Lettuce is one of the economically important leaf vegetables and is cultivated mainly in temperate climate areas. Cultivar identification based on the distinctness, uniformity, and stability (DUS) test is a prerequisite for new cultivar... more
Lettuce is one of the economically important leaf vegetables and is cultivated mainly in temperate climate areas. Cultivar identification based on the distinctness, uniformity, and stability (DUS) test is a prerequisite for new cultivar registration. However, DUS testing based on morphological features is time-consuming, labor-intensive, and costly, and can also be influenced by environmental factors. Thus, molecular markers have also been used for the identification of genetic diversity as an effective, accurate, and stable method. Currently, genome-wide single nucleotide polymorphisms (SNPs) using next-generation sequencing technology are commonly applied in genetic research on diverse plant species. This study aimed to establish an effective and high-throughput cultivar identification system for lettuce using core sets of SNP markers developed by genotyping by sequencing (GBS). GBS identified 17 877 high-quality SNPs for 90 commercial lettuce cultivars. Genetic differentiation an...
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2015년, 조 바이러스 발생양상을 구명하기 위하여 전국적인 조사를 실시하였다. 주요재배단지 7개 지역에서 이상 증상과 바이러스 병징을 보이는 식물체 100점을 수집하여, RT-PCR 진단과 RNA sequencing 방법을 이용하여 전체 4종의 바이러스를 동정하였다. 수집한 시료에서는 Barley virus G (BVG)가 10점, Rice stripe virus (RSV)는 4점, Northern cereal... more
2015년, 조 바이러스 발생양상을 구명하기 위하여 전국적인 조사를 실시하였다. 주요재배단지 7개 지역에서 이상 증상과 바이러스 병징을 보이는 식물체 100점을 수집하여, RT-PCR 진단과 RNA sequencing 방법을 이용하여 전체 4종의 바이러스를 동정하였다. 수집한 시료에서는 Barley virus G (BVG)가 10점, Rice stripe virus (RSV)는 4점, Northern cereal mosaic virus (NCMV), Sugarcane yellow leaf virus (ScYLV)가 각각 1점씩 검출되었다. 이들 중에서 BVG와 NCMV는 국내 조에서 첫 발생보고이며, ScYLV는 Polerovirus속의 신종으로 예상된다. 본 연구결과는 조 식물체의 무병종자와 저항성 품종개발을 위한 기초연구 자료로 이용 가능할 것으로 생각된다.
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Molecular plant-aphid interactions: A novel gene families of putative salivary effectors in pea aphid (Acyr-thosiphon pisum).
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Research Interests: Biology, Medicine, Phylogeny, Domain Analysis, Plant diseases, and 15 moreProtein Kinases, Article, Phytophthora, Brassica rapa, Amino Acid Sequence, Base Sequence, Hypersensitive Response, Protein Binding, PLANT PROTEINS, Host Plant, Biochemistry and cell biology, Molecular Biology Reports, Plant Leaves, Molecular Sequence Data, and Sequence homology
HpaG is a type III-secreted elicitor protein of Xanthomonas axonopodis pv. glycines. We have determined the critical amino acid residues important for hypersensitive response (HR) elicitation by random and site-directed mutagenesis of... more
HpaG is a type III-secreted elicitor protein of Xanthomonas axonopodis pv. glycines. We have determined the critical amino acid residues important for hypersensitive response (HR) elicitation by random and site-directed mutagenesis of HpaG and its homolog XopA. A plasmid clone carrying hpaG was mutagenized by site-directed mutagenesis, hydroxylamine mutagenesis, and error-prone PCR. A total of 52 mutants were obtained, including 51 single missense mutants and 1 double missense mutant. The HR elicitation activity was abolished in the two missense mutants [HpaG(L50P) and HpaG(L43P/L50P)]. Seven single missense mutants showed reduced activity, and the HR elicitation activity of the rest of the mutants was similar to that of wild-type HpaG. Mutational and deletion analyses narrowed the region essential for elicitor activity to the 23-amino-acid peptide (H2N-NQGISEKQLDQLLTQLIMALLQQ-COOH). A synthetic peptide of this sequence possessed HR elicitor activity at the same concentration as the...
