• Korean Journal of Medicinal Crop Science
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• v.17 no.1
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• pp.26-32
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• 2009

The region containing 18S rRNA gene, ITS 1 and part of the 5.8S rRNA gene of the Atractylodes japonica Koidz was amplified by PCR and the product cloned in a pBluescript SK II plasmid. DNA sequence of the cloned DNA was determined and submitted to the GenBank (accession number EU678363). Phylogenetic analysis of the ITS 1 DNA showed close similarity with the other plant species of the family Compositae. The extract of the plant materials of five different members of the family Compositae was analyzed by HPLC to detect atractylon. Extract of the A. japonica Koidz showed presence of significant amount of atractylon. However, noticeable amount of atractylon was not detected by the same analyses from the extracts of the other plants belonging to the family Compositae including Artemisia capillaris, Chrysantemum zawadskii, Eclipta prostrata or Taraxacum platycarpum.

• 한국균학회소식:학술대회논문집
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• 2014.05a
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• pp.45-45
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• 2014

Individualities of precious health mushroom called Zhenghonggu@ from respective protections scattered among all main mountains of Fujian China were collected and recognized locally, then compared with Russula griseocarnosa. Their internal transcribed spacer (ITS) region (ITS1, ITS2 and 5.8S rDNA) of the nuclear rDNA were amplified, AMOVA analyzed, nested clade analyzed and then compared with the ITS sequences of relative Russula species from other regions of China to confirm the taxonomic status of Zhenghonggu$^@$ and its population structure. Total 23 haplotypes from different protections of Fujian can be clustered into three clades similar to the three lineages of Dahongjun$^@$ from southeastern China reported by Li et al. The geographic distribution characteristic of these three phylogeny clades may be closely coupled with the vegetation regionalization and/or the differences of coenosium construction of Fagaceae that is the host of Russula griseocarnosa. The correlation of taxonomy, phylogeny and geographical distribution of Russula are discussed.

• Journal of Life Science
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• v.11 no.2
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• pp.126-134
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• 2001

The phylogenetic tree displayed the presence of five groups in the Phellinus genus, which were distinguished based on their morphology. Most of the p. linteus appeared a cluster which was highly significant with the exception of P. linteus KACC 500122 and KACC 500411. They formed the sister taxa of P 1inteus where P. baumii, Phellinus sp. MPNU 7003, MPNU 7007, and MPNU 7010 had similar morphological characteristics. Also, P. nigricans IMSNU 32024 and P. pini var, carniformans IMSNU 32031 were grouped in the same cluster with P. igniarius KCTC 6227, KCTC 6228, and P. chrysoloma KCTC 6225 extracted from the Gen-Bank database. P. torulosus IMSNU 32028 and Phellinus sp. MPNU 7011 formed a closed group, however, these species had a distant taxa when compared with the other Phellinus species. The nucleotide sequences of the internal transcribed spacer (ITS) regions of ribosomal DNA (rDNA) including the 5.85 rDNA were determined from 24 strains of the Phellinus genus in order to analyze their phylogenetic relationship. These fungi were divided into two basic groups based on their ITS length, however, this grouping was different from that based on their morphological characteristics. Although various ITS sequences were ambiguously aligned, conserved sites were also identified. Accordingly, a neighbor-joining tree was constructed using the nucleotide sequence data of the conserved sites of the ITS regions and the 5.8S rDNA.

• Ocean Science Journal
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• v.40 no.3
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• pp.155-166
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• 2005

New PCR primers (N=18) were designed for the isolation of complete SSU to LSU rDNA sequences from the dinoflagellate Alexandrium tamarense. Standard PCR, employing each primer set selected for amplifications of less than 1.5 kb, successfully amplified the expected rDNA regions of A. tamarense (Korean isolate, HY970328M). Complete SSU, LSU rDNAs and ITS sequences, including 5.8S rDNA, were recorded at 1,800 bp, 520 bp and 3,393 bp, respectively. The LSU rDNA sequence was the first report in Alexandrium genus. No intron was found in the LSU rRNA coding region. Twelve D-domains within the LSU rDNA were put together into 1,879 bp (44.4% G+C), and cores into 1514 bp (42.8% G+C). The core sequence was significantly different (0.0867 of genetic distance, 91% sequence similarity) in comparison with Prorocentrum micans (GenBank access. no. X16108). The D2 region was the longest in length (300 bp) and highly variable among the 12 D-domains. In a phylogenetic analysis using complete LSU rDNA sequences of a variety of phytoplankton, A. tamarense was clearly separated with high resolution against other species. The result suggests that the sequence may resolve the taxonomic ambiguities of Alexandrium genus, particularly of the tamarensis complex.

