Publications by authors named "Bong Choon Lee"

24 Publications

  • Page 1 of 1

Soybean Viromes in the Republic of Korea Revealed by RT-PCR and Next-Generation Sequencing.

Microorganisms 2020 Nov 12;8(11). Epub 2020 Nov 12.

Research Institute of Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul 08826, Korea.

Soybean ( L.) is one of the most important crop plants in the Republic of Korea. Here, we conducted a soybean virome study. We harvested a total of 172 soybean leaf samples showing disease symptoms from major soybean-growing regions in the Republic of Korea. Individual samples were examined for virus infection by RT-PCR. Moreover, we generated eight libraries representing eight provinces by pooling samples and four libraries from single samples. RNA-seq followed by bioinformatics analyses revealed 10 different RNA viruses infecting soybean. The proportion of viral reads in each transcriptome ranged from 0.2 to 31.7%. Coinfection of different viruses in soybean plants was very common. There was a single dominant virus in each province, and this geographical difference might be related to the soybean seeds that transmit viruses. In this study, 32 viral genome sequences were assembled and successfully used to analyze the phylogenetic relationships and quasispecies nature of the identified RNA viruses. Moreover, RT-PCR with newly developed primers confirmed infection of the identified viruses in each library. Taken together, our soybean virome study provides a comprehensive overview of viruses infecting soybean in eight geographical regions in the Republic of Korea and four single soybean plants in detail.
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http://dx.doi.org/10.3390/microorganisms8111777DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7698195PMC
November 2020

Development of a transcranial direct current stimulation (tDCS) device based on polarity interchangeable electrodes.

Technol Health Care 2020 ;28(S1):311-319

Department of Radiological Science, Health Sciences Division, Dongseo University, Busan, Korea.

Background: Transcranial direct current stimulation (tDCS) is a noninvasive brain stimulation technique that can help modulate cortical excitability by transmitting direct current (DC) between a pair of scalp electrodes. To date, most studies on tDCS have been relatively short-lived, and the DC stimulations only lasted a few minutes. Conventional tDCS devices usually have some problems such as needing a lot of patches and lead lines.

Objective: Since conventional tDCS devices are unsuitable for use in long-term stimulations, we developed a new tDCS which can easily be used by unskilled persons.

Methods: We developed a new tDCS device that does not have lead lines for tDCS electrodes and has a simple structure.

Result: This device can achieve stimulation with polarity interchangeable DC without physically swapping the anode and cathode. The performance of the proposed device was verified through an experiment.

Conclusion: The developed tDCS device can contribute to long-term research as it uses neuroelectric stimulation.
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http://dx.doi.org/10.3233/THC-209031DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7369044PMC
April 2021

Sweet potato viromes in eight different geographical regions in Korea and two different cultivars.

Sci Rep 2020 02 13;10(1):2588. Epub 2020 Feb 13.

Research Institute of Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul, 08826, Republic of Korea.

The sweet potato in the family Convolvulaceae is a dicotyledonous perennial plant. Here, we conducted a comprehensive sweet potato virome study using 10 different libraries from eight regions in Korea and two different sweet potato cultivars by RNA-Sequencing. Comprehensive bioinformatics analyses revealed 10 different virus species infecting sweet potato. Moreover, we identified two novel viruses infecting sweet potato referred to as Sweet potato virus E (SPVE) in the genus Potyvirus and Sweet potato virus F (SPVF) in the genus Carlavirus. Of the identified viruses, Sweet potato feathery mottle virus (SPFMV) was the dominant virus followed by Sweet potato virus C (SPVC) and SPVE in Korea. We obtained a total of 30 viral genomes for eight viruses. Our phylogenetic analyses showed many potyvirus isolates are highly correlated with geographical regions. However, two isolates of SPFMV and a single isolate of Sweet potato virus G (SPVG) were genetically distant from other known isolates. The mutation rate was the highest in SPFMV followed by SPVC and SPVG. Two different sweet potato cultivars, Beni Haruka and Hogammi, were infected by seven and five viruses, respectively. Taken together, we provide a complete list of viruses infecting sweet potato in Korea and diagnostic methods.
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http://dx.doi.org/10.1038/s41598-020-59518-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7018812PMC
February 2020

Barley RNA viromes in six different geographical regions in Korea.

Sci Rep 2018 09 5;8(1):13237. Epub 2018 Sep 5.

