• Korean Journal of Medicinal Crop Science
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• v.24 no.1
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• pp.55-61
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• 2016

Background : Plant breeding requires the collection of genetically diverse genetic resources. Studies on the characteristics of Platycodon grandiflorum resources have not been carried out so far. The present study was carried out to discriminate P. grandiflorum based on morphological characteristics and genetic diversity using simple sequence repeat (SSR) markers. Methods and Results :We collected 11 P. grandiflorum cultivars: Maries II, Hakone double white, Hakone double blue, Fuji white, Fuji pink, Fuji blue, Astra white, Astra pink, Astra blue, Astra semi-double blue and Jangbaek. Analyses of the morphological characteristics of the collection were conducted for aerial parts (flower, stem and leaf) and underground parts (root). Next, the genetic diversity of all P. grandiflorum resources was analyzed using SSR markers employing the DNA fragment analysis method. We determined that the 11 P. grandiflorum cultivars analyzed could be classified by plant length, leaf number and root characteristic. Based on the genetic diversity analysis, these cultivars were classified into four distinct groups. Conclusions : These findings could be used for further research on cultivar development using molecular breeding techniques and for conservation of the genetic diversity of P. grandiflorum. Moreover, the markers could be used for genetic mapping of the plant and marker-assisted selection for crop breeding.

• Mycobiology
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• v.37 no.3
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• pp.183-188
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• 2009

The molecular phylogeny in nine different commercial cultivated strains of Pleurotus nebrodensis was studied based on their internal transcribed spacer (ITS) region and RAPD. In the sequence of ITS region of selected strains, it was revealed that the total length ranged from 592 to 614 bp. The size of ITS1 and ITS2 regions varied among the strains from 219 to 228 bp and 211 to 229 bp, respectively. The sequence of ITS2 was more variable than ITS1 and the region of 5.8S sequences were identical. Phylogenetic tree of the ITS region sequences indicated that selected strains were classified into five clusters. The reciprocal homologies of the ITS region sequences ranged from 99 to 100%. The strains were also analyzed by RAPD with 20 arbitrary primers. Twelve primers were efficient to applying amplification of the genomic DNA. The sizes of the polymorphic fragments obtained were in the range of 200 to 2000 bp. RAPD and ITS analysis techniques were able to detect genetic variation among the tested strains. Experimental results suggested that IUM-1381, IUM-3914, IUM-1495 and AY-581431 strains were genetically very similar. Therefore, all IUM and NCBI gene bank strains of P. nebrodensis were genetically same with some variations.

• The Plant Pathology Journal
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• v.31 no.4
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• pp.388-401
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• 2015

Sweet potatoes (Ipomea batatas L.) are grown extensively, in tropical and temperate regions, and are important food crops worldwide. In Korea, potyviruses, including Sweet potato feathery mottle virus (SPFMV), Sweet potato virus C (SPVC), Sweet potato virus G (SPVG), Sweet potato virus 2 (SPV2), and Sweet potato latent virus (SPLV), have been detected in sweet potato fields at a high (~95%) incidence. In the present work, complete genome sequences of 18 isolates, representing the five potyviruses mentioned above, were compared with previously reported genome sequences. The complete genomes consisted of 10,081 to 10,830 nucleotides, excluding the poly-A tails. Their genomic organizations were typical of the Potyvirus genus, including one target open reading frame coding for a putative polyprotein. Based on phylogenetic analyses and sequence comparisons, the Korean SPFMV isolates belonged to the strains RC and O with >98% nucleotide sequence identity. Korean SPVC isolates had 99% identity to the Japanese isolate SPVC-Bungo and 70% identity to the SPFMV isolates. The Korean SPVG isolates showed 99% identity to the three previously reported SPVG isolates. Korean SPV2 isolates had 97% identity to the SPV2 GWB-2 isolate from the USA. Korean SPLV isolates had a relatively low (88%) nucleotide sequence identity with the Taiwanese SPLV-TW isolates, and they were phylogenetically distantly related to SPFMV isolates. Recombination analysis revealed that possible recombination events occurred in the P1, HC-Pro and NIa-NIb regions of SPFMV and SPLV isolates and these regions were identified as hotspots for recombination in the sweet potato potyviruses.

