• Journal of Species Research
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• v.8 no.3
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• pp.313-317
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• 2019

Bats influence overall ecosystem health by regulating species diversity and being a major source of zoonotic viruses. Hence, there is a need to elucidate their migration, population structure, and phylogenetic relationship. The complete mitochondrial genome is widely used for studying the genome-level characteristics and phylogenetic relationship of various animals due to its high mutation rate, simple structure, and maternal inheritance. In this study, we determined the complete mitogenome sequence of the bird-like noctule (Nyctalus aviator) by Illumina next-generation sequencing. The sequences obtained were used to reconstruct a phylogenic tree of Vespertilionidae to elucidate the phylogenetic relationship among its members. The mitogenome of N. aviator is 16,863-bp long with a typical vertebrate gene arrangement, consisting of 13 protein-coding genes (PCGs), 22 transfer RNA genes, 2 ribosomal RNA genes, and 1 putative control region. Overall, the nucleotide composition is as follows: 32.3% A, 24.2% C, 14.3% G, and 29.2% T, with a slight AT bias (61.5%). The base composition of the 13 PCGs is as follows: 30.3% A, 13.4% G, 31.0% T, and 25.2% C. The phylogenetic analysis, based on 13 concatenated PCG sequences, infers that N. aviator is closely related to N. noctula with a high bootstrap value (100%).

• Journal of Microbiology and Biotechnology
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• v.14 no.4
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• pp.816-821
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• 2004

A reliable molecular phylogenetic method to identify Hericium erinaceum, the most industrially valuable species in the Hericium genus, was established. Sequencing and phylogenetic analyses of the PCR-amplified ITS and 5.8S rDNA from Hericium fungi, including 6 species and 23 isolates, showed that variation in nucleotide sequences and size exists in both ITS1 and ITS2 regions, but not in the 5.8S region. These two ITS regions provided different levels of information on the relationship of H. erinaceum to other Hericium species. Based on the ITS1 sequence, both the parsimony and neighbor joining trees clearly distinguished Asian H. erinaceum isolates from other Hericium species and isolates. The intraspecific divergence of the ITS2 region was suitable to dissect the Asian H. erinaceum isolates into a few groups.

• Journal of Veterinary Science
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• v.24 no.2
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• pp.29.1-29.12
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• 2023

Background: Feline panleukopenia virus (FPV) is a widespread and highly infectious pathogen in cats with a high mortality rate. Although Yanji has a developed cat breeding industry, the variation of FPV locally is still unclear. Objectives: This study aimed to isolate and investigate the epidemiology of FPV in Yanji between 2021 and 2022. Methods: A strain of FPV was isolated from F81 cells. Cats suspected of FPV infection (n = 80) between 2021 and 2022 from Yanji were enrolled in this study. The capsid protein 2 (VP2) of FPV was amplified. It was cloned into the pMD-19T vector and transformed into a competent Escherichia coli strain. The positive colonies were analyzed via VP2 Sanger sequencing. A phylogenetic analysis based on a VP2 coding sequence was performed to identify the genetic relationships between the strains. Results: An FPV strain named YBYJ-1 was successfully isolated. The virus diameter was approximately 20-24 nm, 50% tissue culture infectious dose = 1 × 10^-4.94/mL, which caused cytopathic effect in F81 cells. The epidemiological survey from 2021 to 2022 showed that 27 of the 80 samples were FPV-positive. Additionally, three strains positive for CPV-2c were unexpectedly found. Phylogenetic analysis showed that most of the 27 FPV strains belonged to the same group, and no mutations were found in the critical amino acids. Conclusions: A local FPV strain named YBYJ-1 was successfully isolated. There was no critical mutation in FPV in Yanji, but some cases with CPV-2c infected cats were identified.

• Mycobiology
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• v.50 no.2
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• pp.150-154
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• 2022

Rhytisma lonicericola was identified as a tar spot fungus on Lonicera sp. in 1902, and has since been recorded on several species of Lonicera in China, Japan, and Korea. Most of the previous records of R. lonicericola have been based on a list of disease occurrences in the absence of any formal morphological identification or molecular analyses. Using six newly obtained specimens collected in the past 2 years, we confirmed the tar spot fungus found on L. japonica in Korea as R. lonicericola based on morphological examinations and molecular phylogenetic analyses. This fungus was distinguished from R. xylostei, another tar spot fungus on Lonicera, by ascospore size and geographical distributions. We present detailed mycological information and, for the first time, DNA sequence data useful for the identification of R. lonicericola.

• Parasites, Hosts and Diseases
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• v.57 no.2
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• pp.127-134
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• 2019

Sinuolinea capsularis Davis, 1917 is myxosporean that infect the urinary system of the host fish. Insufficient morphological and molecular data of S. capsularis exits, and it is therefore difficult to make an accurate identification of the parasite. We tried a series of morphological and molecular analysis to identify an myxosporean isolated from urinary bladder of cultured olive flounder, Paralichthys olivaceus, from Jeju island in the Republic of Korea. Some of them were observed under a light microscope and SEM, and remain samples were used molecular and phylogenetic analysis. Mature spores were subspherical, measuring $13.9{\pm}0.6{\mu}m$ in length and $13.8{\pm}0.8{\mu}m$ in width. Two spherical polar capsules on opposite sides in the middle of the spore had a diameter range of $4.3{\pm}0.4{\mu}m$. Scanning electron microscopy revealed that spores a severely twisted the suture line. By the morphological comparison and analysis, it was identified as S. capsularis. In addition, we obtained the partial 18S rDNA of S. capsularis and first registered it in NCBI. Phylogenetic analysis showed that S. capsularis clustered with Zschokkella subclade infecting the urinary system of marine fish, and it supported the infection site tropism effect on phylogeny of marine myxosporeans as well as the origin of Sinuolinea is not monophyly.

