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Iris yellow spot, caused by Iris yellow spot orthotospovirus (IYSV) (Genus:  Orthotospovirus , Family:  Tospoviridae ), is an important disease of  Allium  spp. The complete N gene sequences of 142 IYSV isolates of curated sequence data from GenBank were used to determine the genetic diversity and evolutionary pattern.  In silico  restriction fragment length polymorphism (RFLP) analysis, codon-based maximum likelihood studies, genetic differentiation and gene flow within the populations of IYSV genotypes were investigated. Bayesian phylogenetic analysis was carried out to estimate the evolutionary rate.  In silico  RFLP analysis of N gene sequences categorized IYSV isolates into two major genotypes  viz ., IYSV Netherlands (IYSV  NL  ; 55.63%), IYSV Brazil (IYSV  BR  ; 38.73%) and the rest fell in neither group [IYSV other (IYSV  other  ; 5.63%)]. Phylogenetic tree largely corroborated the results of RFLP analysis and the IYSV genotypes clustered into IYSV  NL   and IYSV  BR   genotypes. Genetic diversity test revealed IYSV  other   to be more diverse than IYSV  NL   and IYSV  BR  . IYSV  NL   and IYSV  BR   genotypes are under purifying selection and population expansion, whereas IYSV  other   showed decreasing population size and hence appear to be under balancing selection. IYSV  BR   is least differentiated from IYSV  other   compared to IYSV  NL   genotype based on nucleotide diversity. Three putative recombinant events were found in the N gene of IYSV isolates based on RDP analysis, however, RAT substantiated two among them. The marginal likelihood mean substitution rate was 5.08 × 10 –5  subs/site/year and 95% highest posterior density (HPD) substitution rate between 5.11 × 10 –5  and 5.06 × 10 –5 . Findings suggest that IYSV continues to evolve using population expansion strategies. The substitution rates identified are similar to other plant RNA viruses.

frontiers in microbiology

Viruses Without Borders: Global Analysis of the Population Structure, Haplotype Distribution, and Evolutionary Pattern of Iris Yellow Spot Orthotospovirus (Family Tospoviridae, Genus Orthotospovirus)