• Microbiology and Biotechnology Letters
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• v.46 no.2
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• pp.162-170
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• 2018

Non-typhoidal Salmonella is one of the main pathogens causing food-borne illness in humans, with up to 20% of cases resulting from consumption of pork products. Over the gastroenteritis signs, multidrug resistant Salmonella has arisen. In this study, pan-susceptible phenotypic strains of Salmonella enterica serotype Weltevreden recovered from pig production chain in Chiang Mai, Thailand during 2012-2014 were chosen for analysis. The aim of this study was to use whole genome sequencing (WGS) data with an emphasis on antimicrobial resistance gene investigation to assess their pathogenic potential and genetic diversity determination based on whole genome Multilocus Sequence Typing (wgMLST) to expand epidemiological knowledge and to provide additional guidance for disease control. Analyis using ResFinder 3.0 for WGS database tracing found that one of pan-susceptible phenotypic strain carried five classes of resistance genes: aminoglycoside, beta-lactam, phenicol, sulfonamide, and tetracycline associated genes. Twenty four and 36 loci differences were detected by core genome Multilocus Sequence Typing (cgMLST) and pan genome Multilocus Sequence Typing (pgMLST), respectively, in two matching strains (44/13 vs A543057 and A543056 vs 204/13) initially assigned by conventional MLST and Pulsed-field Gel Electrophoresis (PFGE). One hundread percent discriminant ability can be achieved using the wgMLST technique. WGS is currently the ultimate molecular technique for various in-depth studies. As the findings stated above, a new of "gold standard typing method era" for routine works in genome study is being set.

• The Plant Pathology Journal
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• v.16 no.2
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• pp.110-117
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• 2000

Potato virus X (PVX-KO) showing mild mosaic and stunting symptoms on potato (Solanum tuberosum) in Kangwon area has been isolated and characterized. EM observation of the purified virus particles showed flexuous rod shape of about 520 nm in length. The coat protein (CP) of the virus had a molecular weight of 31 kDa in SDS-PAGE analysis, and the viral RNA was approximately 6.4 kb in size in denatured agarose gel electro-phoresis. In gel-immunodiffusion tests, it reacted strongly with an antiserum to common PVX from BIOREABAAG (USA). A rabbit antiserum was produced using purified virus and used for routine PVX detection by ELISA. Cultivated potatoes in Kangwon and other areas were frequently infected with PVX-KO. Both Datura stramonium and Nicotiana tabaccum cultivars developed necrotic local lesions 5 days after inoculation, and systemic mosaic symptoms with vein clearing 2 weeks after inoculation. All the features agree with the description of other PVX strains. To confirm and determine PVX strains, reverse transcription-polymerase chain reaction experiment was conducted using specific primers for viral CP. Amplified DNA fragments were cloned and sequenced. Results showed nucleotide sequence homologies of about 88 to 99% to other PVX strains. Based on CP amino acid sequence deduced from nucleotide sequences and host range studies PVX-KO is considered a member of the type X subgroup of PVX.

• The Korean Journal of Food And Nutrition
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• v.19 no.4
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• pp.496-501
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• 2006

This study was to isolate a bacterium producing a alkaline protease from mud flats of the west seaside of Korea and to investigate the biochemical analysis of the alkaline protease producing from the isolate. The isolate was named as Gelidibacter sp. HK-1 based on 16S rRNA sequence, Gram staining and the photograph of electron microsceope. Optimum temperature for growth and pretense production of the isolate was $25^{\circ}C$. Growth of the isolate was reached at stationary phase after 10hrs followed by inoculation. Maximum activity of protease produced from the isolate was shown after 14hrs. Optimum temperature and pH for the protease activity were $45^{\circ}C$ and pH 9, respectively. Molecular weight of the pretense was about 50KD and the partial amino acid sequence of the pretense was Ala-Try-Ala-Leu-Asn-Thr-Ser-Val-Thr-Glu-Thr-Phe-Ala-Lys. The partial amino acid sequences of the protease showed significant homology with a pretense produced from Streptomyces avermitilis.

