• Molecules and Cells
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• 제25권2호
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• pp.258-264
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• 2008

Deschampsia antarctica is the only monocot that thrives in the tough conditions of the Antarctic region. It is an invaluable resource for the identification of genes associated with tolerance to various environmental pressures. In order to identify genes that are differentially regulated between greenhouse-grown and Antarctic field-grown plants, we initiated a detailed gene expression analysis. Antarctic plants were collected and greenhouse plants served as controls. Two different cDNA libraries were constructed with these plants. A total of 2,112 cDNA clones was sequenced and grouped into 1,199 unigene clusters consisting of 243 consensus and 956 singleton sequences. Using similarity searches against several public databases, we constructed a functional classification of the ESTs into categories such as genes related to responses to stimuli, as well as photosynthesis and metabolism. Real-time PCR analysis of various stress responsive genes revealed different patterns of regulation in the different environments, suggesting that these genes are involved in responses to specific environmental factors.

• 대한의생명과학회지
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• 제23권3호
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• pp.223-229
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• 2017

Fungal infections by human pathogenic fungi are increasing globally in elderly, children and immune suppressed or deficient patients. Aspergillus fumigatus is one of the well-known pathogenic fungi and causes aspergilloses in human world widely. However, current identification and classification methods based on its phenotypic characteristics still have limitations. Therefore, currently, molecular biological tools using their DNA sequences are used for genotype identification and classification. In the present study, in order to analyze genetic variations of A. fumigatus clinical isolates, a total of six housekeeping genes were amplified by PCR using specific primer pairs and multi-locus sequence typing (MLST) assay. Results from phylogenetic tree analysis showed that most A. fumigatus strains (88.9%) from respiratory specimens were classified into cluster A and B, and approximately half of A. fumigatus strains (46%) from non-respiratory specimens were classified into cluster C and D. Although the sample size was limited, genetic characteristics of A. fumigatus clinical isolates according to their origins were very similar and well-correlated with other clinical data.

• Journal of Microbiology and Biotechnology
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• 제20권4호
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• pp.757-762
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• 2010

Cronobacter is a major foodborne pathogen in powdered infant formula and can lead to serious developmental after-effect and death to infants. The contamination of Cronobacter may be a high risk for the powdered foods. To isolate and identify Cronobacter from the powdered foods such as powdered infant formula and Saengsik in Korea, a conventional culture method, rapid identification system, PCR, and 16S rDNA sequencing were performed. As the results of isolation, seven Cronobacter spp. were isolated from seven out of 102 powdered infant formulas and 41 Cronobacter were isolated from 41 out of 86 Saengsiks. Forty-eight Cronobacter isolates were identified to be C. sakazakii and C. dublenisis by 16S rDNA sequence analysis. Most of the isolates were C. sakazakii and 13% of the isolates were C. dublinesis. One fourth of the C. sakazakii isolates showed different biochemical characteristics of negative nitrate reduction and nonmotility activities compared with the other strains reported previously.

• 생명과학회지
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• 제16권1호
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• pp.71-75
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• 2006

We analyzed the phylogenic relationships of 23 partial 18S rDNA sequences of 22 species (1 species has 2 strains) belonging to Sarcorptiforms include 4 new sequences, using several tools. Although geographic distributions are quite far from, sequence similarity of two strains of Dermatophygoides pteronyssinus isolated from Japan and New Zealand were very high. This result suggests that mite migration by animals including human occurred in the two continents. We investigated the Endeostigmata taxonomic relationship between the Prostigmata and Oribatida subgroups using small fragments (340-400 bp) of their 185 rDNA sequences. But Endeostigmata was not grouped with Oribatida or Prostigmata. In conclusion, it is first reported phylogenic relationship for classified mites included in Sarcoptiformes using 185 rDNA sequence analysis and its system is a very powerful tool for classification of mites.

