• 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.

• The Korean Journal of Mycology
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• v.44 no.4
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• pp.377-381
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• 2016

Abnormal chloranthy was observed on Prunus mume trees grown in an orchard in Uiseong, Gyeongbuk province, Korea in 2015. Flower buds showing chloranthy were covered with numerous orange-colored sori, which were confirmed to contain spermogonia and aeciospores by stereo microscopy and light microscopy. When observed using scanning electron microscope, the aeciospores were globose, ellipsoid, or ovoid, and measured $22.8{\sim}35.6{\times}19.8{\sim}36.8{\mu}m$, with a verrucae wall ornamentation. To construct a phylogeny, the large and small subunit regions of rDNA were sequenced and compared with those of allied species by the maximum likelihood method. The isolated fungus species showed high similarities with Caeoma makinoi (Teleomorph: Blastospora smilacis), which was previously isolated from P. mume in Japan. Therefore, we initially report this fungal agent parasitic on P. mume as C. makinoi in Korea and name the disease it causes as "flower bud chloranthy disease".

• Korean Journal of Plant Taxonomy
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• v.45 no.4
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• pp.306-317
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• 2015

This study was conducted to address the taxonomic status of the Korean endemic species Saxifraga octopetala, which is sometimes considered conspecific to Micranthes manchuriensis. Extensive molecular phylogenetic analysis using nrITS sequences as well as morphological examination of type specimens of the two species were undertaken to ascertain the phylogenetic position and species delimitation of S. octopetala. In the resulting nrITS trees, a total of 65 accessions representing S. octopetala grouped together and nested within the Micranthes clade, exhibiting a close relationship with M. nelsoniana and M. manchuriensis. Multiple accessions of M. manchuriensis collected from China and Russia also formed a clade, showing a sister group relationship with M. nelsoniana var. pacifica and M. fusca. The ambiguous species entity of S. octopetala is thought to have originated from Nakai's misinterpretation of Wilford's collection (type specimens of M. manchuriensis), which is a complex collection including an inflorescence of M. nelsoniana. In spite of apparent morphological similarity between S. octopetala and M. manchuriensis, they differ in the presence and absence of underground stolons. The distinct position of S. octopetala within the Micranthes clade on the nrITS tree suggests that it should retain species status in Micranthes. Thus a new combination (Micranthes octopetala) is proposed.

• Korean Journal of Microbiology
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• v.46 no.3
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• pp.262-269
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• 2010

To investigate a quantitative evaluation of the actinobacteria, we have collected samples from various kinds of bamboo forest soil. Each different layers contained $2.7{\times}10^6-2.7{\times}10^8$ CFU/g of actinobacteria which was the highest in litter layers of Sasa boreali forest soil. We obtained 330 actinobacteria from different layers of bamboo forest soil; litter (100 strains), humus (70 strains), and rhizosphere soil (160 strains). Based on the colony morphology (aerial mycelium, substrate mycelium, and soluble pigment), isolates were divided into thirty-six groups and we selected 50 representative isolates. 16S rRNA gene sequence analysis showed Streptomyces was major actinobacteria (94%) and they were categorized as cluster I (2 strains), II (35 strains), III (6 strains), and IV (7 strains), respectively. The diversity index of 50 Streptomyces collected from the bamboo forest soil was calculated with the Shannon-Wiener method. Bamboo litter showed higher diversity index level of 3.33 than that of humus and rhizosphere soil. Also, antibiotic activities of our isolates were investigated against Botrytis cinerea, Xanthomonas campestris, Xanthomonas axonopodis pv. vesicatoria, and Bacillus cereus and found in 74, 16, 25, and 24 strains, respectively.

• Korean Journal of Plant Taxonomy
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• v.36 no.2
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• pp.91-108
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• 2006

Phylogenetic analyses were conducted to evaluate evolution and relationship of 16 taxa of Korean Geranium including 3 outgroups using ITS (internal transcribed spacer) squences of nuclear ribosomal DNA. Phylogenetic studies used most parsimony and neighbor-joining methods including bootstrapping and jackknifing analysis. As the result, Korean Geranium forms monophyletic group. In the parsimony tree G. koraiense var. hallasanense situated as the most basal clade and Erianthum group forms one clade by high bootstrap ans jackknife values (100% of bootstrap and jackknife values). G.dahuricum as one of the Krameri group is closely related with Palustre group by very weak relationship (37% of bootstrap and 44% of jackknife values) and the node collapse in the strict tree. G. Knuthii which was one of wilfordii group is closely related with Koreanum group. G. sibiricum, one of Sibiricum group, is the most closest relationship with G. soboliferum and these species are sister to G. krameri. G. tripartitum and G. wilfordii which are wilfordii group are linked to G. nepalense, G. thunbergii f. pallidum and G. thunbergii. This result suggested that the phylogenetic analysis of ITS sequences should be useful to address phylogenetic questions on the genus Korean Geranium.

