Publications by authors named "Chang-Gi Back"

22 Publications

  • Page 1 of 1

Using RNA-Sequencing Data to Examine Tissue-Specific Garlic Microbiomes.

Int J Mol Sci 2021 Jun 24;22(13). Epub 2021 Jun 24.

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

Garlic () is a perennial bulbous plant. Due to its clonal propagation, various diseases threaten the yield and quality of garlic. In this study, we conducted in silico analysis to identify microorganisms, bacteria, fungi, and viruses in six different tissues using garlic RNA-sequencing data. The number of identified microbial species was the highest in inflorescences, followed by flowers and bulb cloves. With the Kraken2 tool, 57% of identified microbial reads were assigned to bacteria and 41% were assigned to viruses. Fungi only made up 1% of microbial reads. At the species level, was the most dominant bacteria while was the most abundant fungi. Several allexiviruses were identified. Of them, the most abundant virus was garlic virus C followed by shallot virus X. We obtained a total of 14 viral genome sequences for four allexiviruses. As we expected, the microbial community varied depending on the tissue types, although there was a dominant microorganism in each tissue. In addition, we found that Kraken2 was a very powerful and efficient tool for the bacteria using RNA-sequencing data with some limitations for virome study.
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http://dx.doi.org/10.3390/ijms22136791DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8268838PMC
June 2021

Comparative Study of Metagenomics and Metatranscriptomics to Reveal Microbiomes in Overwintering Pepper Fruits.

Int J Mol Sci 2021 Jun 8;22(12). Epub 2021 Jun 8.

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

Red pepper (, L.), is one of the most important spice plants in Korea. Overwintering pepper fruits are a reservoir of various microbial pepper diseases. Here, we conducted metagenomics (DNA sequencing) and metatranscriptomics (RNA sequencing) using samples collected from three different fields. We compared two different library types and three different analytical methods for the identification of microbiomes in overwintering pepper fruits. Our results demonstrated that DNA sequencing might be useful for the identification of bacteria and DNA viruses such as bacteriophages, while mRNA sequencing might be beneficial for the identification of fungi and RNA viruses. Among three analytical methods, KRAKEN2 with raw data reads (KRAKEN2_R) might be superior for the identification of microbial species to other analytical methods. However, some microbial species with a low number of reads were wrongly assigned at the species level by KRAKEN2_R. Moreover, we found that the databases for bacteria and viruses were better established as compared to the fungal database with limited genome data. In summary, we carefully suggest that different library types and analytical methods with proper databases should be applied for the purpose of microbiome study.
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http://dx.doi.org/10.3390/ijms22126202DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8227054PMC
June 2021

QTL Mapping for Gummy Stem Blight Resistance in Watermelon ( spp.).

Plants (Basel) 2021 Mar 8;10(3). Epub 2021 Mar 8.

Department of Horticulture, Institute of Agricultural Science & Technology, Jeonbuk National University, Jeonju 54896, Korea.

Watermelon () is an economically important fruit crop worldwide. Gummy stem blight (GSB) is one of the most damaging diseases encountered during watermelon cultivation. In the present study, we identified quantitative trait loci (QTLs) associated with GSB resistance in an F population derived from a cross between maternal-susceptible line '920533' () and the paternal-resistant line 'PI 189225' (). The resistance of 178 F plants was assessed by two different evaluation methods, including leaf lesion (LL) and stem blight (SB). To analyze the QTLs associated with GSB resistance, a linkage map was constructed covering a total genetic distance of 1070.2 cM. QTL analysis detected three QTLs associated with GSB resistance on chromosome 8 and 6. Among them, two QTLs, and on chromosome 8 identified as major QTLs, explaining 10.5 and 10.0% of the phenotypic variations localizing at same area and sharing the same top markers for both LL and SB traits, respectively. A minor QTL, , explains 9.7% of phenotypic variations detected on chromosome 6 only for the SB trait. High-throughput markers were developed and validated for the selection of resistant QTLs using watermelon accessions, and commercial cultivars. Four potential candidate genes were predicted associated with GSB resistance based on the physical location of flanking markers on chromosome 8. These findings will be helpful for the development of watermelon cultivars resistant to GSB.
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http://dx.doi.org/10.3390/plants10030500DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7999335PMC
March 2021

Occurrence of Cercospora Leaf Spot Caused by cf. on Melon in Korea.

