• Korean Journal of Plant Taxonomy
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• v.50 no.3
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• pp.318-326
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• 2020

We found an unrecorded species, Carex molestiformis Reznicek & Rothrock, in Byeokparyeong, Daehwa-myeon, Pyeongchang-gun, Gangwon-do, South Korea. This species is native to southern parts of the United States (ca. 11 states, including Arkansas, Missouri, and Oklahoma). These plants are usually distributed densely in stream flood plains, bottomlands, stream banks, and along roadsides. Belonging to section Ovales Kunth, perennial herbs with gynecandrous spikes, C. molestiformis is closely related to C. maackii Maxim. and C. scoparia Willd. and is distinguished from them by the number (2-4) of spikes in each inflorescence and the width (2.63.4 mm) and number (69) of veins of perigynia. A new Korean name of C. molestiformis 'Ga-Neun-Ta-Rae-Sa-Cho' was given, as it has slender overall appearance compared with C. maackii (Ta-Rae-Sa-Cho). We also provide a description, illustrations, photographs and a key of related taxa in Korea. We compared three DNA barcode region (chloroplast DNA matK, ndhF and nuclear ribosomal DNA internal transcribed spacer) sequences from C. molestiformis with those of C. maackii and C. scoparia, determining eight species-specific single nucleotide polymorphism sites for C. molestiformis.

• ALGAE
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• v.33 no.1
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• pp.49-54
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• 2018

Red algal mitochondrial genomes (mtDNAs) can provide useful information on species identification. mtDNAs of Pyropia / Porphyra (Bangiales, Rhodophyta) have shown diverse variation in their size and gene structure. In particular, the introns and intronic open reading frames found in the ribosomal RNA large subunit gene (rnl) and cytochrome c oxidase subunit 1 gene (cox1) significantly vary the mitochondrial genome size in Pyropia / Porphyra species. In this study, we examined the exon / intron structure of rnl and cox1 genes of Pyropia yezoensis at the intraspecific level. The combined data of rnl and cox1 genes exhibited 12 genotypes for 40 P. yezoensis strains, based on the existence of introns. These genotypes were more effective to identify P. yezoensis strains in comparison to the traditional DNA barcode cox1 marker (5 haplotypes). Therefore, the variation in gene structure of rnl and cox1 can be a novel molecular marker to discriminate the strains of Pyropia species.

• Journal of Species Research
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• v.10 no.2
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• pp.154-158
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• 2021

An endemic endangered species, Aster altaicus var. uchiyamae (Danyang aster) B2015-0044, is cultivated at the Shingu Botanical Garden, which serves as the ex situ conservation institution for this species. In this work, we sequenced the chloroplast genome of A. altaicus var. uchiyamae B2015-0044. We found that the chloroplast (cp) genome of B2015-0044 was 152,457 base pairs(bps) in size: 84,247 bps of large single copy regions(LSC), 25,007 bps of inverted repeats(IRs), and 18,196 bps of small single copy regions. The B2015-0044 cp genome contains 79 protein-coding genes (PCGs), 4 RNA genes, 29 tRNA genes, and 3 pseudogenes. These results were identical to a previously reported cp genome (Park et al., 2017), except for two sites in introns and three in intergenic spacer (IGS) regions. For the intronic differences, we found that clpP.i1 had a 1-bp small simple repeat (SSR) (T) and petD.i had a 3-bp SSR (ATT). We found 1-bp SSRs in the IGSs of trnT_ggu~psbD and psbZ~trnG_gcc, C and A, respectively. The IGS of(ndhF)~rpl32 had a SNP. Based on our results, the cp genome of the A. altaicus var. uchiyamae can be classified into two genotypes, [C]¹-[A]¹²-[T]¹²-[ATT]⁴-C and [C]²-[A]¹¹-[T]¹¹-[ATT]²-A.

• The Plant Pathology Journal
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• v.38 no.4
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• pp.304-312
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• 2022

Boxwood is a representative ornamental shrub that is widely used in landscaping horticulture. After pruning, damaged leaves or stems of boxwoods are unavoidably vulnerable to infection by various plant pathogens. Several boxwood diseases caused by fungi, such as Volutella blight and Macrophoma leaf spot, have been reported worldwide including Republic of Korea. In this study, we isolated and identified fungal pathogens of boxwood diseases that occurred in Korea and characterized their morphological and taxonomic characteristics. Boxwood samples showing blight symptoms were collected in Seoul, Republic of Korea, and the putative fungal pathogens Pseudonectria buxi, P. foliicola, and Neofusicoccum buxi were successfully identified. Investigation of the morphological features of the field isolates, including mycelial growth and conidial morphology, and phylogenetic analysis of multiple DNA barcode loci revealed that there were some morphological and genetic variations among isolates, but all of the analyzed isolates were closely related to the corresponding reference strains. We also found that P. foliicola strains were more virulent than P. buxi, and the N. buxi strains isolated in this study were weak pathogens or saprophytes. The results of our study will contribute to the development of control strategies for boxwood diseases caused by fungi and accelerate research on the complex ecology of boxwood diseases.

