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Research Article
Adyatma Irawan Santosa
Ankara University Faculty of Agriculture: Ankara Universitesi Ziraat Fakultesi
Corresponding Author
ORCiD: https://orcid.org/0000-0002-2826-5444
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This work is licensed under a CC BY 4.0 License. Read Full License
Leek yellow stripe virus (LYSV, Potyvirus), a pathogen affecting Allium spp. worldwide, has been suspected to consist of two types: S and N, based on genetic and host species differences. In this study, phylogenetic and evolutionary analyses were performed to P1 and CP regions of genome of global LYSV isolates to clarify the variation among members of S-type and N-type. Constructed phylogenetic trees clearly divided isolates into S-type and N-type, with N-type was further split into L and N groups, according to hosts. Significant nucleotide (nt) and amino acids (aa) sequence variation were observed on full ORF, P1, HC-Pro, P3, VPg coding regions. The dN/dS values of P1 and CP confirmed that both genes are under strong negative selection pressure. Neutrality tests on Eastern Asian isolates argued that ancestor of current LYSV isolates may had evolved with garlic while they were in Asia before spread to other world regions through garlic propagative materials. The genetic differentiation and gene flow analysis showed that there was very frequent gene flow from S-type to L and N groups and these phylogroups differentiated from each other over time. Host differences, substantial nt and aa variation, inconsistent serological test results, and phylogenetic and diversity analyses results highly suggested that LYSV can be separated into two types: S and N.
Keywords
diversity analysis, evolutionary analysis, leek yellow stripe virus, phylogenetic analysis
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This is a preprint. It has not completed peer review.
Research Article
Adyatma Irawan Santosa
Ankara University Faculty of Agriculture: Ankara Universitesi Ziraat Fakultesi
Corresponding Author
ORCiD: https://orcid.org/0000-0002-2826-5444
Badges
Prescreen
This manuscript passed our Prescreen assessment
Complete author information
Appropriate declaration statements
Potential risks to human health
Prescreen
History
CURRENT STATUS: Posted
Version 1
Posted 01 Apr, 2021
Community comments: 2
Metrics
Comments: 0
PDF Downloads: ...
HTML Views: ...
Subject Areas
Virology
License:
This work is licensed under a CC BY 4.0 License. Read Full License
Leek yellow stripe virus (LYSV, Potyvirus), a pathogen affecting Allium spp. worldwide, has been suspected to consist of two types: S and N, based on genetic and host species differences. In this study, phylogenetic and evolutionary analyses were performed to P1 and CP regions of genome of global LYSV isolates to clarify the variation among members of S-type and N-type. Constructed phylogenetic trees clearly divided isolates into S-type and N-type, with N-type was further split into L and N groups, according to hosts. Significant nucleotide (nt) and amino acids (aa) sequence variation were observed on full ORF, P1, HC-Pro, P3, VPg coding regions. The dN/dS values of P1 and CP confirmed that both genes are under strong negative selection pressure. Neutrality tests on Eastern Asian isolates argued that ancestor of current LYSV isolates may had evolved with garlic while they were in Asia before spread to other world regions through garlic propagative materials. The genetic differentiation and gene flow analysis showed that there was very frequent gene flow from S-type to L and N groups and these phylogroups differentiated from each other over time. Host differences, substantial nt and aa variation, inconsistent serological test results, and phylogenetic and diversity analyses results highly suggested that LYSV can be separated into two types: S and N.
Figure 1
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