Research Interests: Bacteriology, Biology, Medicine, Biological Sciences, Mutagenesis, and 15 moreProtein Secretion, Pseudomonas, Polymerase Chain Reaction, Erwinia, Amino Acid Sequence, Elicitor, Hypersensitive Response, Mutagens, Plasma Membrane, Hydroxylamine, Host Plant, Molecular Sequence Data, DNA mutational analysis, Mutation analysis, and Medical and Health Sciences
Burkholderia glumae produces toxoflavin, a phytotoxin with a broad host range, which is a key virulence factor in bacterial rice grain rot. Based on genetic analysis, we previously reported that ToxR, a LysR-type regulator, activates both... more
Burkholderia glumae produces toxoflavin, a phytotoxin with a broad host range, which is a key virulence factor in bacterial rice grain rot. Based on genetic analysis, we previously reported that ToxR, a LysR-type regulator, activates both the toxABCDE (toxoflavin biosynthesis genes) and toxFGHI (toxoflavin transporter genes) operons in the presence of toxoflavin as a coinducer. Quorum sensing regulates the expression of the transcriptional activator ToxJ that is required for tox gene expression. Here, we used gel mobility shift and DNase I protection analyses to demonstrate that both ToxR and ToxJ bind simultaneously to the regulatory regions of both tox operons. ToxR and ToxJ both bound to the toxA and toxF regulatory regions, and the sequences for the binding of ToxR to the regulatory regions of both tox operons possessed T-N 11 -A motifs. Following random mutagenesis of toxR , 10 ToxR mutants were isolated. We constructed a reporter strain, S6K34 ( toxR ′ A ′::Ω toxF ::Tn 3 - gus...
Research Interests: Genetics, Microbiology, Bacteriology, Gene regulation, Biology, and 15 moreMedicine, Gene expression, Biological Sciences, Mutagenesis, Mutation, Bacteria, Gene, Burkholderia, Genetic Analysis, Host Range, DNA binding proteins, Molecular Structure, DNA mutational analysis, binding sites, and Medical and Health Sciences
한해살이풀로서(Ha와 Lee, 2001), 원산지는 중앙아시아와 동북아시아로 알려져 있다 (Li와 Wu, 1996). 동유럽, 중앙아시아, 동아시아 지역에서는 주요 곡물로서 재배되고 있으며, 아프리카, 아메리카, 호 주 등에서는 조류 등의 사료용으로 일부 재배되고 있다(De Wet 등, 1979). 국내에서 조는 1960년대까지 주요 작물로 널 리 재배되었으며(Kim 등, 2009), 주로 엿, 떡, 소주 등의 일부 재료로... more
한해살이풀로서(Ha와 Lee, 2001), 원산지는 중앙아시아와 동북아시아로 알려져 있다 (Li와 Wu, 1996). 동유럽, 중앙아시아, 동아시아 지역에서는 주요 곡물로서 재배되고 있으며, 아프리카, 아메리카, 호 주 등에서는 조류 등의 사료용으로 일부 재배되고 있다(De Wet 등, 1979). 국내에서 조는 1960년대까지 주요 작물로 널 리 재배되었으며(Kim 등, 2009), 주로 엿, 떡, 소주 등의 일부 재료로 이용되었다(Ha와 Lee, 2001). 이후, 조의 재배는 벼와 밀 등 주요 작물과 비교하여 수량과 수익성이 낮아 생산량 이 지속적으로 감소하였다. 통계청 보고에 따르면, 조의 생 산량은 2004년 2,644톤에서 2009년 1,360톤으로 급격히 감 소하였다(Kim, 2012; 통계청). 최근 건강에 대한 관심이 높아 지면서 조와 같은 잡곡은 웰빙식품, 기능성식품에 대한 소 비자의 선호도가 높아지며 관심이 증대하고 있지만(Lee 등, 2012), 수량과 직접적인 관련이 있는 병해충에 관한 체계적 인 연구들은 부족한 실정이다. 조의 경우 현재까지 2종의 바이러스(Rice black-streaked dwarf virus [RBSDV], Rice stripe virus [RSV])만이 보고되어 있어 바이러스 무병종자의 보급과 저항성 품종 개발 등의 연구에 제한적일 수밖에 없다. 따라 서 본 연구에서는 국내 조에서 발생하는 바이러스 조사를 수행하였으며, next generation sequencing (NGS)와 reverse
Research Interests: Biology and Plant Disease
We sequenced an approximately 29-kb region from Xanthomonas axonopodis pv. glycines that contained the Hrp type III secretion system, and we characterized the genes in this region by Tn 3-gus mutagenesis and gene expression analyses. From... more
We sequenced an approximately 29-kb region from Xanthomonas axonopodis pv. glycines that contained the Hrp type III secretion system, and we characterized the genes in this region by Tn 3-gus mutagenesis and gene expression analyses. From the region, hrp (hypersensitive response and pathogenicity) and hrc ( hrp and conserved) genes, which encode type III secretion systems, and hpa ( hrp -associated) genes were identified. The characteristics of the region, such as the presence of many virulence genes, low G+C content, and bordering tRNA genes, satisfied the criteria for a pathogenicity island (PAI) in a bacterium. The PAI was composed of nine hrp , nine hrc , and eight hpa genes with seven plant-inducible promoter boxes. The hrp and hrc mutants failed to elicit hypersensitive responses in pepper plants but induced hypersensitive responses in all tomato plants tested. The Hrp PAI of X. axonopodis pv. glycines resembled the Hrp PAIs of other Xanthomonas species, and the Hrp PAI core r...
