• The Korean Journal of Mycology
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• v.42 no.2
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• pp.138-143
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• 2014

Several isolates were collected from apple, pepper, strawberry, cucumber and tomato having typical gray mold symptoms. All the isolates were identified as Botrytis cinerea by using morphological characteristics and PCR-RFLP method. It was difficult to analyze the phylogenetic relationship of these isolates by using ITS region, HSP60 and G3PDH because these genes were highly homologous in their nucleotide in inter-species of B. cinerea and intra-species of genus Botrytis. However, phylogenetic analysis using combined sequences (RPB2, HSP60 and G3PDH genes) clearly showed that all isolate of B. cinerea were different from Botrytis spp. Furthermore, it was also confirmed that strawberry isolate was distantly related to apple, pepper, cucumber and tomato isolates that were closely related to each other in nucleotide level.

• Asian-Australasian Journal of Animal Sciences
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• v.32 no.2
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• pp.176-182
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• 2019

Objective: This study was conducted to investigate basic information on genetic structure and characteristics of Limousin population in Hungary. Obtained results will be taken into consideration when adopting the new breeding strategy by the Association of Hungarian Limousin and Blonde d'Aquitaine Breeders (AHLBB). Methods: Genetic diversity and phylogenetic relationship of 3,443 Limousin cattle from 16 different herds were investigated by performing genotyping using 18 microsatellite markers. Amplified DNA was genotyped using an automated genetic analyzer. Results: Mean of effective alleles ($n_e$) of the populations was 3.77. Population C had the lowest number of effective alleles (3.01) and the lowest inbreeding coefficient ($F_{IS}$) value (-0.15). Principal component analysis of estimated genetic distance ($F_{ST}$) values (p<0.000) revealed two herds (C and E) distinct from the majority of other Limousin herds. The pairwise $F_{ST}$ values of population C compared to the others (0.066 to 0.120) fell into the range of moderate genetic distance: 0.050 to 0.150, while population E displayed also moderate genetic distance ($F_{ST}$ values in range 0.052 to 0.064) but only to six populations (G, H, J, L, N, and P). $F_{ST(C-E)}$ was 0.148, all other pairs -excluding C and E herds- displayed low genetic distance ($F_{ST}$<0.049). Population D, F, I, J, K, L, N, O, and P carried private alleles, which alleles belonged to 1.1% of the individuals. Most probable number of clusters (K) were 2 and 7 determined by Structure and BAPS software. Conclusion: This study showed useful genetic diversity and phylogenetic relationship data that can be utilized for the development of a new breeding strategy by AHLBB. The results presented could also contribute to the proper selection of animals for further whole genome scan studies of Limousins.

• Korean Journal of Fisheries and Aquatic Sciences
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• v.54 no.5
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• pp.698-702
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• 2021

Yellow head virus (YHV) is a rod-shaped positive-sense single-stranded RNA virus, classified into the genus Okavirus, family Roniviridae, and order Nidovirales. In this study, 200 fleshy prawns (Fenneropenaeus chinensis) collected from the vicinity of Narodo in Goheung-gun, Korea, were screened for the presence of yellow head complex viruses and related genotype such as YHV genotype 8. The detection rate of YHV genotype 8 among the 200 fleshy prawns, determined using nested RT-PCR (reverse transcription polymerase chain reation), was 39.0%. Phylogenetic analysis of the ORF1b gene of YHV showed that eight distinct genetic lineages were detected. The four strains of YHV genotype 8 obtained in this study formed a robust clade with the YHV genotype 8 group that was first isolated from fleshy prawns in China suspected to have acute hepatopancreatic necrosis disease (AHPND).

• Journal of Veterinary Science
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• v.23 no.4
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• pp.57.1-57.9
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• 2022

Background: Classical swine fever virus (CSFV), the causative agent of classical swine fever (CFS), is a highly contagious disease that poses a serious threat to Chinese pig populations. Objectives: Many provinces of China, such as Shandong, Henan, Hebei, Heilongjiang, and Liaoning provinces, have reported epidemics of CSFV, while the references to the epidemic of CSFV in Yunnan province are rare. This study examined the epidemic characteristics of the CSFV in Yunnan province. Methods: In this study, 326 tissue samples were collected from different regions in Yunnan province from 2015 to 2021. A reverse transcription-polymerase chain reaction (RT-PCR), sequences analysis, and phylogenetic analysis were performed for the pathogenic detection and analysis of these 326 clinical specimens. Results: Approximately 3.37% (11/326) of specimens tested positive for the CSFV by RT-PCR, which is lower than that of other regions of China. Sequence analysis of the partial E2 sequences of eleven CSFV strains showed that they shared 89.0-100.0% nucleotide (nt) and 95.0-100.0% amino acid (aa) homology, respectively. Phylogenetic analysis showed that these novel isolates belonged to the subgenotypes 2.1c and 2.1d, with subgenotype 2.1c being predominant. Conclusions: The CSFV was sporadic in China's Yunnan province from 2015 to 2021. Both 2.1c and 2.1d subgenotypes were found in this region, but 2.1c was dominant.

