• 한국버섯학회지
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• 제12권3호
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• pp.154-162
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• 2014

Oyster mushrooms including of P. ostreatus, P. eryngii, P. pulmonarius and P. cornucopiae are one of the famous mushrooms for foods in Korea. RAPD were carried out using 14 of oligoprimers to analyze the phylogenetic relationship among 57 strains of 32 Pleurotus species. Most of species formed the minimum clade with strains within species and was divided respectively species. Therefore clade was separated well in accordance species. Pleurotus species formed again clade to be added in close related to other species, and were discriminated by sixteen clades with each representative species including high similarity groups. Sixteen clades were composed representative species according to each clade. There were clade I of P. pulmonarius(P. sajor-caju, P. opuntiae, P. sapidus), clade II of P. eryngii(P. fuscus var. ferulae, P. fossulatus), clade III of P. ostreatus(P. ostreatus var. columbinus, P. spodoleucus, P. floridanus), clade IV of P. florida, clade V of P. djamor(P. flabellatus, P. incarnates, P. salmoneo-stramineus), clade VII of P. populinus(P. subareolatus), clade VIII of P. cystidiosus(P. cystidiosus var. formosensis), clade X of P. dryinus(P. dryinus var. pometi), clade XIV of P. cornucopiae(P. citrinopilieatus, P. euosmus), and clade XV of P. australis. These species were representative species each clades. Five species, P. ulmarius(clade VI), P. griseus(clade IX), P. calyptratus(clade XI), P. lampas(clade XII), P. smithii(clade XIII)and P. serotinus (clade XVI) were used each one strain in analysis, so they were clustered other groups.

• 미생물학회지
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• 제43권4호
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• pp.285-291
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• 2007

볼티모어의 분류체계에 의하면 바이러스는 복제 및 단백질합성 전략에 따라 6개의 집단으로나눌 수 있다. 몇 종류의 작은 DNA 바이러스를 제외한 대부분의 바이러스는 게놈 복제를 위한 자신의 핵산중합효소를 유전자로 암호화하고 있다. 바이러스 핵산중합효소에는 DNA-의존DNA 중합효수, RNA-의존RNA 중합효소, RNA-의존 DNA 중합효소 세 종류가 있으며, 이들은 모두 4개의 공통된 모티프(motif)를 가진다. 우리는 볼티모어의 분류체계와 바이러스의 핵산중합효소와의 관계를 아미노산 서열을 통해 분자 계통분류학적 분석을 통해 알아보고자 하였다. NCBI GenBank에서 얻은 바이러스 중합효소의 아미노산 서열을 CLUSTAL X 프로그램으로 다중서열하고, Neighbor-joining, Maximum-likelihood, Bayesian의 세 가지 방법으로 계통도를 그려보았다. 미세한 차이는 있었으나, 세 가지 방법 모두에서 볼티모어의 분류법과 일치하는 결과를 보였고, 특이하게도 두 가닥 RNA 바이러스는 숙주의 종류에 따라, (-)RNA 바이러스는 게놈의 절편화에 따라 각각2개의 소집단으로 나뉘어지는 것을 볼 수 있었다.

• 한국어류학회지
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• 제22권4호
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• pp.273-278
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• 2010

왜매치 Abbottina springeri Banarescu and Nalbant의 분자계통학적 위치를 밝히기 위해 한국에 서식하는 버들매치속 2종과 모래주사속 5종의 핵 유전자인 recombination activating gene 1 (RAG1)의 염기서열을 분석하였다. RAG1 유전자 염기서열 정보에 기초한 계통수에서 배들매치 A. rivularis는 단계통군을 형성하는 왜매치, Biwia zezera 및 모래주사속 종들과 분리되었다. 이 계통 내에서 B. zezera는 왜매치와 모래주사속 5종을 구성된 단계통 그룹과 자매계통 관계를 보였다. 분자계통수 상에서 버들매치속 2종은 다계통군으로 나타났고, 이러한 결과는 골격 특징들에 근거한 이들의 계통적 관계를 밝힌 선행연구와 잘 일치하였다. 따라서 입의 피질돌기 유무와 부레의 골낭 유무와 크기 등과 같은 형태적 특징들에 근거한 버들배치속과 모래주사속의 현분류체계는 진화 역사를 잘 반영하지 못하는 것으로 여겨진다.

• Parasites, Hosts and Diseases
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• 제54권6호
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• pp.777-786
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• 2016

Raillietina species are prevalent in domestic chickens (Gallus gallus domesticus) in Phayao province, northern Thailand. Their infection may cause disease and death, which affects the public health and economic situation in chicken farms. The identification of Raillietina has been based on morphology and molecular analysis. In this study, morphological observations using light (LM) and scanning electron microscopies (SEM) coupled with molecular analysis of the internal transcribed spacer 2 (ITS2) region and the nicotinamide adenine dinucleotide dehydrogenase subunit 1 (ND1) gene were employed for precise identification and phylogenetic relationship studies of Raillietina spp. Four Raillietina species, including R. echinobothrida, R. tetragona, R. cesticillus, and Raillietina sp., were recovered in domestic chickens from 4 districts in Phayao province, Thailand. LM and SEM observations revealed differences in the morphology of the scolex, position of the genital pore, number of eggs per egg capsule, and rostellar opening surface structures in all 4 species. Phylogenetic relationships were found among the phylogenetic trees obtained by the maximum likelihood and distance-based neighbor-joining methods. ITS2 and ND1 sequence data recorded from Raillietina sp. appeared to be monophyletic. The query sequences of R. echinobothrida, R. tetragona, R. cesticillus, and Raillietina sp. were separated according to the different morphological characters. This study confirmed that morphological studies combined with molecular analyses can differentiate related species within the genus Raillietina in Thailand.

