• 한국균학회지
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• 제49권1호
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• pp.11-19
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• 2021

In 2017, Talaromyces variabilis was isolated during a survey of fungal diversity in field soils in Korea. This isolate was described based on its morphological and molecular characteristics and it was identified molecularly using the partial 18S-ITS1-5.8S-ITS2-28S rDNA region and calmodulin (CaM)-encoding gene sequence data. Thus, this study reported morphological and multigene sequence characterization of T. variabilis.

• 한국동물위생학회지
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• 제42권3호
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• pp.161-167
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• 2019

The poultry red mite (PRM), Dermanyssus gallinae, causes great economic losses to poultry industries in Korea. The molecular epidemiological characterization of PRM has been investigated in some countries, but those analysis has been not conducted yet in Korea. The aim of this study is to determine the genetic diversity of PRMs in Korea compared with those from other countries. Here, 13 PRM samples collected from Korea were analyzed with a part of the mitochondrial cytochrome oxidase subunit I (COI) gene and nuclear internal transcribed spacers (ITS) region. All the samples showed an identical COI sequence, which has also been reported in European countries and Japan. Phylogenetic diversity analysis showed that the mites from Korea were genetically related to those in other countries. The nuclear ITS region sequences were classified into three sequence types. Additionally, one of the ITS sequences was an intermediate type, implying that a hybridization event occurred among the mite populations in Korea. These findings suggested PRMs from Korea showed low genetic diversity with respect to mitochondrial COI gene, but three different populations inhabited in Korea with respect to nuclear ITS region sequences.

• Journal of Microbiology and Biotechnology
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• 제1권1호
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• pp.45-49
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• 1991

The complete nucleotide sequence of alkalophilic Bacillus sp. K-17 $\beta$-xylosidase gene and its flanking regions were established. A 1263-bp of an open reading frame for $\beta$-xylosidase was observed. The molecular weight (50, 521 dalton), deduced from the nucleotide sequence of $\beta$-xylosidase gene, agreed with the result obtained by SDS-polyacrylamide gel electrophoresis of the purified enzyme (51, 000 dalton). The Shine-Dalgarno sequence, 5'-GAGGAGG-3', was found 8 bp upstream of the initiation codon ATG. The -10 sequence (TAAAAT) in the promoter region for $\beta$-xylosidase gene was similar to the consensus sequence for Bacillus subtilis RNA polymerase, whereas the -35 sequence (TCGATCA) different from all the known -35 regions in the promoter for Bacillus subtilis RNA polymerase.

• 한국산림과학회지
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• 제96권4호
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• pp.425-431
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• 2007

Rhizina undulata의 PCR 검정 및 유전적 특성 분석을 목적으로, rDNA ITS 영역의 염기배열 해석 및 PCR 방법에 의한 토양으로부터 R. undulata의 진단법을 개발하였다. 18S rDNA 부분의 염기서열 분석 결과, 공시한 4종의 균주 모두 1,375 nt의 크기로 동일하였으며, 염기배열도 100% 일치하였다. 한편, rDNA ITS 영역의 염기배열은 585 nt이었고, PDK-1, PTT-1 및 PDJ-9 균주는 염기배열이 100% 동일하였으나, PDS-5균주에서는 두 곳에서 염기의 치환이 발견되었다. 이와 같은 염기배열을 분석하여 제작한 R. undulata rDNA ITS 영역 특이적 primer를 이용한 PCR 검정 결과, R. undulata 균주들에서만 약 525 bp 크기의 ITS 영역 특이적인 증폭산물이 검출되었다. PCR 방법에 의하여 검출할 수 있는 토양 중의 R. undulata 최소 균사량의 한계를 확인하기 위해서, 순수 배양한 R. undulata 균사현탁액을 순차 희석하여 100g의 사양토에 혼합한 다음, 농도별로 균사 혼합한 각각의 토양 시료로부터 추출한 total DNA의 PCR 증폭산물을 분석한 결과, PCR 방법에 의하여 100g의 토양 중에 1 ng의 R. undulata 균사가 함유되어 있는 경우까지 검출이 가능하였다.

• Ocean Science Journal
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• 제40권3호
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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.

• Genomics & Informatics
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• 제16권4호
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• pp.23.1-23.5
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• 2018

Virus taxonomy was initially determined by clinical experiments based on phenotype. However, with the development of sequence analysis methods, genotype-based classification was also applied. With the development of genome sequence analysis technology, there is an increasing demand for virus taxonomy to be extended from in vivo and in vitro to in silico. In this study, we verified the consistency of the current International Committee on Taxonomy of Viruses taxonomy using an in silico approach, aiming to identify the specific sequence for each virus. We applied this approach to norovirus in Caliciviridae, which causes 90% of gastroenteritis cases worldwide. First, based on the dogma "protein structure determines its function," we hypothesized that the specific sequence can be identified by the specific structure. Firstly, we extracted the coding region (CDS). Secondly, the CDS protein sequences of each genus were annotated by the conserved domain database (CDD) search. Finally, the conserved domains of each genus in Caliciviridae are classified by RPS-BLAST with CDD. The analysis result is that Caliciviridae has sequences including RNA helicase in common. In case of Norovirus, Calicivirus coat protein C terminal and viral polyprotein N-terminal appears as a specific domain in Caliciviridae. It does not include in the other genera in Caliciviridae. If this method is utilized to detect specific conserved domains, it can be used as classification keywords based on protein functional structure. After determining the specific protein domains, the specific protein domain sequences would be converted to gene sequences. This sequences would be re-used one of viral bio-marks.

