Bean yellow mosaic virus subgroup; search for the group specific sequences in the 3' terminal region of the genome

Detection and discovery of plant viruses in soybean by metagenomic sequencing

BACKGROUND

Viruses negatively impact soybean production by causing diseases that affect yield and seed quality. Newly emerging or re-emerging viruses can also threaten soybean production because current control measures may not be effective against them. Furthermore, detection and characterization of new plant viruses requires major efforts when no sequence or antibody-based resources are available.

METHODS

In this study, soybean fields were scouted for virus-like disease symptoms during the 2016-2019 growing seasons. Total RNA was extracted from symptomatic soybean parts, cDNA libraries were prepared, and RNA sequencing was performed using high-throughput sequencing (HTS). A custom bioinformatic workflow was used to identify and assemble known and unknown virus genomes.

RESULTS

Several viruses were identified in single or mixed infections. Full- or nearly full-length genomes were generated for tobacco streak virus (TSV), alfalfa mosaic virus (AMV), tobacco ringspot virus (TRSV), soybean dwarf virus (SbDV), bean pod mottle virus (BPMV), soybean vein necrosis virus (SVNV), clover yellow vein virus (ClYVV), and a novel virus named soybean ilarvirus 1 (SIlV1). Two distinct ClYVV isolates were recovered, and their biological properties were investigated in Nicotiana benthamiana, broad bean, and soybean. In addition to infections by individual viruses, we also found that mixed viral infections in various combinations were quite common.

CONCLUSIONS

Taken together, the results of this study showed that HTS-based technology is a valuable diagnostic tool for the identification of several viruses in field-grown soybean and can provide rapid information about expected viruses as well as viruses that were previously not detected in soybean.

P3N-PIPO of Clover yellow vein virus exacerbates symptoms in pea infected with white clover mosaic virus and is implicated in viral synergism

Mixed infection of pea (Pisum sativum) with Clover yellow vein virus (ClYVV) and White clover mosaic virus (WClMV) led to more severe disease symptoms (a phenomenon called viral synergism). Similar to the mixed ClYVV/WClMV infection, a WClMV-based vector encoding P3N-PIPO of ClYVV exacerbated the disease symptoms. Infection with the WClMV vector encoding ClYVV HC-Pro (a suppressor of RNA silencing involved in potyviral synergisms), also resulted in more severe symptoms, although to a lesser extent than infection with the vector encoding P3N-PIPO. Viral genomic RNA accumulated soon after inoculation (at 2 and 4 days) at higher levels in leaves inoculated with WClMV encoding HC-Pro but at lower levels in leaves inoculated with WClMV encoding P3N-PIPO than in peas infected with WClMV encoding GFP. Our results suggest that ClYVV P3N-PIPO is involved in the synergism between ClYVV and WClMV during pea infection through an unknown mechanism different from suppression of RNA silencing.

Cross-protection against bean yellow mosaic virus (BYMV) and clover yellow vein virus by Attenuated BYMV isolate M11

Attenuated isolate M11 of Bean yellow mosaic virus (BYMV), obtained after exposing BYMV-infected plants to low temperature, and its efficacy in cross-protecting against infection by BYMV isolates from gladiolus, broad bean (Vicia faba) and white clover (Trifolium repens) was assessed with western blotting and reverse transcription-polymerase chain reaction. The level of cross-protection varied depending on the challenge virus isolates. Cross-protection was complete against BYMV isolates from gladiolus, but incomplete against BYMV isolates from other hosts. M11 also partially cross-protected against an isolate of Clover yellow vein virus. A comparison of the nucleotide sequence of M11 and those of BYMV isolates from gladiolus and from other hosts showed higher homology among gladiolus isolates than the homology between gladiolus isolates and nongladiolus isolates. In the phylogenetic trees, constructed using the nucleotide sequences of an overall polyprotein of the genomes, five gladiolus isolates clustered together, completely separated from the three BYMV isolates from other hosts. A comparison of the amino acid sequences between M11 and its parental isolate IbG, and analysis of recombinant infectious clones between M11 and IbG revealed that an amino acid at position 314 was involved in the attenuation of BYMV.

