• Journal of Life Science
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• v.21 no.3
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• pp.341-348
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• 2011

In an effort to gain greater understanding of the maternal lineages of the Jeju native pig (JNP), we analyzed the mitochondrial DNA (mtDNA) CYTB gene and compared it with those of other pig breeds. PCR-RFLP analysis was conducted with six pig breeds including JNP, and then the RFLP patterns allowed for the separation of the pig breeds into two distinct haplotypes (mtCYTB1 and mtCYTB2). The JNP CYTB sequences were detected in both the European and Asian breed clusters on the phylogenetic tree. The J2 group was sorted with the indigenous cluster of Asian pig lineages and was related closely to Chinese native pig breeds, but a second group, J1, was sorted with the European pig lineages and appeared to be related to Spanish Iberian native pigs, rather than to Asian breeds. These results indicate that the JNP currently raised on Jeju Island have two major maternal origins estimated in Asian and European pigs. We concluded that the JNP that share a common lineage with indigenous Asian pigs were domesticated in the distant past, originating from pigs that were already being raised elsewhere at that time, and that the European pig breeds introduced in the twentieth century have also contributed to the formation of this pig population.

• Journal of Life Science
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• v.20 no.11
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• pp.1697-1703
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• 2010

Asarum consists of low-growing herbs and is a genus in the Aristolochiaceae family with species found in the north temperate zones with most species in Asia. We evaluated the nine taxa with the trnL - trnT region of the chloroplast genome to estimate phenotypic relationships within genus Asarum in Korea. Alignment of the DNA sequences required the addition of numerous gaps. Sequence variation within the Asarum was mostly due to nucleotide inserts/deletions, although several indels and inserts were found. Another source of sequence divergence was length variation due to stretches of short repeats that occur at the trnL - trnT region in all the Asarum. A + T content for nine Korean species of genus Asarum ranged between 74.7% and 78.3%. These values were higher than those for the angiosperm alignments of the total trnL and trnT region (64.5~67.1%). Within genus Asarum, A. patens was strikingly different from the others in the three phylogenetic analyses (MP, ML, and NJ). However, some internal nodes were poorly supported. Within Korean Asarum, four species were unsolved portions. Possible reasons for the striking non-congruence between the previous morphological traits and the trnL - trnT based on phylogeny were discussed.

• Parasites, Hosts and Diseases
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• v.58 no.1
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• pp.73-79
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• 2020

Echinostoma revolutum is a zoonotic food-borne intestinal trematode that can cause intestinal bleeding, enteritis, and diarrhea in human and birds. To identify a suspected E. revolutum trematode from a red-crowned crane (Grus japonensis) and to reveal the genetic characteristics of its mitochondrial (mt) genome, the internal transcribed spacer (ITS) and complete mt genome sequence of this trematode were amplified. The results identified the trematode as E. revolutum. Its entire mt genome sequence was 15,714 bp in length, including 12 protein-coding genes, 22 transfer RNA genes, 2 ribosomal RNA genes and one non-coding region (NCR), with 61.73% A+T base content and a significant AT preference. The length of the 22 tRNA genes ranged from 59 bp to 70 bp, and their secondary structure showed the typical cloverleaf and D-loop structure. The length of the large subunit of rRNA (rrnL) and the small subunit of rRNA (rrnS) gene was 1,011 bp and 742 bp, respectively. Phylogenetic trees showed that E. revolutum and E. miyagawai clustered together, belonging to Echinostomatidae with Hypoderaeum conoideum. This study may enrich the mitochondrial gene database of Echinostoma trematodes and provide valuable data for studying the molecular identification and phylogeny of some digenean trematodes.

• 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.