• Molecules and Cells
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• v.27 no.2
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• pp.205-209
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• 2009

The loci of the 5S and 45S rRNA genes were localized on chromosomes in five species of Capsicum, namely, annuum, chacoense, frutescens, baccatum, and chinense by FISH. The 5S rDNA was localized to the distal region of one chromosome in all species observed. The number of 45S rDNA loci varied among species; one in annuum, two in chacoense and frutescens, and chinense, and four in baccatum, with the exceptions that 'CM334' of annuum had three loci and 'tabasco' of frutescens gad one locus. 'CM334'-derived BAC clones, 384B09 and 365P05, were screened with 5S rDNA as a probe, and BACs 278M03 and 262A23 were screened with 25S rDNA as a probe. Both ends of these BAC clones were sequenced. FISH with these BAC probes on pachytenes from 'CM334' plant showed one 5S rDNA locus and three 45S rDNA loci, consistent with the patterns on the somatic chromosomes. The 5S rDNA probe was also applied on extended DNA fibers to reveal that its coverage measured as long as 0.439 Mb in the pepper genome. FISH techniques applied on somatic and meiotic chromosomes and fibers have been established for chili to provide valuable information about the copy number variation of 45S rDNA and the actual physical size of the 5S rDNA in chili.

• ALGAE
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• v.25 no.2
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• pp.65-70
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• 2010

The genus Chaetoceros provides highly diversified diatoms in marine systems. Morphological descriptions of the genus are well-documented, yet the DNA taxonomy of Chaetoceros has not been satisfactorily established. Here, the molecular divergences of the 18S-28S rDNA of Chaetoceros were assessed. DNA similarities were relatively low in both 18S (93.1 $\pm$ 3.9%) and 28S rDNA (81.0 $\pm$ 4.6%). Phylogenies of the 18S, 28S rDNAs showed that Chaetoceros was divided according to individual species, clustering the same species into single clades. Statistical analysis with corrected genetic (p-) distance scores showed that nucleotide divergence of Chaetoceros 28S rDNA significantly differed from that of 18S rDNA (Student's t-test, p < 0.05). This finding suggests that the 28S rDNA may be treated as a more suitable marker for species-level taxonomic distinctions of Chaetoceros.

• The Plant Pathology Journal
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• v.25 no.1
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• pp.21-25
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• 2009

Jujube trees infected with phytoplasma exhibit symptoms of typical witches' broom, such as yellowing, abnormally small leaves, short internodes and proliferation of shoots. A 1.2 kb fragment of the 16S rDNA from jujube phytoplasma was generated by R16F2n/R16R2 primer pair from earlier amplified P1/P7 PCR products of cloned jujube witches' broom phytoplasmas. Enzymatic restriction fragment length polymorphism (RFLP) and sequence analysis of 16S rDNA revealed that the jujube tree was infected with 16S rDNA I and V groups of phytoplasmas. Extensive comparative analyses of restriction enzyme profiles from Alu I, Hha I, Msp I, and Rsa I clearly classified the two into different phytoplasma groups. The phylogenie analyses based on 16S rDNA showed that the similarity of the two different clones was 87.5%. This is the first report of a mixed phytoplasmal infection in a single jujube tree.

• Korean Journal of Medicinal Crop Science
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• v.14 no.3
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• pp.178-182
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• 2006

This study was conducted to investigate the variation in sequence, the base composition and the sequence similarity of 18S rDNA (18S ribosomal RNA coding region) in the 10 Polygonatum spp. collections. The entire 18S rDNA region of 10 Polygonatum spp. collections ranged from 913 bp to 914 bp. There were 8 variable sites in the entire 18S region, and they were attributable to nucleotide substitution and deletion. $T{\rightarrow}C$ transition happened in 4 sites, and $A{\rightarrow}G$ transition happened in 1 site. $C{\rightarrow}A$ transversion happened in 1 site, and deletion happened in 2 sites. Transition rates were five times that of transversion. Base compositions of 18S rDNA were $23.09{\sim}23.33%$ in adenine, $23.33{\sim}23.52%$ in guanine, $25.60{\sim}25.85%$ in thymine and $27.38{\sim}27.79%$ in cytosine. The A + T content of 18S rDNA of 10 Polygonatum spp. collections averages 48.99%, ranging from 48.80% to 49.18%, and the G + C content averages 51.01%, ranging from 50.82% to 51.20%. Pairwise sequence comparisons indicated that 18S rDNA sequence similarity ranged from 99.7% to 100%.