Mycobiology 2020 Jul 20;48(5):418-422. Epub 2020 Jul 20.

Horticultural and Herbal Crop Environment Division, National Institute of Horticultural and Herbal Science, Rural Development Administration, Wanju, Korea.

In 2016, a cercosporoid fungus was found from leaf spot symptoms on melon in Korea. The fungus isolated from the plant was identified based on morphological characteristics and sequence analyses of five genes (ITS rDNA, translation elongation factor 1-α, actin, calmodulin, and histone H3). The fungal isolate was found to be pathogenic to melon. The results confirm that the fungus associated with leaf spot on melon was cf. . This is the first report of cf. causing Cercospora leaf spot on melon in Korea.
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http://dx.doi.org/10.1080/12298093.2020.1792133DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7580573PMC
July 2020

First report of bacterial shot-hole disease caused by pv. on plumcot in South Korea.

Plant Dis 2020 Sep 29. Epub 2020 Sep 29.

National Institute of Horticultural & Herbal Science, Horticultural and Herbal Crop Environment Division, 100, Nongsaengmyeong-ro, Iseo-myeon, Wanju-gun, Jeollabuk-do, Korea (the Republic of), 565-852;

Plumcot is an interspecific hybrid product between Japanese plums () and apricots () obtained by the NIHHS, Korea in 1999 [1]. At the early of 2017, black spots-like symptoms were observed on plumcot fruits and leaves at cultivation areas in Naju (34.965595, 126.665853) province. Further investigation shows that approximately 60% of the plumcot leaves in the affected orchard were infected, which caused 40% total production loss. At the early stage of infection, disease symptoms appear as small, angular and water-soaked spots and develop into circular brown spots at the later stages of infection. As the disease progresses, the leaf tissues around the spots became yellow and the lesions enlarged. When the adjacent lesions merged and the necrotic tissues fall off, shot-hole symptoms appear on the leaves. To identify the causal agent of this disease, infected leaf tissues were excised and surface-sterilized with 1% NaOCl for 30 secs prior to rinsing with sterile water, thrice . Tissue samples were then placed in sterile water (0.5 mL) for 5 min before its aliquots were streaked onto Luria-Bertani (LB) agar. Plates then were incubated at 28°C. To obtain pure colonies, bacteria were re-streak into a new LB agar and colonies showing typical spp. morphology (i.e. convex, smooth, yellow, and mucoid) were subjected to Gram staining assay. For molecular identification, 16S ribosomal DNA () and gyrase B () genes were amplified using a 9F/1512r and UP-1/UP-2Sr primers [2,3] respectively from 5 gram-negative isolates. PCR products were sequenced and analysed using BLASTN. Result shows that and genes are 99-100% identical to a similar genomic region of pv. isolated in almond (MK156163), peach (MG049922) and apricot (KX950802) respectively [4,5,6]. and gene sequences were deposited in the GenBank (LC485472 and LC576824), whereas pathogen isolate was deposited into Korean Agricultural Culture Collection (KACC19949). Pathogenicity test was performed using bacterial suspension (10 cfu/mL) inoculated on the abaxial and adaxial surface of plumcot detached leaves. For inoculation, 10 healthy young leaves were used whereas, 5 young leaves mock-inoculated with sterile LB broth were used as a control. Both leaf samples were kept in a closed container to maintain 100% humidity before being incubated at 25°C. The water-soaked symptoms were observed visually on the inoculated leaves 2 to 3 days post-inoculation. No water-soaked symptoms were observed on the control leaves. Morphology and sequences of molecular markers used showed that the 3 bacterial colonies re-isolated from the inoculated leaves were identical to the original isolate, fulfilling Koch's postulate. Pathogenicity tests were repeated twice and the results obtained were consistent with the first experiment. As a new variety of stone fruit cultivated in Korea, information about pathogens and registered agrochemicals to control disease outbreak in plumcot are still limited. Therefore, the identification of as a causal agent to the black spot disease is critical for the development of disease management strategies and to identify appropriate agrochemicals to control the occurrence of this disease in the field. To our knowledge, this is the first report of as a causal agent to the shot-hole disease on the plumcot in Korea.
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http://dx.doi.org/10.1094/PDIS-06-20-1227-PDNDOI Listing
September 2020

