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

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.

SUBMITTER: Tabassum A

PROVIDER: S-EPMC8488366 | biostudies-literature |

REPOSITORIES: biostudies-literature

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Project description:TaxonomyIris yellow spot virus (IYSV) is in the genus Tospovirus, family Bunyaviridae, with a single-stranded, tri-segmented RNA genome with an ambisense genome organization. Members of the other genera in the family infect predominantly vertebrates and insects.Geographical distributionIYSV is present in most Allium-growing regions of the world.Physical propertiesVirions are pleomorphic particles of 80-120 nm in size. The particle consists of RNA, protein, glycoprotein and lipids.GenomeIYSV shares the genomic features of other tospoviruses: a segmented RNA genome of three RNAs, referred to as large (L), medium (M) and small (S). The L RNA codes for the RNA-dependent RNA polymerase (RdRp) in negative sense. The M RNA uses an ambisense coding strategy and codes for the precursor for the GN /GC glycoprotein in the viral complementary (vc) sense and a non-structural protein (NSm) in the viral (v) sense. The S RNA also uses an ambisense coding strategy with the coat protein (N) in vc sense and a non-structural protein (NSs) in the v sense.TransmissionThe virus is transmitted by Thrips tabaci Lindeman (Order: Thysanoptera; Family: Thripidae; onion thrips) and with less efficiency by Frankliniella fusca Hinds (tobacco thrips). HOST: IYSV has a relatively broad host range, including cultivated and wild onions, garlic, chives, leeks and several ornamentals. Some weeds are naturally infected by IYSV and may serve as alternative hosts for the virus.SymptomsIYSV symptoms in Allium spp. are yellow- to straw-coloured, diamond-shaped lesions on leaves and flowering scapes. Diamond-shaped lesions are particularly pronounced on scapes. As the disease progresses, the lesions coalesce, leading to lodging of the scapes. In seed crops, this could lead to a reduction in yield and quality. Early to mid-season infection in bulb crops results in reduced vigour and bulb size.ControlResistant varieties are not available, but a limited number of accessions with field tolerance have been identified. Integrated disease management tactics, including sanitation, crop rotation, thrips management, maintenance of optimal plant vigour, soil fertility, irrigation and physical separation of bulb and seed crops, can mitigate the effect of the disease. Virus code: 00.011.0.85.009 Useful link: http://www.alliumnet.com/.

Project description:BACKGROUND AND AIMS:Two Phragmites australis taxa are recognized in Europe: P. australis ssp. altissimus, also known as Phragmites isiaca, in the Mediterranean region and P. australis in the temperate region. Another taxonomic group in the Mediterranean is Phragmites frutescens. European genotypes are diverse genetically, cytologically and morphologically, and are related to African, Asiatic and American genotypes. We investigated chloroplast DNA (cpDNA) diversity in Europe and defined the current borders of the European gene pool. METHODOLOGY:We analysed chloroplast variation with parsimony and genetic distance methods, and compared it with that of nuclear amplified fragment length polymorphism and microsatellites. We also investigated the phenological pattern of 188 genotypes collected worldwide in a common garden in Denmark. We assumed that non-flowering genotypes could indicate climatic, geographic and/or reproductive barriers to dispersal and would have been recorded in the genetic pattern as groups genetically isolated from, or within, the European pool. PRINCIPAL RESULTS:The European P. australis gene pool extends from North America to the Far East and South Africa. However, African and North American genotypes are differentiating from the European genotypes. Mediterranean P. australis is genetically different from temperate P. australis and shares several similarities with Phragmites mauritianus in Africa and Phragmites karka in Asia. Phragmites frutescens shares the cpDNA sequences with both these tropical species. Two DNA bands can distinguish Mediterranean P. australis from P. frutescens and P. mauritianus and from temperate P. australis, and reveal possible hybrids among these species in the Mediterranean region. Phenological data confirmed possible gene flow within the temperate region of Europe, whereas the Mediterranean genotypes did not set inflorescences in Denmark, suggesting reproductive barriers between temperate and Mediterranean P. australis. CONCLUSIONS:European P. australis appears as one of four main Phragmites groups known in the world. Further research is needed to understand the implications of long-distance dispersal at the population level.

Dataset Information

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

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