First Report of Bean common mosaic virus in Cudrania tricuspidata in Korea.

Cudrania tricuspidata (Moraceae) is a deciduous tree widely distributed in East Asia, including China, Korea, and Japan. It produces delicious fruit, and its cortex and root bark have been used as a traditional medicine to treat neuritis and inflammation. As C. tricuspidata has become known as a functional food, its cultivation area and production gradually have increased in Korea. However, information of viral disease in C. tricuspidata is very limited. In September 2012, open-field-grown C. tricuspidata trees showing virus-like symptoms of mosaic, yellowing, and distortion on the leaves were found in Naju, Korea. The fruit production in the diseased trees decreased to 20 to 40% of that in healthy trees. To identify causal agent(s), total RNA was isolated from the symptomatic leaves and used to generate a transcriptome library using the TruSeq Stranded Total RNA with Ribo-Zero Plant kit (Illumina, San Diego, CA) according to the manufacturer's instruction. The transcriptome library was analyzed by next-generation sequencing (NGS) using an Illumina HiSeq2000 sequencer. NGS reads were quality filtered and de novo assembled by the Trinity pipeline, and the assembled contigs were analyzed against the viral reference genome database in Genbank by BLASTn and BLASTx searches (3). The entire NGS procedure was perofrmed by Macrogen Inc. (Seoul, South Korea). Among the analyzed contigs, one large contig (10,043 bp) was of viral origin. Nucleotide blast searches showed that the contig has a maximum identity of 89% (with 100% coverage) to the isolate MS1 (Genbank Accession No. EU761198) of Bean common mosaic virus (BCMV), which was isolated from Macroptilium atropurpureum in Australia. The presence of BCMV was confirmed by a commercially available double-antibody sandwich (DAS)-ELISA kit (Agdia, Elkhart, IN). To confirm the BCMV sequence obtained by NGS, two large fragments covering the entire BCMV genome were amplified by reverse transcription-polymerase chain reaction (RT-PCR) using two sets of specific primers (5'-AAAATAAAACAACTCATAAAGACAAC-3' and 5'-AGACTGTGTCCCAGAGCATTTC-3' to amplify the 5' half of the BCMV genome; 5'-GCATCCTGAGATTCACAGAATTC-3' and 5'-GGAACAACAAACATTGCCGTAG-3' to amplify the 3' half of the BCMV genome) and sequenced. To obtain the complete genome sequence, the 5' and 3' terminal sequences were analyzed by the 5' and 3' rapid amplification of cDNA ends (RACE) method as described previously (1). The assembled full-length sequence of BCMV isolated from C. tricuspidata was 10,051 nucleotides in length without a poly(A) tail. It was deposited in Genbank under the accession number KM076650. BCMV, a member of the genus Potyvirus, is one of the most common viruses naturally infecting legumes, including Phaseolus vulgaris (2). In general, BCMV is known to have a restricted host range outside legume species (2). Therefore, the identification of BCMV from C. tricuspidata in this report is very exceptional. Because BCMV is easily transmitted by various aphids like other potyviruses, a large-scale survey may be required for exact investigation of the BCMV incidence in C. tricuspidata to prevent rapid spread of the virus. To the best of our knowledge, this is the first report of BCMV in C. tricuspidata. References: (1) H.-R. Kwak et al. Plant Pathol. J. 29:274, 2013. (2) M. Saiz et al. Virus Res. 31:39, 1994. (3) S.-E. Schelhorn et al. PLoS Comput. Biol. 9:e1003228, 2013.

First Report of Clover yellow vein virus on Glycine max in Korea.

