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

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.

Analysis of Coat Protein of Peanut stunt virus Subgroup II Isolates from Alfalfa Fields in West Iran

“…A combination for high haplotype diversity and low genetic diversity, assessed by mitochondrial DNA markers, is taken as evidence of a recent population expansion after a genetic bottleneck and this also was found for Turnip mosaic virus (TuMV) (Tomitaka and Ohshima ) and Cauliflower mosaic virus (CaMV) (Farzadfar et al. ).…”

A Distinct Subpopulation of Cauliflower mosaic virus (CaMV) in South Iran

“…capitata alba therefore were considered as (L/MMo) biotype as previously described (Farzadfar and Pourrahim ; Farzadfar et al. ).…”

“…New recombination site between ORFs 2 and 6 was found in two isolates (IRNKerman and IRNRKerman2) from south Iran which added to four recombination events were indicated in the LIR and ORFs 1, 2, 3 and 7 (events 2, 3 and 4) corresponding to 5′ extremity of 35S RNA and in ORF6 (event 1) corresponding to 5′ extremity of 19S RNA (Farzadfar et al. ). These sites have been previously predicted as hot spots of template switching in CaMV (Froissart et al.…”

“…Hakatasuwari leaves using DNeasy Plant Mini kit (QIAGEN, Valencia, California) according to the manufacturer's instructions, and high‐fidelity Platinum™ Pfx DNA polymerase (Invitrogen, Carlsbad, CA, USA) with specific primers designed in previous study (Farzadfar and Pourrahim ; Farzadfar et al. ). DNA amplicons were sequenced in both directions, and sequence data were assembled using BIOEDIT version 5.0.9 (Hall ).…”

“…Moreover, recombination analysis revealed that a genomic exchange is responsible for the emergence of CaMV strains (Farzadfar et al. ). Using new sequences of Iranian CaMV isolates from south Iran, we found the new recombinant subpopulation by concatenate fragments of three ORFs 2, 4 and 6 according to aphid transmission, coat protein and inclusion body protein/translation transactivator (TAV) genes, respectively.…”