First Report of Verticillium Wilt Caused by Infection on Chinese Cabbage in Korea.

Plant Dis 2020 Sep 23. Epub 2020 Sep 23.

National Institute of Horticultural & Herbal Science, Horticultural and Herbal Crop Environment Division, Wanju-gun, Jeollabuk-do, Korea (the Republic of);

Chinese cabbage () is one of the most important vegetables in Korea due to its role as the main ingredient for the making of Kimchi. In June 2014, disease symptoms of leaves wilt, dry, and drop off on Chinese cabbage were observed in a Chinese cabbage farm located at Taebeak (37°26'50.7"N 128°95'50.0"E), Gangwon province, Korea. This disease was observed on approximately 35% of the plants in the field, causing an almost 10% decrease in total production. At the early stage of infection, the color at the edge of the plant foliage changed from green to yellow. As the disease progressed, infected leaves wilted, dried off, and detached from the plant. Soft rot that occurred at the base of the leaf stem and root tissues caused the infected leaves to dry and fell off the plant. To identify the causal agent, a small piece of infected leaf tissues was sterilized with 1% sodium hypochlorite solution for 1 min and rinsed with sterile water before it was transferred onto potato dextrose agar (PDA) media. The plates were then incubated at 25°C for 10 days in the dark. Fungal colonies grown on PDA media were of white-creamy in color with an abundance of mycelia and later develop into black color due to the formation of microsclerotia embedded in the media. Microscopic examination showed conidiophores and phialides were both appeared in a verticillate arrangement, whereas conidia were hyaline, smooth-walled, and ellipsoidal to oval with average size 5.4×2.5 µm (n=100). Microsclerotia appeared in elongate to an irregularly spherical shape and greatly variable in size. The morphological attributes of the fungal isolate described above were comparable to the characteristics of Kleb. () described by Hawksworth and Talboys (1970), and isolated from Chinese cabbage in Japan reported in Kishi (1998). Pathogenicity test was performed by soaking twelve individual Chinese cabbage seedlings for 15 min into fungal pathogen conidial suspension (1x10 conidium/ml) before transferred into soil tray. The same number of non-inoculated seedlings on the soil tray was used as a control. Inoculated and control plants were then covered with a plastic bag for 24 hours to maintain high humidity before transferred into the greenhouse (25°C). Seven days post-inoculation (dpi), treated plant leaves turned yellow, and soft rot was observed. At 10-dpi, plant leaf tissues dried off and severe soft rot occurred. Pathogenicity test was repeated three times and consistent results were obtained. The re-isolated fungal pathogen from the inoculated plants showed identical morphological characteristics to the original isolates, thus fulfilling Koch's postulates. For further identification, PCR amplification targeting and regions were performed (Liu et al., 1999; White et al., 1990). Each PCR product was sequenced and deposited in the GenBank under the accession LC549667 and LC061275, respectively. Sequence analysis using BLAST showed that the nucleotide sequences of ITS and RPB2 DNA fragments are 99-100% identical to the reference strain of available in the NCBI database (MG585719, HE972023, XM_009652520 and DQ522468, respectively). Therefore, based on the results of morphological and molecular analyses, the fungal pathogen isolated from Chinese cabbage in this study was identified as and deposited in the National Institute of Horticultural and Herbal Science germplasm collection (NIHHS 13-252). Recently, due to high demand and a more competitive price, more Chrysanthemum farmers in Korea switch their crops to Chinese cabbage. Interestingly, the occurrence of infection was also reported to occur in Chrysanthemum plants in Korea (Han et al. 2007), which indicates a serious problem ahead to these farmers. Therefore, in this current study, the identification of pathogenic to Chinese cabbage will provide vital knowledge for the development of disease management strategies to minimize the loss of crop production. To our knowledge, this is the first report that causes Verticillium wilt disease on Chinese cabbage in Korea.
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http://dx.doi.org/10.1094/PDIS-05-20-1132-PDNDOI Listing
September 2020