Glycine max (Soybean) is the most important edible crop in Korea. In Korea, eight viruses have been reported to infect soybean, including Alfalfa mosaic virus (AMV), Cowpea mosaic virus (CPMV), Cucumber mosaic virus (CMV), Soybean dwarf virus (SbDV), Soybean mosaic virus (SMV), Soybean yellow common mosaic virus (SYCMV), Soybean yellow mottle virus (SYMMV), and Peanut stunt virus (PSV) (1). In 2012, Glycine max were observed in Daegu, South Korea, with mosaic and mottling symptoms on leaves. Samples with virus-like symptoms (n = 151) were collected from Daegu including legume genetic resource field. Virus particles were filamentous rod shaped, average length 760 nm, and were analyzed by RT-PCR using specific primers for several Potyviruses and previously reported viruses infecting soybean. Only two samples showing mosaic and mottling symptoms were identified as Clover yellow vein virus (ClYVV) based on RT-PCR using primers specific for ClYVV (5'-GTTGGCTTGGTTGACACTGA-3' and 5'-CTTCGATCATGGATGCACA-3'). The sequences of amplified fragments were 97 to 98% similar with ClYVV. ClYVV is a distinct species in the genus Potyvirus and family Potyviridae. ClYVV is transmitted by several species of aphids and by mechanical inoculation (2). ClYVV was first reported on Gentiana scabra, and the disease has never been reported in soybean fields in Korea. The biological properties and full genome sequence of the selected ClYVV isolate of apparent virus symptoms between two samples were analyzed. The ClYVV isolate was inoculated to local lesion plants, re-isolated from local lesions three times, and propagated in Nicotiana benthamiana, and then named ClYVV-Gm. The ClYVV-Gm induced local lesions on inoculated leaves of N. tabacum cv. Xanthi-nc, Tetragonia expansa, and systemic symptoms on upper leaves of Chenopodium amaranticolor, C. quinoa, and N. clevelandii. The ClYVV-Gm caused mosaic and mottling symptoms on Glycine max cv. Kwangan and Phaseolus vulgaris. The genome of ClYVV-Gm was determined to be 9,584 nucleotides in length (GenBank Accession No. KF975894), and it shared 83% to 97% nucleotide identity with the sequences of 27 previously reported ClYVV isolates including Vicia fava and Pisum sativum. Despite low occurrence of ClYVV in Glycine max, ClYVV has a broad host range including tobacco, weed species, and soybean, which can lead to spreading of the virus. Our results indicate that emergence of ClYVV could become a problem to Leguminosae in Korea. To our knowledge, this is the first biological and molecular report of ClYVV infecting Glycine max in Korea. References: (1) Y. H. Lee et al. Korea Soybean Digest 29:7, 2012. (2) T. Sasaya et al. Phytopathology 87:1014, 1997.

First Report of Broad bean wilt virus 2 in Leonurus sibiricus in Korea.

Leonurus sibiricus L. (family Lamiaceae) has been used as a traditional herbal remedy to treat various gynecologic diseases. Although it is a widely distributed subtropical weed in Southeast Asia, L. sibiricus have been commercially cultivated on a small scale in many geographic areas of Korea. In August 2012, field-grown L. sibiricus plants showing mosaic, yellowing, and stunting symptoms were collected near a pepper field in Andong, Korea. Since L. sibiricus is only consumed as a raw material of traditional medicine in Korea, symptomatic plants lose commercial value entirely. To identify the causal agent(s) of the virus-like symptoms, total RNA was extracted from the symptomatic leaves, and a transcriptome library was generated using the TruSeq Stranded Total RNA with Ribo-Zero plant kit (Illumina, San Diego, CA) according to the standard protocol. Next-generation sequencing (NGS) was performed using an Illumina HiSeq2000 sequencer. De novo assembly of the quality filtered NGS reads (101-bp paired-end reads) were performed using the Trinity pipeline and the assembled contigs (92,329 contigs) were analyzed against the viral reference genome database in GenBank by BLASTn and BLASTx searches (3). The entire NGS procedure was performed by Macrogen Inc. (Seoul, South Korea). Among the analyzed contigs, only two large contigs were clearly of viral origin. Nucleotide blast searches showed that the first and second contigs (5,914 and 3,534 bp, respectively) have maximum identities of 91 and 95% to RNA1 of the isolate RP3 (GenBank Accession No. JX183225) and RNA2 of the isolate RP7 (JX183234) of Broad bean wilt virus 2 (BBWV-2), which were isolated from pepper in Korea. The NGS results were confirmed by analyzing the sequences of the fragments covering the entire BBWV-2 genome amplified by RT-PCR using specific primers for BBWV-2 as described previously (1). To obtain the complete genome sequence, terminal sequences of both RNA segments were analyzed by the 5' and 3' rapid amplification of cDNA ends (RACE) method as described previously (1). The assembled full-length sequences of BBWV-2 RNA1 and RNA2 isolated from L. sibiricus were 5,951 and 3,575 nucleotides in length, respectively, and deposited in GenBank under the accessions KM076648 and KM076649, respectively. BBWV-2 belongs to the genus Fabavirus in the family Secoviridae and it is known to have a wide host range. To investigate the host range of the BBWV-2 isolated from L. sibiricus, sap from the symptomatic leaves of L. sibiricus was inoculated to the test plants including Nicotiana benthamiana, Capsicum annuum (red pepper), and C. annuum var. gulosum (Paprika). RT-PCR detection and sequencing of the amplicons showed that all the inoculated test plants were infected with the BBWV-2 isolated from L. sibiricus. Currently, BBWV-2 is epidemic in pepper fields in Korea (1,2). Because BBWV-2 is easily transmitted by various aphids, and L. sibiricus is widely distributed in both wild and cultivated fields in Korea, this host might serve as a potential source of BBWV-2 to other crops such as pepper. To the best of our knowledge, this is the first report of BBWV-2 in L. sibiricus. References: (1) H.-R. Kwak et al. Plant Pathol. J. 29:274, 2013. (2) H.-R. Kwak et al. Plant Pathol. J. 29:397, 2013. (3) S.-E. Schelhorn et al. PLoS Comput. Biol. 9:e1003228, 2013.

