• The Korean Journal of Mycology
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• v.42 no.4
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• pp.341-343
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• 2014

Camarops ustulinoides (Henn.) Nannf., belonging to the family Boliniaceae (Order Boliniales), is reported as new to Korea. The morphological characteristics and molecular phylogenetic analysis based on the nucLSU region sequence confirm the recognition of this taxon. Illustrated descriptions of C. ustulinoides are provided.

• The Korean Journal of Mycology
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• v.51 no.1
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• pp.1-6
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• 2023

Tilia mandshurica trees with rust symptoms have consistently been noticed during disease surveys in Korea since 2006. Based on the morphological examination and molecular sequence analysis of the internal transcribed spacer and large subunit of ribosomal DNA, Pucciniastrum tiliae was identified as the causal fungus of rust disease. This is the first report of P. tiliae infection on T. mandshurica in Korea.

• Journal of Plant Biotechnology
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• v.46 no.2
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• pp.79-87
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• 2019

One of wild diploid Solanum species, Solanum chacoense, is one of the excellent resources for potato breeding because it is resistant to several important pathogens, but the species is not sexually compatible with potato (S. tuberosum) causing the limitation of sexual hybridization between S. tuberosum and S. chacoense. Therefore, diverse traits regarding resistance from the species can be introgressed into potato via somatic hybridization. After cell fusion, the identification of fusion products is crucial with molecular markers. In this study, S. chacoense specific markers were developed by comparing the chloroplast genome (cpDNA) sequence of S. chacoense obtained by NGS (next-generation sequencing) technology with those of five other Solanum species. A full length of the cpDNA sequence is 155,532 bp and its structure is similar to other Solanum species. Phylogenetic analysis resulted that S. chacoense is most closely located with S. commersonii. Sequence alignment with cpDNA sequences of six other Solanum species identified two InDels and 37 SNPs specific sequences in S. chacoense. Based on these InDels and SNPs regions, four markers for distingushing S. chacoense from other Solanum species were developed. These results obtained in this research could help breeders select breeding lines and facilitate breeding using S. chacoense in potato breeding.

• Microbiology and Biotechnology Letters
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• v.43 no.1
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• pp.22-30
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• 2015

CSF is a major concern for the swine industry, representing currently the most epizootically dangerous disease to the species. Numerous CSFV isolates with various degrees of virulence have already been isolated worldwide, ranging from low virulent strains that do not result in any apparent clinical signs to highly virulent strains that cause a severe per acute hemorrhagic fever with very high mortality. The molecular epidemiology of CSFVs has proven to be an essential tool for effective disease control and the development of safe and effective vaccines. Therefore, this study cloned and sequenced local CSFV isolates, and conducted a phylogenetic analysis based on the E2 glycoprotein encoding sequences.The RNA was extracted from PK15 cell culture passaged CSFV isolates, the cDNA prepared, and the complete E2 gene amplified with a product size of 1186 bp. The gelpurified PCR product was cloned into a pGEMT easy vector and the positive clone commercially sequenced. Aligning the nucleotide (1119 bp) and amino acid (373) sequences with 29 reference strains revealed nucleotide and amino acid sequence identities of 82.60-97.80% and 88.70-98.70%, respectively, indicating a higher mutation rate of the field CSFV strains. The phylogenetic analysis based on the complete E2 amino acid sequences also revealed a reliable differentiation of all the analyzed strains into specific genetic groups and subgroups, plus the local isolate (CSFV-E2) was found to cluster with the CSFV subgroup 2.2. Thus, the full-length E2 cds proved to be most suitable for a reliable and statistically significant phylogenetic analysis of CSFV isolates.