Research Institute of Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul, 08826, Republic of Korea.

Barley is a kind of cereal grass belonging to the family Poaceae. To examine viruses infecting winter barley in Korea, we carried out a comprehensive study of barley RNA viromes using next-generation sequencing (NGS). A total of 110 barley leaf samples from 17 geographical locations were collected. NGS followed by extensive bioinformatics analyses revealed six different barley viromes: Barley yellow mosaic virus (BaYMV), Barley mild mosaic virus (BaMMV), Barley yellow dwarf virus (BYDV), Hordeum vulgare endornavirus (HvEV), and Barley virus G (BVG). BaYMV and HvEV were identified in all libraries, while other viruses were identified in some specific library. Based on the number of virus-associated reads, BaYMV was a dominant virus infecting winter barley in Korea causing yellow disease symptoms. We obtained nearly complete genomes of six BaYMV isolates and two BaMMV isolates. Phylogenetic analyses indicate that BaYMV and BaMMV were largely grouped based on geographical regions such as Asia and Europe. Single nucleotide polymorphisms analyses suggested that most BaYMV and BaMMV showed strong genetic variations; however, BaYMV isolate Jeonju and BaMMV isolate Gunsan exhibited a few and no SNPs, respectively, suggesting low level of genetic variation. Taken together, this is the first study of barley RNA viromes in Korea.
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http://dx.doi.org/10.1038/s41598-018-31671-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6125401PMC
September 2018

Identification of viral domains integrated into Arabidopsis proteome.

Mol Phylogenet Evol 2018 11 17;128:246-257. Epub 2018 Aug 17.

Research Institute of Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul 08826, Republic of Korea; The Taejin Genome Institute, Gadam-gil 61, Hoeongseong 25239, Republic of Korea. Electronic address:

Horizontal gene transfer (HGT) contributes to the genome evolution of living organisms. In particular, several recent studies provide convincing data on the integration of viral sequences into diverse organisms. Here, we identified 101 viral domains integrated into the model plant Arabidopsis proteome. Functional analysis based on gene ontology (GO) terms indicates that viral domains in the Arabidopsis proteome were involved in various stress responses with binding functions. Protein interaction networks support the strong protein interactions of viral domains with other Arabidopsis proteins. A proteome-wide analysis gave a comprehensive evolutionary view of viral domains integrated into 41 plant proteomes, revealing the specific and conserved integration of viral domains into plant proteomes. Phylogenetic analyses revealed the possible HGT between viral domains and plant proteomes. Our results provide an overview of the integration of viral domains into plant proteomes and their possible functional roles associated with plant defense mechanisms.
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http://dx.doi.org/10.1016/j.ympev.2018.08.009DOI Listing
November 2018

Complete genome sequence of peanut virus C, a putative novel ilarvirus.

Arch Virol 2018 Aug 12;163(8):2265-2269. Epub 2018 Apr 12.

Crop Production Technology Research Division, National Institute of Crop Science, Rural Development Administration, Miryang, 50424, Republic of Korea.

We determined the complete genome sequence of a putative novel ilarvirus, tentatively named "peanut virus C" (PVC), identified in peanut (Arachis hypogaea). The three segmented genomic RNA molecules of PVC were 3474 (RNA1), 2925 (RNA2), and 2160 (RNA3) nucleotides in length, with five predicted open reading frames containing conserved domains and motifs that are typical features of ilarviruses. The three genomic RNAs shared nucleotide sequence similarity (74% identity and 93% query coverage for RNA1, 75% identity and 85% query coverage for RNA2, and 72% identity and 70% query coverage for RNA3) with the most closely related ilarvirus, parietaria mottle virus. These results suggest that PVC is a novel member of the genus Ilarvirus in the family Bromoviridae.
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http://dx.doi.org/10.1007/s00705-018-3827-5DOI Listing
August 2018

Peach RNA viromes in six different peach cultivars.

Sci Rep 2018 01 30;8(1):1844. Epub 2018 Jan 30.

Research Institute of Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul, 08826, Republic of Korea.

