Selection Pressure and Founder Effects Constrain Genetic Variation in Differentiated Populations of Soilborne Bymovirus <i>Wheat yellow mosaic virus</i> (<i>Potyviridae</i>) in China

Sun, Bing‐Jian; Sun, Liying; Tugume, Arthur K.; Adams, Michael J.; Yang, Jason; Xie, Liji; Chen, J.-P.

doi:10.1094/phyto-01-13-0013-r

Cited by 22 publications

(16 citation statements)

References 75 publications

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“…All coat protein domains tested were found to be under extreme purifying selection, an observation already reported for members of the Secoviridae [14]–[16] and other plant-infecting RNA viruses [44]–[47]. It has been suggested that such extreme purifying selection is a result of selection constraints imposed by specific molecular interactions during vector transmission [47], [48].…”

Section: Discussionsupporting

confidence: 57%

An Evolutionary Analysis of the Secoviridae Family of Viruses

2014

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The plant-infecting Secoviridae family of viruses forms part of the Picornavirales order, an important group of non-enveloped viruses that infect vertebrates, arthropods, plants and algae. The impact of the secovirids on cultivated crops is significant, infecting a wide range of plants from grapevine to rice. The overwhelming majority are transmitted by ecdysozoan vectors such as nematodes, beetles and aphids. In this study, we have applied a variety of computational methods to examine the evolutionary traits of these viruses. Strong purifying selection pressures were calculated for the coat protein (CP) sequences of nine species, although for two species evidence of both codon specific and episodic diversifying selection were found. By using Bayesian phylogenetic reconstruction methods CP nucleotide substitution rates for four species were estimated to range from between 9.29×10−3 to 2.74×10−3 (subs/site/year), values which are comparable with the short-term estimates of other related plant- and animal-infecting virus species. From these data, we were able to construct a time-measured phylogeny of the subfamily Comovirinae that estimated divergence of ninety-four extant sequences occurred less than 1,000 years ago with present virus species diversifying between 50 and 250 years ago; a period coinciding with the intensification of agricultural practices in industrial societies. Although recombination (modularity) was limited to closely related taxa, significant and often unique similarities in the protein domains between secovirid and animal infecting picorna-like viruses, especially for the protease and coat protein, suggested a shared ancestry. We discuss our results in a wider context and find tentative evidence to indicate that some members of the Secoviridae might have their origins in insects, possibly colonizing plants in a number of founding events that have led to speciation. Such a scenario; virus infection between species of different taxonomic kingdoms, has significant implications for virus emergence.

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Section: Discussionsupporting

confidence: 57%

An Evolutionary Analysis of the Secoviridae Family of Viruses

2014

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“…The site at Yantai was mostly infested with WYMV, but Chinese wheat mosaic virus (CWMV), an unrelated virus (genus Furovirus, family Virgaviridae) transmitted by the same vector (Diao et al, 1999), was occasionally detected, while only WYMV was detected in Xiping and Yangzhou. There are known to have differences between these WYMV populations (Sun et al, 2013). N12-1 was highly resistant to WYMV in Yantai, Xiping and Yangzhou; a small number of transgenic plants developed disease symptom in Yantai, which is due to the CWMV infection (detected by ELISA).…”

Section: Wymv Resistance Of the Transgenic Wheat In Field Trialsmentioning

confidence: 99%

Durable field resistance to wheat yellow mosaic virus in transgenic wheat containing the antisense virus polymerase gene