• Journal of Microbiology and Biotechnology
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• v.30 no.11
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• pp.1680-1687
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• 2020

Fungal endophytes are symbiotic microorganisms that are often found in asymptomatic plants. This study describes the genetic diversity of the fungal endophytes isolated from the roots of plants sampled from the west coast of Korea. Five halophytic plant species, Limonium tetragonum, Suaeda australis, Suaeda maritima, Suaeda glauca Bunge, and Phragmites australis, were collected from a salt marsh in Gochang and used to isolate and identify culturable, root-associated endophytic fungi. The fungal internal transcribed spacer (ITS) region ITS1-5.8S-ITS2 was used as the DNA barcode for the classification of these specimens. In total, 156 isolates of the fungal strains were identified and categorized into 23 genera and two phyla (Ascomycota and Basidiomycota), with Dothideomycetes and Sordariomycetes as the predominant classes. The genus Alternaria accounted for the largest number of strains, followed by Cladosporium and Fusarium. The highest diversity index was obtained from the endophytic fungal group associated with the plant P. australis. Waito-C rice seedlings were treated with the fungal culture filtrates to analyze their plant growth-promoting capacity. A bioassay of the Sm-3-7-5 fungal strain isolated from S. maritima confirmed that it had the highest plant growth-promoting capacity. Molecular identification of the Sm-3-7-5 strain revealed that it belongs to Alternaria alternata and is a producer of gibberellins. These findings provided a fundamental basis for understanding the symbiotic interactions between plants and fungi.

• Journal of Plant Biotechnology
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• v.47 no.1
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• pp.15-25
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• 2020

Allium L. is one of the largest genera of the Amaryllidaceae family, with more than 920 species including many economically important species used as vegetables, spices, medicines, or ornamental plants. Currently, DNA barcoding tools are being successfully used for the molecular taxonomy of Allium. A total of 46 Allium species were collected from their native areas, and DNA was extracted using the IBRC DNA extraction kit. We used specific primers to PCR amplify matK. DNA sequences were edited and aligned for homology, and a phylogenetic tree was constructed using the neighbor-joining method. The results show thymine (38.5%) was the most frequent and guanine (13.9%) the least frequent nucleotide. The matK regions of the populations were quite highly conserved, and the amount of C and CT was calculated at 0.162 and 0.26, respectively. Analysis of the nucleotide substitution showed C-T (26.22%) and A-G (8.08%) to have the highest and lowest percent, respectively. The natural selection process dN/dS was 1.16, and the naturality test results were -1.5 for Tajima's D and -1.19 for Fu's Fs. The NJ dendrogram generated three distinct clades: the first contained Allium austroiranicum and A. ampeloprasum; the second contained A. iranshahrii, A. bisotunense, and A. cf assadi; and the third contained A. rubellum and other species. In this study, we tested the utility of the matK region as a DNA barcode for discriminating Allium. species.

• 한국균학회소식:학술대회논문집
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• 2015.11a
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• pp.41-41
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• 2015