• Korean Journal of Plant Taxonomy
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• v.38 no.4
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• pp.371-388
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• 2008

Phylogenetic studies were conducted for 35 populations of the subfamily Coryloideae (Betulaceae) based on waxy gene of nuclear DNA and atpB-rbcL intergenic spacer region of chloroplast DNA. Waxy data analysis suggest that Coryloideae is monophyletic; Corylus is monophyletic and basally branching within the subfamily Coryloideae; Ostryopsis is sister to the Carpinus and Ostrya clade, and the Ostrya is monophyletic (BS=86, PP=99). AtpB-rbcL intergenic spacer region analysis shows that Ostryopsis appeared as the most basal clade within the Coryloideae; Corylus is monophyletic(BS=98, PP=100) and placed between Carpinus-Ostrya and Ostryopsis clade; Carpinus and Ostrya formed a clade with a high support value(BS=100, PP=100). Carpinus sect. Carpinus is monophyletic, whereas sect. Distegocarpus is paraphyletic in the waxy tree. Corylus formed two subclades, but discordance at the infrageneric classification based on morphological characters. In the atpB-rbcL tree, Carpinus and Corylus taxa form a polytomy within the each clade. Results from the two data sets differ mainly in the relative position of Ostryopsis, the monophyly of Ostrya, and the relationships within the Carpinus-Ostrya clade. Further studies are needed for clarify the taxonomic position and the generic limitation.

• Korean Journal of Plant Resources
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• v.24 no.4
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• pp.358-369
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• 2011

The internal transcribed spacer (ITS) regions of nuclear ribosomal DNA from genus Chrysosplenium were sequenced to address phylogenetic relationship. ITS including 5.8S sequence varied in length from 647 bp to 653 bp. Among them, 219 sites were variable sites with parsimony-informative. The aligned sequences were analyzed by maximum parsimony (MP) and neighbor-joining (NJ) methods. In the strict consensus trees of parsimony analysis, the monophyly of Chrysosplenium was supported by 100% bootstrap value. The first clade, C. pseudofauriei was at the basal position of the genus, and others formed two clades with high bootstrap support. The second clade included Ser. Pilosa and Ser. Oppositifolia and third clade included Ser. Alternifolia and Ser. Flagellifera. The NJ trees showed essentially the same topology. Finally, DNA sequences of ITS regions were useful phylogenetic marker in this genus. Based on the ITS and ridge seed morphological results, C. sphaerospermum Maxim. and C. valdepilosum (Ohwi) S.H. Kang & J.W. Han were discussed their scientific names and taxonomic positions.

• Korean Journal of Plant Taxonomy
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• v.38 no.3
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• pp.197-222
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• 2008

A recently published Korean Flora, "The genera of vascular plants of Korea (GFK)", includes the descriptions and keys for 217 families, 1,044 genera, and 3,209 species of Korean vascular plants. We reclassified these taxa according to the recent APG classification system, which resulted in 64 orders, 204 families, 1,044 genera and 3,209 species. Twenty-two families from the GFK were abandoned because of changes to the familial delimitations in the APG system. In contrast, the number of families in the Liliaceous group was increased. The Liliaceae in the GFK included 31 genera and 109 species. These taxa are now assigned to 10 families in four different orders including Liliales, Asparagales, Alismatales, and Dioscoreales because of the drastic changes to the monocot classification system in the past 20 years. In addition, the family name of the Aucubaceae was changed to Garryaceae. As a result, the number of families in the GFK has been reduced to 204. The results were summarized in four tables and two figures at the levels of unofficial higher taxonomic hierarchies, orders, families and genera. This new information can provide a guidelines for selecting the phylogenetic analysis unit for the Korean tree of life (KTOL) project. Futhermore, the updated classification system also provides an important summarization for the systematic community for placing the Korean flora in a modern phylogenetic context.

• Journal of Life Science
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• v.13 no.3
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• pp.291-297
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• 2003

A human endogenous retroviral family (HERV-W) has recently been described that is related to multiple sclerosis-associated retrovirus (MSRV) sequences that have been identified in particles recovered from monocyte cultures from patients with multiple sclerosis. Two pol fragments (HWP-FB10 and HWP-FBl2) of HERV-W family were identified and analysed by the PCR approach with cDNA library of human fetal brain. They showed 89 percent nucleotide sequence similarity with that of the HERV-W (accession no. AF009668). Deletion/insertion or point mutation in the coding region of the pol fragments from human fetal brain resulted in amino acid frameshift that induced a mutated protein. Phylogenetic analysis of the HERV-W family from GenBank database indicates that the HWP-FB10 is very closely related to the AC000064 derived from human chromosome 7q21-q22. Further studies on the genetic relationship with neighbouring genes and functional role of these new HERV-W pol sequences are indicated.

• The Korean Journal of Mycology
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• v.46 no.2
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• pp.193-199
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• 2018

The fungus, Podosphaera pannosa, was identified in 1991 as the cause of powdery mildew symptoms on peach (Prunus persica var. persica) fruit from Korea based on the morphological characteristics of the conidial state. Recently, however, in Serbia and France, the cause of 'rusty spot' found on peach fruit was identified as P. leucotricha, and the cause of 'powdery mildew' on nectarine (Prunus persica var. nucipersica) fruit was identified as P. pannosa. To confirm the identity of the Korean pathogen, we collected four samples of powdery mildew from Korean peach fruit: three with the 'powdery mildew' symptom and one with the 'rusty spot' symptom. Morphological examination of the four samples confirmed P. pannosa as the pathogen. Internal transcribed spacer sequences of rDNA were analyzed for molecular characterization. A phylogenetic tree showed that the Korean isolates were clustered into a clade containing P. pannosa from Rosa species, with high sequence similarities of more than 99%. Thus, we showed that the powdery mildew and rusty spot symptoms on peach fruits from Korea are associated with P. pannosa.