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A phylogeographical study of the cauliflower mosaic virus population in mid-Eurasia Iran using complete genome analysis

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Abstract

The full-length sequences of 34 Iranian cauliflower mosaic virus (CaMV) isolates were compared with others from public nucleotide sequence databases to provide a comprehensive overview of the genetic variability and patterns of genetic exchange in CaMV isolates from Iran. Based on the severity of symptoms and their ability to infect Brassica oleracea var. capitata, Iranian CaMV isolates were grouped into two distinct biotypes: latent/mild mottle (LI/MMo) and severe (S) infection. Recombination breakpoints were detected between the large intergenic region (LIR) and open reading frame (ORF) V (event 2); between ORF VII and ORF II (event 3), between ORF I and ORF III (event 4), and within ORF VI (event 1). Phylogenetic analysis indicated that Iranian CaMV isolates clustered into two subgroups belonging to group I (GI) that were distinct from North American and European isolates from group II (GII). Northeast Iranian isolates (subgroup B) and CaMV isolates from subgroup A closely corresponded to the S and LI/MMo biological groups, respectively. Genome-wide pairwise identity analysis of the CaMV isolates revealed three regions of pairwise identity representation: 92–94 % for GII and 94–96 % and 98–100 % for subgroups A and B. The within-population diversity was lower than the between-population diversity, suggesting the contribution of a founder effect on diversification of CaMV isolates. Amino acid sequences were conserved, with ω values ranging from 0.074 to 0.717 in different proteins. Thirteen amino acids in the deduced proteins of ORFs I, II, III, VI and VII were under positive selection (ω > 1), whereas purifying selection applied to the proteins encoded by ORFs IV and V. This study suggests that variation in the CaMV population can be explained by host-range differentiation and selection pressure. Moreover, recombination analysis revealed that a genomic exchange is responsible for the emergence of CaMV strains, providing valuable new information for understanding the diversity and evolution of caulimoviruses.

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Authors and Affiliations

  1. Department of Plant Virus Research, Iranian Research Institute of Plant Protection, P.O.Box 19395-1454, Chamran Highway, Tehran, Iran

    Shirin Farzadfar & Reza Pourrahim

  2. Department of Advanced Technology Fusion, Graduate School of Science and Engineering, Saga University, 1 Honjo-Machi, Saga, 840-8502, Japan

    Hassan Ebrahimi

Authors
  1. Shirin Farzadfar
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  2. Reza Pourrahim
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  3. Hassan Ebrahimi
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Corresponding author

Correspondence to Shirin Farzadfar.

Electronic supplementary material

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705_2013_1910_MOESM1_ESM.jpg

Supplementary Fig. S1. Symptoms induced by cauliflower mosaic virus isolates IRNCCK3 (a and b) and IRNRKh22 (c and d) belonging to the phylogenetic groups GI and GII, respectively, on the indicator cabbage plants B. oleracea var. capitata alba (a and c) and B. oleracea var. capitata cv. Ryozan 2-go (b and d). Healthy plant of B. oleracea var. capitata alba (h). (JPEG 104 kb)

Supplementary Table S1and S2-revised (DOCX 29 kb)

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Farzadfar, S., Pourrahim, R. & Ebrahimi, H. A phylogeographical study of the cauliflower mosaic virus population in mid-Eurasia Iran using complete genome analysis. Arch Virol 159, 1329–1340 (2014). https://doi.org/10.1007/s00705-013-1910-5

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