• The Korea Journal of Herbology
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• v.28 no.3
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• pp.75-84
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• 2013

Objectives : The origin of Breeae Herba (So-gye) and Cirsii Herba (Dae-gye) is differently prescribed in Korean and Chinese modern pharmacopoeia. Since the similar morphological characteristics and chaotic plant names, moreover, the aerial part of Carduus crispus have been used as the Cirsii Herba. To develop a reliable method for correct identification of these herbal medicines and to evaluate the genetic relationship of these closely related plant species, we analyzed sequences of DNA barcode regions. Methods : Thirty-one samples of 6 medicinal plants (B. segeta, B. setosa, C. japonicum var. maackii, C. setidens, C. chanroenicum, and C. crispus) were collected from different habitate and nucleotide sequences of DNA barcode regions (rDNA-ITS, matK, and rbcL) were analyzed after amplification using appropriate primers reported in previous studies. The nucleotides of species-specific authentic marker and phylogenetic relations were estimated based on the entire sequences of DNA barcodes by the analysis of ClastalW and UPGMA, respectively. Results : In comparative analysis of DNA barcode sequences, we obtained specific nucleotides to discriminate the medicinal plant of Breeae/Cirsii Herba in species level and evaluated the phylogenetic relationship of these species. Futhermore, we identified distinct marker nucleotides enough to authenticate respective species. These sequence differences at corresponding positions were avaliable genetic markers to determine the botanical origins of Breeae Herbal as well as Cirsii Herba. Conclusions : These marker nucleotides would be useful to identify the official herbal medicines by providing of definitive information that can identify each plant species and distinguish from unauthentic adulterants and substitutes.

• Animal Bioscience
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• v.35 no.6
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• pp.826-837
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• 2022

Objective: Cambodia is located within the distribution range of the red junglefowl, the common ancestor of domestic chickens. Although a variety of indigenous chickens have been reared in Cambodia since ancient times, their genetic characteristics have yet to be sufficiently defined. Here, we conducted a large-scale population genetic study to investigate the genetic diversity and population genetic structure of Cambodian indigenous chickens and their phylogenetic relationships with other chicken breeds and native chickens worldwide. Methods: A Bayesian phylogenetic tree was constructed based on 625 mitochondrial DNA D-loop sequences, and Bayesian clustering analysis was performed for 666 individuals with 23 microsatellite markers, using samples collected from 28 indigenous chicken populations in 24 provinces and three commercial chicken breeds. Results: A total of 92 haplotypes of mitochondrial D-loop sequences belonging to haplogroups A to F and J were detected in Cambodian chickens; in the indigenous chickens, haplogroup D (44.4%) was the most common, and haplogroups A (21.0%) and B (13.2%) were also dominant. However, haplogroup J, which is rare in domestic chickens but abundant in Thai red junglefowl, was found at a high frequency (14.5%), whereas the frequency of haplogroup E was considerably lower (4.6%). Population genetic structure analysis based on microsatellite markers revealed the presence of three major genetic clusters in Cambodian indigenous chickens. Their genetic diversity was relatively high, which was similar to findings reported for indigenous chickens from other Southeast Asian countries. Conclusion: Cambodian indigenous chickens are characterized by mitochondrial D-loop haplotypes that are common to indigenous chickens throughout Southeast Asia, and may retain many of the haplotypes that originated from wild ancestral populations. These chickens exhibit high population genetic diversity, and the geographical distribution of three major clusters may be attributed to inter-regional trade and poultry transportation routes within Cambodia or international movement between Cambodia and other countries.

• Journal of Environmental Science International
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• v.32 no.5
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• pp.315-328
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• 2023

Cyanobacteria have been used as pollution indicator species in freshwater ecosystems, and identifying their fluctuations can be an important part about management of surface waters globally. Cyanotoxins produced by cyanobacteria are directly or indirectly a threat to human and environmental health. In order to confirm the potential risk of these cyanotoxins, the fluctuations of phytoplankton and phylogenetic analysis of cyanotoxin synthetase genes were conducted at each point in the Yeongsan River water system in Gwangju from November 2021 to October 2022. Diatoms which grow well in winter were dominant at 99.4 ~ 99.5%, and diatoms and green algae were dominant from the spring to autumn when the water temperature rises. Stephanodiscus spp. were dominant at 92.7 to 97.5 % at all sites in the winter, and Aulacoseira spp., which grow in warm water temperatures, were dominant in summer and autumn. Microcystis aeruginosa was dominant at 25.2% in summer only at site 5. mcyB and anaC have been detected as cyanotoxin synthetase genes. The phylogenetic tree of anaC could be divided into two groups (Group 1 & Group 2). Group 1 contained Aphanizomenon sp. and Cuspidothrix issatschenkoi. It is combined with Aphanizomenon sp. and Cuspidothrix issatschenkoi, which are known to produce cyanotoxins.