Chen¹,

Sun²,

HongYa³

et al. 2013

Plant Biotechnology Journal

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Summary Wheat yellow mosaic virus (WYMV) has spread rapidly and causes serious yield losses in the major wheat‐growing areas in China. Because it is vectored by the fungus‐like organism Polymyxa graminis that survives for long periods in soil, it is difficult to eliminate by conventional crop management or fungicides. There is also only limited resistance in commercial cultivars. In this research, fourteen independent transgenic events were obtained by co‐transformation with the antisense NIb8 gene (the NIb replicase of WYMV) and a selectable gene bar. Four original transgenic lines (N12, N13, N14 and N15) and an offspring line (N12‐1) showed high and durable resistance to WYMV in the field. Four resistant lines were shown to have segregated and only contain NIb8 (without bar) by PCR and herbicide resistance testing in the later generations. Line N12‐1 showed broad‐spectrum resistance to WYMV isolates from different sites in China. After growing in the infested soil, WYMV could not be detected by tissue printing and Western blot assays of transgenic wheat. The grain yield of transgenic wheat was about 10% greater than the wild‐type susceptible control. Northern blot and small RNA deep sequencing analyses showed that there was no accumulation of small interfering RNAs targeting the NIb8 gene in transgenic wheat plants, suggesting that transgene RNA silencing, a common mechanism of virus‐derived disease resistance, is not involved in the process of WYMV resistance. This durable and broad‐spectrum resistance to WYMV in transgenic wheat will be useful for alleviating the damage caused by WYMV.

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“…It is clear that studying the genetic variation and evolution of plant viruses proposes an important strategy for agricultural production due to the warming climate and the harsh ecosystem [8–10]. Evolution analysis of RNA viruses was achieved by codon usage bias, phylogenetic tree, genetic distance, selection pressure, genetic differentiation and gene flow which have been examined in some ss-RNA viruses [11,12] and ds-RNA viruses [4,13]. However, evolutionary analysis has only been conducted in a few viruses with overlapping open reading frames (ORFs).…”

Section: Introductionmentioning

confidence: 99%

Molecular characteristics of segment 5, a unique fragment encoding two partially overlapping ORFs in the genome of rice black-streaked dwarf virus

Zhang

Yao

et al. 2019

PLoS ONE

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Rice black-streaked dwarf virus (RBSDV), a ds-RNA virus in Fijivirus genus with family Reoviridae, which is transmitted by the small brown planthopper, is responsible for incidence of maize rough dwarf disease (MRDD) and rice black-streaked dwarf disease (RBSDD). To understand the variation and evolution of S5, a unique fragment in the genome of RBSDV which encodes two partially overlapping ORFs (ORF5-1 and ORF5-2), we analyzed 127 sequences from maize and rice exhibiting symptoms of dwarfism. The nucleotide diversity of both ORF5-1 (π = 0.039) and ORF5-2 (π = 0.027) was higher than that of the overlapping region (π = 0.011) (P < 0.05). ORF5-2 was under the greatest selection pressure based on codon bias analysis, and its activation was possibly influenced by the overlapping region. The recombinant fragments of three recombinant events (14NM23, 14BM20, and 14NM17) cross the overlapping region. Based on neighbor-joining tree analysis, the overlapping region could represent the evolutionary basis of the full-length S5, which was classified into three main groups. RBSDV populations were expanding and haplotype diversity resulted mainly from the overlapping region. The genetic differentiation of combinations (T127-B35, T127-J34, A58-B35, A58-J34, and B35-J34) reached significant or extremely significant levels. Gene flow was most frequent between subpopulations A58 and B35, with the smallest |Fst| (0.02930). We investigated interactions between 13 RBSDV proteins by two-hybrid screening assays and identified interactions between P5-1/P6, P6/P9-1, and P3/P6. We also observed self-interactive effects of P3, P6, P7-1, and P10. In short, we have proven that RBSDV populations were expanding and the overlapping region plays an important role in the genetic variation and evolution of RBSDV S5. Our results enable ongoing research into the evolutionary history of RBSDV-S5 with two partly overlapping ORFs.

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Selection Pressure and Founder Effects Constrain Genetic Variation in Differentiated Populations of Soilborne Bymovirus Wheat yellow mosaic virus (Potyviridae) in China

Cited by 22 publications

References 75 publications

An Evolutionary Analysis of the Secoviridae Family of Viruses

An Evolutionary Analysis of the Secoviridae Family of Viruses

Durable field resistance to wheat yellow mosaic virus in transgenic wheat containing the antisense virus polymerase gene

Molecular characteristics of segment 5, a unique fragment encoding two partially overlapping ORFs in the genome of rice black-streaked dwarf virus

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