Research Article: Positive selection and recombination shaped the large genetic differentiation of Beet black scorch virus population

Date Published: April 25, 2019

Publisher: Public Library of Science

Author(s): Shirin Farzadfar, Reza Pourrahim, Naomi Forrester.

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

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.

Partial Text

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]. Beet black scorch virus (BBSV) belonging to the genus 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. Later, 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]. Symptomless infections have also been observed in sugar beet [7]. BBSV is transmitted by the chytrid vector Olpidium brassicae zoospores in a non-persistent manner [8]. In addition, the virus is also mechanically transmissible to a number of herbaceous hosts and induces necrotic local lesions on Chenopodium spp., Tetragonia expansa and Spinacia oleracea. Nicotiana spp., Solanum lycopersicum, Physalis floridana and Lactuca sativa are asymptomatic hosts [9].

The objectives of this investigation were to better understand the sequence diversity and genetic structure of BBSV population using different approaches. The four new Iranian BBSV isolates sequenced in this study (ac. no. MH705129 to MH705132) were all 3644 nts in length, with genome organization identical to that of the type BBSV member. The presented sequence data is the most common variant within each sample. Phylogenetic analysis using 3′UTR region grouped the BBSV isolates into two groups. Most of the BBSV isolates from China, Europe, and one from North America were in phylogroup GII. Group GI isolates from Iran fell into two subgroups. Almost all of the BBSV isolates from North-East Iran (Khorasan district, geographically the nearest county to Xinjiang province in China) were not clustered with Chinese or European isolates in Group II. The Iranian BBSV isolates in the subgroup II-IranC originating from North-West Iran (Kermanshah district, Fig 2) were clustered in Group II. Overall, the PATRISTIC plots using ML trees indicated that the coding and 3′UTR regions were closely linked and showed similar evolutionary pattern (Fig 3).

The evolutionary analysis of BBSV indicates that: a) Genetic differentiation has occurred among two original populations of BBSV (Table B in S1 File), one in the Middle East (Iran) and the other one in East Asia. b) Differentiation has divided Iranian BBSV isolates into two groups. This suggests the wide spread dissemination of the virus in sugar beet growing areas in Iran. c) Three BBSV subpopulations have been observed in Iran (based on the analysis of 3′UTR sequences). The subpopulation in North-East Iran appears to have diverged most recently. d) Recombination has a considerable role in the evolution of viruses by decreasing mutational bar, producing genetic diversification, and generating new strains. Our analysis using RDP4 [20] indicated a recombination event in the Chinese Xinjiang/m81 isolate and a putative inter-recombination breakpoint in 3′UTR of Iranian isolates in subgroup I-IranA. e) Fitness to the host plant or to the chytrid vector may illustrate how diversifying selection influences different sites in the BBSV genome. Furthermore, the positively selected site(s) in different ORFs of BBSV indicate(s) differentiation among evolved subgroups (Tables 3 and 4). BBSV isolates belonging to subgroups I-IranA and I-IranB are dispersed in Iran, whereas except for the USA isolate, all other isolates in BBSV subgroup II-Chinese were collected from China in East Asia. As previously described by Moury [38] different evolution patterns may have originated by biological variation and/or dispensation diversities. Beet has long been cultivated in Iran and some parts of Iran are considered as an origin point of the domestic beet [39]. However, improved beet seeds were introduced about 120 years ago to Iran. At that time each original population of BBSV might have passed through sequential bottleneck transmissions in different host varieties. These host changes may have selected for the introduction of changes at various sites during several generations. In addition, resting spores of O. brassica can remain dormant in infested soil for long times; e.g. as reported for Polymyxa betae, the vector of BNYVV [40]. Beet soil-borne viruses are transmitted primarily via the movement of soils containing viruliferous resting vector spores [40], so the transmission of BBSV from unknown natural hosts to sugar beet fields may well have been an important factor in this evolution.

 

Source:

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

 

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