• The Plant Pathology Journal
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• 제25권2호
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• pp.142-150
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• 2009

The complete genome sequences of RNA3 and RNA4 of the 13 different Rice stripe virus (RSV) isolates were determined and characterized in this study to address the possible causes of the recent re-emergence of RSV that affected many rice fields in Korea. The genome size of each RNA segment varied among isolates and significant differences were observed in the intergenic region. There was up to 4% average divergence in the RNA4 nucleotide sequence among 13 Korean isolates and only 1.4% in the RNA3. Phylogenetic relationships among different Korean isolates revealed that there were at least 2 types of RNA3 and 4 distinct types of RNA4 genomes present in Korea. However, Korean isolates with one type of RNA3 predominate over the other while the occurrences of the RSV Korean isolates with the 4 types of RNA4 genome were not correlated to specific geographical areas. Results further indicate that RNA4 had diverged more than RNA3 and these differences in accumulation of mutations in the individual RNA segments indicate that genetic reassortment were likely to contribute to the genetic divergence in the 13 Korean isolates. All of the Korean-RNA3 sequences except for one isolate grouped with Chinese isolates (JY and Z). In contrast, the RNA 4 sequences segregated together with either Chinese (JY and Z) and Japanese (M and T) isolates but genetic relationships of Korean isolates- RNAs 3 and 4 segments to Chinese-Y isolate were low. Altogether, these results suggest that the occurrence of mixtures of RNAs 3 and 4 genotypes in the natural population of RSV may have contributed to the sudden outbreak in Korea.

• The Plant Pathology Journal
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• 제34권3호
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• pp.199-207
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• 2018

Tomato chlorosis virus (ToCV) is a whitefly-transmitted and phloem-limited crinivirus. In 2013, severe interveinal chlorosis and bronzing on tomato leaves, known symptoms of ToCV infection, were observed in greenhouses in Korea. To identify ToCV infection in symptomatic tomato plants, RT-PCR with ToCV-specific primers was performed on leaf samples collected from 11 tomato cultivating areas where ToCV-like symptoms were observed in 2013 and 2014. About half of samples (45.18%) were confirmed as ToCV-infected, and the complete genome of 10 different isolates were characterized. This is the first report of ToCV occurring in Korea. The phylogenetic relationship and genetic variation among ToCV isolates from Korea and other countries were also analysed. When RNA1 and RNA2 are analysed separately, ToCV isolates were clustered into three groups in phylogenetic trees, and ToCV Korean isolates were confirmed to belong to two groups, which were geographically separated. These results suggested that Korean ToCV isolates originated from two independent origins. However, the RNA1 and RNA2 sequences of the Yeonggwang isolate were confirmed to belong to different groups, which indicated that ToCV RNA1 and RNA2 originated from two different origins and were reassorted in Yeonggwang, which is the intermediate point of two geographically separated groups.

• 한국어류학회지
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• 제12권4호
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• pp.223-229
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• 2000

한국산 미꾸리과 어류의 계통유전학적 관계를 고찰하고자 8종의 mitochondrial cytochrome b의 유전자 서열을 비교한 결과 대부분 이전의 형태학적 연구의 결과와 일치하였다. 그러나 종개속 Orthrias과 쌀미꾸리속 Lefua의 분류학적 위치는 미꾸리과 Cobitidae와 paraphyletic group으로 나타났으며 이 두 속의 sequence divergence는 0.184~0.272으로 나타나 미꾸리과와 잉어과 사이의 divergence와 유사하였다. 한편 참종개속 Iksookimia 2종과 북방종개 Cobitis melanoleuca는 각각 다르게 분화한 결과를 보여 주었으며 또한 중국산 미꾸리와 한국산 영덕 미꾸리의 sequence divergence는 0.099로 종간의 divergence를 보여주어 주목되었다. 미꾸리과 어류 가운데 참종개속의 일부 어류는 분류학적 위치로 보아 이들의 기원이 미꾸리과의 속간 잡종기원으로 생각된다.

• Parasites, Hosts and Diseases
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• 제37권3호
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• pp.181-188
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• 1999

We investigated the value of mitochondrial small subunit rRNA gene (mt SSU rDNA) PCR-RFLP as a taxonomic tool for Acanthamoeba isolates with close inter-relationships. Twenty-five isolates representing 20 species were included in the analysis. As in nuclear 18s rDNA analysis, two type strains (A. astronyxis and A. tubiashi) of morphological group 1 diverged earliest from the other strains, but the divergence between them was less than in 18s riboprinting. Acanthamoeba griffini of morhological group 2 branched between pathogenic (A. culbertsoni A-1 and A. healyi OC-3A) and nonpathogenic (A.palestinensis Reich, A. pustulosa GE-3a, A. royreba Oak Ridge, and A lenticulata PD2S) strains of morphological group 3. Among the remaining isolates of morphological group 2, the Chang strain had the identical mitochondrial riboprints as the type strain of A. hatchetti. AA2 and AA1, the type strains of A. divionensis and A. paradivionensis, respectively, had the identical riboprints as A. quina Vil3 and A. castellanii Ma. Although the branching orders of A. castellanii Neff, A. polyphaga P23, A. triangularis SH621, and A. lugdunensis L3a were different from those in 18S riboprinting analysis, the results obtained from this study generally coincided well with those from 18S riboprinting. Mitochondrial riboprinting may have an advantage over nuclear 18S rDNA riboprinting beacuse the mt SSU rDNAs do not seem to have introns that are found in the 18S genes of Acanthamoeba and that distort phylogenetic analyses.

• Journal of Life Science
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• 제11권2호
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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.

• Mycobiology
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• 제37권3호
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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.