• Journal of Microbiology and Biotechnology
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• 제34권5호
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• pp.1146-1153
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• 2024

The increasing economic losses associated with growth retardation caused by Enterocytozoon hepatopenaei (EHP), a microsporidian parasite infecting penaeid shrimp, require effective monitoring. The internal transcribed spacer (ITS)-1 region, the non-coding region of ribosomal clusters between 18S and 5.8S rRNA genes, is widely used in phylogenetic studies due to its high variability. In this study, the ITS-1 region sequence (~600-bp) of EHP was first identified, and primers for a polymerase chain reaction (PCR) assay targeting that sequence were designed. A newly developed nested-PCR method successfully detected the EHP in various shrimp (Penaeus vannamei and P. monodon) and related samples, including water and feces collected from Indonesia, Thailand, South Korea, India, and Malaysia. The primers did not cross-react with other hosts and pathogens, and this PCR assay is more sensitive than existing PCR detection methods targeting the small subunit ribosomal RNA (SSU rRNA) and spore wall protein (SWP) genes. Phylogenetic analysis based on the ITS-1 sequences indicated that the Indonesian strain was distinct (86.2% nucleotide sequence identity) from other strains collected from Thailand and South Korea, and also showed the internal diversity among Thailand (N = 7, divided into four branches) and South Korean (N = 5, divided into two branches) samples. The results revealed the ability of the ITS-1 region to determine the genetic diversity of EHP from different geographical origins.

• Journal of Microbiology
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• 제42권3호
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• pp.233-238
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• 2004

Transcriptional regulation of the Schizosaccharomyces pombe y-glutamylcysteine synthetase (GCS) gene was examined using the two GCS-lacZ fusion plasmids pUGCS101 and pUGCS102, which harbor 607 bp and 447 bp upstream regions, respectively. The negatively-acting sequence was located in the -607 - -447 bp upstream region of the GCS gene. The upstream sequence responsible for induction by menadione(MD) and L-buthionine-(S, R)-sulfoximine (BSO) resides in the -607 - -447 bp region, whereas the sequence which codes for nitric oxide induction is located within the -447 bp region, measured from the translational initiation point. Carbon source-dependent regulation of the GCS gene appeared to be dependent on the nucleotide sequence within -447 bp region. The transcription factor Papl is involved in the induction of the GCS gene by MD and BSO, but not by nitric oxide. Induction of the GCS gene occurring due to low glucose concentration does not depend on the presence of Pap1. These data imply that induction by MD and BSO may be mediated by the Pap1 binding site, probably located in the -607 - -447 region, and also that the nitric oxide-mediated regulation of the S. pombe GCS gene may share a similar mechanism with its carbon-dependent induction.

• 한국잠사곤충학회지
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• 제43권1호
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• pp.1-8
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• 2001

Nucleotide sequence in internal transcribed spacer (ITS) regions of ribosomal DNA among mulberry varieties (Morus species) were analyzed in order to identify the possibility of classification for the species. The variations in the ITS regions were compared among 9 mulberry varieties and one variety of Cudrania species as an outgroup. ITS 1 region of the varieties ranging from 219 to 220 bp in length was 49-50 bp shorter than ITS 2 region. Of 510 sites in the ITS 1 and 2 regions, 148 sites were potentially variable, of which 52% and 48% sites were distributed in ITS 1 and ITS 2 regions, respectively. By pairwise comparisons on the nucleotide sequences in the ITS 1 and 2 regions among 9 mulberry varieties, they were classified into 5 groups. Divergence values of the sequences, however, were considerably low ranging from 0 to 1.3%. Especially, there was no divergence among Backasipmunja, Chungilppong and Milsungpong and Jungyasang, Ssarigol II and Yulbon, respectively.

• The Plant Pathology Journal
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• 제16권4호
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• pp.231-235
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• 2000

The 3,000 nucleotides of 3'-terminal region of the genomic RNA of a new isolate of carlavirus from a Korean native lily (Lilum lancitoium) was cloned and its nucleotide sequences were determined. The coat protein (CP) gene of the virus showed 72.0% to 72.8% nucleotide sequence identities and 86.9% to 88.0% amino acid sequence identities with those of the four strains (two Korean, one Dutch, and one Japanese isolates) of lily symptomless virus (LSV). Interestingly, different amino acid sequences between the new isolate and LSV strains were located at the N-terminal region of the CP. Pairwise amino acid sequence comparison of the CP gene revealed sequence identities of 22.0% to 71.1% between the virus and other 9 carlavirus species. The 25 kDa and 12 kDa proteins genes of the virus share 30.7% to 76.3% and 31.1% to 85.8% amino acid sequence identities, respectively, with those of 8 other carlaviruses. The 16 kDa protein gene of the virus shares 16.7% to 72.9% amino acid sequence identities with that of 9 other carlaviruses. These data indicate that the virus, designated as lily latent virus (LiLV), is a distinct of the Carlavirus genus and distinguished from the known strains of LSV.