• Animal Bioscience
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• v.36 no.4
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• pp.671-678
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• 2023

Objective: Previous studies isolated the thermophilic ammonium-tolerant (TAT) bacterium Bacillus sp. TAT105 that grew in composting swine manure with the assimilation of ammonium nitrogen and reduced ammonia emissions during composting. Those studies also investigated the potential for applications of TAT105 to composting. It was observed that the concentration of TAT bacteria, phylogenetically close to TAT105, increased during composting. The objectives of this study were to identify the phylogenetic placement of these TAT bacteria and investigate their distribution in various composts. Methods: The phylogenetic placement of TAT105 was examined based on the sequence of 16S ribosomal RNA gene. The genomic DNA homology between TAT105 and the type strains of bacterial species that were phylogenetically close to TAT105 were examined by DNA-DNA hybridization. Moreover, the tolerances of these strains to NH₄Cl and NaCl were analyzed using a cultivation method. Concentrations of TAT bacteria in various composts were evaluated using an agar medium specific to TAT bacteria and polymerase chain reaction followed by restriction fragment length polymorphism analysis. Results: TAT105 was most closely related to Bacillus thermolactis and Bacillus kokeshiiformis. Many variants of these species have been detected in various environments, including composts. The type strains of these species displayed TAT characteristics that were similar to those of TAT105. Among the composts examined in this study, TAT bacteria were detected at high concentrations (10⁵ to 10⁹ colony forming units per gram of dry matter) in most of the composts made from cattle manure, swine manure, bark, and excess sludge. Conclusion: TAT bacteria comprised B. thermolactis, B. kokeshiiformis, and their phylogenetically close relatives. They were considered to be adaptable to composting of some certain materials, and a favorable target for searching for strains with some useful function that could be applied to composting of these materials.

• Korean Journal of Agricultural Science
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• v.37 no.3
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• pp.341-350
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• 2010

Blue mold is the most important postharvest disease of apples in Korea. Apple fruits with blue mold symptoms were collected from storages in different locations in Korea and were investigated for their association with Penicillium species. A total of sixty five isolates of Penicillium were sampled from the collected apples. Based on DNA sequence analysis of ${\beta}$-tublin gene and ITS and lsu rDNA (ID region) and morphological characteristics, they were identified as P. crustosum, P. expansum, P. italicum, P. solitum and P. sp.. P. sp. which is closely related to P. hirsutum is a new species, not reported before. P. expansum (35%) was predominant species followed by P. crustosum. The phylogenetic tree inferred from combined ${\beta}$-tublin and ID region sequence showed good correlation with species that are defined by morphological characteristics. In pathogenicity test, apples were wound-inoculated with conidial suspension and incubated at $20-22^{\circ}C$. The most severe and destructive species was P. expansum. The species caused a decayed area 42-50mm in diameter after 8-10days. Decayed area caused by P. crustosum and P. sp. was 26-32mm and 20-26mm, respectively. This is the first record of P. crustosum, P. italicum and P. sp. from apple in Korea.

• Microbiology and Biotechnology Letters
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• v.33 no.2
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• pp.90-95
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• 2005

An Actinomycetes producing an anti-VRSA (vancomycin-resistant Staphylococcus aureus) substance was isolated from soil. The cultural, morphological, physiological and phylogenetic analyses of an isolated strain were investigated for identification. Cultural characteristics based on ISP (International Streptomyces Project) were as follows: white aerial mycelium, yellow reverse side, and good growth on various medium. Also, the isolate did not produce the soluble pigment. Morphological characteristics were showed cylindrical spore chain and smooth spore surface by SEM (Scanning Electron Microscope). Physiological characteristics were showed LL-type by DAP isomer analysis and detected glycine, glutamic acid and alanine. A phylogenetic analysis of the 16S rDNA provided a clue that the isolated strain was actually a member of the genus Streptomyces, because the determined sequence exhibited a higher homology with Streptomyces echinatus. The isolate was identified to be a genus of Streptomyces sp.. The optimal culture conditions for the maximum production of anti-VRSA substance by Streptomyces sp. were attained in a culture medium composed of $2.0\%$ (w/v) glucose, and $0.4\%$ (w/v) yeast extract. The anti-VRSA substance was highly produced after 5 days of culture. Optimal pH and temperature conditions for the production of anti-VRSA substance were pH 7.0 and $28^{\circ}C$, respectively.