• The Plant Pathology Journal
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• v.31 no.3
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• pp.212-218
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• 2015

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 $1pg/{\mu}l$ 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.

• Journal of Plant Biotechnology
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• v.45 no.2
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• pp.102-109
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• 2018

Thistle is a perennial plant that is widely used for medicinal purposes. Information on the genetic diversity of thistle populations are great important for their conservation and germ plasmic utilization. Although thistle is an important medicinal plant species registered in South Korea, no molecular markers are currently available to distinguish them from other similar species from different countries. In this study, we developed single nucleotide polymorphism (SNP) markers derived from the nuclear ribosomal DNA internal transcribed spacer (ITS) regions of genomic sequences to identify distinct Korean-specific thistle species via an amplification refractory mutation system (ARMS)-PCR and high resolution melting (HRM) curve analyses. We performed molecular authentication of four different kinds of thistle species from different regions using DNA sequences in the ITS intergenic region. We also developed a quantitative PCR assay using species-specific ITS primers, which allowed us to estimate the ratio of Korean-specific thistle species using varying ratios of mixed genomic DNA templates from the two species. The SNP markers developed in this study are useful for rapidly identifying specific thistle species from different countries.

• Mycobiology
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• v.32 no.3
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• pp.123-127
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• 2004

Sweet persimmons have been increasingly cultivated in the southern part of Korea. However, anthracnose disease caused by Colletotrichum species is one of the major hindrances in cultivation and productions. In this study, we used polymerase chain reaction(PCR) to detect Colletotrichum species with the AFLP(amplified fragment length polymorphism) method. In AFLP, we used E3(5'-GACTGCGTACCAATTCTA-3') and M1(5'-GATGAGTCCTGAGTAACAG-3') primer combination and, as a result, 262 bp segment was observed in Colletotrichum species only. Specific PCR primers were designed from the sequence data and used to detect the presence of the fungus in genomic DNA isolated from symptomless sweet persimmon plants. Based on sequence data for specific segments, Co.B1(5'-GAGAGAGTAGAATTGCGCTG-3') and Co.B2(5'-CTACCATTCTTCTA GGTGGG-3') were designed to detect Colletotrichum species. The 220 bp segment was observed in Colletotrichum species only, but not in other fungal and bacterial isolates.

• The Plant Pathology Journal
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• v.26 no.4
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• pp.409-416
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• 2010

Fusarium species, a large group of plant pathogens, potentially pose quarantine concerns worldwide. Here, we focus on the development of a method for detecting four Fusarium species in quarantined plants in Korea: F. solani f. sp. cucurbitae, F. stilboides, F. redolens, and F. semitectum var. majus. Species-specific primers were designed from the nucleotide sequences of either the translation elongation factor-1 alpha (TEF1) gene or RNA polymerase II subunit (RPB2) gene. Two different primer sets derived from TEF1, all specific to F. solani f. sp. cucurbitae, were able to differentiate the two races (1 and 2) of this species. A set of nested primers for each race was designed to confirm the PCR results. Similarly, two primer sets derived from RPB2 successfully amplified specific fragments from five F. stilboides isolates grouped within a single phylogenetic clade. A specific TEF1 primer set amplified a DNA fragment from only four of the 12 F. redolens strains examined, which were grouped within a single phylogenetic clade. All of the F. semitectum var. majus isolates could be specifically detected with a single RPB2 primer set. The specificity of the primer sets developed here was confirmed using a total of 130 Fusarium isolates.

• 한국균학회소식:학술대회논문집
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• 2018.05a
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• pp.35-35
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• 2018

Arbuscular mycorrhizal fungi (AMF) are one of the most widespread symbionts globally. Owing to their enhanced nutrient absorption capacity, AMF significantly contribute to the survival of individual plants and the ecosystem functioning. Community structures of AMF are affected by many environmental factors Inland wetlands have a different environment from common forest soils, therefore, plants inhabiting wetlands may have characteristic AMF communities. The purpose of this study was to compare the AMF communities in wetlands, among the species of host plants. We sampled the roots of 3 host plant species, Phragmites communis, Miscanthus sacchariflorus, and Trisetum bifidum with rhizospheres from 3 isolated areas in Upo wetland, Korea. We extracted DNA from AMF spores in rhizospheres and the roots of 3 plant species. We amplified 18S rDNA of AMF using AMF specific primer. As a result, we confirmed 9 species from 5 genera in AMF spores, and 5 species from 3 genera in plant roots. Funneliformis caledonium was the most dominant species in field soils, on the other hand, Diversispora aurantia was the most dominant species in plant roots. We confirmed that species diversity and abundance of AMF communities were different among host plant species. These results showed that the AMF community had specific to host plants in the inland wetland.

• Korean Journal of Plant Resources
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• v.12 no.4
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• pp.303-311
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• 1999

This study had been performed to clarify the distribution of specific plants and hydrophytes in the 27 sites of drainage basins located in Youngsan River at the period of June 1997 to July 1999. Hydrophytes were composed of 32 familis 86 species and hygrophytes 36 familis 135 species. Among hydrophytes, emerged plant, floating-leaved plant, submerged plants and free floating hydrophytes were 52, 15, 12, and 7 species respectively in this investigation. Threatened species were Drosera rotundifolia, Utricularia racemosa, Utricularia bifida, Utricularia japonica, Hydrocharis dubia, Endangered species were Brasenia schreberi and Euryale ferox.

