• The Korean Journal of Mycology
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• v.48 no.4
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• pp.511-518
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• 2020

This study was conducted to isolate and identify the fungal pathogen caused unreported post-harvest disease on apples (cv. Fuji) fruit in Korea. The disease symptoms on apples appeared as irregular, light to dark brown, slightly sunken spots. The three fungal strains were isolated from infected tissues of apple fruits and their cultural and morphological characteristics were completely consistent with those of Plenodomus collinsoniae. The phylogenetic analysis using the internal transcribed spacer (ITS) regions, beta-tubulin (TUB), and the second largest subunit of RNA polymerase II (RPB2) sequences revealed the closest relationship of the isolates with Plenodomus collinsoniae at the species level. The pathogenicity test showed the same dark brown spots on Fuji apple cultivar. Therefore, P. collinsoniae is a newly reported fungal agent causing post-harvest disease on apples in Korea.

• Fisheries and Aquatic Sciences
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• v.24 no.5
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• pp.181-190
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• 2021

Grouper is one of the most economically important fishes with various morphological forms and characteristics, meaning it is often difficult to identify species and distinguish between life stages, sometimes leading to morphological misidentification. Therefore, identification using a molecular deoxyribose nucleic acid (DNA) approach was needed as an alternative means to identify closely related species. This study aims to determine the molecular phylogeny of grouper from the northern part of the Bird's Head Seascape of Papua. The DNA sequence of each cytochrome oxidase I (COI) gene was used to study the molecular relationship among closely related species of grouper. The results showed that there were 16 Epinephelinae that have been compared to a gene bank (National Centre for Biotechnology Information, NCBI) in the sequence length of 623 base pairs. The closest genetic distance was found between Cephalopholis miniata and Cephalopholis sexmaculata (0.036), while the furthest genetic distance was observed between Plectropomus laevis and Cephalopholis spiloparaea (0.247). This finding was further reinforced by the morphological characters of each species. This finding highlighted that five genera were represented as a monophyletic group (clade), i.e., Epinephelus, Cephalopholis, Plectropomus, Saloptia and Variola.

• Proceedings of the Korean Society of Plant Pathology Conference
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• 2003.10a
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• pp.115.2-116
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• 2003

Complete genomic nucleotide sequence of Daphe virus S (DVS), a member of the genus Carlavirus, causing leaf distortion and chlorotic spot disease symptoms in daphne plants, has been determined in this study. The genome of DVS contained six open reading fames coding for long viral replicase, triple gene block, 36 kDa viral coat protein (CP) and 12 kDa from the 5' to 3' ends, which is a typical genome structure of carlaviruses. Two Korean isolates of DVS isolates were 98.1％ and 93.6％ amino acid identical in the CP and 12kDa, respectively. The CP gene of DVS shares 25.2-55.2％ and 42.9-56.1％ similarities with that of 19 other carlaviruses at the amino acid and nucleotide levels, respectively. The 3'-proximal 12 kDa gene of DVS shares 20.2-57.8％ amino acid identities with that of 18 other members of the genus. The 3' noncoding region of DVS consists of 73 nucleotides with long excluding poly A tract, and shares 69.1-77.1％ identities to the known carlaviruses. In the phylogenetic analyses of the two proteins, DVS was closely related to Helenium virus S and Chrysanthemum virus B. This is the first complete sequence information for the DVS, and further confirms the classification of DVS as a distinct species of the genus Carlavirus.

• The Korean Journal of Mycology
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• v.50 no.3
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• pp.183-194
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• 2022

Two fungal strains, designated KNUF-21-006 and KNUF-21-028, were isolated from soil samples collected from Gyeongbuk Province, Korea. The strain KNUF-21-006 was similar to other Pestalotiopsis species in terms of morphological characteristics, including whitish to pale brown mycelium, conidial shape, and size. The isolate had aerial hyphae that produced black fruiting bodies on the mycelium. The conidia were fusoid to ellipsoid, four-septate, and appendage-bearing. Phylogenetic analysis using the internal transcribed spacer (ITS) region, translation elongation factor 1-alpha (TEF), and β-tubulin (TUB) gene sequences confirmed that the closest relationship of the isolate at the species level was with Pestalotiopsis clavata. The strain KNUF-21-028 exhibits similar morphological characteristics to other Botryotrichum species, including white aerial mycelium with sulcate and irregular margins, conidial shape, and size. The conidia were globose, single, and hyaline. Upon molecular analysis-using the ITS region, large subunit (LSU) rRNA gene, and TUB gene sequences-the fungus was identified as Botryotrichum iranicum. This is the first record of these fungal species in Korea.

