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Population genetic analysis of potato virus X based on the CP gene sequence.

ABSTRACT: To investigate the genetic variation and molecular evolution of potato virus X (PVX), 87 coat protein (CP) gene sequences were retrieved from GenBank and analyzed. Of the PVX isolates studied, one recombinant isolate (X3) was detected from South America population of the virus. The other isolates belonged to two lineages, Eurasia and America, with the significant FST value (0.60). Non-synonymous nucleotide diversity to synonymous nucleotide diversity (? = dN/dS) was less than 1 indicating that the CP gene has been under negative selection or neutral evolution. Further analysis showed that all of the codons in both lineages were under negative selection pressure. No significant genetic differentiation was found between Chinese, Indian, Iranian, Japanese, and the UK populations whereas South America population was distinctly differentiated from other populations. Different evolutionary constraints found for the two lineages suggest that possible mutations and genetic drift were important evolutionary forces driving the genetic diversification of PVX population.

SUBMITTER: Hajizadeh M

PROVIDER: S-EPMC5377869 | biostudies-literature | 2017 Mar

REPOSITORIES: biostudies-literature

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Population genetic analysis of potato virus X based on the CP gene sequence.

Hajizadeh Mohammad M Sokhandan-Bashir Nemat N

Virusdisease 20170206 1

To investigate the genetic variation and molecular evolution of potato virus X (PVX), 87 coat protein (CP) gene sequences were retrieved from GenBank and analyzed. Of the PVX isolates studied, one recombinant isolate (X3) was detected from South America population of the virus. The other isolates belonged to two lineages, Eurasia and America, with the significant F<sub>ST</sub> value (0.60). Non-synonymous nucleotide diversity to synonymous nucleotide diversity (ω = dN/dS) was less than 1 indica ...[more]

PMID: 28466060

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Project description:Transmission is a crucial part of a viral life cycle and transmission mode can have an important impact on virus biology. It was demonstrated that transmission mode can influence the virulence and evolution of a virus; however, few empirical data are available to describe the direct underlying changes in virus population structure dynamics within the host. Potato virus Y (PVY) is an RNA virus and one of the most damaging pathogens of potato. It comprises several genetically variable strains that are transmitted between plants via different transmission modes. To investigate how transmission modes affect the within-plant viral population structure, we have used a deep sequencing approach to examine the changes in the genetic structure of populations (in leaves and tubers) of three PVY strains after successive passages by horizontal (aphid and mechanical) and vertical (via tubers) transmission modes. Nucleotide diversities of viral populations were significantly influenced by transmission modes; lineages transmitted by aphids were the least diverse, whereas lineages transmitted by tubers were the most diverse. Differences in nucleotide diversities of viral populations between leaves and tubers were transmission mode-dependent, with higher diversities in tubers than in leaves for aphid and mechanically transmitted lineages. Furthermore, aphid and tuber transmissions were shown to impose stronger genetic bottlenecks than mechanical transmission. To better understand the structure of virus populations within the host, transmission mode, movement of the virus within the host, and the number of replication cycles after transmission event need to be considered. Collectively, our results suggest a significant impact of virus transmission modes on the within-plant diversity of virus populations and provide quantitative fundamental data for understanding how transmission can shape virus diversity in the natural ecosystems, where different transmission modes are expected to affect virus population structure and consequently its evolution.

Dataset Information

Population genetic analysis of potato virus X based on the CP gene sequence.

Publications

Population genetic analysis of potato virus X based on the CP gene sequence.

Similar Datasets

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