Oomycetes belong to the kingdom Straminipila, a remarkably diverse group which includes brown algae and planktonic diatoms, although they have previously been classified under the kingdom Fungi. These organisms have evolved both saprophytic and pathogenic lifestyles, and more than 60% of the known species are pathogens on plants, the majority of which are classified into the order Peronosporales (includes downy mildews, Phytophthora, and Pythium). Recent phylogenetic investigations based on DNA sequences have revealed that the diversity of oomycetes has been largely underestimated. Although morphology is the most valuable criterion for their identification and diversity, morphological species identification is time-consuming and in some groups very difficult, especially for non-taxonomists. DNA barcoding is a fast and reliable tool for identification of species, enabling us to unravel the diversity and distribution of oomycetes. Accurate species determination of plant pathogens is a prerequisite for their control and quarantine, and further for assessing their potential threat to crops. The mitochondrial cox2 gene has been widely used for identification, taxonomy and phylogeny of various oomycete groups. However, recently the cox1 gene was proposed as a DNA barcode marker instead, together with ITS rDNA. To determine which out of cox1 or cox2 is best suited as universal oomycete barcode, we compared these two genes in terms of (1) PCR efficiency for 31 representative genera, as well as for historic herbarium specimens, and (2) in terms of sequence polymorphism, intra- and interspecific divergence. The primer sets for cox2 successfully amplified all oomycete genera tested, while cox1 failed to amplify three genera. In addition, cox2 exhibited higher PCR efficiency for historic herbarium specimens, providing easier access to barcoding type material. In addition, cox2 yielded higher species identification success, with higher interspecific and lower intraspecific divergences than cox1. Therefore, cox2 is suggested as a partner DNA barcode along with ITS rDNA instead of cox1. Including the two barcoding markers, ITS rDNA and cox2 mtDNA, the multi-locus phylogenetic analyses were performed to resolve two complex clades, Bremia lactucae (lettuce downy mildew) and Peronospora effuse (spinach downy mildew) at the species level and to infer evolutionary relationships within them. The approaches discriminated all currently accepted species and revealed several previously unrecognized lineages, which are specific to a host genus or species. The sequence polymorphisms were useful to develop a real-time quantitative PCR (qPCR) assay for detection of airborne inoculum of B. lactucae and P. effusa. Specificity tests revealed that the qPCR assay is specific for detection of each species. This assay is sensitive, enabling detection of very low levels of inoculum that may be present in the field. Early detection of the pathogen, coupled with knowledge of other factors that favor downy mildew outbreaks, may enable disease forecasting for judicious timing of fungicide applications.

• Mycobiology
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• v.42 no.2
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• pp.100-108
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• 2014

Twelve plant species were collected from the east coast of Korea to identify culturable endophytes present in their roots. The fungal internal transcribe spacer (ITS) region (ITS1-5.8SrRNA-ITS2) was used as a DNA barcode for identification of fungi. A total of 194 fungal strains were identified and categorized into 31 genera. The genus Penicillium accounted for the largest number of strains, followed by the genus Aspergillus. Furthermore, using 5 statistical methods, the diversity indices of the fungi were calculated at the genus level. After comprehensive evaluation, the endophytic fungal group from Phragmites australis ranked highest in diversity analyses. Several strains responsible for plant growth and survival (Penicillium citrinum, P. funiculosum, P. janthinellum, P. restrictum, and P. simplicissimum), were also identified. This study provides basic data on the sheds light on the symbiotic relationship between coastal plants and fungi.

• Animal Systematics, Evolution and Diversity
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• v.36 no.3
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• pp.240-250
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• 2020

Member of the genus Tobrilus Andrássy, 1959, which belongs to Tobrilidae Filipjev, 1918, are known as free-living nematodes in freshwater habitat. This genus was previously unknown from Korea. Five Tobrilus species are here reported for the first time from Korea: Tobrilus aberrans (Schneider, 1925), Tobrilus diversipapillatus (Daday, 1905), Tobrilus gracilis (Bastian, 1865), Tobrilus longus (Leidy, 1851), and Tobrilus wesenbergi (Micoletzky, 1925). Specimens were collected from sediments of the Nakdong River in Korea. Morphological characters and measurements of the specimens generally agree with the original descriptions of Tobrilus species, except for some differences that can be attributed to intraspecific variation among populations(e.g., nerve ring position [% pharynx] and reproductive length). Each species can be distinguished from other members of the genus by specific characters (e.g., cephalic setae length and position, buccal cavity and pocket shape, vulva position, degree of development of reproductive system, and tail length and shape). Here, five species in the genus Tobrilus are fully redescribed and illustrated using optical microscopy images. DNA barcode sequence information (the D2-D3 region of 28S rDNA) is also provided for molecular species identification.

• Animal Systematics, Evolution and Diversity
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• v.36 no.3
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• pp.251-257
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• 2020

The genus Plectus Bastian, 1865 represents a group of free-living freshwater nematodes belonging to the family Plectidae Örley, 1880. However, only one species has been reported thus far from Korea. Plectus aquatilis Andrássy, 1985 and Plectus cirratus Bastian, 1865 are reported for the first time from Korea, from sediments collected from the Nakdong River. Plectus aquatilis is distinguished from other Plectus species by its three longitudinal alae in the lateral field, thin and directed cephalic setae, continuous lip region (head not set-off), and rectangular shaped tail. Plectus cirratus is distinguished from other Plectus species by its large body, two longitudinal alae in the lateral field, larger stoma, and longer tail. Morphological characters and measurements of the specimens generally agree with the original descriptions of Plectus species. Here, the morphological characters (detailed morphometrics) of two species in the genus Plectus are fully redescribed and illustrated using optical microscopy. DNA barcode sequence information from the 18S rDNA gene is also provided for molecular species identification and compared with sequences from other Plectus species available on GenBank.