Many recent studies have demonstrated that several known and unknown viruses infect many horticultural plants. However, the elucidation of a viral population and the understanding of the genetic complexity of viral genomes in a single plant are rarely reported. Here, we conducted metatranscriptome analyses using six different peach trees representing six individual peach cultivars. We identified six viruses including five viruses in the family Betaflexiviridae and a novel virus belonging to the family Tymoviridae as well as two viroids. The number of identified viruses and viroids in each transcriptome ranged from one to six. We obtained 18 complete or nearly complete genomes for six viruses and two viroids using transcriptome data. Furthermore, we analyzed single nucleotide variations for individual viral genomes. In addition, we analyzed the amount of viral RNA and copy number for identified viruses and viroids. Some viruses or viroids were commonly present in different cultivars; however, the list of infected viruses and viroids in each cultivar was different. Taken together, our study reveals the viral population in a single peach tree and a comprehensive overview for the diversities of viral communities in different peach cultivars.
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http://dx.doi.org/10.1038/s41598-018-20256-wDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5789896PMC
January 2018

Genome Assembly and Single Nucleotide Variations for Soybean Mosaic Virus Using Soybean Seed Transcriptome Data.

Plant Pathol J 2017 Oct 1;33(5):478-487. Epub 2017 Oct 1.

Department of Agricultural Biotechnology, Research Institute of Agriculture and Life Sciences, and Plant Genomics and Breeding Institute, College of Agriculture and Life Sciences, Seoul National University, Seoul 08826, Korea.

Soybean is the most important legume crop in the world. Several diseases in soybean lead to serious yield losses in major soybean-producing countries. Moreover, soybean can be infected by diverse viruses. Recently, we carried out a large-scale screening to identify viruses infecting soybean using available soybean transcriptome data. Of the screened transcriptomes, a soybean transcriptome for soybean seed development analysis contains several virus-associated sequences. In this study, we identified five viruses, including soybean mosaic virus (SMV), infecting soybean by transcriptome assembly followed by blast search. We assembled a nearly complete consensus genome sequence of SMV China using transcriptome data. Based on phylogenetic analysis, the consensus genome sequence of SMV China was closely related to SMV isolates from South Korea. We examined single nucleotide variations (SNVs) for SMVs in the soybean seed transcriptome revealing 780 SNVs, which were evenly distributed on the SMV genome. Four SNVs, C-U, U-C, A-G, and G-A, were frequently identified. This result demonstrated the quasispecies variation of the SMV genome. Taken together, this study carried out bioinformatics analyses to identify viruses using soybean transcriptome data. In addition, we demonstrated the application of soybean transcriptome data for virus genome assembly and SNV analysis.
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http://dx.doi.org/10.5423/PPJ.OA.03.2017.0060DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5624490PMC
October 2017

Genome Sequence of Grapevine Virus T, a Novel Foveavirus Infecting Grapevine.

Genome Announc 2017 Sep 14;5(37). Epub 2017 Sep 14.

Department of Agricultural Biotechnology, College of Agriculture and Life Sciences, Seoul National University, Seoul, Republic of Korea

Here, we report the genome sequence of grapevine virus T (GVT), a novel single-stranded RNA virus identified from a transcriptome of grapevine. The genome of GVT is 8,701 nucleotides in length and encodes five open reading frames. GVT is a putative member of the genus in the family .
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http://dx.doi.org/10.1128/genomeA.00995-17DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5597771PMC
September 2017

Genome Sequence of Grapevine Virus K, a Novel Vitivirus Infecting Grapevine.

Genome Announc 2017 Sep 14;5(37). Epub 2017 Sep 14.

Department of Agricultural Biotechnology, College of Agriculture and Life Sciences, Seoul National University, Seoul, Republic of Korea

Here, we report the genome sequence of grapevine virus K (GVK), a novel single-stranded RNA virus identified from a transcriptome of grapevine. The genome of GVK is 7,476 nucleotides in length and encodes 5 open reading frames. GVK is a putative member of the genus in the family .
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http://dx.doi.org/10.1128/genomeA.00994-17DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5597770PMC
September 2017

Complete genome sequence of rice virus A, a new member of the family Tombusviridae.

Arch Virol 2017 Oct 10;162(10):3247-3250. Epub 2017 Jul 10.

Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, 305-806, South Korea.

