• Mycobiology
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• 제47권4호
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• pp.368-377
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• 2019

The genus Macrolepiota (Agaricales, Basidiomycota) is easy to recognize at the genus level because of big, fleshy basidiocarps with squamules covering the pileus; a single or double annulus; and big, thick-walled basidiospores with a germ pore. However, morphological identification is often unreliable in Macrolepiota due to similar morphological features among species. Due to the uncertainty of previous morphological identification in the genus Macrolepiota, it is necessary to re-examine Korean Macrolepiota using molecular data. We reexamined 34 Macrolepiota specimens collected from 2012 to 2018 in Korea using a reverse taxonomic approach, whereby species identification was first done based on the internal transcribed spacer (ITS) region analysis, followed by morphological confirmation. We identified the presence of four species: M. detersa, M. mastoidea, M. procera, and M. umbonata sp. nov. Two species (M. detersa and M. mastoidea) were previously unrecorded from Korea and M. umbonata is a new species. Detailed descriptions of all four species and taxonomic key are provided in this study. Macrolepiota procera and M. umbonata are distributed through the country, but M. detersa and M. mastoidea are distributed only in limited areas. According to our results, the combination of ITS locus and morphology proved to be a robust approach to evaluate the taxonomic status of Macrolepiota species in Korea. Additional surveys are needed to verify the species diversity and clarify their geographic distribution.

• The Plant Pathology Journal
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• 제39권4호
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• pp.384-396
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• 2023

Colletotrichum acutatum species complex is one of the most important groups in the genus Colletotrichum with a high species diversity and a wide range of host plants. C. acutatum and related species have been collected from different plants and locations in Korea and deposited into the Korean Agricultural Culture Collection (KACC), National Institute of Agricultural Sciences since the 1990s. These fungal isolates were previously identified based mainly on morphological characteristics, and a limitation of molecular data was provided. To confirm the identification of species, 64 C. acutatum species complex isolates in KACC were used in this study for DNA sequence analyses of six loci: nuclear ribosomal internal transcribed spacers (ITS), betatubulin 2 (TUB2), histone-3 (HIS3), glyceraldehyde3-phosphate dehydrogenase (GAPDH), chitin synthase 1 (CHS-1), and actin (ACT). The molecular analysis revealed that they were identified in six different species of C. fioriniae (24 isolates), C. nymphaeae (21 isolates), C. scovillei (12 isolates), C. chrysanthemi (three isolates), C. lupini (two isolates), and C. godetiae (one isolate), and a novel species candidate. We compared the hosts of KACC isolates with "The List of Plant Diseases in Korea", previous reports in Korea and global reports and found that 23 combinations between hosts and pathogens could be newly reported in Korea after pathogenicity tests, and 12 of these have not been recorded in the world.

• Animal cells and systems
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• 제16권6호
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• pp.488-497
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• 2012

A DNA barcode based on 648 bp of cytochrome c oxidase I (COI) gene aims to build species-specific libraries for animal groups. However, it is hard to recover full-length (648 bp) barcode gene from environmental fecal samples due to DNA degradation. In this study, we designed a new primer set (K_Bird), which amplifies a 226 bp fragment targeted an inner position of full-length COI barcode based on 102 species of Korean birds to improve amplification success, and we attempted to identify bird species from 39 avian fecal samples collected during 4 months from Jinan, South Korea. Simultaneously, we conducted a dietary analysis using a universal DNA mini-barcode (Uni_Minibar) from same fecal samples. In silico analysis on newly designed mini-barcode represented that genetic distances were 0.5% in species and 9.1% in genera. Intraspecific variations of 149 species out of 174 species (86%) between Korea and North America were within the threshold (5.3% threshold in this study). From environmental fecal samples collected in Jinan, we identified seven avian species, which have high similarity (99-100%) with registered COI sequences in GenBank. Eight kinds of prey species, such as moth, spider, fly, and dragonfly, were identified in dietary analysis. We suppose that our strategy applying mini-barcode for environmental fecal samples, might be a useful and convenient tool for species identification and dietary analysis for birds.

• 식물분류학회지
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• 제46권2호
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• pp.163-174
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• 2016

Gnetum (Gnetaceae, Gnetales) is a gymnosperm genus with ca. 35 species distributed in tropical forests around the world. Due to its dioecious habit and lack of diagnostic characters from vegetative tissue, the identification of Gnetum species is not easy without seeds or reproductive structures. To identify and verify their phylogenetic positions, we applied DNA barcoding to Cambodian Gnetum collections gathered between 2010 and 2015, with previously designed cp matK gene primers. We newly sequenced partial matK sequences from 72 Gnetum collections, 43 out of 72 from Cambodia, and analyzed 115 Gnetum accessions using the neighbor-joining method. The resulting neighbor-joining tree categorized Cambodian Gnetum samples into three clades of species: G. macrostachyum, G. montanum, and G. aff. gracilipes. The recognition of G. aff. gracilipes in Cambodia is reported here for the first time. Taxonomic information for the three recognized Cambodian Gnetum species is provided and the benefits of the taxonomic reevaluation assisted by DNA barcoding are emphasized in this work.

• 한국가구학회지
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• 제26권2호
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• pp.163-170
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• 2015

This study was conducted to identify wood species for 51 excavated wooden shoes in the 12~16 Chungjin district of Jongno. Wood species of 31 Pinus sp., 12 Torreya nucifera S. et Z., 4 Ginkgo biloba L., 2 Salix sp., 1 Kalopanax pictus (Thunb.) Nakai. and 1 Morus sp. were identified. Wood used for wooden shoes was a species that can be mainly obtained easily around. Among them, Torreya nucifera S. et Z. grows in warm temperate zone of Korea, which shows that interregional cooperation has occurred.