• Korean journal of applied entomology
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• v.37 no.1
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• pp.23-30
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• 1998

Restriction fragment length polymorphism (RFLP) of a DNA has been a useful tool for analyzing genetic variation. This research was performed to establish an RFLP analytic method on the mitochondrial DNA (mtDNA) of the beet armyworm, Spodoptera exigua (Hiibner). To do this, total size of the mtDNA was measured and polymerase chain reaction (PCR) primers were selected. Its mitochondrial genome size was ca. 16kb. From a serial PCR test of 29 primers refered to the compilation of Simon et al. (1994), 22 primers were selected to amplify its mtDNA fragments. These primers resulted in short (300-700 bp) or long (1000-2000 bp) DNA products which represented a total or partial sequence of each of CO-I, CO-11, Cyt-B, ND-1, 12s rRNA, 16s rRNA, and some tRNAs. PCR-RFLP was performed in some variable mtDNA regions with 8 kinds of 4bp recognizing restriction enzymes. Different populations from Andong, Kyungsan, and Sunchun did not show any restriction site polymorphisms but had some length variation in certain regions of mtDNA.

• Journal of Microbiology and Biotechnology
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• v.11 no.3
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• pp.428-434
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• 2001

A viscous substance producer strain BS62, which was isolated from conventional Chungkookjang, was examined for its productivity of levansucrase and levan during soybean fermentation at $37{\circ}C$. After one day of cultivation, the enzyme activity reached the highest level, 8 units $ml^{-1}$. Extracts of fermented soybeans were precipitated by ethanol and hydrolyzed by either 0.1 N HCl or invertase, and the hydrolyzates were analyzed using thin layer and ion chromatographies. Fructose was the only sugar detected. This suggest that fructose was derived from the levan produced by the strain BS62 during soybean fermentation. The aerobic, endospore-forming bacterium BS62 was identified as a Bacillus subtilis sp., based on the composition of its cellular fatty acids and phylogeny, which was determined by its 16S rDNA sequence.

• The Plant Pathology Journal
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• v.40 no.2
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• pp.171-191
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• 2024

Identification of Helicotylenchus species is very challenging due to phenotypic plasticity and existence of cryptic species complexes. Recently, the use of rDNA barcodes has proven to be useful for identification of Helicotylenchus. Molecular markers are a quick diagnostic tool and are crucial for discriminating related species and resolving cryptic species complexes within this speciose genus. However, DNA barcoding is not an error-free approach. The public databases appear to be marred by incorrect sequences, arising from sequencing errors, mislabeling, and misidentifications. Herein, we provide a comprehensive analysis of the newly obtained, and published DNA sequences of Helicotylenchus, revealing the potential faults in the available DNA barcodes. A total of 97 sequences (25 nearly full-length 18S-rRNA, 12 partial 28S-rRNA, 16 partial internal transcribed spacer [ITS]-rRNA, and 44 partial cytochrome c oxidase subunit I [COI] gene sequences) were newly obtained in the present study. Phylogenetic relationships between species are given as inferred from the analyses of 103 sequences of 18S-rRNA, 469 sequences of 28S-rRNA, 183 sequences of ITS-rRNA, and 63 sequences of COI. Remarks on suggested corrections of published accessions in GenBank database are given. Additionally, COI gene sequences of H. dihystera, H. asiaticus and the contentious H. microlobus are provided herein for the first time. Similar to rDNA gene analyses, the COI sequences support the genetic distinctness and validity of H. microlobus. DNA barcodes from type material are needed for resolving the taxonomic status of the unresolved taxonomic groups within the genus.