• Journal of Life Science
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• v.14 no.4
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• pp.593-607
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• 2004

The nucleotide sequence for a nuclear-encoded small subunit rDNA (SSU rDNA) was determined for 43 species of the class Dinophyceae, including harmful algae Cochlodinium polykrikoides and Gyrodinium aureolum. These sequences and data analyses were performed by parsimony, distances and maximum likelihood methods in PHYLIP (Phylogenetic Inference Package) version 3.573c. The species Noctiluca scintillans, Gonyaulax spinifern and Crypthecodinium cohnii occupied a basal position within the Dino- phyceae in our analyses. The genera Alexandrium and Symbiodinium were monophyletic (supported by a bootstrap value of >70%), whereas the genera Gymnedinium and Gyrodinium formed polyphyletic nodes, for which bootstrap support was strong (>70%) in the neighbor-joining and maximum likelihood methods except for the PHYLIP parsimony analysis (=59%). The sequence divergence between G. aureolum and G. dorsum/ G. galathenum was the largest at 7.4% (45 bp), whereas G. aureolum and G. mikimotoi showed an extremely low value of genetic divergence of 0.9% (5 bp). The genetic divergence between C. polykrikoides and G. aureolum was a low value of 5.2% (31 bp). In the phylogenetic analysis, the placement of G. aureolum and C. polykrikoides was closer to the genus Gymnodinium than to the genus Gyrodinium, which was supported by a moderate bootstrap value.

• Journal of Microbiology and Biotechnology
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• v.20 no.10
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• pp.1440-1445
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• 2010

Rhodococcus sp. JDC-11, capable of utilizing di-n-butyl phthalate (DBP) as the sole source of carbon and energy, was isolated from sewage sludge and confirmed mainly based on 16S rRNA gene sequence analysis. The optimum pH, temperature, and agitation rate for DBP degradation by Rhodococcus sp. JDC-11 were 8.0, $30^{\circ}C$, and 175 rpm, respectively. In addition, low concentrations of glucose were found to inhibit the degradation of DBP, whereas high concentrations of glucose increased its degradation. Meanwhile, a substrate utilization test showed that JDC-11 was also able to utilize other phthalates. The major metabolites of DBP degradation were identified as monobutyl phthalate and phthalic acid by gas chromatography-mass spectrometry, allowing speculation on the tentative metabolic pathway of DBP degradation by Rhodococcus sp. JDC-11. Using a set of new degenerate primers, a partial sequence of the 3,4-phthalate dioxygenase gene was obtained from JDC-11. Moreover, a sequence analysis revealed that the phthalate dioxygenase gene of JDC-11 was highly homologous to the large subunit of the phthalate dioxygenase from Rhodococcus coprophilus strain G9.

• The Plant Pathology Journal
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• v.25 no.1
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• pp.91-94
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• 2009

An unreported disease of garlic was observed in commercial fields in Jiangsu province, China. The symptoms started as water soaked lesions at the base of the leaves. Later, water-soaked areas developed on stems and spread to the internal tissues, followed by yellowing and necrosis along leaf edges and soft rot of the stems. The causal organism isolated from symptomatic plants was identified as Pseudomonas fluorescens based on its biochemical and physiological characteristics and confirmed by the cellular fatty acid composition and Biolog data as well as 168 rRNA gene sequence analysis. The bacterial isolates caused similar symptoms when inoculated onto garlic plants. In addition, leek and shallot were susceptible to the P. fluorescens pathogen. However, the P. fluorescens pathogen failed to cause any symptoms when it was inoculated onto 15 other plants. This is the first report of a bacterial disease of garlic caused by P. fluorescens in China.

• Korean Journal of Environment and Ecology
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• v.32 no.6
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• pp.566-574
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• 2018

The purpose of this study was to identify the phylogenetic relationships of the plants in the Korean genus Suaeda and to find out the molecular markers that could confirm the interspecies relationships in the family tree through molecular phylogenetic studies. We used the nuclear ribosomal DNA ITS and the chloroplast DNA matK, psbA-trnH, and trnL-trnF as the molecular markers. We could not distinguish between S. japonica and S. maritima and between S. maritima and S. australis in the ITS region and could not distinguish between S. japonica and S. australis with the base sequence in the psbA-trnH and trnL-trnF region. However, we analyzed the combinations of four molecular marker regions and confirmed that each of five plant species of the genus Suaeda formed the independent line. Therefore, it is considered that combinations of molecular markers would be useful for the analysis of phylogenetic relationships in the genus Suaeda. Further investigations of the ecological and morphological characteristics would be needed to understand the phylogenetic relationship and lineage diversification in the genus Suaeda.