Causing Anthracnose on Orchids in Korea.

Mycobiology 2020 Jun 2;48(4):321-325. Epub 2020 Jun 2.

Horticultural and Herbal Crop Environment Division, National Institute of Horticultural and Herbal Science, Rural Development Administration, Wanju, Korea.

A species was isolated from leaves of exhibiting symptoms of anthracnose. In this study, the isolates obtained were identified based on recent taxonomic approaches for the genus . The identity of the causal pathogen was confirmed using morphological data and phylogenetic analysis of combined multi-gene dataset (internal transcribed spacer, glyceraldehyde 3-phosphate dehydrogenase, chitin synthase-1, actin, histone3, beta-tubulin, and calmodulin). Pathogenicity testing revealed that the isolates were pathogenic to . Based on these results, the fungal pathogen occurring on orchids was identified as which is a newly recorded species in Korea.
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http://dx.doi.org/10.1080/12298093.2020.1768626DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7476528PMC
June 2020

Comparative Microbiome Study of Mummified Peach Fruits by Metagenomics and Metatranscriptomics.

Plants (Basel) 2020 Aug 18;9(8). Epub 2020 Aug 18.

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

The dried peach fruits clinging to peach trees or lying on the ground nearby are known as mummified peach fruits. Here, we examined the microbiome communities of three different mummified peach fruits from the nectarine cultivar "Hahong" by DNA- and RNA-sequencing. We found the dominance of followed by , , and in the mummified peach fruits. Moreover, we found a high number of Proteobacteria, including , , , and . Furthermore, we identified several viruses and viroids. Bacteriophages were identified by DNA- and RNA-sequencing, while viruses and viroids with RNA genomes were identified by only RNA-sequencing. Moreover, we identified a novel mycovirus referred to as umbra-like virus 1 (MULV1) from . Our results revealed the co-inhabitance of fungi and bacteria in the mummified peach fruits, although dominant microorganisms were present. RNA-sequencing revealed that several fungal and bacterial genes were actively transcribed. Comparative analyses suggested that RNA-sequencing provides more detailed information on microbial communities; however, combining DNA- and RNA-sequencing results increased the diversity of microorganisms, suggesting the importance of databases and analysis tools for microbiome studies. Taken together, our study provides a comprehensive overview of microbial communities in mummified peach fruits by DNA shotgun sequencing and RNA-sequencing.
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http://dx.doi.org/10.3390/plants9081052DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7464454PMC
August 2020

High-Quality Genome Assembly of , the Causal Agent of Onion Downy Mildew.

Mol Plant Microbe Interact 2020 May 1;33(5):718-720. Epub 2020 Apr 1.

National Institute of Agricultural Sciences, Rural Development Administration, Jeonju 54874, Republic of Korea.

is an obligate biotrophic oomycete that causes downy mildew on onion (). Onion is an important crop worldwide, but its production is affected by this pathogen. We sequenced the genome of using the PacBio sequencing platform, and de novo assembly resulted in 74 contigs with a total contig size of 29.3 Mb and 48.48% GC content. Here, we report the first high-quality genome sequence of and its comparison with the genome assemblies of other oomycetes. The genome is a very useful resource to serve as a reference for analysis of isolates and for comparative genomic studies of the biotrophic oomycetes.
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http://dx.doi.org/10.1094/MPMI-10-19-0280-ADOI Listing
May 2020

Loop-Mediated Isothermal Amplification for the Detection of pv. in Peaches.