• Mycobiology
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• 제32권1호
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• pp.24-34
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• 2004

Molecular approaches, internal transcribed spacer(ITS) sequences of ribosomal DNA, and Universal Rice Primer Polymerase Chain Reaction(URP-PCR) were used to investigate the genetic diversity, taxonomic complexity, and relationships of Trichoderma species in mushroom farms. Forty-one isolates of 13 Trichoderma spp. were used in this study and clustered into eight groups. The DNA fingerprint patterns and ITS1 region sequence alignment data showed similar results, but not in some species, such as T. virens, T. atroviride, T. harzianum, and T. aureoviride. Results of this study have proven that the morphology-based taxonomic system has some limitations in terms of classification. The data obtained in this study would be a good index for classifying indistinguishable Trichoderma strains.

• 한국식물병리학회지
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• 제12권2호
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• pp.176-181
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• 1996

Aster yomena로부터 분리한 오이 모자이크 바이러스(cucumber mosaic virus) (CMV-As)의 RNA4로부터 완전한 길이의 cDNA를 합성하고 그 전체적인 염기서열(1,043 nt`s)을 결정하였다. CMV-As RNA4는 73개의 염기로 구성된 5`말단의 leader 부위, 657개의 염기로 구성된 외피단백질(coat protein) 유전자 부위 및 312개의 염기로 구성된 3` 말단의 비번역 부위로 구성되어 있음을 확인하였다. 외피단백질 유전자 부위의 염기서열을 다른 계통의 CMV와 비교해 볼 때 그 염기서열이 보전적으로 존재하고 있으나 그 외의 부분은 다양함을 확인하였다. 특히 3` 말단부위의 61개의 염기로 구성된 부위(959-1019)는 다른 계통의 CMV에서는 상당히 유사하지만 CMV-As도 다른 CMV처럼 tRNA와 유사한 구조를 역시 형성함을 확인하였다. CMV-As의 RNA4 염기서열을 다른 계통의 CMV와 비교할 때 CMV-I17F와 가장 유사하였으며(91.9%) S형의 CMV-M과는 가장 낮은 동일성을 보였다(71.1%). 외와 같은 염기성열의 비교 결과와 EcoRI 제한효소 인식부위의 존재로 미루어 CMV-As는 WT형으로 분류된다.

• 대한본초학회지
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• 제30권3호
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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.

• 원예과학기술지
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• 제35권3호
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• pp.344-360
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• 2017

Zoysia 속 잔디는 학교운동장 및 공원, 골프장, 스포츠경기장과 같이 다양한 장소에 식재되고 있는 중요한 잔디이다. 해안가에서 자생하는 Zoysia 속 들잔디와 갯잔디는 외부 형태적 특성이 유사하여 외부 형태적 분류 뿐 만 아니라 분자생물학적 분류도 필요하다. 본 연구에서는 nrDNA-ITS(Internal Transcribed Spacer)의 DNA 바코드 분석을 통해서 자생하는 들잔디와 갯잔디의 분자생물학적 신속한 분류체계를 확립하고자 하였다. 이를 위해 난지형 잔디인 Zoysia 속 들잔디(Z. japonica) 및 갯잔디(Z. sinica)와 한지형 대표 잔디인 크리핑 벤트그라스(A. stolonifera) 및 켄터키 블루그라스(P. pratensis)의 nrDNA-ITS 염기서열을 확보하였다. 확보된 들잔디및 갯잔디, 크리핑 벤트그라스, 켄터키 블루그라스의 ITS 염기서열 전체 구간은 각 686bp와 687bp, 683bp, 681bp으로 확인되었으며, nrDNA-ITS 내부 염기서열구간 분석 결과, ITS1의 크기는 248-249bp, ITS2는 270̵-274bp, 5.8S rDNA는 163-164bp의 차이로, 각 4종의 잔디가 ITS 염기서열을 이용하여 식별되었다. 특히, 들잔디와 갯잔디 nrDNA-ITS 염기서열은 19 염기(2.8%) 차이를 나타냈으며, ITS1과 ITS2의 G + C 함량은 55.4-63.3% 임을 확인하였다. 이러한 들잔디와 갯잔디의 ITS 염기서열 차이를 바탕으로 CAPS 마커로 전환하여 대조구 및 수집된 자생 Zoysia 속 잔디 영양체 62개체를 분석한 결과, 외부형태학적 분류법으로 들잔디 개체, 갯잔디 개체로 동정되었지만, ITSCAPS 마커를 이용한 분자생물학적 분류법으로 들잔디 36개체와 갯잔디 22개체 뿐만 아니라 들잔디와 갯잔디간의 자연교배종 4개체도 식별하였다. 이상의 결과에서 들잔디와 갯잔디는 ITS 염기서열 및 ITS 기반 CAPS를 통하여 식별할 수 있을 것으로 판단된다.

