Molecular characterization of a novel umbra-like virus from Thuja orientalis (arborvitae) in South Korea.

A novel umbra-like virus was identified in arborvitae in South Korea using RNA sequencing (RNA-seq). The virus identified was tentatively named "arborvitae umbra-like virus" (AULV) and contained a 4,300-nucleotide genome organized into four non-structural open reading frames (ORFs). Cloning and Sanger sequencing were used to confirm the viral contig sequence and determine the size of the genome. Genome analysis indicated that ORF2 encodes an RNA-dependent RNA polymerase that is probably expressed through ribosomal frameshifting. ORF3 encodes a putative long-distance movement protein, while the functions of ORFs 1 and 4 are unknown. The virus lacks a coat protein gene. The genome of AULV shares 27.3%-48.4% nucleotide sequence identity with closely related umbraviruses. Phylogenetic analysis based on the complete genome sequences and amino acid sequences of the RNA-dependent RNA polymerase revealed that AULV forms a monophyletic lineage with Guiyang paspalum paspaloides tombus-like virus (GPpTV1). We suggest that AULV is a novel umbra-like virus belonging to the family Tombusviridae.

Genome sequence and characterization of a novel fabavirus infecting Cirsium setidens (gondre) in South Korea.

The complete nucleotide sequence of a novel gondre (Cirsium setidens)-infecting virus, provisionally named "cirsium virus A" (CiVA), was determined by high-throughput and Sanger sequencing, revealing a genome organization typical of fabaviruses. RNA1 and RNA2 are 5,828 and 3,478 nucleotides long, excluding the 3'-terminal poly(A) tails, each containing a single open reading frame. The highest sequence identity values for the CiVA coat protein and proteinase-polymerase, compared with known fabavirus sequences, were 59.09% and 69.68%, respectively, falling below the current thresholds for Fabavirus species demarcation. Our findings support classifying CiVA as a novel putative member of the genus Fabavirus, subfamily Comovirinae, family Secoviridae.

Complete genome sequence and genome characterization of a novel potyvirus from Lamprocapnos spectabilis.

The genome of a new potyvirus from a Lamprocapnos spectabilis plant in South Korea was sequenced by high-throughput sequencing and confirmed by Sanger sequencing. The new potyvirus was tentatively named "lamprocapnos virus A" (LaVA); its complete genome contains 9,745 nucleotides, excluding the 3'-terminal poly(A) tail. The LaVA genome structure is similar to that of members of the genus Potyvirus and contains an open reading frame encoding a large putative polyprotein of 3,120 amino acids (aa) with conserved motifs. The complete genome shared 48%-56% nucleotide sequence identity and the polyprotein shared 41%-52% aa sequence identity with those of other potyviruses. These values are below the standard thresholds for potyvirus species demarcation. Phylogenetic analysis based on polyprotein sequences showed that LaVA belongs to the genus Potyvirus. To our knowledge, this is the first report of the complete genome sequence and genome characterization of a potyvirus infecting Lamprocapnos spectabilis.

Complete Genome Sequence of a Papaya ringspot virus Isolate from South Korea That Infects Cucurbita pepo.

The complete genome sequence of a Papaya ringspot virus (PRSV) isolate from South Korea (SK) infecting squash (Cucurbita pepo) was obtained using paired-end RNA sequencing. A BLASTn search of the PRSV SK isolate full-genome sequence showed nucleotide sequence identity ranging from 81% to 83% with previously reported PRSV isolates (GenBank accession numbers KX655874 and EF017707).

The first complete sequence and genome structure of daphne virus Y.

From Daphne odora Thunb., an ornamental shrub in the Republic of Korea, a potyvirus was identified that has an RNA genome of 9,448 nucleotides (excluding the 3'-terminal poly(A) tail) encoding a polyprotein of 3,065 amino acids, with nine putative protease cleavage sites producing ten proteins. Since this potyvirus shared the highest nucleotide sequence identity (91 %; query coverage 5 %) with the available partial sequence of daphne virus Y (DVY) from New Zealand (EU179854), it was considered a Korean isolate of DVY. This is the first molecular characterization of the complete genome sequence of a DVY isolate.

Complete genome sequence and construction of infectious full-length cDNA clones of tobacco ringspot Nepovirus, a viral pathogen causing bud blight in soybean.

Tobacco ringspot virus (TRSV, genus Nepovirus), causes severe diseases in soybean and tobacco plants. TRSV-induced bud blight disease significantly reduced both the yield and quality of soybeans. The function of the encoded viral gene product involved in TRSV infection was unclear due to the limitation of reverse genetics studies on the viral genome. Here, we represent the successful construction of infectious full-length cDNA clones of TRSV genome (RNA1 and RNA2). The cDNAs of TRSV RNA1 and RNA2 were cloned into the binary vector pPZP211 immediately downstream of a double cauliflower mosaic virus 35S promoter and upstream of the nopaline synthase terminator. Seven days after agrobacterium-mediated co-inoculation of these two constructs, Nicotiana benthamiana plants developed a systemic infection with necrotic ringspot symptoms and weak stunting of the leaves, similar to that induced by natural TRSV. The systemic infection was confirmed by transmission electron microscopy and Western blot analysis. Simultaneously, soybean, tomato, and Arabidopsis ecotype Estland were mechanically inoculated with sap prepared from TRSV-agroinfiltrated N. benthamiana leaves, showing typical symptoms of bud blight, necrotic spots, and lethal systemic necrosis, respectively. The system developed herein will be an appealing way to determine TRSV viral gene functions and study host-TRSV interactions.