Plant Pathol J 2019 Dec 12;35(6):635-643. Epub 2019 Dec 12.

School of Applied Biosciences, Kyungpook National University, Daegu 41566, Korea.

To detect pv, a loop-mediated isothermal amplification (LAMP) detection method were developed. The LAMP assay was designed to test crude plant tissue without pre-extraction, or heating incubation, and without advanced analysis equipment. The LAMP primers were designed by targeting an ABC transporter ATP-binding protein, this primer set was tested using the genomic DNA of and non- strains, and a ladder product was generated from the genomic DNA of pv strain but not from 12 other species strains and 6 strains of other genera. The LAMP conditions were checked with the healthy leaves of 31 peach varieties, and no reaction was detected using either the peach leaves or the peach DNA as a template. Furthermore, the high diagnostic accuracy of the LAMP method was confirmed with 13 pv strains isolated from various regions in Korea, with all samples exhibiting a positive reaction in LAMP assays. In particular, the LAMP method successfully detected the pathogen in diseased peach leaves and fruit in the field, and the LAMP conditions were proven to be a reliable diagnostic method for the specific detection and identification of pv in peach orchards.
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http://dx.doi.org/10.5423/PPJ.OA.07.2019.0197DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6901255PMC
December 2019

Whole-Genome Sequence of Erwinia persicina B64, Which Causes Pink Soft Rot in Onions.

Microbiol Resour Announc 2019 Jan 3;8(1). Epub 2019 Jan 3.

National Institute of Horticultural and Herbal Science, Rural Development Administration, Wanju, Republic of Korea.

Erwinia persicina B64 was isolated from rotten onions in cold-storage facilities. Here, we report the complete genome sequence of E. persicina B64, which contains 5,070,450 bp with 55.17% GC content. The genome of this isolate is composed of one chromosome and two plasmids.
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http://dx.doi.org/10.1128/MRA.01302-18DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6318354PMC
January 2019

Cutaneous Microflora from Geographically Isolated Groups of , an Insect Vector of Diverse Plant Pathogens.

Mycobiology 2017 Sep 30;45(3):160-171. Epub 2017 Sep 30.

Horticultural & Herbal Crop Environment Division, National Institute of Horticultural & Herbal Science, Rural Development Administration, Wanju 55365, Korea.

Larvae of , an insect vector that transports plant pathogens, were sampled from geographically isolated regions in Korea to identify their cutaneous fungal and bacterial flora. Sampled areas were chosen within the distribution range of ; each site was more than 91 km apart to ensure geographical segregation. We isolated 76 microbial (fungi and bacteria) strains (site 1, 29; site 2, 29; site 3, 18 strains) that were identified on the basis of morphological differences. Species identification was molecularly confirmed by determination of universal fungal internal transcribed spacer and bacterial 16S rRNA gene sequences in comparison to sequences in the EzTaxon database and the NCBI GenBank database, and their phylogenetic relationships were determined. The fungal isolates belonged to 2 phyla, 5 classes, and 7 genera; bacterial species belonged to 23 genera and 32 species. Microbial diversity differed significantly among the geographical groups with respect to Margalef's richness (3.9, 3.6, and 4.5), Menhinick's index (2.65, 2.46, and 3.30), Simpson's index (0.06, 0.12, and 0.01), and Shannon's index (2.50, 2.17, and 2.58). Although the microbial genera distribution or diversity values clearly varied among geographical groups, common genera were identified in all groups, including the fungal genus , and the bacterial genera and . According to classic principles of co-evolutionary relationship, these genera might have a closer association with their host insect vector than other genera identified. Some cutaneous bacterial genera (e.g., ) displaying weak interdependency with insect vectors may be hazardous to agricultural environments via mechanical transmission via . This study provides comprehensive information regarding the cutaneous microflora of , which can help in the control of such pests for crop management.
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http://dx.doi.org/10.5941/MYCO.2017.45.3.160DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5673511PMC
September 2017

New Recorded Species in Three Genera of the Sordariomycetes in Korea.

