• Weed & Turfgrass Science
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• 제4권1호
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• pp.26-34
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• 2015

최근에 전 세계적으로 동물, 식물뿐만 아니라 균류, 해조류 등에서 활발하게 이용하는 DNA 바코드는 게놈 DNA의 단편을 이용해 종들 간의 DNA 변이를 발견하여 형태적 지식 없이 정확하게 종을 동정하고 분류하는 방법이다. 고등식물에서는 단일마커로 바코드 조건을 충족할 수 없어 엽록체 DNA의 rbcL과 matK 유전자를 표준마커로 이용하고 있다. 본 연구는 식물 표준 바코드마커와 핵 DNA의 ITS 부위를 이용하여 국내 벼과 식물 252 분류군 중 주로 농경지에서 발생하는 잡초 총 84분류군 403생태형을 바코드하여 데이터베이스를 구축하기 위하여 수행하였다. 바코드 결과 PCR 증폭과 염기서열 분석 성공률은 rbcL에서 가장 높았으며 matK에서 가장 낮았다. 그러나 바코드 갭과 종식별 해상력은 matK에서 가장 높았다. 80.9%의 염기서열 분석 성공률을 보인 ITS는 matK와의 조합에서 92.9% 까지 종 식별 해상력을 높일 수 있어 벼과 바코드에 매우 유용한 조합이었다. 벼과의 바코드데이터는 미국의 국립생물공학정보센터에 기탁하여 genbank 번호를 부여받아 공개하였다. 그러므로 형태적으로 동정이 어려운 벼과 잡초를 matK와 ITS 부위의 염기서열을 분석하여 미국의 국립생물공학정보센터에 기탁한 데이터와 비교함으로써 쉽고 간편하게 동정할 수 있게 되었다.

• ALGAE
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• 제17권2호
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• pp.75-81
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• 2002

In this study the length of ITS2 from four species of the Ulvaceae in Jeju Island varied between 167 and 203 bp. The resuits of this investigation showed that two genus, Ulva and Enteromorpha are grouped in a monophyletic assemblage with 100% bootstrap support in all phylogenetic trees. However, a thorough eamination of these characters from representatives does not provided a way to identify any unique morphological features of clasdes in this tree. This study reveals that Ulva conglobata and Ulva pertusa belong to one clade in the phylogenetic tree with the samples from Jeju Island, Korea.

• Mycobiology
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• 제36권4호
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• pp.203-210
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• 2008

In previous studies investigating the genus Xanthoparmelia, thirteen different species have been reported from South Korea alone. However, there currently has been no revisional study performed until now. To explore the genus Xanthoparmelia, a phenotypic analysis was performed based on morphological, anatomical and chemical characters, while an investigation of Xanthoparmelia phylogeny was based on nuclear ribosomal (nr) DNA ITS sequences. A thorough examination of the specimens deposited in the Korean Lichen Research Institute (KoLRI) confirmed that eight species of Xanthoparmelia occur inside South Korea. Our analysis further confirmed the colors of the lower surface and medullar chemistry are important taxonomic characters in Xanthoparmelia. This study also presents a detailed description of each species and a key to the genus.

• Mycobiology
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• 제37권3호
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• pp.189-196
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• 2009

A taxonomic study of Peltigera in South Korea was performed. The phylogenetic analysis based on nr DNA internal transcribed spacer sequences suggests that Peltigera is a well-supported monophyletic group. Important characteristics are the phycobiont type of thallus and the vein type at the lower cortex (wide and flat, or narrow and ridged). The vertical or horizontal arrangement of the apothecia is also important in distinguishing species in this genus. Eleven species of Peltigera were revealed and confirmed, which included one new record, P. elisabethae. A description of each species is presented with morphological, anatomic, and chemical characteristics, and comparisons between similar species are made. A key to the species is also presented.