• Journal of Plant Biotechnology
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• v.38 no.3
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• pp.234-240
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• 2011

The genus Paeonia belongs to the family Paeoniaceae having significant medicinal and ornamental importance. The present investigation was undertaken with an aim to understand phylogenetic relationships of three Paeonia species (P. lactiflora, P. obovata, and P. suffruticosa) that are widely distributed in China, Korea, and Japan, using nuclear ribosomal DNA (nrDNA) internal transcribed spacer (ITS) sequence and to compare the phylogeny results with investigations reported earlier using existed sequences of the same species. The size variation obtained among sequenced nrDNA ITS region was narrow and ranged from 722 to 726 bp. The highest interspecific genetic distance (GD) was found between P. lactiflora and P. suffruticosa or P. obovata. The phylogram obtained using our nrDNA ITS sequences showed non-congruence with previous hypothesis of the phylogeny between section Paeonia and section Moutan of genus Paeonia. This result was supported by the phylogenetic relations showed in the phylogram constructed with existed sequences in NCBI. The present study suggested that P. obovata belonging to section Paeonia was phylogenetically closer to P. suffruticosa representing section Moutan of genus Paeonia than P. lactiflora belonging to section Paeonia. The main reason of the paraphyly of section Paeonia is thought to be nucleotide additivity directly caused by origin hybridization. This study provides more sequence sources of genus Paeonia, and will help for further studies in intraspecies population, and their phylogentic analysis and molecular evolution.

• Korean Journal of Plant Resources
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• v.27 no.6
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• pp.680-686
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• 2014

Acanthopanacis Cortex has been used for oriental medicinal purposes in Asian countries especially in Korea and China. In the Korean Pharmacopeia, the cortexes of the dried roots, stems and branches of all species in Eleutherococcus and Eleutherococcus sessiliflorus are known as 'Ogapi'. Mostly the cortexes of E. gracilistylus roots and E.senticosus roots were used as 'Ogapi' in China and Japan, respectively. Therefore, the purpose of this study was to determine and compare the molecular authentication of Korean 'Ogapi' by using the ribosomal internal transcribed spacer (ITS) region. The ITS region has the highest possibility of effective and successful identification for the widest variety of molecular authentication. The ITS region was targeted for molecular analysis with Single nucleotide polymorphisms (SNPs) specific for morphologically similar to E. gracilistylus, E. senticosus, E. sessiliflorus from their adulterant, moreover, E. sieboldianus were detected within sequence data. Thus, based on these SNP sites, specific primers were designed and multiplex PCR analysis were conducted for molecular authentication of four plants (E. gracilistylus, E. senticosus, E. sessiliflorus, and E. sieboldianus). The findings of results indicated that ITS region might be established multiplex-PCR analysis systems and hence were proved to be an effective tools for molecular evaluation and comparison of 'Ogapi' with other plants.

• Proceedings of the Korean Society of Plant Pathology Conference
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• 2003.10a
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• pp.125.3-126
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• 2003

A near full-length sequence of a new tobamovirus infecting Hibiscus rosa-sinensis L. was determined. The genome consists of 58 nucleotides (nt) 5' UTR, followed by a 4.9 kb ORF which methyl transferase helicase domain (128 kDa), readthrough protein RNA dependent RNA polymerase (RdRp) 185 kDa and a 52 kDa protein. The 128 kDa protein had a maximum homology of 51.4 ％ to TMGMV and amino acids (an) were 54.3 ％ identical to TMV- vulgare strain. The 185 kDa RdRp had a maximum homology of 53.5％ to TMV-Ob and KGMMV-Y and a 59.6％ homology at the an level to CGMMV-SH. The MP gene encodes 282 aa and its theoretical molecular weight is 30.4 kDa. The nt and an sequence identities of MP ranged from 38.8％ to 43.9％ and 30.9％ to 37.9％, respectively. The CP gene encodes 163 residues and with a theoretical molecular weight of 18.2 kDa The (nt) and aa sequences of the CP were 46.9 ％ to 51.6％ and 45.3％ to 57.1％ identical to other tobamoviruses, respectively. The predicted virion origin of assembly (OAS) was located in the CP gene. Phylogenetic trees generated based on the nt and as sequences of RdRp, MP and CP genes indicated that this new virus clustered with subgroup II tobamoviruses. Although the CP ORF of this virus shared a high nt and aa sequence identity with Sunn-hemp mosaic virus (SHMV), Western analysis showed that it is serologically unrelated to SHMV. We propose the name Hibiscus virus S (HVS) for this Singapore isolate. This is the first report on a near full-length sequence of a Tobamovirus that infects hibiscus.