• Korean Journal of Plant Resources
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• v.31 no.1
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• pp.37-51
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• 2018

Molecular phylogenetic analysis was conducted to evaluate the taxonomic relationships of genus Arisaema L. distributed in Korea and the molecular phylogenetic characteristics of three authentic Arisaema species for the herbal medicine Arisaematis Rhizoma (the rhizomes of A. amurense, A. heterophyllum, and A. erubescens). The sequences of three DNA barcodes (rDNA-ITS, matK, and rbcL) were analyzed using 50 samples of nine taxa consisted of eight Korean and one Chinese Arisaema with one outgroup (Dracunculus vulgaris). Both individual and combined phylogenetic analyses of three DNA barcode sequences revealed that the treated nine taxa are independently classified into six distinct clades (Clade I, A. amurense f. amurense and A. amurense f. serratum; Clade II, A. serratum and A. takesimense; Clade III, A. ringens; Clade IV, A. erubescens; Clade V, A. heterophyllum; Clade VI, A. thunbergii subsp. thunbergii and A. thunbergii subsp. geomundoense). These six clades were reasonably divided into three individual sections, Pedatisecta, Sinarisaema, and Tortuosa. Futhermore, the results of comparative DNA barcode sequences analyses provided a significant information for the taxonomic reconsideration of Arisaema L. at the specific and intraspecific level. However, we could not confirm the taxonomic characteristics or identity among the three authentic medicinal species through the molecular phylogenetic analyses of genus Arisaema L. for Arisaematis Rhizoma.

• Korean Journal of Ecology and Environment
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• v.36 no.3 s.104
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• pp.221-234
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• 2003

Phylogenetic studies would clarify the diversity of fishes if the morphological analysis based on plesimorphy characters combined with new genetic analysis on molecular level, inferring more accurate and objective phylogeny and the taxonomy. Current molecular phylogenetic approach using mitochondrial genome provides the framework for a new hypothesis not only inferring the relationships between ancestor descendants but raveling the intra-, interspecies variation.

• Journal of Microbiology
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• v.41 no.3
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• pp.232-238
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• 2003

Previous phylogenetic studies on human immunodeficiency virus type 1 (HIV-1) isolated from Korean patients suggest that the major subtype of Korean isolate is subtype B. In this subtype, some of the Korean isolates seem to be clustered exclusively of foreign isolates. Presence of this so-called “Korean clade” among Korean isolates is unique but needs verification since the number of Korean isolates used in previous studies was limited. This study aimed to identify the presence of the “Korean clade” by molecular phylogenetic analysis using all the Korean nef gene sequences registered in the NCBI GenBank (N=243) together with 32 reference strains and 77 foreign isolates. Extensive analysis of the nef gene nucleotide sequences by neighbor-joining method revealed the following. Most (83.1 ％) of the Korean isolates belonged to subtype B, and 81.2％ of subtype B were clustered together and excluded foreign isolates (bootstrap value=91.9％ ). Within Korean subtype B cluster, no characteristic subcluster formation was evident since the bootstrap values for the subcluster were very low. Due to limited information, the phylogenetic analysis failed to identify the epidemiological linkage among specific groups such as homosexuals and hemophiliacs within the Korean subtype B cluster. Detailed analysis and epidemiological information are needed to clarify the origin and significance of the Korean subtype B cluster.

• Korean Journal of Veterinary Service
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• v.37 no.3
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• pp.157-164
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• 2014

Clostridium chauvoei is the etiologic agent of blackleg, a high mortality rated disease infection mainly cattle. In the present study, the partial sequences of 16S rRNA and flagellin gene of C. chauvoei isolated in Jeonbuk, Korea were determined and compared with those of reference strain. Oligonucleotide primers were designed to amplify a 811 bp fragment of 16S rRNA gene and 1229 bp fragment of flagellin gene. Sequencing analysis of 16S rRNA gene showed high homology to the reference strains ranging 82.3% to 100%, while flagellin gene were different from published foreign clostridia, showing 98.7% to 72.0% nucleotide sequence homology. Phylogenetic analysis based on 16S rRNA gene revealed the close phylogenetic relationship of C. chauvoei and C. septicum in cluster I, which includes C. carnis, C. tertium, C. quinii, C. celatum, C. perfringens, C. absonum, C. botulinum B. Phylogentic analysis also revealed that flagellin gene formed a single cluster with C. chauvoei, C. septicum, C. novyi A, C. novyi B, C. tyrobutylicum, C. acetobutylicum. The genetic informations obtained from this study could be useful for the molecular study of C. chauvoei.

• The Korean Journal of Mycology
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• v.47 no.2
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• pp.95-104
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• 2019

The genus Ochrolechia is a widespread, lichen genus in Korea. Despite being common, little is known about the species diversity and geographical distribution of Ochrolechia. In this study, we detailed the identification procedure of the genus Ochrolechia in a Korean collection and provided the description of each species. Using 104 specimens collected from 2003 to 2017, we identified four species of the genus Ochrolechia via morphological and/or molecular phylogenetic analysis: O. parellula, O. trochophora, O. yasudae and O. akagiensis. Among them, O. akagiensis had not been previously reported in Korea. Moreover, the species identified as O. frigida and O. tartarea in past studies were corrected as O. yasudae and O. parellula, respectively, based on morphological and/or molecular evidence. Phylogenetic analysis using the internal transcribed spacer regions including 5.8S rRNA gene showed that the four species separated clearly, indicating that the morphological identification corresponds to the phylogenetic identification. We provide a taxonomic key for the four species of the genus Ochrolechia.