• The Korea Journal of Herbology
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• v.29 no.6
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• pp.35-43
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• 2014

Objectives : Official Arisaematis Rhizoma is described only three species, Arisaema amurnse, Arisaema erubescens, and Arisaema heterophyllum, in national Pharmacopoeia. However, other Arisaema species, Arisaema ringens, Arisaema takesimense and Arisaema serratum, also have been distributed as an inauthentic Arisaematis Rhizoma in the herbal market. To develop a reliable molecular authentication method for Arisaematis Rhizoma in species level, we analyzed DNA barcode regions using six Arisaema species. Methods : Thirty-eight samples of six Arisaema plants species (A. amurense, A. amurense f. serratum, A. heterophyllum, A. takesimense, and A. serratum) were collected from different habitate and nucleotide sequences of DNA barcode regions (rDNA-ITS, matK, and rbcL gene) were analyzed after PCR amplification. The species-specific sequences and phylogenetic relations were estimated using entire sequences of three DNA barcodes based on the analysis of ClastalW and UPGMA, respectively. Results : The comparative analysis of DNA barcode sequences were revealed inter-species specific nucleotides to distinguish the medicinal plant of Arisaema Rhizoma in species levels excluding between A. amurense and its subspecies (A. amurense f. serratum) and A. takesimense and A. serratum, respectively. However, we obtained sequence differences enough to discriminate authentic and inauthentic Arisaematis Rhizoma. Therefore, we suggest that these SNP type molecular genetic markers were an reliable method avaliable to identify official herbal medicines. Conclusions : These marker nucleotides could be useful to identify the official herbal medicines by providing definitive information that can identify original medicinal plant and distinguish from inauthentic adulterants and substitutes.

• Journal of Species Research
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• v.4 no.2
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• pp.127-136
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• 2015

As an outcome of the study on the bacterial species diversity in Korea, we report 24 unrecorded bacterial species of Korea belonging to the phylum Firmicutes. The unrecorded species excavated through this study were assigned to 12 different genera of 7 families, namely Bacillus, Halobacillus, Lysinibacillus and Thalassobacillus of Bacillaceae, Brevibacillus and Paenibacillus of Paenibacillaceae, Viridibacillus of Planococcaceae, Salinicoccus and Staphylococcus of Staphylococcaceae, Enterococcus of Enterococcaceae, Lactobacillus of Lactobacillaceae, and Lactococcus of Streptococcaceae, respectively. The bacterial isolates were obtained from various ecosystems in Korea. The isolates were identified based on 16S rRNA gene sequences, and those exhibiting at least 99% sequence similarity with known bacterial species but never reported in Korea were selected as unrecorded species. The selected isolates were subjected to further taxonomic characterization including the analysis of cell shape and fine structure using electron microscope, colony color and shapes, enzyme activities and carbon source utilization. The descriptive information on the 24 unrecorded species are provided.

• Journal of Ecology and Environment
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• v.31 no.1
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• pp.75-81
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• 2008

Rates of molecular evolution are known to vary widely among taxonomic groups. A number of studies, examining various taxonomic groups, have indicated that body size is negatively and clutch size is positively correlated with the rates of nucleotide substitutions among vertebrate species. Generally, either smaller body mass or larger clutch size is associated with shorter generation times and higher metabolic rates. However, this generality is subject to ongoing debate, and large-scale comparative studies of species below the Order level are lacking. In this study, phylogenetically independent methods were used to test for relationships between rates of the mitochondrial cytochrome b evolution and a range of life history traits, such as body mass and clutch size in the Order Galliformes. This analysis included data from 67 species of Galliformes birds and 2 outgroup species in Anseriformes. In contrast to previous studies, taxa were limited to within-Order level, not to Class or higher. I found no evidence to support an effect of life history traits on the rate of molecular evolution within the Galliformes. These results suggest that such relationship may be too weak to be observed in comparisons of closely related species or may not be a general pattern that is applicable to all nucleotide sequences or all taxonomic groups.