• Journal of Microbiology and Biotechnology
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• v.4 no.4
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• pp.256-263
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• 1994

The aceB gene, encoding for malate synthase, one of the key enzymes of glyoxylate bypass, was isolated from a pMT1-based Corynebacterium glutamicum gene library via complementation of an Escherichia coli aceB mutant on an acetate minimal medium. The aceB gene was closely linked to aceA, separated by 598 base pairs, and transcribed in divergent direction. The aceB expressed a protein product of Mr 83, 000 in Corynebacterium glutamicum which was unusually large compared with those of other malate synthases. A DNA-sequence analysis of the cloned DNA identified an open-reading frame of 2, 217 base pairs which encodes a protein with the molecular weight of 82, 311 comprising 739 aminoo acids. The putative protein product showed only limited amino acid-sequence homology to its counteliparts in other organisms. The N-terminal region of the protein, which shows no apparent homology with the known sequences of other malate synthases, appeared to be responsible for the protein s unusually large size. A potential calciumbinding domain of EF-hand structure found among eukaryotes was detected in the N-terminal region of the deduced protein.

• ALGAE
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• v.31 no.4
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• pp.303-315
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• 2016

Compsopogon specimens collected in China were examined based on morphology and DNA sequences. Five molecular markers from different genome compartments including rbcL, COI, 18S rDNA, psbA, and UPA were identified and used to construct a phylogenetic relationship. Phylogenetic analyses indicated that two different morphological types from China clustered into an independent clade with Compsopogon specimens when compared to other global samples. The Compsopogon clade exhibited robust support values, revealing the affiliation of the samples to Compsopogon caeruleus. Although the samples were distributed in a close geographical area, unexpected sequence divergences between the Chinese samples implied that they were introduced by different dispersal events and from varied origins. It was speculated that Compsopogon originated in North America, a portion of the Laurentia landmass situated in the Rodinia supercontinent at approximately 573.89-1,701.50 million years ago during the Proterozoic era.Although Compsopogonhad evolved for a rather long time, genetic conservation had limited its variability and rate of evolution, resulting in the current monospecific global distribution. Additional global specimens and sequence information were required to increase our understanding of the evolutionary history of this ancient red algal lineage.

• Proceedings of the Korean Biophysical Society Conference
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• 2003.06a
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• pp.53-53
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• 2003

Calumenin was previously identified as a high affinity Ca$\^$2+/ binding protein in mouse cardiac sarcoplasmic reticulum (SR). For the present study, a 48 kDa skeletal homologue of calumenin was identified by sucrose-density gradient of rabbit skeletal SR membranes, concanavalin A treatment, 2D-gel electrophoresis, $\^$45/Ca$\^$2+/ overlay, Stains-all staining, and MALDI-TOF analysis. We attempted to clone the skeletal calumenin by RT-PCR based on mouse cardiac and human calumenin sequences. The deduced amino acid sequence (315 residues) of the skeletal calumenin showed high identity to mouse cardiac calumenin (90％). As seen in the cardiac calumenin, the deduced sequence contains a 19 amino acid N-terminal signal sequence and a HDEF C-terminal sequence, a putative retrieval signal to ER. Also, the skeletal calumenin contains one N-glycosylation site, three PKC phosphorylation sites, eight casein kinase 2 phosphorylation sites, and 6 EF-hand domains. GST-calumenin showed a conformational change and increased mobility in the presence of Ca$\^$2+/ in SDS-PAGE. Three calumenin interacting proteins (ryanodine receptor 1, glycogen phosphorylase, and phosphofructo kinase) were identified by pull-down assay with GST-calumenin and solubilized SR. All the interactions were Ca$\^$2+/dependent. The present results suggest that calumenin plays an important role in Ca$\^$2+/ homeostasis of muscle cells.