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

Shirin Farzadfar,Reza Pourrahim,Naomi Forrester

doi:10.1371/journal.pone.0215574

Shirin Farzadfar, Reza Pourrahim + Show 1 more

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https://doi.org/10.1371/journal.pone.0215574

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Abstract

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.

Highlights

Soilborne viruses, especially those persistently transmitted by plasmodiophorid and chytrid vectors, are economically important and cause considerable losses to sugar beet (Beta vulgaris) production worldwide [1]
The phylogenetic trees based on all open reading frames (ORFs) (Figures A, B and C in S2 File) indicted that Beet black scorch virus (BBSV) isolates fell into two main groups
Most of the Iranian isolates clustered in GI with two subpopulations IranA (I-IranA) and IranB (I-IranB)

Summary

Introduction

Especially those persistently transmitted by plasmodiophorid and chytrid vectors, are economically important and cause considerable losses to sugar beet (Beta vulgaris) production worldwide [1]. Betanecrovirus, family Tombusviridae [2, 3, 4], was first reported in Chinses Inner Mongolia [5, 6, 7] This virus induces severe systemic disease symptoms of black scorching leaves tips, necrotic fibrous roots and severe stunting of affected sugar beet plants in fields throughout North-West and Eastern China. BBSV was reported from the USA [7], and Europe [1] with no black scorching on the leaves but showing exacerbated symptoms similar to that of rhizomania as induced by Beet necrotic yellow vein virus-BNYVV (genus Benyvirus, Benyviridae family) [1, 7]. Nicotiana spp., Solanum lycopersicum, Physalis floridana and Lactuca sativa are asymptomatic hosts [9]

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