An evaluation of the virus population in rice plants using next-generation sequencing technologies resulted in the discovery of a new RNA virus, tentatively named rice virus A (RVA). The complete RVA genome sequence was determined and analyzed, revealing a genome organization resembling that of viruses classified in the genera Aureusvirus, Tombusvirus and Zeavirus within the family Tombusviridae. With 4,832 nucleotides, the RVA genome may be the largest monopartite genome sequenced to date in the family Tombusviridae. The 453-amino acid RVA coat protein shares the highest identity with the gp3 protein of an unclassified carascovirus, SF1 (GenBank accession no. KF510027) isolated from San Francisco wastewater, rather than the coat protein of any known member of the family Tombusviridae. These novel characteristics represent a significant divergence from the genomes of viruses belonging to the sixteen existing genera of the family Tombusviridae, demonstrating that RVA is likely a new family member.
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http://dx.doi.org/10.1007/s00705-017-3472-4DOI Listing
October 2017

The pepper virome: natural co-infection of diverse viruses and their quasispecies.

BMC Genomics 2017 06 8;18(1):453. Epub 2017 Jun 8.

Department of Agricultural Biotechnology, College of Agriculture and Life Sciences, Seoul National University, Seoul, 151-921, Republic of Korea.

Background: The co-infection of diverse viruses in a host plant is common; however, little is known about viral populations and their quasispecies in the host.

Results: Here, we report the first pepper viromes that were co-infected by different types of viral genomes. The pepper viromes are dominated by geminivirus DNA-A followed by a novel carlavirus referred to as Pepper virus A. The two pepper cultivars share similar viral populations and replications. However, the quasispecies for double-stranded RNA virus and two satellite DNAs were heterogeneous and homogenous in susceptible and resistant cultivars, respectively, indicating the quasispecies of an individual virus depends on the host.

Conclusions: Taken together, we provide the first evidence that the host plant resistant to viruses has an unrevealed antiviral system, affecting viral quasispecies, not replication.
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http://dx.doi.org/10.1186/s12864-017-3838-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5465472PMC
June 2017

Integrated analyses using RNA-Seq data reveal viral genomes, single nucleotide variations, the phylogenetic relationship, and recombination for Apple stem grooving virus.

BMC Genomics 2016 08 9;17:579. Epub 2016 Aug 9.

Department of Agricultural Biotechnology, College of Agriculture and Life Sciences, Seoul National University, Seoul, 151-921, Republic of Korea.

Background: Next-generation sequencing (NGS) provides many possibilities for plant virology research. In this study, we performed integrated analyses using plant transcriptome data for plant virus identification using Apple stem grooving virus (ASGV) as an exemplar virus. We used 15 publicly available transcriptome libraries from three different studies, two mRNA-Seq studies and a small RNA-Seq study.

Results: We de novo assembled nearly complete genomes of ASGV isolates Fuji and Cuiguan from apple and pear transcriptomes, respectively, and identified single nucleotide variations (SNVs) of ASGV within the transcriptomes. We demonstrated the application of NGS raw data to confirm viral infections in the plant transcriptomes. In addition, we compared the usability of two de novo assemblers, Trinity and Velvet, for virus identification and genome assembly. A phylogenetic tree revealed that ASGV and Citrus tatter leaf virus (CTLV) are the same virus, which was divided into two clades. Recombination analyses identified six recombination events from 21 viral genomes.

Conclusions: Taken together, our in silico analyses using NGS data provide a successful application of plant transcriptomes to reveal extensive information associated with viral genome assembly, SNVs, phylogenetic relationships, and genetic recombination.
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http://dx.doi.org/10.1186/s12864-016-2994-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4977635PMC
August 2016

De novo transcriptome assembly of Setatria italica variety Taejin.

Genom Data 2016 Jun 5;8:121-2. Epub 2016 May 5.

Department of Agricultural Biotechnology, College of Agriculture and Life Sciences, Seoul National University, Seoul 151-921, Republic of Korea; The Taejin Genome Institute, Gadam-gil 61, Hoeongseong 25239, Republic of Korea.

Foxtail millet (Setaria italica) belonging to the family Poaceae is an important millet that is widely cultivated in East Asia. Of the cultivated millets, the foxtail millet has the longest history and is one of the main food crops in South India and China. Moreover, foxtail millet is a model plant system for biofuel generation utilizing the C4 photosynthetic pathway. In this study, we carried out de novo transcriptome assembly for the foxtail millet variety Taejin collected from Korea using next-generation sequencing. We obtained a total of 8.676 GB raw data by paired-end sequencing. The raw data in this study can be available in NCBI SRA database with accession number of SRR3406552. The Trinity program was used to de novo assemble 145,332 transcripts. Using the TransDecoder program, we predicted 82,925 putative proteins. BLASTP was performed against the Swiss-Prot protein sequence database to annotate the functions of identified proteins, resulting in 20,555 potentially novel proteins. Taken together, this study provides transcriptome data for the foxtail millet variety Taejin by RNA-Seq.
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http://dx.doi.org/10.1016/j.gdata.2016.05.001DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4878839PMC
June 2016

De novo transcriptome assembly of two Vigna angularis varieties collected from Korea.