• Mycobiology
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• 제50권5호
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• pp.382-388
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• 2022

White mold (or Sclerotinia stem rot), caused by Sclerotinia species, is a major air, soil, or seed-transmitted disease affecting numerous crops and wild plants. Microscopic or culture-based methods currently available for their detection and identification are time-consuming, laborious, and often erroneous. Therefore, we developed a multiplex quantitative PCR (qPCR) assay for the discrimination, detection, and quantification of DNA collected from each of the three economically relevant Sclerotinia species, namely, S. sclerotiorum, S. minor, and S. nivalis. TaqMan primer/probe combinations specific for each Sclerotinia species were designed based on the gene sequences encoding aspartyl protease. High specificity and sensitivity of each probe were confirmed for sclerotium and soil samples, as well as pure cultures, using simplex and multiplex qPCRs. This multiplex assay could be helpful in detecting and quantifying specific species of Sclerotinia, and therefore, may be valuable for disease diagnosis, forecasting, and management.

• Mycobiology
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• 제51권6호
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• pp.436-444
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• 2023

Aspergillus species play a crucial role in terrestrial environments as degraders and are well known for producing various secondary metabolites. Recently, Aspergillus species have been discovered in marine environments, exhibiting adaptability to high salinity and producing diverse secondary metabolites with valuable properties. However, limited research has focused on their marine diversity, leading to inaccurate species identification. The current study addresses this gap by investigating diverse marine habitats in the Republic of Korea, including sediment, seawater, seaweed, and marine animals. From three coasts of the Korean Peninsula, 472 Aspergillus strains were isolated from the various marine habitats. A total of 41 species were accurately identified using multigenetic markers: internal transcribed spacer, calmodulin, and b-tubulin. The findings underscore the importance of accurate identification and provide a basis for elucidating the functional role of marine-derived Aspergillus species in marine ecosystems.

• Animal Systematics, Evolution and Diversity
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• 제29권4호
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• pp.272-278
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• 2013

Accurate identification of fish and fish products, from eggs to adults, is important in many areas. Grey mullets of the family Mugilidae are distributed worldwide and inhabit marine, estuarine, and freshwater environments in all tropical and temperate regions. Various Mugilid species are commercially important species in fishery and aquaculture of many countries. For the present study we have chosen two Mugilid genes with different phylogenetic signals: relatively variable mitochondrial cytochrome oxidase subunit I (COI) and conservative nuclear rhodopsin (RHO). We examined their diversity within and among 9 Mugilid species belonging to 4 genera, many of which have been examined from multiple specimens, with the goal of determining whether DNA barcoding can achieve unambiguous species recognition of Mugilid species. The data obtained showed that information based on COI sequences was diagnostic not only for species-level identification but also for recognition of intraspecific units, e.g., allopatric populations of circumtropical Mugil cephalus, or even native and acclimatized specimens of Chelon haematocheila. All RHO sequences appeared strictly species specific. Based on the data obtained, we conclude that COI, as well as RHO sequencing can be used to unambiguously identify fish species. Topologies of phylogeny based on RHO and COI sequences coincided with each other, while together they had a good phylogenetic signal.

• 식물분류학회지
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• 제48권3호
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• pp.206-217
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• 2018

The nucleotide sequences of the chloroplast rbcL, matK, and psbA-trnH and nuclear internal transcribed spacer (ITS) regions were determined from all species of Viburnum in Korea with multiple accessions to reconstruct the phylogeny and to evaluate the utility of the DNA sequences as DNA barcodes. The results of phylogenetic analyses of the cpDNA and ITS data are consistent with the findings of previous studies of Viburnum. Four morphologically closely related species, V. dilatatum, V. erosum, V. japonicum, and V. wrightii, were included in a strongly supported sister clade of V. koreanum and V. opulus. Viburnum odoratissimum is suggested to be sister to the V. dilatatum/V. koreanum clade in the cpDNA data, while V. odoratissimum is a sister to V. furcatum in the ITS data. Viburnum burejaeticum and V. carlesii are strongly supported as monophyletic. Our analyses of DNA barcode regions from multiple accessions of the species of Viburnum in Korea confirm that six out of ten species in Korea can be discriminated at the species level. The V. dilatatum complex can be separated from the remaining species according to molecular data, but the resolution power to differentiate a species within the complex is weak. This study suggests that regional DNA barcodes are useful for molecular species identification in the case of Viburnum when flowering or fruiting materials are not available.

• Journal of Microbiology and Biotechnology
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• 제22권8호
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• pp.1107-1112
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• 2012

Outbreaks of foodborne diseases associated with Vibrio species such as V. parahaemolyticus, V. vulnificus, and V. cholerae frequently occur in countries having a dietary habit of raw seafood consumption. For rapid identification of different Vibrio species involved in foodborne diseases, whole-cell protein pattern analysis for 13 type strains of 12 Vibrio species was performed using SDS-PAGE analysis. Pathogenic Vibrio species such as V. parahaemolyticus, V. vulnificus, V. cholerae, V. alginolyticus, V. fluvialis, and V. mimicus were included in the 12 Vibrio species used in this study. Each of the 12 Vibrio species showed clearly specific band patterns of its own. Two different strains of V. parahaemolyticus showed two different SDS-PAGE whole-cell protein patterns, giving the possibility of categorizing isolated strains in the same V. parahaemolyticus species into two subgroups. The 36 Vibrio isolates collected from sushi restaurants in Busan were all identified as V. parahaemolyticus by comparing their protein patterns with those of Vibrio type strains. The identified isolates were categorized into two different subgroups of V. parahaemolyticus. The whole-cell protein pattern analysis by SDS-PAGE can be used as a specific, rapid, and simple identification method for Vibrio spp. involved in foodborne diseases at the subspecies level.