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

Afsha Tabassum; S V Ramesh; Ying Zhai; Romana Iftikhar; Cristian Olaya; Hanu R Pappu

doi:10.3389/fmicb.2021.633710

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

Front Microbiol. 2021 Sep 20:12:633710. doi: 10.3389/fmicb.2021.633710. eCollection 2021.

Authors

Afsha Tabassum¹, S V Ramesh², Ying Zhai¹, Romana Iftikhar¹, Cristian Olaya¹, Hanu R Pappu¹

Affiliations

¹ Department of Plant Pathology, Washington State University, Pullman, WA, United States.
² Indian Council of Agricultural Research-Central Plantation Crops Research Institute, Kasaragod, India.

Abstract

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.

Keywords: BEAST; evolutionary genomics; gene flow; genetic differentiation; genetic recombination; in silico RFLP; iris yellow spot orthotospovirus; phylogenetics.