• The Korean Journal of Mycology
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• v.51 no.4
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• pp.361-371
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• 2023

The study was undertaken to isolate and characterize wild yeast strains from soil samples collected in Seoul, Korea. Among the 19 yeast strains obtained, 17 were previously recorded species. The remaining two strains, Wickerhamomyces sp. GW1-4 and Archaeorhizomyces sp. YB4-103 were new species candidates. The genomic and microbiological characteristics of GW1-4 and YB4-103 were investigated. Phylogenetic analyses based on the 26S rRNA gene sequences and internal transcribed sequences, GW1-4 and YB4-103, represent a distinct lineage within the family Phaffomycetaceae and Archaeorhizomycetaceae, respectively. The GW1-4 and YB4-103 strains had the highest sequence homology with Wickerhamomyces xylosivorus NBRC 111553^T (88.97%) and Archaeorhizomyces finlayi CBS 128710^T (87.55%), respectively.

• The Korean Journal of Mycology
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• v.51 no.3
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• pp.191-204
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• 2023

This study introduces one specimen each of the genera Gymnopilus, Marasmius, and Mycena as an unrecorded species found in the Hwasun Gotjawal and Jeju Gotjawal Provincial Park of the Hangyeong-Andeok terrain, South Korea. Morphological analyses of macroscopic and microscopic features, and molecular analysis of the nuclear ribosomal internal transcribed spacer region were conducted to identify the specimens. Our results indicated that the newly identified specimens were Gymnopilus dilepis, Marasmius tenuissimus, and Mycena seminau. Here, we describe these newly identified mushroom species and provide baseline data on their diversity in Gotjawal, South Korea.

• Korean Journal of Environmental Biology
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• v.42 no.2
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• pp.187-192
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• 2024

Pseudolithoderma subextensum is a crustose brown algal species in the family Lithodermataceae and order Sphacelariales. This species is distributed in several regions across the world including, Europe, Western Atlantic, Middle East and Asia (Hong Kong and Japan). Recent floristic surveys along the Korean coastal shores have revealed new records of encrusting brown algae. In this study, we report P. subextensum as a new record from Korea. Morpho-anatomical and molecular studies on Ralfsia-like specimens from Korea identified some of them as P. subextensum. Pseudolithoderma subextensum is characterized by dark chestnut brown crust with a hypothallial basal layer and erect perithallial filaments, tufts of hairs occasionally arising from the basal layer, several discoid shaped chloroplasts per cell, plurangia arising terminally on erect filaments and without sterile cells, and unangia arising terminally on erect filaments, elongated cylindrical and without paraphyses. Phylogenetic analyses based on COI-5P (545bp) reveal that P. subextensum are nested within Lithodermataceae and forms the same clade with P. roscoffense. The genetic divergences for COI-5P between them is 24.5%.

• The Plant Pathology Journal
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• v.26 no.1
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• pp.93-98
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• 2010

A virus isolate causing symptoms of yellow mosaic, fern leaves, malformation and plant necrosis on Rudbeckia bicolor was prevalent around Pyeongchang area in Korea. The causal virus was identified as Cucumber mosaic virus (CMV) using characteristics from biological, serological and molecular analyses and named as CMV-Rb. CMV-Rb caused mosaic on Nicotiana benthamiana, N. tabacum, Capsicum annuum, and Lycopersicon esculentum. However, typical local lesions did not develop on inoculated Pisum sativum, Cucurbita moschata, Datura stramonium and Tetragonia expansa plants. Full-length genome sequences of CMV-Rb RNAs 1, 2 and 3 were obtained using 12 primer pairs by RT-PCR analysis. The genome of CMV-Rb RNA segments 1, 2, and 3 consists of 3363nt, 3049nt, and 2214nt in length, respectively. In order to ascertain their taxonomic identity, nucleotide and the deduced amino acid sequence analyses RNAs 1, 2 and 3 of CMV-Rb isolates were conducted with previously reported sequences of CMV strains and/or isolates. CMV-Rb RNAs showed about 90 to 99% sequence identity to those of subgroup I strains suggesting that CMV-Rb is more closely related to CMV isolates belong to subgroup I. To our knowledge, this is the first report of CMV on Rudbeckia bicolor in Korea.