• Proceedings of the Korean Society of Crop Science Conference
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• 2022.10a
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• pp.216-216
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• 2022

The starch-branching enzymes (BEs) are responsible for synthesizing the amylopectin, which plays an important role in determining the structural and physical properties of starch granules. BE has two differently functioning isoforms (BEI and BEIIa/b) based on their difference in the chain-length pattern by the degree of polymerization (DP), which mainly contributes to the amylopectin chain length distribution in starch biosynthesis. In this study, we investigated functional haplotypes and evolutionary analyses of SBE1 in 374 rice accessions (320 Korean bred and 54 wild). The analyses were performed based on the classified subpopulations. Haplotype analysis generates a total of 8 haplotypes, of which only four haplotypes were functional carrying four functional SNPs in four different exons of SBE1 on chromosome 6. Nucleotide diversity analysis showed a highest pi-value in aromatic group (0.0029), while the lowest diversity value was in temperate japonica (0.0002), indicating the signal of this gene evolution origin. Different directional selections could be estimated by negative Tajima's D value of temperate japonica (-1.1285) and positive Tajima's D value of tropical japonica (0.9456), where the selective sweeps were undergone by both positive purifying and balancing selections. Phylogenetic analysis indicates a closer relationship of the wild with most of the cultivated subgroups indicating a common ancestor for SBE1 gene. FST-values indicate distant genetic relationships of temperate japonica from all other classified groups. PCA and population structure analysis show an admixed structure of wild and cultivated subpopulations in some proportions.

• The Korean Journal of Mycology
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• v.39 no.1
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• pp.11-15
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• 2011

To provide basic information for Verticillium spp., molecular methods were applied to analyze genetic characteristics within Verticillium spp. including Verticillium dahliae, isolated from diseased plants in two regions of Korea. Five Korean isolates of V. dahliae causing Verticillium wilt on chrysanthemum were analyzed, together with six other Verticillium spp., using mitochondrial small subunit rRNA gene (rns) sequence and random-amplified polymorphic DNA (RAPD). In a phylogenetic tree based on rns region sequences, Korean V. dahliae isolates formed a single clade with foreign isolates, whereas the other Verticillium spp. formed separate groups. In addition to rns sequence analysis, a dendrogram based on RAPD fragment patterns also showed clustering of all V. dahliae isolates into one group, separate from the six different Verticillium spp., and the V. dahliae isolates formed three subgroups which corresponded to the regions of origin, Kumi, Busan city and Canada. This indicates that high genetic variation exists between regions, although the fungus was isolated from the same host plant, chrysanthemum. These results provide the foundation for the study of genetic diversity and relationships among V. dahliae isolates in Korea.

• Journal of Aquaculture
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• v.17 no.3
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• pp.197-208
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• 2004

Five commercially valuable Korean Veneroid, Protothaca jedoensis, Ruditapes philippinarum, Saxidomus purpuratus, Cyclina sinensis and Meretrix lusoria were recognized by comparing internal and external morphological characters. As length of the primary tooth was directly grown proportional to shell size but all other characters were not measured according to size of shell. Hence, the morphological characters of these Veneroids may be estimated from the size of the unique primary tooth and it might be enough to be a good criterion for identification of species among Veneriods. Numerical index of hinge plate length of these species was assessed systematically, irrespective of measuring the length, height and width of the shell. The highest internal and external morphological similarity was observed between P. jedoensis and R. philippinarum and the lowest similarity was observed between P. jedoensis and M. lusoria. These similarities may be affected by multiple environmental factors as well as genetic characters. For artificial seed production of P. jedoensis, R. philppinarum, a closest relative among the five species, must be focussed.