Genom Data 2016 Jun 5;8:119-20. Epub 2016 May 5.

Department of Agricultural Biotechnology, College of Agriculture and Life Sciences, Seoul National University, Seoul 151-921, Republic of Korea; The Taejin Genome Institute, Gadam-gil 61, Hoengseong 25239, Republic of Korea.

The adzuki bean (Vigna angularis), a member of the family Fabaceae, is widely grown in Asia, from East Asia to the Himalayas. The adzuki bean is known as an ingredient that adds sweetness to diverse desserts made in Eastern Asian countries. Libraries prepared from two V. angularis varieties referred to as Taejin Black and Taejin Red were paired-end sequenced using the Illumina HiSeq 2000 system. The raw data in this study can be available in NCBI SRA database with accession numbers of SRR3406660 and SRR3406553. After de novo transcriptome assembly using Trinity, we obtained 324,219 and 280,056 transcripts from Taejin Black and Taejin Red, respectively. We predicted a total of 238,321 proteins and 179,519 proteins for Taejin Black and Taejin Red, respectively, by the TransDecoder program. We carried out BLASTP on the predicted proteins against the Swiss-Prot protein sequence database to predict the putative functions of identified proteins. Taken together, we provide transcriptomes of two adzuki bean varieties by RNA-Seq, which might be usefully applied to generate molecular markers.
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http://dx.doi.org/10.1016/j.gdata.2016.05.004DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4878840PMC
June 2016

De novo transcriptome assembly of Sorghum bicolor variety Taejin.

Genom Data 2016 Jun 5;8:117-8. Epub 2016 May 5.

Department of Agricultural Biotechnology, College of Agriculture and Life Sciences, Seoul National University, Seoul 151-921, Republic of Korea; The Taejin Genome Institute, Gadam-gil 61, Hoengseong, 25239, Republic of Korea.

Sorghum (Sorghum bicolor), also known as great millet, is one of the most popular cultivated grass species in the world. Sorghum is frequently consumed as food for humans and animals as well as used for ethanol production. In this study, we conducted de novo transcriptome assembly for sorghum variety Taejin by next-generation sequencing, obtaining 8.748 GB of raw data. The raw data in this study can be available in NCBI SRA database with accession number of SRX1715644. Using the Trinity program, we identified 222,161 transcripts from sorghum variety Taejin. We further predicted coding regions within the assembled transcripts by the TransDecoder program, resulting in a total of 148,531 proteins. We carried out BLASTP against the Swiss-Prot protein sequence database to annotate the functions of the identified proteins. To our knowledge, this is the first transcriptome data for a sorghum variety derived from Korea, and it can be usefully applied to the generation of genetic markers.
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http://dx.doi.org/10.1016/j.gdata.2016.05.002DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4878842PMC
June 2016

The complete genomic sequence of a tentative new polerovirus identified in barley in South Korea.

Arch Virol 2016 Jul 5;161(7):2047-50. Epub 2016 May 5.

Biosystems and Bioengineering Program, University of Science and Technology (UST), Daejeon, 305-350, South Korea.

The complete nucleotide sequence of a new barley polerovirus, tentatively named barley virus G (BVG), which was isolated in Gimje, South Korea, has been determined using an RNA sequencing technique combined with polymerase chain reaction methods. The viral genomic RNA of BVG is 5,620 nucleotides long and contains six typical open reading frames commonly observed in other poleroviruses. Sequence comparisons revealed that BVG is most closely related to maize yellow dwarf virus-RMV, with the highest amino acid identities being less than 90 % for all of the corresponding proteins. These results suggested that BVG is a member of a new species in the genus Polerovirus.
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http://dx.doi.org/10.1007/s00705-016-2881-0DOI Listing
July 2016

One-step multiplex reverse transcription-polymerase chain reaction for the simultaneous detection of three rice viruses.

J Virol Methods 2013 Nov 11;193(2):674-8. Epub 2013 Jul 11.

National Institute of Crop Science, RDA, Suwon, Republic of Korea.