• Mycobiology
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• 제35권3호
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• pp.117-123
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• 2007

Seventy-two lichen specimens of Cetrelia collected in South Korea since 2003 were examined by both phenotypic and phylogenetic analyses. The phenotypic analysis was based on morphological and chemical characters, and the phylogenetic analysis was based on nrDNA ITS sequences. The result suggested that the presence and absence of isidia, soredia, lobules and medullar reaction C+ or C- are the important characters in the taxonomy of this genus. Four species of Cetrelia, C. chicitae, C. braunsiana, C. japonica, and C. pseudolivetorum have been identified in this study. Description of each species is presented with morphological and chemical characters. A key to the Cetrelia species is also presented.

• BMB Reports
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• 제41권10호
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• pp.693-698
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• 2008

The full-length cDNA of LebZIP2 (Lycopersicon esculentum bZIP2) encodes a protein of 164 amino acids and contains a N-terminal basic-region leucine zipper domain. Analysis of the deduced tomato LebZIP2 amino acid sequence revealed that it shares 85% sequence identity with both tobacco bZIP and pepper CcbZIP. LebZIP2 mRNA is expressed at a high level exclusively in flowers. Presently, LebZIP2 was strongly increased also following NaCl and mannitol treatments. No significant LebZIP2 expression was evident following cold treatment. Transient LebZIP2 overexpression resulted in increased NbNOA1 and NbNR transcript levels in Nicotiana benthamiana leaves. Our results indicate that LebZIP2 might play roles as an abiotic stress-signaling pathway and as a transcriptional regulator of the NbNOA1 or NbNR genes.

• 식물분류학회지
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• 제41권3호
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• pp.259-266
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• 2011

Elsholtzia hallasanensis, E. springia, and E. splendens var. fasciflora (Lamiaceae) were reported recently as new species or new varieties of E. splendens according to their morphological characteristics. To reappraise the taxonomic status of these additional taxa and to determine the relationships between all Korean Elsholtzia taxa except E. saxatilis, which is distributed in North Korea, molecular studies based on the nrDNA (ITS) and cpDNA (rpl16, and trnH-psbA) sequences of seven taxa of Elsholtzia and one outgroup were carried out. The molecular data support that E. angustifolia and E. minima are distinct species from E. splendens and E. ciliata, respectively, because they have several private marker genes and show monophyly. The molecular data also support that E. splendens has a very close taxonomic relationship with both E. hallasanensis and E. springia. We found that E. splendens var. fasciflora, with multiple inflorescence, was based on several private marker genes and on the monophyly of its trees, suggesting that it can be considered as a variety. Elsholtzia springia, with the same sequences and the same morphological characteristics with E. hallasanensis after transplanting, should be treated as a synonym of E. hallasanensis. Moreover, we consider the taxonomic status of E. hallasanensis as E. splendens var. hallasanensis (Y. Lee) N.S. Lee & C.S. Lee, stat. nov.

• 식물분류학회지
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• 제45권4호
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• pp.306-317
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• 2015

본 연구에서는 간혹 흰바위취(Micranthes manchuriensis)와 동일종으로 취급되기도 하는 한국 고유종 구실바위취(Saxifraga octopetala)의 분류학적 지위를 알아보고자 수행되었다. 구실바위취의 계통학적 위치와 종의 경계를 확인하기 위해 두 종의 기준표본에 대한 형태적 검토와 핵 리보솜 DNA의 ITS 지역 염기서열에 대한 집중적인 계통분석을 시행하였다. 총 65개 구실바위취 개체는 ITS 계통수에서 하나의 무리를 이루면서 Micranthes 분기군(clade)에 포함되었고, 톱바위취 및 흰바위취와 가까운 계통 유연관계를 나타내었다. 중국과 러시아에서 채집된 다수의 흰바위취 개체 역시 독자적인 분기군을 형성하면서 M. nelsoniana var. pacifica 및 M. fusca와 자매군을 이루었다. 구실바위취의 실체가 모호했던 것은 흰바위취 개체와 톱바위취의 화서를 함께 포함하고 있는 복합표본인 Wilford의 채집품(흰바위취의 기준표본)을 Nakai가 잘못 관찰하였기 때문으로 생각되었다. 구실바위취와 흰바위취의 높은 형태적 유사성에도 불구하고 이들은 지하 포복경의 특징에 있어서 차이를 보였다. ITS 계통수에서 구실바위취가 Micranthes 내에 자리하는 것으로 나타나 구실바위취는 Micranthes 내에서 종의 지위를 유지하여야 할 것으로 판단되었고, 이에 따라 신조합명(Micranthes octopetala)을 발표하였다.