• Asian-Australasian Journal of Animal Sciences
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• v.18 no.6
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• pp.755-761
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• 2005

Blood samples were collected from eight native Japanese breeds of chickens (Miyadi-dori, Ohiki, Onaga-dori, Shoukoku, Tosa-Jidori, Tosa-Kukin, Toutenkou and Uzurao) and two foreign breeds of chickens (White Leghorn and Rhode Island Red) to examine the genetic variability and relationships among the breeds by using a microsatellite DNA technique. Except for the Shoukoku breed, the other Japanese chicken breeds all originate from Kochi Prefecture. Ohiki, Onaga-dori, Tosa-Jidori, Toutenkou and Uzurao are fancy fowl, and Miyadi-dori and Tosa-Kukin are utility fowl. Among the fancy fowl, Ohiki, Onaga-dori, and Toutenkou males have thick and long feathers in the saddle and tail. Genetic variabilities of the 20 microsatellites examined, varied depending on the breed: the mean number of alleles per locus ranged from 2.05 (Miyadi-dori) to 3.90 (Rhode Island Red); proportion of polymorphic loci ranged from 0.75 (Miyadi-dori) to 1.00 (Rhode Island Red, Shoukoku and Uzurao); and mean expected heterozygosity ranged from 0.330 (Miyadi-dori) to 0.607 (Rhode Island Red). Unique microsatellite alleles were detected in each breed. Using the neighbour-joining method, phylogenetic trees were constructed based on the genetic distances of D$_{A}$ and D$_{ST}$. Among the breeds originating from Kochi Prefecture, fancy and utility breeds belonged to different clusters. Among the fancy breeds, those having thick and long feathers in the tail and saddle showed a close genetic relationship to the Shoukoku breed, which also has thick and long feathers in the tail and saddle.

• Asian Pacific Journal of Cancer Prevention
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• v.17 no.9
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• pp.4357-4361
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• 2016

Background: Whether there is any relationship between human papilloma virus (HPV) and breast carcinoma is not clear. Some previous studies have indicated a possible role in oncogenesis in the breast. In this study, we therefore analyzed the presence of HPV infection in breast tissues of Iranian women from Yazd city. Materials and Methods: In a cross-sectional study, formalin-fixed paraffin-embedded tissues from 87 patients with breast cancer and 84 cases with breast fibrocystic lesions (control group) were selected from a tissue archive. Grade of tumors and fibrocystic tissues were determined by two pathologists. The nested-PCR method was performed for detection of HPVs in samples. HPV genotypes were determined by sequencing and the phylogenetic tree depicted by MEGA software. Results: Of the 87 women with breast cancer, 22.9% (20 isolates) had positive results for HPV DNA. In the control group no HPV was detected. The HPV genotypes in positive samples were HPV-16 (35%) HPV-18 (15%), HPV-6 (45%) and HPV-11 (5%). The data did not approved a significant correlation between tissue pathology of breast cancer and the HPV genotype frequency. Conclusions: The data did not provide any evidence for a role of high risk HPV types in oncogenesis in the breast.

• Journal of Life Science
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• v.14 no.1
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• pp.115-120
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• 2004

Lepista nuda is a world-wide species which has and international reputation as a excellent edible species. In this study, we investigated the genetic variation and taxonomic relationship of L. nuda and other five Tricholomataceae species were analyzed by random amplied polymorphic DNA (RAPD). 15 kinds of random primers were used. The distance matrix was calculated using UPGMA and phyolgenetic relationship were inferred by neighnor-joining (NJ) method. Various bands of 100bp∼1600bp were observed in electrophoretic patterns of RAPD. Nei's genetic distance was calculated using a total of 228 DNA bands identified, and phylogenetic tree was made. The Nei's genetic variations of L. nuda, Lepista surdida, Collybia peronata, Collybia confluens, Lyophyllum cinerascens, Laccara laccata were 0∼21.3%, 21.2∼28.0%, 15.4∼23.0%, 14∼21.8%, 16.5∼34.6%, and 12.4∼27.4%, respectively The consistency index, the retention index and homoplasy index were 0.5217, 0.5769 and 0.5156, respectively. Also, two groups could be made by NJ tree. The genetic distance between L. nuda and C. confluens was closer than that between L. nuda and L. sordida.