Two Resistance Modes to Clover yellow vein virus in Pea Characterized by a Green Fluorescent Protein-Tagged Virus

ABSTRACT This study characterized resistance in pea lines PI 347295 and PI 378159 to Clover yellow vein virus (ClYVV). Genetic cross experiments showed that a single recessive gene controls resistance in both lines. Conventional mechanical inoculation did not result in infection; however, particle bombardment with infectious plasmid or mechanical inoculation with concentrated viral inocula did cause infection. When ClYVV No. 30 isolate was tagged with a green fluorescent protein (GFP) and used to monitor infection, viral cell-to-cell movement differed in the two pea lines. In PI 347595, ClYVV replicated at a single-cell level, but did not move to neighboring cells, indicating that resistance operated at a cell-to-cell step. In PI 378159, the virus moved to cells around the infection site and reached the leaf veins, but viral movement was slower than that in the susceptible line. The viruses observed around the infection sites and in the veins were then recovered and inoculated again by a conventional mechanical inoculation method onto PI 378159 demonstrating that ClYVV probably had mutated and newly emerged mutant viruses can move to neighboring cells and systemically infect the plants. Tagging the virus with GFP was an efficient tool for characterizing resistance modes. Implications of the two resistance modes are discussed.

Sequence of the 3'-terminal region of a Zimbabwe isolate of cowpea aphid-borne mosaic virus (CABMV)

The 3'-terminal 1221 nucleotides of a Zimbabwe isolate of cowpea aphid-borne mosaic potyvirus (CABMV) genome have been sequenced. The sequence comprises an open reading frame (ORF) of 990 nucleotides and a 3' non-coding-region of 231 nucleotides followed by a poly-A. The ORF has high similarity to NIb and coat proteins (CP) of potyviruses. A potential CP Q/S cleavage site was identified, yielding a CP of 30.5 kDa containing 275 amino acids. The CABMV sequence is closely related to that of South African passiflora virus (SAPV) which should therefore be regarded as a strain of CABMV.

The complete nucleotide sequences of the coat protein cistron and the 3' non-coding region of a newly-identified potyvirus infecting sweetpotato, as compared to those of sweetpotato feathery mottle virus

Complementary DNA representing 728 nucleotides of the 3' end of the genomic RNA of sweetpotato virus G (SPV-G) a newly-identified potyvirus infecting sweetpotato, was cloned and sequenced. This sequence was combined with that previously determined for the 5' terminal part of the coat protein cistron of the virus. The whole sequence contained a single open reading frame (ORF) of 1065 nucleotide, with the capacity to encode a coat protein of 355 amino acids, significantly larger than that of other potyviruses. The ORF was followed by an untranslated region of 222 nucleotides and a poly (A) tail. The coat protein of SPV-G was only distantly related to that of known potyviruses, with the exception of sweetpotato feathery mottle virus (SPFMV). Indeed, sequence identity in the C-terminal three quarters of the coat protein (more than 80%) and in the 3' untranslated region (more than 70%) indicate that SPV-G should be considered as closely related to, though distinct from SPFMV. This subset relationship is similar to that previously reported for members of the bean yellow mosaic virus subgroup or the bean common mosaic virus subgroup.

Evolutionary relationships among bean common mosaic virus strains and closely related potyviruses

Bean common mosaic virus (BCMV) consists of a large number of strains with complex and controversial relationships among them and with other potyviruses that infect legumes. In order to elucidate the BCMV taxonomic pattern and its evolutionary implications, a phylogenetic analysis has been carried out. The analysis of the coat protein gene and 3' non-coding region (NCR) sequences recently obtained by us and other currently available potyviral sequences confirms the clustering of viruses comprised in BCMV strains with other closely related potyviruses and reveals the great informative content of 3' NCR, suggesting a more relevant role for this region in phylogenetic analysis.

A proposal for a bean common mosaic subgroup of potyviruses

In order to elucidate the taxonomic positions of bean common mosaic virus (BCMV) and blackeye cowpea mosaic virus (B1CMV), several strains of these viruses were compared on the basis of host ranges, antigenic properties established with antisera to virions and to N-terminal peptide domains of their coat proteins, and high performance liquid chromatographic peptide profiles. The comparison includes three strains of BCMV, viz. NL1, NL3 and NY15, four strains of B1CMV, viz. Fla, Ind, NR, and W, and the Moroccan isolate (Mor) of cowpea aphid-borne mosaic virus (CABMV), formerly designated as B1CMV-Mor. Based on these parameters, Fla, NR, and W are strains of one virus, whereas NL3, Ind and CABMV-Mor (and possibly NL1 and NY15) are separate viruses. In view of these characteristics which allow similar viruses to be separated, we propose that these viruses be included in a bean common mosaic subgroup of the genus Potyvirus.

A summary of potyvirus taxonomy and definitions

The current taxonomic status of the family Potyviridae is presented with suggestions for resolving some taxonomic problems. Terms such as strain, pathotype, serotype, variant, mutant, and isolate are discussed in relation to the family.