• Mycobiology
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• v.34 no.1
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• pp.7-13
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• 2006

Arbuscular mycorrhizas (AM) have mutualistic symbiosis with plants and thus efforts have been placed on application of these symbiotic relationships to agricultural and environmental fields. In this study, AM fungi were collected from 25 sites growing with 16 host plant species in Korea and cultured with Sorghum bicolor in greenhouse condition. AM fungal spores were extracted and identified using both morphological and molecular methods. Using morphological characters, total 15 morpho-speices were identified. DNA was extracted from single spore of AM fungi and a partial region on 18S rDNA was amplified using nested PCR with AM fungal specific primers AML1/AML2. A total of 36 18S rDNA sequences were analyzed for phylogenetic analysis and 15 groups of AM fungi were identified using both morphological and molecular data of spores. Among the species, 4 species, Archaeospora leptoticha, Scutellospora castanea, S. cerradensis, S. weresubiae were described for the first time in Korea and two species in Glomus and a species in Gigaspora were not identified. Morphological and molecular identification of AM fungal spores in this study would help identify AM fungal community colonizing roots.

• The Plant Pathology Journal
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• v.37 no.4
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• pp.329-338
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• 2021

Alternaria leaf blight is one of the most common diseases in watermelon worldwide. In Korea, however, the Alternaria species causing the watermelon leaf blight have not been investigated thoroughly. A total of 16 Alternaria isolates was recovered from diseased watermelon leaves with leaf blight symptoms, which were collected from 14 fields in Korea. Analysis of internal transcribed spacer (ITS) region, glyceraldehyde-3-phosphate dehydrogenase (GAPDH), and RNA polymerase II second largest subunit (RPB2) were not competent to differentiate the Alternaria isolates. On the contrary, analysis of amplicon size of the histone H3 (HIS3) gene successfully differentiated the isolates into three Alternaria subgroups, and further sequence analysis of them identified three Alternaria spp. Alternaria tenuissima, A. gaisen, and A. alternata. Representative Alternaria isolates from three species induced dark brown leaf spot lesions on detached watermelon leaves, indicating that A. tenuissima, A. gaisen, and A. alternata are all causal agents of Alternaria leaf blight. Our results indicate that the Alternaria species associated watermelon leaf blight in Korea is more complex than reported previously. This is the first report regarding the population structure of Alternaria species causing watermelon leaf blight in Korea.

• Mycobiology
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• v.51 no.5
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• pp.300-312
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• 2023

Hydnum is a genus of ectomycorrhizal fungi belonging to the Hydnaceae family. It is widely distributed across different regions of the world, including North America, Europe, and Asia; however, some of them showed disjunct distributions. In recent years, with the integration of molecular techniques, the taxonomy and classification of Hydnum have undergone several revisions and advancements. However, these changes have not yet been applied in the Republic of Korea. In this study, we conducted an integrated analysis combining the morphological and molecular analyses of 30 specimens collected over a period of approximately 10 years in the Republic of Korea. For molecular analysis, the sequence data of the internal transcribed spacer (ITS) region, the large subunit of nuclear ribosomal RNA gene (nrLSU), and a portion of translation elongation factor 1-a (TEF1) were employed as molecular markers. Through this study, we identified eight species that had previously not been reported to occur in the Republic of Korea, including one new species, Hydnum paucispinum. A taxonomic key and detailed descriptions of the eight Hydnum species are provided in this study.

• Mycobiology
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• v.43 no.4
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• pp.408-414
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• 2015

Amanita (Agaricales, Basidiomycota) is one of the most well-known genera composed of poisonous mushrooms. This genus of almost 500 species is distributed worldwide. Approximately 240 macrofungi were collected through an ongoing survey of indigenous fungi of Mt. Jeombong in Inje County, Korea in 2014. Among these specimens, 25 were identified as members of Amanita using macroscopic features. Specimens were identified to the species level by microscopic features and molecular sequence analyses of the internal transcribed spacer and large subunit of nuclear ribosomal RNA. We molecularly identified 13 Amanita species, with seven species matching previously recorded species, four species (A. caesareoides, A. griseoturcosa, A. imazekii, and A. sepiacea) new to Korea, and two unknown species.