Mycobiology 2017 Jun 30;45(2):64-72. Epub 2017 Jun 30.

School of Applied Biosciences, College of Agriculture and Life Sciences, Kyungpook National University, Daegu 41566, Korea.

In an ongoing survey of Korean indigenous fungi, three fungal strains belonging to the Sordariomycetes were isolated from soil samples. These strains were designated KNU16-001, KNU16-002, and KNU16-009, and identified as , , and , respectively, based on morphological characterization and phylogenetic analysis using internal transcribed spacer region sequences of ribosomal DNA. This is the first report of these species in Korea.
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http://dx.doi.org/10.5941/MYCO.2017.45.2.64DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5541150PMC
June 2017

First Report of Leaf Spot Caused by on Black Chokeberry () in Korea.

Mycobiology 2016 Sep 30;44(3):187-190. Epub 2016 Sep 30.

School of Ecology & Environmental System, College of Ecology & Environmental Sciences, Kyungpook National University, Sangju 37224, Korea.

In July 2015, diseased leaves of black chokeberry () were observed in Danyang and Gochang, Korea. The symptoms appeared as circular or irregular brown leaf spots, from which was isolated. The isolates were cultured on potato dextrose agar, and their morphological characteristics were observed under a light microscope. The colonies were whitish to ash colored. The pathogenicity test on healthy black chokeberry leaves produced circular brown spots, in line with the original symptoms. Molecular analyses of the ITS, GPD, RPB2, and TEF genes were conducted to confirm the identity of the pathogen. The phylogeny of the multi-gene sequences indicated that the causal agent was . This study is the first report of leaf spot on black chokeberry ().
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http://dx.doi.org/10.5941/MYCO.2016.44.3.187DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5078132PMC
September 2016

First Report of Fusarium subglutinans Causing Leaf Spot Disease on Cymbidium Orchids in Korea.

Mycobiology 2015 Sep 30;43(3):343-6. Epub 2015 Sep 30.

Horticultural and Herbal Crop Environment Division, National Institute of Horticultural and Herbal Science, Rural Development Administration, Wanju 55365, Korea.

In 2006~2010, leaf spot symptoms, that is, small, yellow spots that turned into dark brown-to-black lesions surrounded by a yellow halo, were observed on Cymbidium spp. in Gongju, Taean, and Gapyeong in Korea. A Fusarium species was continuously isolated from symptomatic leaves; in pathogenicity testing, isolates caused leaf spot symptoms consisting of sunken, dark brown lesions similar to the original ones. The causal pathogen was identified as Fusarium subglutinans based on morphological and translation elongation factor 1-alpha sequence analyses. This is the first report of F. subglutinans as the cause of leaf spot disease in Cymbidium spp. in Korea.
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http://dx.doi.org/10.5941/MYCO.2015.43.3.343DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4630443PMC
September 2015

Development of a Species-specific PCR Assay for Three Xanthomonas Species, Causing Bulb and Flower Diseases, Based on Their Genome Sequences.

Plant Pathol J 2015 Sep 30;31(3):212-8. Epub 2015 Sep 30.

College of Agriculture and Life Sciences, Kyungpook National University, Daegu 702-701, Korea ; Institute of Plant Medicine, Kyungpook National University, Daegu 702-701, Korea.