• The Plant Pathology Journal
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• v.40 no.5
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• pp.425-437
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• 2024

A large number of species in the genus Colletotrichum have been reported as causal agents of anthracnose on crops and wild plants in Korea. Many Colletotrichum isolates from the country preserved in the Korean Agricultural Culture Collection (KACC) were previously identified based on host plants and morphological characteristics, and it may lead to species misidentification. Thus, accurate fungal species identification using multilocus sequence analyses is essential for understanding disease epidemiology and disease management strategies. In this study, combined DNA sequence analyses of internal transcribed spacer, gapdh, chs-1, his3, act, tub2, and gs were applied to re-identify 27 Colletotrichum isolates in KACC. The phylogenetic analyses showed that the isolates resulted in 11 known species, they belong to the C. dematium species complex (C. hemerocallidis, C. jinshuiense, and C. spinaciae), the C. magnum complex (C. kaifengense and C. cf. ovatense), the C. orchidearum complex (C. cattleyicola, C. plurivorum, C. reniforme, and C. sojae) and the C. orbiculare complex (C. malvarum and C. orbiculare). Of them, C. cattleyicola, C. hemerocallidis, C. kaifengense, and C. reniforme were unrecorded species in Korea. In the view of host-fungus combinations, 10 combinations are newly reported in the world and 12 are new reports in Korea, although their pathogenicity on the host was not confirmed.

• Journal of Microbiology
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• v.42 no.4
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• pp.299-304
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• 2004

To investigate the presence of infectious agents in human atherosclerotic arterial tissues. Atherosclerotic plaques were removed from 128 patients undergoing carotid endarterectomy or other bypass proce­dures for occlusive disease, and from twenty normal arterial wall samples, obtained from transplant donors with no history of diabetes, hypertension, smoking, or hyperlipidemia. Using the polymerase chain reaction (PCR) or reverse transcription-PCR, these samples were analyzed for the presence of Chlamydia pneumoniae, cytomegalovirus, enterovirus, adenovirus, herpes simplex viruses types 1 and 2, and Epstein-Barr virus. The amplicons were then sequenced, and phylogenetic analyses were per­formed. Enteroviral RNA was found in 22 of 128 atherosclerotic vascular lesions $(17.2\%),$ and C. pneu­moniae and cytomegalovirus were each found in 2 samples $(1.6\%).$ In contrast, adenovirus, herpes simplex viruses, and Epstein-Barr virus were not identified in any of the atherosclerotic samples. Enterovirus was detected in 6/24 $(25.0\%)$ aortas, 7/33 $(21.2\%)$ carotid arteries, 6/40 $(15.0\%)$ femoral arteries, and 3/31 $(9.7\%)$ radial arteries of patients with chronic renal failure. There were no infectious agents detected in any of the control specimens. Using phylogenetic analysis, the enterovirus isolates were clustered into 3 groups, arranged as echovirus 9 and coxsackieviruses Bl and B3. Enteroviral RNA was detected in $17.2\%$ of atherosclerotic plaques, but was not observed in any of the control spec­imens. This suggests a connection between enteroviral infection and atherosclerosis. These findings dif­fer from those of other studies, which found more frequent incidence of C. pneumoniae and cytomegalovirus infection in atherosclerotic plaques.

• Journal of Microbiology
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• v.44 no.6
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• pp.591-599
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• 2006

To address the diversity of cyclodextrin-producing P. graminis strains isolated from wheat roots and rhizospheres of maize and sorghum sown in Australia, Brazil, and France, restriction fragment length polymorphism analysis of part of genes encoding RNA polymerase (rpoB-RFLP) and DNA gyrase subunit B (gyrB-RFLP) was used to produce genetic fingerprints. A phylogenetic tree based on rpoB gene sequences was also constructed. The isolates originated from Brazil could be separated from those from Australia and France, when data from the rpoB-based phylogenetic tree or gyrB-RFLP were considered. These analyses also allowed the separation of all P. graminis strains studied here into four clusters; one group formed by the strains GJK201 and $RSA19^T$, second group formed by the strains MC22.02 and MC04.21, third group formed by the strains TOD61, TOD 221, TOD302, and TOD111, and forth group formed by all strains isolated from plants sown in Cerrado soil, Brazil. As this last group was formed by strains isolated from sorghum and maize sown in the same soil (Cerrado) in Brazil, our results suggest that the diversity of these P. graminis strains is more affected by the soil type than the plant from where they have been isolated.

