• 한국패류학회지
• /
• 제13권1호
• /
• pp.1-7
• /
• 1997

한국산 가리비, 큰가리비(Patinopecten yessoensis)와 주문진가리비(Chlamys swifti), 2종에 대한 28S ribosomal RNA 유전자의 PCR- 산물을 이용 RFLP 및 염기서열을 밝히고, 이미 보고된 2과 3종의 염기서열과 상동성을 비교 분석하였다. 그 결과 28S rRNA유전자를 이용하여 7가지 제한효소를 처리한 PCR-RFLP의 종간 차이에서 Taq I 제한효소에서만 차이를 볼 수 있었다. 한편 두종간에 28S rRNA유전자의 D1 부위의 염기서열에서 231개 부위 중 14군데에서 변이를 보였다.

• 한국패류학회지
• /
• 제21권2호
• /
• pp.147-161
• /
• 2005

백합 상과의 계통분류학적 유연관계를 알아보기 위하여 14 종의 이치 아강 이매패류와 3 종의 익형 아강 패류를 대상으로 28S rRNA의 일부 염기서열을 분석한 뒤 GenBank에 등록된 관련 종들의 염기서열을 취득하여 PAUP 프로그램을 이용하여 최대 절약분석을 실시한 결과 다음과 같은 결과를 얻었다. 분석된 1,480 개의 형질 (gap 포함) 중 560 개의 형질이 parsimony 결과 informative하였다. 하나의 가장 절약적인 분지도를 구했을 경우 전체 분지의 길이는 2765였고 consistency index (Cl) = 0.4843, homoplasy index (Hl) = 0.5157, Retention index (Rl) = 0.6291 로 나타났다. 동일 종 표본, Corbicula fluminea와 Sinonovacula constricts의 경우 각각 3.1%, 1.2%의 차이를 보였다. Pitarinae-Cyclininae-Meretrinae가 하나의 분지를 이루고 있었고, Samaranginae-Chioninae-Dorsininae가 다른 하나의 분지를 이루고 있었다.

• 생명과학회지
• /
• 제22권2호
• /
• pp.232-238
• /
• 2012

금정산성 막걸리$^{(R)}$는 전통적인 수제누룩과 쌀로부터 발효된 한국의 전통적인 술이다. 본 연구에서는 막걸리 발효기간 동안 세균과 진균의 다양성을 특성화하기 위해 16S와 28S rRNA 유전자를 목적으로 하는 PCRDenaturing Gradient Gel Electrophoresis (PCR-DGGE) 분석을 수행하였다. 막걸리 발효기간 동안 PCR-DGGE profile에서 검출된 세균은 16S rRNA 유전자 서열에 기초한 동정결과 Lactobacillus spp. (L. curvatus, L. kisonensis, L. plantarum, L. sakei 및 L. gasseri), Pediococcus spp. (P. acidilactici, P. parvulus, P. agglomerans및 P. pentosaceus), Pantoea spp. (P. agglomerans 및 P. ananatis) 그리고 Citrobacter freundii로 총 12종이었으며, 배양2일 이후 L. curvatus가 주된 우점 종을 형성하였다. 반면 PCR-DGGE profile에서 검출된 진균은 28S rRNA 유전자 서열에 기초한 동정결과 Pichia kudriavzevii, Saccharomyces cerevisiae, Asidia idahoensis, Kluyveromyces marxianus, Saccharomycopsis fibuligera 및 Torulaspora delbrueckii로 6종이었으며 주된 우점 진균은 배양0일에서 2일에 P. kudriavzevii에서 배양 3일에서 6일에 S. cerevisiae로 전환되었다. 결과적으로 PCR-DGGE분석은 막걸리발효기간 동안 미생물의 구조와 다양성을 이해하는 데 유용한 도구임을 보여주었다.

• 생명과학회지
• /
• 제8권1호
• /
• pp.32-39
• /
• 1998

진딧물이 하나의 ribosomal RNA 유전자(rDNA)단위는 총 길이가 13,061bp이며 총 G/C비율은 59%이다. 그것을 구성하고 있는 각 영역의 길이와 G/C비율은 다음과 같다. 5’ETS는 G/C비율이 69%이고 843bp이다 . 18S rRNA 는 2,469bp이며 G/C비율은 59%이다. ITS I길이는 229bp이며 70%의 G/C비율이다. 5.8S rRNA는 160bp이며 63%의 G/C비율이다. ITS II는 325bp이며 70%dml G/C비율이다. 28S rRNA는 4, 147bp이고 60%의 G/C비율이다. IGS는 4,888bp로 55%의 G/C비율이다.