Research Interests: Microbiology, Phytopathology, Bacteriology, Plant Biology, Biology, and 15 moreMedicine, Genetic Diversity, Biological Sciences, Mutation, DNA Extraction, Gene Dosage, Phenotype, Genetic variation, Plant Pathogen, Plant Pathology, Amino Acid Sequence, Pathogenicity, Lycopersicon esculentum, Molecular Sequence Data, and Medical and Health Sciences
Glycinecin A, a bacteriocin produced by Xanthomonas campestris pv. glycines, inhibits the growth of X. campestris pv. vesicatoria. We have cloned and expressed the genes encoding glycinecin A in Escherichia coli. Recombinant glycinecin A... more
Glycinecin A, a bacteriocin produced by Xanthomonas campestris pv. glycines, inhibits the growth of X. campestris pv. vesicatoria. We have cloned and expressed the genes encoding glycinecin A in Escherichia coli. Recombinant glycinecin A was purified from cell extracts by ammonium sulfate precipitation followed by chromatography on Q-Sepharose, Mono Q (ion exchange), and size exclusion columns. Purified glycinecin A is composed of two polypeptides, is active over a wide pH range (6 to 9), and is stable at temperatures up to 60°C. Glycinecin A is a heterodimer consisting of 39- and 14-kDa subunits, as revealed through size exclusion chromatography and cross-linking analysis. Two genes,glyA and glyB, encoding the 39- and 14-kDa subunits, respectively, were identified based on the N-terminal sequences of the subunits. From the nucleotide sequences ofglyA and glyB, we conclude that both genes are translated as bacteriocin precursors that include N-terminal leader sequences. When express...
Research Interests: Multidisciplinary, Gene Cloning, Bacteriocins, Escherichia coli, Link analysis, and 14 moreApplied, Applied Environmental Microbiology, Temperature, Molecular cloning, Ion Exchange, Protein Quaternary Structure, Culture Media, Hydrogen-Ion Concentration, Size Exclusion Chromatography, Ammonium Sulfate, Xanthomonas Campestris, Dimerization, Molecular Sequence Data, and Nucleotide sequence
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Cymbidium mosaic virus (CymMV) is a major virus infecting orchid plants and causing economic loss. In this study, the incidence of viral infection in Calanthe spp. at the Korean Institute of Calanthe was investigated using reverse... more
Cymbidium mosaic virus (CymMV) is a major virus infecting orchid plants and causing economic loss. In this study, the incidence of viral infection in Calanthe spp. at the Korean Institute of Calanthe was investigated using reverse transcription polymerase chain reaction. The CymMV infection rate was 42%, and the two viruses Odontoglossum ringspot virus and Cucumber mosaic virus had frequencies of 8% and 2%, respectively. Additionally, we characterized an isolate of CymMV, CymMV-GW, using biological tests and examined the nucleotide sequence properties of its complete genome. CymMVGW induced chlorotic ringspots and chlorotic spot symptoms in inoculated leaves of Chenopodium amaranticolor and Nicotiana benthamiana, respectively. In this study, we have for the first complete genome sequence of CymMV-GW in Korea. The CymMV-GW genome was 6,225 nucleotides in length, excluding the poly-(A) tail, and showed whole-genome nucleotide and amino acid sequence identities of 97.7% and 100%, respe...
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Apple chlorotic leaf spot virus (ACLSV), Apple stem pitting virus (ASPV), Apple stem grooving virus (ASGV), and Apple scar skin viroid (ASSVd) are economically important viruses that infect pear tree species worldwide. To evaluate the... more
Apple chlorotic leaf spot virus (ACLSV), Apple stem pitting virus (ASPV), Apple stem grooving virus (ASGV), and Apple scar skin viroid (ASSVd) are economically important viruses that infect pear tree species worldwide. To evaluate the prevalence of these viruses in Korea, we investigated infection degree of three viruses and one viroid for the commercial nursery trees of the pear cultivars, Niitaka, Chuwhang, Wonwhang, and Whasan in 2017 and 2018. The results showed that the infection ratio of ACLSV, ASPV, ASGV, and ASSVd for the scion of pear cultivar Niitaka was 10%, 45%, 77%, and 50%, respectively. From the scion of pear cultivar Chuwhang, infection ratios of ASPV, ASGV, and ASSVd were found to be 70%, 50%, and 60%, respectively. From the scion of pear cultivar Whasan, infection ratios of ACLSV, ASPV, ASGV and ASSVd were found to be 40%, 60%, 93%, and 20%, respectively. From the root stock of pear cultivar Wonwhang, infection ratios of ACLSV, ASPV, ASGV, and ASSVd showed 28%, 57%...