Rice stripe virus (RSV), Rice black-streaked dwarf virus (RBSDV), and Rice dwarf virus (RDV) are major rice-infecting viruses in Korea that can cause serious crop losses. A one-step multiplex reverse transcription-polymerase chain reaction (mRT-PCR) was developed for the simultaneous detection of these rice viruses. Three sets of specific primers targeted to the capsid protein coding genes of RSV, RBSDV, and RDV were used to amplify fragments that were 703 bp, 485 bp, and 252 bp, respectively. The one-step mRT-PCR assay proved to be a sensitive and rapid method for detecting the three rice viruses. This method could be used to facilitate better control of rice viruses.
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http://dx.doi.org/10.1016/j.jviromet.2013.07.008DOI Listing
November 2013

A systems approach for identifying resistance factors to Rice stripe virus.

Mol Plant Microbe Interact 2012 Apr;25(4):534-45

Department of Life Sciences, POSTECH, Pohang, Republic of Korea.

Rice stripe virus (RSV) causes disease that can severely affect the productivity of rice (Oryza sativa). Several RSV-resistant cultivars have been developed. However, host factors conferring RSV resistance in these cultivars are still elusive. Here, we present a systems approach for identifying potential rice resistance factors. We developed two near-isogenic lines (NIL), RSV-resistant NIL22 and RSV-susceptible NIL37, and performed gene expression profiling of the two lines in RSV-infected and RSV-uninfected conditions. We identified 237 differentially expressed genes (DEG) between NIL22 and NIL37. By integrating with known quantitative trait loci (QTL), we selected 11 DEG located within the RSV resistance QTL as RSV resistance factor candidates. Furthermore, we identified 417 DEG between RSV-infected and RSV-uninfected conditions. Using an interaction network-based method, we selected 20 DEG highly interacting with the two sets of DEG as RSV resistance factor candidates. Among the 31 candidates, we selected the final set of 21 potential RSV resistance factors whose differential expression was confirmed in the independent samples using real-time reverse-transcription polymerase chain reaction. Finally, we reconstructed a network model delineating potential association of the 21 selected factors with resistance-related processes. In summary, our approach, based on gene expression profiling, revealed potential host resistance factors and a network model describing their relationships with resistance-related processes, which can be further validated in detailed experiments.
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http://dx.doi.org/10.1094/MPMI-11-11-0282DOI Listing
April 2012

Suppression of NS3 and MP is important for the stable inheritance of RNAi-mediated rice stripe virus (RSV) resistance obtained by targeting the fully complementary RSV-CP gene.

Mol Cells 2012 Jan 29;33(1):43-51. Epub 2011 Nov 29.

National Institute of Crop Science, Rural Development Administration, Suwon 441-857, Korea.

Rice stripe virus (RSV) is a viral disease that seriously impacts rice production in East Asia, most notably in Korea, China, and Japan. Highly RSV-resistant transgenic japonica rice plants were generated using a dsRNAi construct designed to silence the entire sequence region of the RSV-CP gene. Transgenic rice plants were inoculated with a population of viruliferous insects, small brown planthoppers (SBPH), and their resistance was evaluated using ELISA and an infection rate assay. A correlation between the expression of the RSV-CP homologous small RNAs and the RSV resistance of the transgenic rice lines was discovered. These plants were also analyzed by comparing the expression pattern of invading viral genes, small RNA production and the stable transmission of the RSV resistance trait to the T3 generation. Furthermore, the agronomic trait was stably transmitted to the T4 generation of transgenic plants.
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http://dx.doi.org/10.1007/s10059-012-2185-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3887747PMC
January 2012

Strain persistence and fluctuation of multiple-antibiotic resistant Campylobacter coli colonizing turkeys over successive production cycles.

Foodborne Pathog Dis 2005 ;2(1):103-10

Department of Food Science, North Carolina State University, Raleigh, North Carolina 27695-2764, USA.