• Mycobiology
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• 제51권1호
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• pp.36-48
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• 2023

Xanthoria elegans is a lichen symbiosis, that inhabits extreme environments and can absorb UV-B. We reported the de novo sequencing and assembly of X. elegans genome. The whole genome was approximately 44.63 Mb, with a GC content of 40.69%. Genome assembly generated 207 scaffolds with an N50 length of 563,100 bp, N90 length of 122,672 bp. The genome comprised 9,581 genes, some encoded enzymes involved in the secondary metabolism such as terpene, polyketides. To further understand the UV-B absorbing and adaptability to extreme environments mechanisms of X. elegans, we searched the secondary metabolites genes and gene-cluster from the genome using genome-mining and bioinformatics analysis. The results revealed that 7 NR-PKSs, 12 HR-PKSs and 2 hybrid PKS-PKSs from X. elegans were isolated, they belong to Type I PKS (T1PKS) according to the domain architecture; phylogenetic analysis and BGCs comparison linked the putative products to two NR-PKSs and three HR-PKSs, the putative products of two NR-PKSs were emodin xanthrone (most likely parietin) and mycophelonic acid, the putative products of three HR-PKSs were soppilines, (+)-asperlin and macrolactone brefeldin A, respectively. 5 PKSs from X. elegans build a correlation between the SMs carbon skeleton and PKS genes based on the domain architecture, phylogenetic and BGC comparison. Although the function of 16 PKSs remains unclear, the findings emphasize that the genes from X. elegans represent an unexploited source of novel polyketide and utilization of lichen gene resources.

• Asian Pacific Journal of Cancer Prevention
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• 제17권9호
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• pp.4259-4265
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• 2016

Background: Colorectal malignancies with high microsatellite instability (MSI-H), either hereditary (Lynch syndrome) or sporadic, demonstrate better prognosis and altered response to 5FU chemotherapy. It is now recommended to perform MSI testing for all new cases of colorectal cancer regardless of being categorized as hereditary or sporadic. For MSI detection, immunohistochemistry or PCR-based protocols using a cohort of various sets of STR markers are recommended. Here we aimed to evaluate a simplified protocol using just a single STR marker, MT1XT20 mononucleotide repeat, for detection of MSI in Lynch syndrome patients. A Promega five-marker MSI testing panel and immunohistochemistry (IHC) were used as the gold standard in conjunction with MT1XT20. Materials and Methods: Colorectal patients with a positive history of familial cancers were selected by evaluating medical records. Based on Amsterdam II criteria for Lynch syndrome 20 families were short listed. DNA was extracted from formalin fixed paraffin embedded tumour and adjacent normal tissues resected from the index case in each family. Extracted DNA was subjected to MT1XT20 mononucleotide marker analysis and assessment with a commercially available five marker MSI testing kit (Promega, USA). IHC also was performed on tissue sections and the results were compared with PCR based data. Results: Eight (40%), seven (35%) and five (25%) cases were MSI positive using with the Promega kit, IHC and MT1XT20, respectively. Among the markers included in Promega kit, BAT26 marker showed instability in all 8 samples. NR24 and NR21 markers showed instability in 7 (87.5%), and BAT25 and MONO 27 in 6 (75%) and 5 (62.5%). Conclusions: Although MT1XT20 was earlier reported as a valid standalone marker for MSI testing in CRC patients, we could not verify this in our Iranian patients. Instead BAT26 among the markers included in Promega MSI testing kit showed instability in all 8 MSI-H CRC samples. Therefore, it seems BAT26 could act well as a single marker for MSI testing in Iranian CRC patients.