The first complete genome sequence of narcissus latent virusfrom Narcissus

AbstractThe complete sequence of a narcissus virus isolated from the Netherlands (Narv-NL) was determined to be 8172 nucleotidesin length with an open reading frame encoding for 2624 amino acids. Phylogenetic analysis indicates that Narv-NLis clustered with high confidence among representative members from the genus Macluravirus, including artichoke latentvirus (ArLV) and Chinese yam necrotic mosaic virus (CYNMV). Sequence analyses indicated Narv-NL shares 67%-69%nucleotide and 51%-68% amino acid sequence identity with ArLV and CYNMV either in the complete ORF or the coatprotein (CP) gene, whereas it had 81%-99 % nucleotide and 80%-99 % amino acid sequence identity with the correspondingCP sequences of narcissus latent virus (NLV) isolates, suggesting that Narv-NL is a member of NLV. To our knowledge,this is the first report of the complete sequence of a NLV isolate

The evolutionary history and global spatio-temporal dynamics of potato virus Y

Abstract Potato virus Y (PVY) is a destructive plant pathogen that causes considerable losses to global potato and tobacco production. Although the molecular structure of PVY is well characterized, the evolutionary and global transmission dynamics of this virus remain poorly understood. We investigated the phylodynamics of the virus by analysing 253 nucleotide sequences of the genes encoding the third protein (P3), cylindrical inclusion protein (CI), and the nuclear inclusion protein (NIb). Our Bayesian phylogenetic analyses showed that the mean substitution rates of different regions of the genome ranged from 8.50 × 10−5 to 1.34 × 10−4 substitutions/site/year, whereas the time to the most recent common ancestor of PVY varied with the length of the genomic regions and with the number of viral isolates being analysed. Our phylogeographic analysis showed that the PVY population originated in South America and was introduced into Europe in the 19th century, from where it spread around the globe. The migration pathways of PVY correlate well with the trade routes of potato tubers, suggesting that the global spread of PVY is associated with human activities.</jats:p

Genetic diversity and molecular evolution of Ornithogalum mosaic virus based on the coat protein gene sequence

Ornithogalum mosaic virus (OrMV) has a wide host range and affects the production of a variety of ornamentals. In this study, the coat protein (CP) gene of OrMVwas used to investigate the molecular mechanisms underlying the evolution of this virus. The 36 OrMV isolates fell into two groups which have significant subpopulation differentiation with an FST value of 0.470. One isolate was identified as a recombinant and the other 35 recombination-free isolates could be divided into two major clades under different evolutionary constraints with dN/dS values of 0.055 and 0.028, respectively, indicating a role of purifying selection in the differentiation of OrMV. In addition, the results from analysis of molecular variance (AMOVA) indicated that the effect of host species on the genetic divergence of OrMV is greater than that of geography. Furthermore, OrMV isolates from the genera Ornithogalum, Lachenalia and Diuri tended to group together, indicating that OrMV diversification was maintained, in part, by host-driven adaptation

Association between Virulence and Triazole Tolerance in the Phytopathogenic Fungus Mycosphaerella graminicola

Host resistance and synthetic antimicrobials such as fungicides are two of the main approaches used to control plant diseases in conventional agriculture. Although pathogens often evolve to overcome host resistance and antimicrobials, the majority of reports have involved qualitative host – pathogen interactions or antimicrobials targeting a single pathogen protein or metabolic pathway. Studies that consider jointly the evolution of virulence, defined as the degree of damage caused to a host by parasite infection, and antimicrobial resistance are rare. Here we compared virulence and fungicide tolerance in the fungal pathogen Mycosphaerella graminicola sampled from wheat fields across three continents and found a positive correlation between virulence and tolerance to a triazole fungicide. We also found that quantitative host resistance selected for higher pathogen virulence. The possible mechanisms responsible for these observations and their consequences for sustainable disease management are discussed.ISSN:1932-620

Genetic diversity analysis of the coat protein gene revealed strong evolutionary constraints on<i> Ornithogalum mosaic virus </i>

Ornithogalum mosaic virus (OrMV) has a wide host range and affects the production of a variety of ornamentals. In this study, the coat protein (CP) gene of OrMVwas used to investigate the molecular mechanisms underlying the evolution of this virus. The 36 OrMV isolates fell into two groups which have a significant subpopulation differentiation with an FST value of 0.470. One isolate was identified as a recombinant and the other 35 recombination-free isolates could be divided into two major clades under different evolutionary constraints with ω-values of 0.055 and 0.028, respectively, indicating a role of purifying selection in the differentiation of OrMV. In addition, the results from molecular variance of analysis (AMOVA) indicated that the effect of host species on the genetic divergence of OrMV is greater than that of geography. In BaTS analysis, OrMV isolates from the genera Ornithogalum, Lachenalia, Diuri tended to group together, indicating that OrMV diversification was maintained, in part, by host-driven adaptation. Furthermore, age calculations suggested that the first divergence event of the OrMV isolates analyzed might take place around 1068 BC.</jats:p

Phylogeography and Evolutionary Dynamics of Tobacco Curly Shoot Virus

Tobacco curly shoot virus (TbCSV), a begomovirus, causes significant economic losses in tobacco and tomato crops across East, Southeast, and South Asia. Despite its agricultural importance, the evolutionary dynamics and emergence process of TbCSV remain poorly understood. This study analyzed the phylodynamics of TbCSV by examining its nucleotide sequences of the coat protein (CP) gene collected between 2000 and 2022. Using various combinations of priors, Bayes factor comparisons identified heterochronous datasets (3 × 100 million chains) generated from a strict molecular clock and Bayesian skyline tree priors as the most robust. The mean substitution rate of the CP gene was estimated at 6.50 × 10−4 substitutions/site/year (95% credibility interval: 4.74 × 10−4–8.50 × 10−4). TbCSV was inferred to have diverged around 1920 CE (95% credibility interval: 1887–1952), with its most probable origin in South Asia. These findings provide valuable insights for the phylogeography and evolutionary dynamics of TbCSV, and contribute to a broader understanding of begomovirus epidemiology