helicase, the RNA-dependent RNA polymerase and the coat protein, showed that the MDR coding region was the most diverse region assessed here, and a possible association between this region and virus adaption to different host or plant tissues is considered. Overall, the nucleotide diversity (π) was low for CSDaV isolates, but the phylogenetic analyses revealed the predominance of two main groups, one of which showed a higher association with CSD-symptomatic plants. Isolates obtained from CSD-symptomatic plants, compared to those obtained from asymptomatic plants, showed higher nucleotide diversity, nonsynonymous and synonymous substitution rates and number of amino acid changes on the coding regions located closer to the 5' end region of the genomic RNA. This work provides new insights into the genetic diversity of the CSDaV, giving support for further epidemiological studies.- "Diversity was studied in the two areas commonly used to examine emaravirus population structure (Bargen et al., 2013; Danesh-Amuz et al., 2014; Dong et al., 2016; Kallinen et al., 2009; Laney et al., 2011; Stewart, 2016; Walia et al., 2014; Supplemental Tables 2 and 3). Nucleotide and aa sequence identity ranged from 98-99% and 99-100% respectively, for the ORFs evaluated. "
[Show abstract] [Hide abstract] ABSTRACT: Yellow ringspot is the only virus-like disease reported in redbud (Cercis spp.) with symptoms including vein clearing, chlorotic ringspots and oak-leaf pattern. A putative new emaravirus was present in all trees displaying typical yellow ringspot symptoms and the name redbud yellow ringspot associated virus is proposed. The virus genome is composed of at least five RNA segments. Two coding regions were studied to determine isolate diversity with results pointing to a homogeneous virus population. Host range was evaluated using graft transmission and by testing species found in close proximity to infected trees. Mite transmission with Aculops cercidis, the predominant species found in redbud trees in the epicenter of the disease, was evaluated but was not found to be a vector of the virus. Based on this study and the accumulated knowledge on emaravirus evolution we propose that speciation is allopatric, with vectors being a major component of the process.- "The SCSMV population would be expanded by fixing advantaged mutations, essentially by enhancing the pathogenicity of the virus via a novel mechanism to suppress the RNAsilencing-based antiviral defense. The P1 site under selection, as identified in this study, can be used in functional genomic studies based on directed mutagenesis and reverse genetics [44]. Additional genomic sequences of SCSMV isolates from other countries are needed to fully assess the genetic variability and phylogenetic history of SCSMV. "
[Show abstract] [Hide abstract] ABSTRACT: Sugarcane streak mosaic virus (SCSMV), an economically important causal agent of mosaic disease of sugarcane, is a member of the newly created genus Poacevirus in the family Potyviridae. In this study, we report the molecular characterization of three new SCSMV isolates from China (YN-YZ211 and HN-YZ49) and Myanmar (MYA-Formosa) and their genetic variation and phylogenetic relationship to SCSMV isolates from Asia and the type members of the family Potyviridae. The complete genome of each of the three isolates was determined to be 9781 nucleotides (nt) in size, excluding the 3′ poly(A) tail. Phylogenetic analysis of the complete polyprotein amino acid (aa) sequences (3130 aa) revealed that all SCSMV isolates clustered into a phylogroup specific to the genus Poacevirus and formed two distinct clades designated as group I and group II. Isolates YN-YZ211, HN-YZ49 and MYA-Formosa clustered into group I, sharing 96.8–99.5 % and 98.9–99.6 % nt (at the complete genomic level) and aa (at the polyprotein level) identity, respectively, among themselves and 81.2–98.8 % and 94.0–99.6 % nt (at the complete genomic level) and aa (at the polyprotein level) identity, respectively, with the corresponding sequences of seven Asian SCSMV isolates. Population genetic analysis revealed greater between-group (0.190 ± 0.004) than within-group (group I = 0.025 ± 0.001 and group II = 0.071 ± 0.003) evolutionary divergence values, further supporting the results of the phylogenetic analysis. Further analysis indicated that natural selection might have contributed to the evolution of isolates belonging to the two identified SCSMV clades, with infrequent genetic exchanges occurring between them over time. These findings provide a comprehensive analysis of the population genetic structure and driving forces for the evolution of SCSMV with implications for global exchange of sugarcane germplasm.
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