First Report of Sweet potato golden vein associated virus Infecting Sweet Potato in Korea.

Sweet potato (Ipomoea batatas) is one of the most important crops in eastern Asia, including Korea. Consumption of sweet potato is increasing gradually because of its growing reputation as a health food. Recently, outbreaks of viruses infecting sweet potatoes have increased all over the world, probably because sweet potatoes are produced via vegetative propagation (1,2). In Korea, most sweet potatoes in fields have been infected by a begomovirus, Sweet potato leaf curl virus (SPLCV), and other viruses such as Sweet potato feathery mottle virus, Sweet potato virus G, and Sweet potato latent virus (3). Many countries have monitored sweet potato virus infections in fields as well as in germplasm collections to select virus-free stocks. In 2013, 20 sweet potato plants showing leaf roll symptoms in Muan, South Korea, were collected and analyzed. Total DNA was isolated from sweet potato leaves (Viral Gene-spin Viral DNA/RNA Extraction Kit, iNtRON Biotechnology, Seongnam, Korea) and viral DNA was amplified by rolling circle amplification (RCA, TempliPhi Amplification Kit, GE Healthcare Life Sciences, Uppsala, Sweden) following the manufacturer's instructions. Amplicons were digested by restriction enzyme SacI (TaKaRa Bio, Shiga, Japan) and products were run on a 1.5% agarose gel. A 2.8-kb DNA fragment was purified from a gel, ligated into a pGEM-T easy vector (Promega, Madison, WI), and sequenced (Macrogen, Seoul, Korea). Based on a BLAST search, most of the sequences (36/38) were identified as SPLCV, but two independent clones 2,824 nt in length from sweet potato cv. Sincheonmi were similar to Sweet potato golden vein associated virus (SPGVaV) isolate US:MS:1B-3 (94.38%, GenBank Accession No. HQ333143). The complete genome sequence of the SPGVaV-Korea isolate contained six ORFs, as expected for a typical monopartite begomovirus. The sequence was deposited in GenBank under accession number KF803170. SPGVaV is a whitefly (Bemisia tabaci)-transmitted virus (genus Begomovirus, family Geminiviridae). A phylogenetic analysis that included other begomoviruses that infect sweet potato showed SPGVaV-Korea to segregate with other SPGVaV isolates. SPGVaV has previously only been reported in Brazil and the United States (1). This is the first report of SPGVaV in sweet potato outside of the Americas. References: (1) L. C. Albuquerque et al. Virol. J. 9:241, 2012. (2) E. Choi et al. Acta Virol. 56:187, 2012. (3) H. R. Kwak et al. Plant Pathol. J. 22:239, 2006.

Molecular characterization of sweet potato leaf curl virus (SPLCV) isolates from Korea: phylogenetic relationship and recombination analysis.

The complete DNA genome of sweet potato leaf curl virus (SPLCV) from samples obtained from eight regions was amplified by PCR and characterized in this study. The DNA genome of one group (SPLCV Korea group 1) consisted of 2828 nucleotides and that of the second group (SPLCV Korea group 2) consisted of 2829 nucleotides. Sequence comparisons showed that the genome sequences of SPLCV Korea isolates were closely related to those of SPLCV Brazil isolates (FJ969834, FJ969835, and FJ969836), SPLCV Japan isolate (AB433788), and SPLCV USA isolate (AF104036) with nucleotide sequence identity values ranging from 96-98%. Analysis of the phylogenetic relationship of SPLCV Korea isolates with other begomoviruses revealed that the majority of SPLCV Korea isolates were clustered with SPLCV Brazil isolates (FJ969834, FJ969835, and FJ969836). Recombination analysis results revealed three recombinations among SPLCV Korea isolates, SPLCV isolates from Brazil and Japan, and ipomoea yellow vein virus (IYVV) Italy isolate.