In this study, we developed a species-specific PCR assay for rapid and accurate detection of three Xanthomonas species, X. axonopodis pv. poinsettiicola (XAP), X. hyacinthi (XH) and X. campestris pv. zantedeschiae (XCZ), based on their draft genome sequences. XAP, XH and XCZ genomes consist of single chromosomes that contain 5,221, 4,395 and 7,986 protein coding genes, respectively. Species-specific primers were designed from variable regions of the draft genome sequence data and assessed by a PCR-based detection method. These primers were also tested for specificity against 17 allied Xanthomonas species as well as against the host DNA and the microbial community of the host surface. Three primer sets were found to be very specific and no amplification product was obtained with the host DNA and the microbial community of the host surface. In addition, a detection limit of 1 pg/μl per PCR reaction was detected when these primer sets were used to amplify corresponding bacterial DNAs. Therefore, these primer sets and the developed species-specific PCR assay represent a valuable, sensitive, and rapid diagnostic tool that can be used to detect three specific pathogens at early stages of infection and may help control diseases.
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http://dx.doi.org/10.5423/PPJ.OA.04.2015.0049DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4564146PMC
September 2015

Complete genome sequence of Spirosoma radiotolerans, a gamma-radiation-resistant bacterium isolated from rice field in South Korea.

J Biotechnol 2015 Aug 22;208:11-2. Epub 2015 May 22.

Department of Bio & Environmental Technology, College of Natural Science, Seoul Women's University, Seoul 139-774, Republic of Korea. Electronic address:

Spirosoma radiotolerans is a Gram-negative, short rod-shaped and gamma-radiation-resistant bacterium isolated from rice field in South Korea (GPS; 37°34'30″N, 127°00'30″E). The complete genome of S. radiotolerans consists of a chromosome (7,029,352bp). From the genome sequence database, we have identified the cluster of genes responsible for DNA recovery from ionizing radiation. The key enzymes for the nucleotide excision repair (NER) were investigated and were identified, suggesting that S. radiotolerans DG5A use (NER) pathways for efficient removal of pyrimidine dimers which are the most abundant type of UV-induced damage. Complete genome information enables further studies on the DNA repair mechanisms during the ionizing radiation.
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http://dx.doi.org/10.1016/j.jbiotec.2015.05.004DOI Listing
August 2015

Survey of Cherry necrotic rusty mottle virus and Cherry green ring mottle virus incidence in Korea by Duplex RT-PCR.

Plant Pathol J 2014 Dec 15;30(4):445-9. Epub 2014 Dec 15.

College of Agriculture and Life Sciences, Kyungpook National University, Daegu 702-701, Korea.

The incidence of Cherry necrotic rusty mottle virus (CNRMV) and Cherry green ring mottle virus (CGRMV) have recently been occurred in Korea, posing a problem for sweet cherry cultivation. Since infected trees have symptomless leaves or ring-like spots on the pericarp, it is difficult to identify a viral infection. In this study, the incidence of CNRMV and CGRMV in sweet cherry in Gyeongbuk province was surveyed using a newly developed duplex reverse transcriptase polymerase chain reaction (RT-PCR) method that can detect both viruses in a single reaction. CNRMV and CGRMV co-infection rates were 29.6%, 53.6%, and 17.6%, respectively, in samples collected from three different sites (Daegu, Gyeongju and Gyeongsan) in Gyeongbuk province during 2012 and 2013. This duplex RT-PCR method offers a simple, rapid, and effective way of identifying CNRMV and CGRMV simultaneously in sweet cherry trees, which can aid in the management of viral infections that could undermine yield.
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http://dx.doi.org/10.5423/PPJ.NT.05.2014.0041DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4262299PMC
December 2014

Draft Genome Sequence of Chryseobacterium sp. Strain P1-3, a Keratinolytic Bacterium Isolated from Poultry Waste.

Genome Announc 2014 Nov 26;2(6). Epub 2014 Nov 26.

School of Applied Biosciences, Kyungpook National University, Daegu, South Korea

Chryseobacterium sp. strain P1-3, harboring keratin degrading activity, has recently been isolated from poultry waste. Here, we report the 4.6-Mbp draft genome sequence of the keratinolytic bacterium with a G+C content of 37.0% and 4,087 protein-coding genes.
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http://dx.doi.org/10.1128/genomeA.01237-14DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4246171PMC
November 2014

Outbreak of Rust Caused by Coleosporium asterum on Solidago virgaurea var. gigantea in Ulleung-do.