• The Korea Journal of Herbology
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• v.30 no.3
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• pp.41-47
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• 2015

Objectives : Due to the morphological similarity of the pericarp and description of multi-species in National Pharmacopoeia of Korea and China, the Zanthoxylum Pericarpium is difficult to authenticate adulterant in species levels. Therefore, we introduced the sequence analysis of DNA barcode and identification of single nucleotide polymorphism(SNP) to establish a reliable tool for the distinction of Zanthoxylum Pericarpium from its adulterants. Methods : To analyze DNA barcode region, genomic DNA was extracted from twenty-four specimens of authentic Zanthoxylum species and inauthentic adulterant and the individual internal transcribed spacer regions (rDNA-ITS and ITS2) of nuclear ribosomal RNA gene were amplified using ITS1, ITS2-S2F, and ITS4 primer. For identification of species-specific sequences, a comparative analysis was performed using entire DNA barcode sequences. Results : In comparison of four Zanthoxylum ITS2 sequences, we identified 16, 4, 6, and 4 distinct species-specific nucleotides enough to distinguish Z. schinifolium, Z. bungeanum, Z. piperitum, and Z. simulans, respectively. The sequence differences were available genetic marker to discriminate four species. Futhermore, phylogenetic relationship revealed a clear classification between different Zanthoxylum species showing 4 different clusters. These results indicated that comparative analysis of ITS2 DNA barcode was an useful genetic marker to authenticate Zanthoxylum Pericarpium in species levels. Conclusions : The marker nucleotides, enough to distinguish Z. schinifolium, Z. piperitum, Z. bungeanum, and Z. simulans, were obtained at 30 SNP marker nucleotides from ITS2 sequences. These differences could be used to authenticate official Zanthoxylum Pericarpium from its adulterants as well as discriminating each four species.

• Korean Journal of Plant Resources
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• v.35 no.2
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• pp.346-361
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• 2022

Food poisoning accidents caused by poisonous plants occur every year. As certain poisonous plants are mistaken for edible plants causing food poisoning, accurate species identification of poisonous plants is required. DNA barcodes suitable for species identification of poisonous plants and database that can be used for accurate species identification are necessary for their use in forensic cases. In this study, species identification of 19 poisonous plants native to Jeju Island using seven DNA barcodes (trnH-psbA, trnL-trnF, trnL intron, rbcL, matK, ITS1-ITS4, 18S rRNA) was performed to construct a database containing sequence information and DNA barcode universality. trnL-trnF barcode and ITS1-ITS4 barcode were the easiest markers for PCR amplification and sequence retrieval, and the combination of the two barcodes enabled single species identification in 18 out of 19 plants. Therefore, when an investigation of unknown poisonous plants is requested, combination of trnL-trnF and ITS1-ITS4 barcodes is considered as a primary marker for species identification. The database of recommended DNA barcodes for each poisonous plant presented in this study will be helpful in plants poisoning cases.

• Research in Plant Disease
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• v.11 no.1
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• pp.56-65
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• 2005

To establish taxonomic system of morphologically similar species of small-spored Alternaria, phylogenetic analysis of internal transcribed spacer (ITS 1, ITS 2 and 5.8S rDNA) and mitochondrial small subunit (mt SSU) rDNA sequences and URP-PCR fingerprinting analysis from 11 species ofAlternaria were performed. Phylogenetic analysis of ITS and mt SSU rDNA sequences revealed that 10 out of 11 species of the smallspored Alternaria were phylogenetically identical with a bootstrap value of 100%. A. infectoria only was phylogenetically differentiated from the other species. The results suggest that the 10 small-spored Alternaria species are very closely related evolutionally and the markers can not be used for differentiation of the smallspored Alternaria species. URP-PCR fingerprinting analysis from eleven species of smallspored Alternaria using 10 URP primers showed that it was possible to differentiate the species, although genetic similarities were found among the species. The Alternaria sp. from common pokeweed could be distinguished from other species by URP-PCR analysis, and it was considered as a new species. A. infectoria could be easily distinguished from the other 10 species by phylogenetic analysis of ITS and mt SSU rDNA sequences and the URPPCR fingerprinting analysis.