• Animal Systematics, Evolution and Diversity
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• v.36 no.4
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• pp.382-386
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• 2020

In this study, Prionospio depauperata Imajima, 1990 is newly reported in Korean fauna. Prionospio depauperata can be distinguished from other relatives by the four pairs of branchiae which are pinnate on chaetigers 2 and 5, and apinnate on chaetigers 3 and 4; caruncle extending to the end of chaetiger 2; and moderate dorsal crest present on chaetigers 7-13. The morphological diagnosis of P. depauperata are provided with the photographs of four Prionospio species. The mitochondrial cytochrome c oxidase subunit 1 (CO1), 16S ribosomal DNA (16S rDNA), and the nuclear 18S ribosomal DNA (18S rDNA) sequences of four Prionospio species from Korean waters, P. depauperata Imajima, 1990, P. japonica Okuda, 1935, P. krusadensis Fauvel, 1929, and P. membranacea Imajima, 1990, were determined for the first time. The inter-specific genetic distances among the congeners of four Prionospio species were 22.3-29.6% in CO1, 10.5-25.0% in 16S rDNA, and 0.3-3.6% in 18S rDNA.

• Korean Journal of Microbiology
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• v.39 no.1
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• pp.36-39
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• 2003

The rapid and reliable 16S rDNA multiplex polymerase chain reaction (PCR) assay was established to characterize bacterial etiologies of middle ear effusion. These etiologies included Haemophilus influenzae, Moraxella catarrhalis and Streptococcus pneumonia, which were detected in middle-ear effusion (MEE) samples taken from patient with otitis media. A total of 39 MEE samples were aspirated from 26 patients. DNA was extracted from MEE samples, and PCR was done with DNA extracts by using the common primers, which is localized at C4 region in the 16S rDNA gene of all bacterial species, and species-specific primers: (i) Haemophilus-specific primer, (ii) Moraxella- specific primer, and (iii) Streptococcus-specific primer. Among 39 samples tested, 24 (61.5%) were positive for H. influenzae, 10 (25.6%) were positive for M. catarrhalis, 3(7.7%) were positive for S. pneumonia, and 11 (28%) were negative for 165 rDNA multiplex PCR reaction. Nine samples (28.6%) exhibited a mixed infection and were positive for both H. infuenzae and M. catarrhalis. We suggested that 16S rDNA multiplex PCR is a useful method to identify rapidly for rapid identification of the pathogenic bacteria and characterization of bacterial etiologies of middle ear effusion.

• Korean Journal of Microbiology
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• v.37 no.1
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• pp.9-14
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• 2001

In order to investigate the pathogenicity and development of differential identification technique in the Yersinia species and other entericbacteria, we isolated 5 strains of Y.pseudotuberculosis from spring water sites in Seoul. The biochemical characteristics of isolated strains revealed that indole, VP($25^{\circ}C$, $37^{\circ}C$), $H_2S$, phenylalanine, lysine, arginine, ornithine, gas from glucose, lactose, sucrose, sorbitol, oxidase and motility($37^{\circ}C$) were all negative and urease, glucose, mannitol, salicin, catalase and motility($25^{\circ}C$) were all positive. To detect the causative agent of pseudotuberculosis(Y.pseudotuberculosis), we carried out a study using a PCR with inv primers complementary to the pathogenic region and found that all strains were positive, this revealed that strains from spring waters were pathogenic. Also 16S rDNA for total 5 strains of Y. pseudotuberculosis were amplified and a stretch of approximately 1,450 nucleotides were sequenced and analyzed. The 16S rDNA nucleotide sequence homologies among Yersinia species ranged 97.5% to 100% and between Y.pseudotuberculosis and other entericbacteria they ranged 93.0% to 95.1%. The Phylogenetic tree generated from the sequence analysis of the 16S rDNA gene showed 3 coherent clusters that could be separated into Y.pseudotuberculsis strains, some Yersinia species strains and other entericbacteria strains.

• Journal of Microbiology
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• v.33 no.2
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• pp.136-141
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• 1995

From a cluster of structural rRNA genes which has previsouly been cloned (Hwang and Kim, in submission; J. Microbiol. Biotechnol.), a 1.0-kb Eco RI fragment of DNA which shows significant homology to the 25S and rRNA s of Tricholoma matsutake was used for sequence analysis. Nucleotide sequence was bidirectionally determined using delection series of the DNA fragment. Comparing the resultant 1016-base sequence with sequences in the database, both the 3'end of 25S-rRNA gene and 5S rRNA gene were searched. The 5S rRNA gene is 118-bp in length and is located 158-bp downstream of 3'end of the 25S rRNA gene. IGSI and IGS2 (partial) sequences are also contained in the fragment. Multiple alignment of the 5S rRNA sequences was carried out with 5S rRNA sequences from some members of the subdivision Basidiomycotina obtained from the database. Polygenetic analysis with distance matrix established by Kimura's 2-parameter method and phylogenetic tree by UPGMA method proposed that T. matsutake is closely related to efibulobasidium allbescens. Secondary structure of 5S rRNA was also hypothesized to show similar topology with its generally accepted eukaryotic counterpart.

• Bulletin of the Korean Chemical Society
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• v.25 no.9
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• pp.1430-1432
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• 2004

• The Plant Pathology Journal
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• v.40 no.2
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• pp.171-191
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• 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.