Mycobiology 2014 Mar 31;42(1):79-81. Epub 2014 Mar 31.

School of Applied Biosciences, Kyungpook National University, Daegu 702-701, Korea. ; Institute of Plant Medicine, Kyungpook National University, Daegu 702-701, Korea.

From June to October 2012, severe outbreaks of rust disease on Solidago virgaurea var. gigantea were observed in 5 different regions of Ulleung-do, Korea. Typical rust symptoms appeared as yellow spots, uredinia on leaves, and massive urediniospores covering the entire plant. Severely infected plants became discolored and died. On the basis of its morphological and molecular characteristics, the causal agent was identified as Coleosporium asterum. This pathogen has been reported as rust disease on S. virgaurea in the Canada and United States. In Korea, rust disease on S. virgaurea var. gigantea was reported as Uromyces rudbeckia in 1992. To the best of our knowledge, C. asterum is a novel rust pathogen on S. virgaurea var. gigantea in Korea.
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http://dx.doi.org/10.5941/MYCO.2014.42.1.79DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4004953PMC
March 2014

Characterization of Species of Cladobotryum which Cause Cobweb Disease in Edible Mushrooms Grown in Korea.

Mycobiology 2012 Sep 30;40(3):189-94. Epub 2012 Sep 30.

School of Applied Biosciences, Kyungpook National University, Daegu 702-701, Korea.

Four Cladobotryum isolates were collected from four different commercially grown mushroom types infected with cobweb disease in Cheongdo-gun and Chilgok-gun of Gyeongbuk Province, Korea in 2010. The isolates were identified as C. mycophilum from Agaricus bisporus and Pleurotus eryngii, C. varium from Flammulina velutipes and Hypsizygus marmoreus. The cultural characteristics of the four isolates were investigated using potato dextrose agar (PDA) media under nine different temperatures ranging from 5~32℃. Rapid growth of the isolates to colony diameters of 47~82 mm was observed at conditions of 18~22℃. No growth was observed at 32℃. C. mycophilum produced a yellowish red pigment while C. varium produced a cream colored pigment after cultivation for 25 days on PDA. Phylogenetic analysis of the internal transcribed spacer region and partial 28S rDNA from the four isolates confirmed they were C. mycophilum and C. varium. Cross pathogenicity tests revealed that the two isolates of C. mycophilum were highly pathogenic toward three mushroom types, but not toward H. marmoreus. The two isolates of C. varium were less pathogenic than those of C. mycophilum, but were pathogenic toward all mushroom types evaluated.
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http://dx.doi.org/10.5941/MYCO.2012.40.3.189DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3483396PMC
September 2012

Biological Characterization of Marssonina coronaria Associated with Apple Blotch Disease.

Mycobiology 2011 Sep 27;39(3):200-5. Epub 2011 Sep 27.

Apple Experiment Station, National Horticultural Research Institute, Gunwi 716-812, Korea.

Marssonina coronaria associated with apple blotch disease causes severe premature defoliation, and is widely distributed in Korea. Thirteen isolates were collected from orchards located in Gyeongbuk Province from 2005~2007. All isolates displayed over 99.6% and 99.2% sequence similarity to each other in internal transcribed spacer regions and partial sequences of 28S rDNA, respectively. The isolates were phylogenetically closely related to Chinese isolates. Selected isolates did not differ in their pathogenicity. The optimum conditions for fungal growth were 20℃ and pH 6 on peptone potato dextrose agar (PPDA). Peptone and mannose were the best nitrogen and carbon source, respectively. Fungal growth was better on PPDA than on common potato dextrose agar. This study provides valuable information for integrated disease management program and facilitates the routine culturing of M. coronaria.
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http://dx.doi.org/10.5941/MYCO.2011.39.3.200DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3385119PMC
September 2011
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