Positive selection and recombination shaped the large genetic differentiation of Beet black scorch virus population.

Beet black scorch virus (BBSV) is a species in the Betanecrovirus genus, in family Tombusviridae. BBSV infection is of considerable importance, causing economic losses to sugar beet (Beta vulgaris) field crops worldwide. Phylogenetic analyses using 3'UTR sequences divided most BBSV isolates into two main groups. Group I is composed of Iranian isolates from all Iranian provinces that have been sampled. Chinese, European, one North American and some other Iranian isolates from North-Western Iran are in Group II. The division of Iranian BBSV isolates into two groups suggests numerous independent infection events have occurred in Iran, possibly from isolated sources from unknown host(s) linked through the viral vector Olpidium. The between-group diversity was higher than the within-group diversity, indicating the role of a founder effect in the diversification of BBSV isolates. The high FST among BBSV populations differentiates BBSV groups. We found no indication of frequent gene flow between populations in Mid-Eurasia, East-Asia and Europe countries. Recombination analysis indicated an intra-recombination event in the Chinese Xinjiang/m81 isolate and an inter-recombination breakpoint in the viral 3'UTR of Iranian isolates in subgroup IranA in Group I. The ω ratios (dNS/dS) were used for detecting positive selection at individual codon sites. Amino acid sequences were conserved with ω from 0.040 to 0.229 in various proteins. In addition, a small fraction of amino acids in proteins RT-ORF1 (p82), ORF4 (p7b) and ORF6 (p24) are positively selected with ω > 1. This analysis could increase the understanding of protein structure and function and Betanecrovirus epidemiology. The recombination analysis shows that genomic exchanges are associated with the emergence of new BBSV strains. Such recombinational exchange analysis may provide new information about the evolution of Betanecrovirus diversity.

Population Analysis of Iranian Potato virus Y Isolates Using Complete Genome Sequence.

In this study, the full-length nucleotide sequences of four Iranian PVY isolates belonging to PVY(N) strain were determined. The genome of Iranian PVY isolates were 9,703-9,707 nucleotides long encoding all potyviral cistrons including P1, HC-Pro, P3, 6K1, CI, 6K2, VPg, NIa-Pro, NIb and CP with coding regions of 825, 1,395, 1,095, 156, 1,902, 156, 564, 732, 1,557 and 801 nucleotides in length, respectively. The length of pipo, embedded in the P3 cistron, was 231 nucleotides. Phylogenetic analysis showed that the Iranian isolates clustered with European recombinant NTN isolates in the N lineage. Recombination analysis demonstrated that Iranian PVY(N) isolates had a typical European PVY(NTN) genome having three recombinant junctions while PVY(N) and PVY(O) were identified as the parents. We used dN/dS methods to detect candidate amino acid positions for positive selection in viral proteins. The mean ω ratio differed among different genes. Using model M0, ω values were 0.267 (P1), 0.085 (HC-Pro), 0.153 (P3), 0.050 (CI), 0.078 (VPg), 0.087 (NIa-pro), 0.079 (NIb) and 0.165 (CP). The analysis showed different sites within P1, P3 and CP were under positive selection pressure, however, the sites varied among PVY populations. To the best of our knowledge, our analysis provides the first demonstration of population structure of PVY(N) strain in mid-Eurasia Iran using complete genome sequences and highlights the importance of recombination and selection pressure in the evolution of PVY.

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

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.

Biological and molecular variation of Iranian Cauliflower mosaic virus (CaMV) isolates.

Seventeen provinces of Iran were surveyed during 2003-2012 to find Brassicaceae hosts of Cauliflower mosaic virus (CaMV). A total 397 samples were collected from plants with virus-like symptoms. Among those tested by ELISA, 255 samples (67.2 %) were found to be infected with CaMV. Mechanical transmission tests showed that the Iranian isolates have similar biological properties on a number of Brassica and Raphanus plant species and cultivars tested. However, the isolates varied in the severity of symptoms they induced and in the capacity to infect B. oleracea var. capitata, on the basis of which they were grouped into two distinct biotypes L/MMo (latent/mild mottle) and severe (S) infection. The molecular diversity of natural population of CaMV were investigated based on the complete sequences of OFR 6 of 36 Iranian isolates collected from different geographically distant regions in Iran alongside the sequences of 14 previously reported isolates. Phylogenetic analyses indicated that the Iranian CaMV isolates belong to two groups (GI and GII). Most of the Iranian isolates fell into GI with other exotic isolates; however, the isolates from North-East Iran with Xinjiang from China fell into GII. The phylogenetic group GII (the North-East Iranian isolates) closely corresponded to the S biological group however other Iranian isolates corresponded to the L/MMo biological group. The within-population diversity was lower than the between population diversity suggesting the contribution of a founder effect on diversification of CaMV isolates. The Iranian isolates were differentiated from other exotic CaMV isolates and clustered into two RFLP groups using Hpy99I which closely corresponded to the biological and phylogenetic groups. This study showed the evolutionary process in CaMV isolates is shaped by a combination of host range differentiation and nucleotide substitution using the approach of population genetics.

Influence of external factors on the production and morphology of biogenic silver nanocrystallites.

Naturally existing biological materials have been garning considerable attention as environmentally benign green-nanofactories for the fabrication of diverse nanomaterials, and with desired size and shape distributions. In the present investigation, we report the size and shape controllable biofabrication of silver nanocrystallites using the growth extract of the fungus, Rhizoctonia solani. Influence of various factors such as growth medium; radiation, in the form of sun light; and seeding duration on the production of silver nanoparticles using aqueous 1 mm silver nitrate solution under ambient conditions is presented. Our results demonstrate that these factors can significantly influence the production, size and shape transformation, and the rate of nanoparticles formation. Multiple characterization techniques involving UV-visible and Fourier transform infrared spectroscopy, X-ray diffraction, energy dispersive X-ray spectroscopy and transmission electron microscopy measurements confirmed the production, surface and structural characteristics, purity and crystalline nature of the biosynthesized silver nanoparticles. Our biogenic synthesis process provides a simple, ecologically friendly, cost-effective synthesis route, and most importantly the ability to have control over the size and shape distributions that lends itself for various biomedical and opto-electronic applications.