• Journal of Microbiology
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• 제45권6호
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• pp.541-546
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• 2007

Red algae are distributed globally, and the group contains several commercially important species. Griffithsia okiensis is one of the most extensively studied red algal species. In this study, we conducted expressed sequence tag (ESTs) analysis and synonymous codon usage analysis using cultured G. okiensis samples. A total of 1,104 cDNA clones were sequenced using a cDNA library made from samples collected from Dolsan Island, on the southern coast of Korea. The clustering analysis of these sequences allowed for the identification of 1,048 unigene clusters consisting of 36 consensus and 1,012 singleton sequences. BLASTX searches generated 532 significant hits (E-value <$10^{-4}$) and via further Gene Ontology analysis, we constructed a functional classification of 434 unigenes. Our codon usage analysis showed that unigene clusters with more than three ESTs had higher GC contents (76.5%) at the third position of the codons than the singletons. Also, the majority of the optimal codons of G. okiensis and Chondrus crispus belonging to Bangiophycidae were G-ending, whereas those of Porphyra yezoensis belonging to Florideophycidae were G-ending. An orthologous gene search for the P. yezoensis EST database resulted in the identification of 39 unigenes commonly expressed in two rhodophytes, which have putative functions for structural proteins, protein degradation, signal transduction, stress response, and physiological processes. Although experiments have been conducted on a limited scale, this study provides a material basis for the development of microarrays useful for gene expression studies, as well as useful information for the comparative genomic analysis of red algae.

• The Plant Pathology Journal
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• 제20권1호
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• pp.46-51
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• 2004

Host resistance is usually parasite-specific and is restricted to a particular pathogen races, and commonly is expressed against specific pathogen genotypes. In contrast, resistance shown by an entire plant species to a species of pathogen is known as non-host resistance. Therefore, non-host resistance is the more common and broad form of disease resistance exhibited by plants. As a first step to understand the mechanism of non-host plant defense, expressed sequence tags (EST) were generated from a hot pepper leaf cDNA library constructed from combined leaves collected at different time points after inoculation with non-host soybean pustule pathogen (Xanthomonas axonopodis pv. Glycines; Xag). To increase gene diversity, ESTs were also generated from cDNA libraries constructed from anthers and flower buds. Among a total of 10,061 ESTs, 8,525 were of sufficient quality to analyze further. Clustering analysis revealed that 55 ％ of all ESTs (4685) occurred only once. BLASTX analysis revealed that 74％ of the ESTs had significant sequence similarity to known proteins present in the NCBI nr database. In addition, 1,265 ESTs were tentatively identified as being full-length cDNAs. Functional classification of the ESTs derived from pathogen-infected pepper leaves revealed that about 25％ were disease- or defense-related genes. Furthermore, 323 (7％) ESTs were tentatively identified as being unique to hot pepper. This study represents the first analysis of sequence data from the hot pepper plant species. Although we focused on genes related to the plant defense response, our data will be useful for future comparative studies.