• The Korean Journal of Ecology
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• v.21 no.1
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• pp.47-63
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• 1998

In order to compare species-specific calcium metabolism, we collected 127 species belonging to 40 different families grown on various habitats including saline, limestone, wetland during the 1996 vegetation period, and analyzed their inorganic ion contents. Plants investigated were divided into 5 groups according to their physiological properties: 1) Chenopodiaceae, Aizoaceae, Caryophyllaceae, Portulacaceae and Phytolaccaceae of Centrospermales and Polygonaceae (Polygonales had a little water-soluble $Ca^{2+}$ but contained high contents of insoluble $Ca^{2+}$ particularly as Ca-oxalate (Chenopodiaceae type), 2) Some plant species such as Rosaceae produced oxalate in amounts insufficient to precipitate all incoming $Ca^{2+}$ and thus contained a surplus of dissolved $Ca^{2+}$ (Rosaceae type), 3) The contents of water-soluble $Ca^{2+}$ in plant species of Crassulaceae. Plantaginaceae, Asclepiadaceae, and Zygophyllaceae were equal to or greater than those of K ($K/Ca{\leq}1$; Crassulaceae type), and 4) K/Ca ratios of Compositae were significantly fluctuated depending on species and soil $Ca^{2+}$ level of their habitats (Compositae type). 5) Certain monocots (Gramineae, Cyperaceae, Juncaceae), in contrast to the dicotyledonous plant families mentioned above, showed a very distinct type of calcium metabolism, that is, the K/Ca ratios of 8~10 were maintained indifferently in the species and their habitat types (Graminae type). These results plants within the same taxon have similar physiological aspects as weel as morphological attributes. To understand calcium metabolism of certain plant species, therefore, it is desirable to approach on the basis of physiological concept (calciotroph or calciophobe) rather than the ecological one (calcicole or calcifuge).

• The Plant Pathology Journal
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• v.30 no.4
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• pp.331-342
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• 2014

Given the lack of a resistant genetic pool in host plants, the introduction of exotic invasive pathogens can result in epidemics that affect a specific ecosystem and economy. Plant quarantine, which is designed to protect endemic plant resources, is a highly invaluable safeguard that should keep biosecurity with increasing international trade and global transportation. A total of 34 species of plant pathogens including Phytophthora infestans were documented as introduced from other countries into Korea from 1900 to 2010. The genus Phytophthora, classified in oomycetes, includes more than 120 species that are mostly recognized worldwide as highly invasive plant pathogens. After 2000, over 50 new species of Phytophthora were identified internationally as plant pathogens occurring in crops and forest trees. In Korea, Phytophthora is also one of the most serious plant pathogens. To date, 22 species (about one-fifth of known species) of the genus have been identified and reported as plant pathogens in the country. The likelihood of new exotic Phytophthora species being introduced into Korea continues to increase, thus necessitating intensive plant quarantine inspections. As new potential threats to plant health in Korea, six Phytophthora species, namely, P. alni, P. inundata, P. kernoviae, P. pinifolia, P. quercina, and P. ramorum, are discussed in this review with focus on history, disease, biology, management, and plant quarantine issues.

• Biotechnology and Bioprocess Engineering:BBE
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• v.9 no.6
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• pp.482-489
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• 2004

Bacillus species were observed and quantified by molecular approaches, using the 16S rDNA primers/probes, in a wastewater treatment plant designed for the purpose of stimulating the growth of Bacillus species. The plant has been operating as a test plant since 1997 in the city of Ina, Japan, with excellent treatment performance. Observations by in situ hybridization, using Bacillus-specific probes, indicated that Bacillus strains were inhabited in the plant and their num­bers decreased during the treatment process. Similar results were obtained from a quantitative PCR analysis using a Bacillus-specific primer set, and the amount of DNA originating from various Bacillus species was maximally $1.91%\$ of the total DNA in the wastewater treatment tank. Clone library analysis using the Bacillus-specific primers suggested that, while the population was no­ticeably increased, the phylogenetic diversity of the increasing Bacillus species was very low.

• The Plant Pathology Journal
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• v.38 no.6
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• pp.656-664
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• 2022

Pectobacterium odoriferum is the primary causative agent in Kimchi cabbage soft-rot diseases. The pathogenic bacteria Pectobacterium genera are responsible for significant yield losses in crops. However, P. odoriferum shares a vast range of hosts with P. carotovorum, P. versatile, and P. brasiliense, and has similar biochemical, phenotypic, and genetic characteristics to these species. Therefore, it is essential to develop a P. odoriferumspecific diagnostic method for soft-rot disease because of the complicated diagnostic process and management as described above. Therefore, in this study, to select P. odoriferum-specific genes, species-specific genes were selected using the data of the P. odoriferum JK2.1 whole genome and similar bacterial species registered with NCBI. Thereafter, the specificity of the selected gene was tested through blast analysis. We identified novel species-specific genes to detect and quantify targeted P. odoriferum and designed specific primer sets targeting HAD family hydrolases. It was confirmed that the selected primer set formed a specific amplicon of 360 bp only in the DNA of P. odoriferum using 29 Pectobacterium species and related species. Furthermore, the population density of P. odoriferum can be estimated without genomic DNA extraction through SYBR Green-based real-time quantitative PCR using a primer set in plants. As a result, the newly developed diagnostic method enables rapid and accurate diagnosis and continuous monitoring of soft-rot disease in Kimchi cabbage without additional procedures from the plant tissue.