• Journal of Microbiology
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• v.44 no.6
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• pp.655-659
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• 2006

Phylogenetic studies of nef, pol, and env gene sequences of HIV-1 isolated from Koreans suggested the presence of a Korean clade in which Korean sequences are clustered to the exclusion of foreign sequences. We attempted to identify and characterize the Korean clade using all vif gene sequences isolated from Koreans registered in the NCBI GenBank database (n = 233). Most (77 %) of the Korean isolates belonged to the Korean clade as a large subcluster in subtype B, designated the Korean clade subtype B ($K_{C}B$). $K_{C}B$ sequences were relatively homogenous compared to Korean subtype B sequences that did not belong to the $K_{C}B$ (non-Korean clade subtype B; $NK_{C}B$). Comparison of amino acid frequencies of $K_{C}B$ and $NK_{C}B$ sequences revealed several positions where the amino acid frequencies were significantly different. These amino acid residues were critical in separating $K_{C}B$ from $NK_{C}B$ or from foreign sequences, since substitution of these amino acids in $K_{C}B$ with the $NK_{C}B$ amino acids relocated the $K_{C}B$ sequences to $NK_{C}B$, and vice versa. Further analyses of $K_{C}B$ will help us to understand the origin and evolutionary history of $K_{C}B$.

• Korean Journal of Plant Taxonomy
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• v.42 no.3
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• pp.185-196
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• 2012

Morphological and geographical examinations as well as phylogenetic analyses using ITS sequences were performed for Asparagus L. in Korea. A total of five species of Asparagus were confirmed to be distributed in South Korea. The shape of cladophylls, length of pedicels, and shape of perianth were considered to be important characteristics for the identification of Koran Asparagus species. A monophyly of each species was evident in the ITS phylogenetic trees in which multiple accessions (5 to 24, depending on species) represented each of the five Korean species. A. rigidulus Nakai, once considered conspecific to A. schoberioides Kunth, formed a distinct lineage in the ITS trees. Pedicels of A. rigidulus, which is distributed mainly in coastal areas, were about two times longer than those of A. schoberioides occurring in inland areas, suggesting that they should be treated as distinct taxa.

• Journal of Microbiology and Biotechnology
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• v.21 no.1
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• pp.5-13
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• 2011

In this study, seven Trichoderma species (33 strains) were classified using secondary metabolite profile-based chemotaxonomy. Secondary metabolites were analyzed by liquid chromatography-electrospray ionization tandem mass spectrometry (LC-ESI-MS-MS) and multivariate statistical methods. T. longibrachiatum and T. virens were independently clustered based on both internal transcribed spacer (ITS) sequence and secondary metabolite analyses. T. harzianum formed three subclusters in the ITS-based phylogenetic tree and two subclusters in the metabolitebased dendrogram. In contrast, T. koningii and T. atroviride strains were mixed in one cluster in the phylogenetic tree, whereas T. koningii was grouped in a different subcluster from T. atroviride and T. hamatum in the chemotaxonomic tree. Partial least-squares discriminant analysis (PLS-DA) was applied to determine which metabolites were responsible for the clustering patterns observed for the different Trichoderma strains. The metabolites were hetelidic acid, sorbicillinol, trichodermanone C, giocladic acid, bisorbicillinol, and three unidentified compounds in the comparison of T. virens and T. longibrachiatum; harzianic acid, demethylharzianic acid, homoharzianic acid, and three unidentified compounds in T. harzianum I and II; and koninginin B, E, and D, and six unidentified compounds in T. koningii and T. atroviride. The results of this study demonstrate that secondary metabolite profiling-based chemotaxonomy has distinct advantages relative to ITS-based classification, since it identified new Trichoderma clusters that were not found using the latter approach.