• 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.

• Journal of fish pathology
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• v.35 no.2
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• pp.215-223
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• 2022

Disease including parasite, bacteria and virus cause serious mortality to salmonid fish in the aquaculture. In this study, we investigated the current disease status of the rainbow trout (Oncorhynchus mykiss) and coho salmon (Oncorhynchus kisutch) in Yanayang, Pyeongchang, Jeongseon and Yeongwol of Gangwon province in 2021 and performed molecular characterization of those pathogen. For parasites, Ichthyophthirius multifiliis was observed at 2 farms. For bacteria, we identified Aeromonas sobria from kidney of rainbow trout using phylogenetic analysis of gyrB gene. A. salmonicida were isolated from necrosis site of gill cover and fin in coho salmon and necrotic lesion of fin in rainbow trout. Phylogenetic analysis using vap gene indicated that A. salmonicida isolated in this study were clustered with previously reported A. salmonicida subsp. salmonicida isolates. For virus, JRt-Nagano type of infectious haematopoietic necrosis virus was detected in rainbow trout, but infectious pancreatic necrosis virus and Oncorhynchus masou virus were not detected. These results provide useful information for the prevention of disease spread and transmission when cultivating new species such as Atlantic salmon in Korea.

• 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.

• 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 Plant Taxonomy
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• v.53 no.2
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• pp.157-165
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• 2023

Paraphlomis koreana (Lamiaceae) was newly named and added to Korean flora in 2014. Paraphlomis belongs to the tribe Paraphlomideae, along with Ajugoides and Matsumurella. However, a recent study has suggested that P. koreana is morphologically similar to Matsumurella chinensis, making them difficult to distinguish from each other. Therefore, we aimed to examine the phylogenetic placement of P. koreana within the tribe and compare its genetic relationship with M. chinensis. We sequenced an additional complete plastid genome for an individual of P. koreana and generated sequences of nuclear ribosomal (nr) DNA regions of internal and external transcribed spacers (ITS and ETS) for two individuals of P. koreana. Maximum likelihood analyses based on two nrDNA regions (ITS and ETS) and four plastid DNA markers (rpl16 intron, rpl32-trnL, rps16 intron, and trnL-F) covering 13 Paraphlomis species and M. chinensis were conducted. Phylogenetic analyses concordantly supported that P. koreana forms a monophyletic group with M. chinensis. Moreover, our study revealed that P. koreana includes nrDNA sequences of M. chinensis as minor intra-individual variants, suggesting that the genetic divergence between the two taxa is incomplete and may represent intraspecific variation rather than distinct species. In conclusion, our findings suggest that the independent species status of P. koreana within Paraphlomis should be reconsidered.

• Journal of fish pathology
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• v.37 no.1
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• pp.25-36
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• 2024

In this study, we analyzed the phylogenetic classification, epitope prediction, and pathogenicity of red sea bream iridovirus (RSIV) isolated from rock bream between 2019 and 2023. Phylogenetics based on genes encoding MCP and ATPase indicated that all five RSIV isolates belonged to RSIV subtype II. The deduced amino acid sequence of the MCP for the amplicons (1362 bp) obtained from RSIV isolates had a length of 453 amino acids. Among these, the amino acid sequences of the RSIV-19, 21, 22, and 23 isolates showed 100% identity, while the RSIV-20 isolate showed 99.78% identity with one residue difference at position 306. As a result of antigenicity analysis based on amino acid sequence, the antigenicity score of the RSIV-20 isolate was 0.6386 and the other RSIV isolates were 0.6365. Additionally, the prediction of their antigenic determinants resulted in a total of 17 identical antigenic plots. When each RSIV was inoculated into rock bream, no significant differences were observed with 100% cumulative mortality in all groups. This study provides data on the potential for genetic variation of RSIV isolated in the same marine area over the past five years, and the antigenicity and pathogenicity results of each isolate are expected to be useful information for selecting future vaccine strains.

• ALGAE
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• v.19 no.3
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• pp.153-160
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• 2004

The intergeneric relationship of Staurastrum complex including genus Arthrodesmus and Xanthidium was studied on the basis of mitochondrial coxⅢ sequence variation. Teiling's suggestion that Staurodesmus was an independent genus apart from genus Staurastrum, Arthrodesmus and Cosmarium was also reevaluated. The phylogeny inferred from coxⅢ gene was not consistent with morphological characteristics of Staurastrum complex. Genus Staurastrum was closely related to genus Xanthidium in the phylogenetic analysis of coxⅢ, but distant to genus Staurodesmus. The taxonomic treatment of genus Staurodesmus as an independent entity could not be determined, because Staurodesmus did not firm a monophyletic Glade. Therefore, genus Staurodesmus could not be treated as an independent genus as Prescott et al. (1982) claimed.

• Mycobiology
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• v.42 no.1
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• pp.12-16
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• 2014

We isolated and examined a new Alternaria sp., which causes leaf spots on Peucedanum japonicum in Korea, by using molecular and morphological methods. Phylogenetic analysis based on a combined internal transcribed spacer region analysis and two protein-coding genes (gpd and Alt a1) demonstrated that the causal fungus was most closely related to A. cinerariae and A. sonchi, and relevant to A. brassicae. However, conidial morphology indicated that it is a novel species within the genus Alternaria, and therefore we have assigned the fungus a new name in this study.

• Korean Journal of Medicinal Crop Science
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• v.14 no.6
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• pp.342-346
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• 2006

Anatomical characters of the Bupleurum latissimum Nakai, an endemic species of Korea, were investigated to confirm its phylogenetic relationships. Compare to other species with anatomical characters, B. latissimum is very similar with B, euphorbioides and B, longeradiatum in point of lacking of pith in the stem, shape of involucres, number of vascular bundles in radical leaf and cauline leaf, and lacking stomata in adaxial leaf surface. The other hand, protruded pollen aperture character appears in B. latissimum and B. euphorbioides. On the based of anatomical characters, therefore, B. latissimum has closest relationships with B. euphorbioides and B. longeradiatum. It also needs molecular study including Asian species in order to confirm phylogenetic position and speciation process apparently.

• Korean Journal of Ichthyology
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• v.21 no.sup1
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• pp.75-75
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• 2009

The previous morphology-based taxonomic frameworks within the family Sygnathidae had emphasized the significance of the male brood pouch and reproductive biology in defining the group. However, several different hypotheses had been proposed by different investigators. This study have beencarried out to determine the phylogenetic relationships among 19 species belonging to the order Syngnathiformes with three Gasterosteiformes species as outgroup taxa by using the mitochondrial cytochrome b and Rag2 nuclear DNA sequences. Phylogenetic analyses based on neighbor-joining distance, maximum parsimony, minimum evolution and maximum likelihood method strongly supported that the family Syngnathidae, the suborder Syngnathoidei and the order Syngnathiformes were all monophyletic group. Much of previous morphological analyses were supported by our molecular data, but some deep relationships were not clearly resolved with regard to members of the suborder Aulostomoidei.