Phylogenetic and diversity analyses revealed that leek yellow stripe virus population consists of three types: S, L, and N

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Santosa A. I., RANDA ZELYÜT F., KARANFİL A., KORKMAZ S., Hartono S., ERTUNÇ F.

Virus Genes, cilt.59, sa.1, ss.121-131, 2023 (SCI-Expanded) identifier identifier

  • Yayın Türü: Makale / Tam Makale
  • Cilt numarası: 59 Sayı: 1
  • Basım Tarihi: 2023
  • Doi Numarası: 10.1007/s11262-022-01956-y
  • Dergi Adı: Virus Genes
  • Derginin Tarandığı İndeksler: Science Citation Index Expanded (SCI-EXPANDED), Scopus, BIOSIS, CAB Abstracts, Chemical Abstracts Core, EMBASE, MEDLINE, Veterinary Science Database
  • Sayfa Sayıları: ss.121-131
  • Anahtar Kelimeler: Diversity analysis, Molecular identification, Phylogenetic analysis, Population study, Selection pressure
  • Bilecik Şeyh Edebali Üniversitesi Adresli: Evet

Özet

© 2022, The Author(s), under exclusive licence to Springer Science+Business Media, LLC, part of Springer Nature.Phylogenetic and evolutionary analyses were performed on the P1 and CP genes of global isolates to clarify the phylogrouping of leek yellow stripe virus (LYSV, genus Potyvirus), a pathogen affecting Allium spp. worldwide, into different types based on genetic variation and host species. The constructed phylogenetic trees divided the isolates into three major groups: S, L, and N. Low nucleotide (nt) and amino acid (aa) percent identities among the three groups were observed on full ORF (75.4–99.0 and 79.1–99.0), P1 (59.1–98.3 and 36.8–98.3), and CP (76.6–100 and 75.7–100) coding regions. The dN/dS values of P1 and CP confirmed that both genes are under strong negative (purifying) selection pressure. Neutrality tests on Eastern Asian isolates suggested that the ancestors of current LYSV isolates evolved with garlic while they were in Asia before spreading to other world regions through garlic propagative materials. Genetic differentiation and gene flow analysis showed extremely frequent gene flow from S group to L and N groups, and these phylogroups differentiated from each other over time. Host differences, inconsistent serological test results, substantial nt and aa variation, and phylogenetic and diversity analyses in this study supported previous reports that LYSV can be separated into three major evolutionary lineages: S, L, and N types.