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spp. have formed harmful cyanobacterial blooms in the Nakdong River during spring, autumn, and now in winter, and the expansion of blooming period and area, associated with the global warming is predicted. The genus has been described to... more
spp. have formed harmful cyanobacterial blooms in the Nakdong River during spring, autumn, and now in winter, and the expansion of blooming period and area, associated with the global warming is predicted. The genus has been described to produce harmful secondary metabolites such as off-flavors and cyanotoxins. Therefore, the production of harmful secondary metabolites from the blooms in the Nakdong River needs to be monitored to minimize the risk to both water quality and public health. Here, we sampled the cyanobacterial blooms in the Nakdong River and isolated ten strains, morphologically classified as Ralfs ex Bornet et Flahault 1888. Phylogenetic analysis using 16S rRNA and internal transcribed spacer (ITS) region nucleotide sequences confirmed this classification. We further verified the harmful secondary metabolites-producing potential of isolates and water samples containing cyanobacterial blooms using PCR with specific primer sets for genes involved in biosynthesis of off-f...
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Research Interests: Microbiology, Computational Biology, Medical Microbiology, HIV, Clinical Microbiology, and 15 moreBiological Sciences, Humans, Female, Animals, Male, Infant, Cattle, Genotype, Feces, Hepatitis E Virus, Biochemistry and cell biology, Child preschool, cattle diseases, Medical and Health Sciences, and HIV infections
The complete genome sequence of an Uiseong isolate of barley virus G (BVG) on proso millet plants in a field in South Korea was determined by RNA sequencing and Sanger sequencing. To our knowledge, this is the first complete genome... more
The complete genome sequence of an Uiseong isolate of barley virus G (BVG) on proso millet plants in a field in South Korea was determined by RNA sequencing and Sanger sequencing. To our knowledge, this is the first complete genome sequence report of BVG infecting proso millet in South Korea.
The complete nucleotide sequences of three representative plasmids, pAG1 from Xanthomonas axonopodis pv. glycines strain AG1, and pXAG81 and pXAG82 from strain 8ra, were determined. The sizes of pAG1, pXAG81, and pXAG82 are 15143, 26721,... more
The complete nucleotide sequences of three representative plasmids, pAG1 from Xanthomonas axonopodis pv. glycines strain AG1, and pXAG81 and pXAG82 from strain 8ra, were determined. The sizes of pAG1, pXAG81, and pXAG82 are 15143, 26721, and 1315 base pairs, respectively. A possible 16, 34, and 1 open-reading frames (ORFs) are present in pAG1, pXAG81, and pXAG82, respectively. pAG1 could encode proteins homologous to AvrBs3, TnpA, TnpR, RepA, HtrA, ParA, M.XmaI, R.XmaI, and six hypothetical proteins. pXAG81 possibly encodes proteins homologous to those involved in conjugal plasmid transfer. Possible oriT sequences similar to those of RP4 were found between mobB and mobC homologs. At the end of the RepA homolog in pAG1 and pXAG81, a putative oriV region at the 3'-end of RepA similar to the integron TNCP23 in pKLC102 of Pseudomonas aeruginosa C strain was found. All 255 isolates carried either pAG1 type or pXAG81 type, and 217 isolates appeared to carry tra gene homologs. Both pAG...
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The complete nucleotide sequences of three representative plasmids, pAG1 from Xanthomonas axonopodis pv. glycines strain AG1, and pXAG81 and pXAG82 from strain 8ra, were determined. The sizes of pAG1, pXAG81, and pXAG82 are 15143, 26721,... more
The complete nucleotide sequences of three representative plasmids, pAG1 from Xanthomonas axonopodis pv. glycines strain AG1, and pXAG81 and pXAG82 from strain 8ra, were determined. The sizes of pAG1, pXAG81, and pXAG82 are 15143, 26721, and 1315 base pairs, respectively. A possible 16, 34, and 1 open-reading frames (ORFs) are present in pAG1, pXAG81, and pXAG82, respectively. pAG1 could encode proteins homologous to AvrBs3, TnpA, TnpR, RepA, HtrA, ParA, M.XmaI, R.XmaI, and six hypothetical proteins. pXAG81 possibly encodes proteins homologous to those involved in conjugal plasmid transfer. Possible oriT sequences similar to those of RP4 were found between mobB and mobC homologs. At the end of the RepA homolog in pAG1 and pXAG81, a putative oriV region at the 3'-end of RepA similar to the integron TNCP23 in pKLC102 of Pseudomonas aeruginosa C strain was found. All 255 isolates carried either pAG1 type or pXAG81 type, and 217 isolates appeared to carry tra gene homologs. Both pAG1 and pXAG81 types contained an avrBs3 homolog varying from three copies in AG1 to eight copies in AG166.