The dynamics of colonization of turkeys by thermophilic campylobacters that are resistant to multiple antibiotics is poorly understood. In this study, we monitored cecal colonization of turkeys by Campylobacter over three successive production cycles at the same farm. Campylobacter isolated from the ceca was predominantly C. coli in all three flocks. Isolates with two distinct fla types that represented a single clonal group based on pulsed-field gel electrophoresis and that were resistant to multiple antibiotics (tetracycline, streptomycin, ampicillin, erythromycin, kanamycin, nalidixic acid, and ciprofloxacin) predominated throughout the three production cycles. The relative prevalence of each fla type, however, varied significantly from one flock to the next. The repeated isolation of these multiresistant C. coli from successive flocks likely reflected persistence of the organisms in currently unknown reservoirs in the production environment or, alternatively, repeated introduction events followed by establishment of these bacteria in each successive flock.
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http://dx.doi.org/10.1089/fpd.2005.2.103DOI Listing
August 2005

Campylobacter colonization of sibling turkey flocks reared under different management conditions.

J Food Prot 2004 Jul;67(7):1463-8

Department of Food Science, North Carolina State University, Raleigh, North Carolina 27695, USA.

Uncertainty exists concerning the key factors contributing to Campylobacter colonization of poultry, especially the possible role of vertical transmission from breeder hens to young birds. A longitudinal study of Campylobacter colonization was performed in two sibling pairs of turkey flocks (four flocks total). Each pair of sibling flocks shared breeder hen populations and was obtained from the same hatchery. One flock of each pair was grown on a commercial farm, and the other was grown in an instructional demonstration unit (Teaching Animal Unit [TAU]). Flocks were located within a 60-mi (96.8-km) radius. The time of placement, feed formulations, stocking density, and general husbandry were the same for both flocks, and each flock was processed at a commercial processing plant following standard feed withdrawal and transport protocols. Both flocks grown on the commercial farms became colonized with Campylobacter between weeks 2 and 3 and remained colonized until processing. Between 80 and 90% of isolates were Campylobacter coli, and the remainder were Campylobacter jejuni. In contrast, neither C. coli nor C. jejuni were isolated from either of the TAU flocks at any time during the production cycle. None of the fla types of Campylobacter from the breeders that provided poults to one of the commercial flocks matched those from the progeny. These results failed to provide evidence for vertical transmission and indicate that this type of transmission either did not occur or was not sufficient to render the TAU turkey flocks Campylobacter positive. Management practices such as proper litter maintenance, controlled traffic between the TAU farm and other turkey flocks, and other less well-defined aspects of turkey production were likely responsible for the absence of Campylobacter in the TAU flocks before harvest.
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http://dx.doi.org/10.4315/0362-028x-67.7.1463DOI Listing
July 2004

G7H, a New Soybean mosaic virus Strain: Its Virulence and Nucleotide Sequence of CI Gene.

Plant Dis 2003 Nov;87(11):1372-1375

National Crop Experiment Station, RDA, Suwon 441-100, Korea.

A new Soybean mosaic virus (SMV) strain was isolated in Korea and designated as G7H. Its virulence on eight differentials and 42 Korean soybean cultivars was compared with existing SMV strains. G7H caused the same symptoms as G7 did on the eight differential cultivars. However, it caused different symptoms on the G7-immune Korean soybean cultivars; G7H caused necrosis in Suwon 97 (Hwangkeumkong) and Suwon 181 (Daewonkong), and a mosaic symptom in Miryang 41 (Duyoukong), while G7 caused only local lesions on those varieties. The nucleotide sequence of the cylindrical inclusion region of G7H was determined and compared with other SMV strains. G7H shared 96.3 and 91.3% nucleotide similarities with G2 and G7, respectively; whereas G7 shared 95.6% nucleotide similarity with G5H.
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http://dx.doi.org/10.1094/PDIS.2003.87.11.1372DOI Listing
November 2003

Molecular characterization of the gene encoding rice allene oxide synthase and its expression.

Biosci Biotechnol Biochem 2002 Dec;66(12):2719-22

Department of Genetic Engineering, Biotechnology Research Institute, Chonnam National University, Gwangju 500-757, Korea.

The gene encoding rice allene oxide synthase, OsAOS, was intronless and had nucleotide sequences with the high GC content of 67%. Deduced amino acid sequences had very high similarity with other AOS proteins, in particular 74% similarity to barley, characterized by the conserved motifs of P450 cytochrome of the CYP74A family. Purified recombinant rice AOS protein expressed in Escherichia coli converted 13-hydroperoxylinolenic acid to allene oxide. Several restriction enzyme digestions and Southern analysis showed that OsAOS was likely to have two copies in its genome. The basal level of OsAOS expression was detected in various tissues and the transcription level was increased by jasmonate treatment.
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http://dx.doi.org/10.1271/bbb.66.2719DOI Listing
December 2002
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