title: Global analysis of population structure, spatial and temporal dynamics of genetic diversity, and evolutionary lineages of Iris yellow spot virus (Tospovirus: Bunyaviridae).
abstract: Thrips-transmitted Iris yellow spot virus is an economically important viral pathogen of Allium crops worldwide. A global analysis of known IYSV nucleocapsid gene (N gene) sequences was carried out to determine the comparative population structure, spatial and temporal dynamics with reference to its genetic diversity and evolution. A total of 98 complete N gene sequences (including 8 sequences reported in this study) available in GenBank and reported from 23 countries were characterized by in-silico RFLP analysis. Based on RFLP, 94% of the isolates could be grouped into NL or BR types while the rest belonged to neither group. The relative proportion of NL and BR types was 46% and 48%, respectively. A temporal shift in the IYSV genotypes with a greater incremental incidence of IYSVBR was found over IYSVNL before 2005 compared to after 2005. The virus population had at least one evolutionarily significant recombination event, involving IYSVBR and IYSVNL. Codon substitution studies did not identify any significant differences among the genotypes of IYSV. However, N gene codons were minimally positively selected, moderately negatively selected denoting the action of purifying selection, thus rejecting the theory of neutral mutation in IYSV population. However, one codon position (139) was found to be positively selected in all the genotypes. Population selection statistics in the IYSVBR, IYSVNL genotypes and in the population as a whole also revealed the action of purifying selection or population expansion, whereas IYSVother displayed a decrease in population size. Genetic differentiation studies showed inherent differentiation and infrequent gene flow between IYSVBR and IYSVNL genotypes corroborating the geographical confinement of these genotypes. Taken together the study suggests that the observed diversity in IYSV population and temporal shift in IYSVBR genotype is attributable to genetic recombination, abundance of purifying selection, insignificant positive selection and population expansion. Restricted gene flow between the two major IYSV genotypes further emphasizes the role of genetic drift in modeling the population architecture, evolutionary lineage and epidemiology of IYSV.
authors: National Institute for Biotechnology and Genetic Engineering, Faisalabad, Pakistan Institute of Engineering and Applied Sciences (PIEAS), Nilore, Islamabad 45650, Pakistan; Washington State University, Department of Plant Pathology, Pullman, WA, USA.
authors: Romana
authors: R
authors: Iftikhar
authors: Directorate of Soybean Research, Indian Council of Agricultural Research (ICAR), Indore, MP 452001, India; Washington State University, Department of Plant Pathology, Pullman, WA, USA.
authors: Shunmugiah V
authors: SV
authors: Ramesh
authors: Department of Entomology, University of California, One Shield Avenue, Davis, CA 95616, USA; Washington State University, Department of Plant Pathology, Pullman, WA, USA.
authors: Sudeep
authors: S
authors: Bag
authors: National Institute for Biotechnology and Genetic Engineering, Faisalabad, Pakistan Institute of Engineering and Applied Sciences (PIEAS), Nilore, Islamabad 45650, Pakistan; Biodiversity Institute of Ontario, University of Guelph, Guelph, ON N1G 2W1, Canada.
authors: Muhammad
authors: M
authors: Ashfaq
authors: Washington State University, Department of Plant Pathology, Pullman, WA, USA. Electronic address: hrp@wsu.edu.
authors: Hanu R
authors: HR
authors: Pappu
mesh_terms: D001483:Base Sequence; D017931:DNA Primers; D004797:Enzyme-Linked Immunosorbent Assay; D019143:Evolution, Molecular; D005814:Genes, Viral; D014644:Genetic Variation; D011110:Polymorphism, Genetic; D012150:Polymorphism, Restriction Fragment Length; D011995:Recombination, Genetic; D020133:Reverse Transcriptase Polymerase Chain Reaction; D017865:Tospovirus / Q000235:genetics*
chemical_list: D017931:DNA Primers
keywords: Gene flow; Nucleocapsid gene; Population genetics; Population selection; RFLP