• Parasites, Hosts and Diseases
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• v.54 no.6
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• pp.743-750
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• 2016

Mus musculus (Rodentia: Muridae) has generally been infected with a rodent hookworm Nippostrongylus brasiliensis. In this report, we present morphological and molecular identification of N. brasiliensis by light and scanning electron microscopy and PCR amplification of mitochondrial cytochrome c oxidase subunit 1 (cox1) gene and the protein sequences encoded by cox1 gene, respectively. Despite the use of N. brasiliensis in many biochemistry studies from India, their taxonomic identification was not fully understood, especially at the species level, and no molecular data is available in GenBank from India. Sequence analysis of cox1 gene in this study revealed that the present specimen showed close identity with the same species available in GenBank, confirming that the species is N. brasiliensis. This study represents the first record of molecular identification of N. brasiliensis from India and the protein structure to better understand the comparative phylogenetic characteristics.

• Journal of Ecology and Environment
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• v.48 no.1
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• pp.32-48
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• 2024

Background: Longitudinal connectivity in river systems strongly affects biological components related to ecosystem functioning, thereby playing an important role in shaping local biodiversity and ecosystem health. Environmental DNA (eDNA)-based metabarcoding has an advantage of enabling to sensitively diagnose the presence/absence of species, becoming an efficient/effective approach for studying the community structure of ecosystems. However, little attention has been paid to eDNA-based biomonitoring for river systems, particularly for assessing the river longitudinal connectivity. In this study, by using eDNA we analyzed and compared species diversity and composition among artificial barriers to assess the longitudinal connectivity of the fish community along down-, mid- and upstream in the Hotancheon from the Geum River basin. Moreover, we investigated temporal variation in eDNA fish community structure and species diversity according to season. Results: The results of species detected between eDNA and conventional surveys revealed higher sensitivity for eDNA and 61% of species (23/38) detected in both methods. The results showed that eDNA-based fish community structure differs from down-, mid- and upstream, and species diversity decreased from down to upstream regardless of season. We found that there was generally higher species diversity at the study sites in spring (a total number of species across the sites [n] = 29) than in autumn (n = 27). Nonmetric multidimensional scaling and heatmap analyses further suggest that there was a tendency for community clusters to form in the down-, mid- and upstream, and seasonal variation in the community structure also existed for the sites. Dominant species in the Hotancheon was Rhynchocypris oxycephalus (26.07%) regardless of season, and subdominant species was Nipponocypris koreanus (16.50%) in spring and Odontobutis platycephala (15.73%) in autumn. Artificial barriers appeared to negatively affect the connectivity of some fish species of high mobility. Conclusions: This study attempts to establish a biological monitoring system by highlighting the versatility and power of eDNA metabarcoding in monitoring native fish community and further evaluating the longitudinal connectivity of river ecosystems. The results of this study suggest that eDNA can be applied to identify fish community structure and species diversity in river systems, although some shortcomings remain still need to be resolved.

• Journal of Ecology and Environment
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• v.37 no.4
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• pp.387-393
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• 2014

We propose Cryptonemia asiatica sp. nov. from Korea and Japan. We used molecular analyses of plastid-encoded rbcL and morphological observations to resolve the taxonomic identities of C. lactuca from Korea, C. luxurians from Japan, and C. seminervis from Spain. Specimens of C. lactuca and C. luxurians fell within the same molecular phylogenetic clade (with 100% bootstrap support) and were clearly separated from specimens of C. luxurians collected from the type locality in Brazil. Our analyses demonstrated identical molecular sequences between C. seminervis specimens from Spain and C. lomation specimens from France. Morphological characteristics of the new species, C. asiatica include prominent midribs through the mid thallus, a cortex 4-6 cells thick, and a blade with undulate margins. Molecular evidence indicates that specimens from Korea and Japan previously assigned to C. lactuca and C. luxurians, respectively, should be reassigned to Cryptonemia asiatica. Binomial C. luxurians from Brazil should be resurrected as the independent species of Cryptonemia.