• 한국응용곤충학회지
• /
• 제42권1호
• /
• pp.65-70
• /
• 2003

곤충자원의 대량사육을 위한 병 발생 예방과 해충의 효과적인 방제를 위하여 흰점박이꽃무지 이병충으로부터 곤충병원 사상균을 분리하였다. 전자현미경 관찰 결과 분리균주 KMA-1은 Metharizium속의 전형적인 쇠사슬형의 분생자를 paliside-like masse에 형성하였다. 따라서, 정확한 동정을 위하여 28S rRNA와 ITS염기 서열을 바탕으로 제작한 특이 프라이머쌍을 사용하여 PCR 반응을 수행하였다. 각각의 프라이머쌍을 사용한 PCR반응으로부터 특이 밴드가 검출되었으며 이 증폭 산물들의 염기 서열을 결정, 비교하였다. 분리 균주 KMA-1의 PCR산물인 28S rRNA와 ITS DNA염기서열을 GenBank데이터베이스에 등록된 염기서열 정보와의 상동성을 검색한 결과, 모두 Metarhizium anisopliae와 가장 높은 서열 상동성을 보였다. 이상의 결과로서 본 실험에서 분리 명명된 KMA-1는 M. anisopliae로 동정되었다.

• Molecules and Cells
• /
• 제40권6호
• /
• pp.410-417
• /
• 2017

Estimation of postmortem interval (PMI) is a key issue in the field of forensic pathology. With the availability of quantitative analysis of RNA levels in postmortem tissues, several studies have assessed the postmortem degradation of constitutively expressed RNA species to estimate PMI. However, conventional RNA quantification as well as biochemical and physiological changes employed thus far have limitations related to standardization or normalization. The present study focuses on an interesting feature of the subdomains of certain RNA species, in which they are site-specifically cleaved during apoptotic cell death. We found that the D8 divergent domain of ribosomal RNA (rRNA) bearing cell death-related cleavage sites was rapidly removed during postmortem RNA degradation. In contrast to the fragile domain, the 5' terminal region of 28S rRNA was remarkably stable during the postmortem period. Importantly, the differences in the degradation rates between the two domains in mammalian 28S rRNA were highly proportional to increasing PMI with a significant linear correlation observed in mice as well as human autopsy tissues. In conclusion, we demonstrate that comparison of the degradation rates between domains of a single RNA species provides quantitative information on postmortem degradation states, which can be applied for the estimation of PMI.

• Parasites, Hosts and Diseases
• /
• 제51권5호
• /
• pp.511-517
• /
• 2013

Species identification using DNA sequences is the basis for DNA taxonomy. In this study, we sequenced the ribosomal large-subunit RNA gene sequences (3,037-3,061 bp) in length of 13 Chinese Theileria stocks that were infective to cattle and sheep. The complete 28S rRNA gene is relatively difficult to amplify and its conserved region is not important for phylogenetic study. Therefore, we selected the D2-D3 region from the complete 28S rRNA sequences for phylogenetic analysis. Our analyses of 28S rRNA gene sequences showed that the 28S rRNA was useful as a phylogenetic marker for analyzing the relationships among Theileria spp. in ruminants. In addition, the D2-D3 region was a short segment that could be used instead of the whole 28S rRNA sequence during the phylogenetic analysis of Theileria, and it may be an ideal DNA barcode.

• The Plant Pathology Journal
• /
• 제38권4호
• /
• pp.323-333
• /
• 2022

Filenchus cylindricus (Thorne & Malek, 1968) Niblack & Bernard, 1985 was reported from the sandy rhizospheric soils of Poa pratensis and for the first time in Korea. Females and males are molecularly characterized and morphological and morphometric data supplied. Identification was made using an integrative approach considering morphological characteristics and inferences drawn from the analyses of the D2-D3 expansion segment of 28S rRNA and ITS1-5.8S-ITS2 of rRNA partial sequences. Females and males from Korea conform to the type descriptions and also to subsequent species descriptions from Iowa and Colorado USA, Sudan and Pakistan. Despite the close morphological and morphometric similarities with F. thornei (Andrássy, 1954) Andrássy, 1963, the two species can be adequately differentiated based on molecular data inference.

• Animal cells and systems
• /
• 제6권2호
• /
• pp.145-151
• /
• 2002

Phylogenetic signal present in the mitochondrial 16S ribosomal RNA gene (16S rDNA) and the nuclear large subunit ribosomal RNA gene (28S rDNA) was explored to assess their utility in resolving family level relationships of the superfamily Tephritoidea. These two genes were chosen because they appear to evolve at different rates, and might contribute to resolve both shallow and deeper phylogenetic branches within a highly diversified group. For the 16S rDNA data set, the number of aligned sites was 1,258 bp, but 1,204 bp were used for analysis after excluding sites of ambiguous alignment. Among these 1,204 sites, 662 sites were variable and 450 sites were informative for parsimony analysis. For the 28S rDNA data set, the number of aligned sites was 1,102 bp, but 1,000 bp were used for analysis after excluding sites of ambiguous alignment. Among these 1000 sites, 235 sites were variable and 95 sites were informative for parsimony analysis. Our analyses suggest that: (1) while 16S rDNA is useful for resolving more recent phylogenetic divergences, 28S rDNA can be used to define much deeper phylogenetic branches; (2) the combined analysis of the 16S and 28S rDNAs enhances the overall resolution without losing phylogenetic signal from either single gene analysis; and (3) additional genes that evolve at intermediate rates between the 16S and 28S rDNAs are needed to further resolve relationships among the tephritoid families.

• The Plant Pathology Journal
• /
• 제40권2호
• /
• pp.171-191
• /
• 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.