• 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.45 no.3
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• pp.160-171
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• 2017

Larvae of Bradysia agrestis, an insect vector that transports plant pathogens, were sampled from geographically isolated regions in Korea to identify their cutaneous fungal and bacterial flora. Sampled areas were chosen within the distribution range of B. agrestis; each site was more than 91 km apart to ensure geographical segregation. We isolated 76 microbial (fungi and bacteria) strains (site 1, 29; site 2, 29; site 3, 18 strains) that were identified on the basis of morphological differences. Species identification was molecularly confirmed by determination of universal fungal internal transcribed spacer and bacterial 16S rRNA gene sequences in comparison to sequences in the EzTaxon database and the NCBI GenBank database, and their phylogenetic relationships were determined. The fungal isolates belonged to 2 phyla, 5 classes, and 7 genera; bacterial species belonged to 23 genera and 32 species. Microbial diversity differed significantly among the geographical groups with respect to Margalef's richness (3.9, 3.6, and 4.5), Menhinick's index (2.65, 2.46, and 3.30), Simpson's index (0.06, 0.12, and 0.01), and Shannon's index (2.50, 2.17, and 2.58). Although the microbial genera distribution or diversity values clearly varied among geographical groups, common genera were identified in all groups, including the fungal genus Cladosporium, and the bacterial genera Bacillus and Rhodococcus. According to classic principles of co-evolutionary relationship, these genera might have a closer association with their host insect vector B. agrestis than other genera identified. Some cutaneous bacterial genera (e.g., Pseudomonas) displaying weak interdependency with insect vectors may be hazardous to agricultural environments via mechanical transmission via B. agrestis. This study provides comprehensive information regarding the cutaneous microflora of B. agrestis, which can help in the control of such pests for crop management.

• Journal of Ginseng Research
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• v.44 no.1
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• pp.135-144
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• 2020

Background: Panax species are important herbal medicinal plants in the Araliaceae family. Recently, we reported the complete chloroplast genomes and 45S nuclear ribosomal DNA sequences from seven Panax species, two (P. quinquefolius and P. trifolius) from North America and five (P. ginseng, P. notoginseng, P. japonicus, P. vietnamensis, and P. stipuleanatus) from Asia. Methods: We conducted phylogenetic analysis of these chloroplast sequences with 12 other Araliaceae species and comprehensive comparative analysis among the seven Panax whole chloroplast genomes. Results: We identified 1,128 single nucleotide polymorphisms (SNP) in coding gene sequences, distributed among 72 of the 79 protein-coding genes in the chloroplast genomes of the seven Panax species. The other seven genes (including psaJ, psbN, rpl23, psbF, psbL, rps18, and rps7) were identical among the Panax species. We also discovered that 12 large chloroplast genome fragments were transferred into the mitochondrial genome based on sharing of more than 90% sequence similarity. The total size of transferred fragments was 60,331 bp, corresponding to approximately 38.6% of chloroplast genome. We developed 18 SNP markers from the chloroplast genic coding sequence regions that were not similar to regions in the mitochondrial genome. These markers included two or three species-specific markers for each species and can be used to authenticate all the seven Panax species from the others. Conclusion: The comparative analysis of chloroplast genomes from seven Panax species elucidated their genetic diversity and evolutionary relationships, and 18 species-specific markers were able to discriminate among these species, thereby furthering efforts to protect the ginseng industry from economically motivated adulteration.

• Journal of Life Science
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• v.17 no.6 s.86
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• pp.756-761
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• 2007

Cenus Malus is a long-lived woody species primarily distributed throughout Asia. Many species of this genus are regarded as agriculturally and ecologically important. The phynetics and genetic diversity among eight species of genus Malus were reconstructed using the random amplified polymorphic DNA (RAPD) markers. In a simple measure of intraspecies variability by the percentage of polymorphic bands, the M. micromalus exhibited the lowest variation (34.7%). The M. pumila showed the highest (50.0%). Mean number of alleles per locus (A) ranged from 1.347 to 1.500 with a mean of 1.437. The phenotypic frequency of each band was calculated and used in estimating genetic diversify (H) within species. The mean of H was 0.190 across species, varying from 0.155 to 0.220. In particular, two cultivated species, M. pumila and M. asiatica, had high expected diversity, 0.314 and 0.307, respectively. On a per locus basis, the proportion of total genetic variation due to differences among species ranged from 0.388 to 0.472 with a mean of 0.423, indicating that 42.3% of the total variation was found among species. The phylogenetic tree showed three distinct elates. One includes M. sieversii, M. pumila, and M. asiatica. Another includes three M. baccata taxa. The other includes M. sieboldii, M. floribunsa, and M. micromalus. One variety and one form of M. sieboldii were well separated each other. RAPD markers are useful in germ-plasm classification of genus Malus and evolutionary studies.

• Korean Journal of Ecology and Environment
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• v.54 no.3
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• pp.229-239
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• 2021

Thamnaconus modestus, distributed in the Northwest Pacific, has high economic value and is used in various seafood. In this study, the morphological and genetic characteristics of T. modestus and T. septentrionalis were compared and analyzed. We observed the external and internal morphology of T. modestus, sketched skeletal elements, and analyzed phylogenetic evolutionary relationships using the cytochrome c oxidase subunit I (COI) gene on mitochondrial DNA compared to T. septentrionalis. The T. modestus observed in this study had blackish-brown patterns irregularly scattered on the gray-brown body, and the fins were blue-green. Genetic analysis results based on the COI sequences of T. modestus showed seven types of base sequence variation; however, the homology was more than 98.8%. In addition, as a result of comparison of the COI nucleotide sequences and phylogenetic analysis in Tetraodontiformes, two T. septentrionalis sequences (JN813099, MW485059) were similar to T. modestus with 99% homology, and the other two T. septentrionalis sequences (EF607583, KP267619) were similar to those of species belonging to another genus Thamnaconus with 95% homology with T. modestus. It was not easy to classify the species based on morphological characteristics, and phylogenetic analysis between T. modestus and T. septentrionalis confirmed the difference in classification. These results provide the external and internal morphology of T. modestus and will be used as important information for the taxonomic study of T. modestus and T. septentrionalis.

• Korean Journal of Plant Taxonomy
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• v.46 no.3
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• pp.314-325
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• 2016

Multiple changes of the photosynthesis pathway are independent evolutionary events occurring in the phylogeny of flowering plants, and such changes have occurred more than five times in Cyperaceae. In the tribe Cypereae, the C4 photosynthetic pathway appeared only once and is regarded as a synapomorphy of the C4 plants within this tribe. The morphological delimitation of genera within Cypereae does not correspond to their molecular phylogenetic relationships. In this study, the molecular phylogeny was compared with the photosynthetic pathways of Korean Cypereae (18 species of Cyperus, 1 species of Kyllinga, and 1 species of Lipocarpha). The photosynthetic pathways were determined by observing the leaf anatomy. The phylogenetic analysis was performed using three DNA regions (nrITS, rbcL, and trnL-F). According to the position of the photosynthetic tissue, 4 species (C. difformis, C. flaccidus, C. haspan, and C. tenuispica) and 16 species (14 Cyperus species, K. brevifolia var. leiolepis, and L. microcephala) were confirmed as C3 and C4 plants, respectively. Tribe Cypereae was divided into the CYPERUS and FICINIA clades, and all species of Korean Cypereae plants belonged to the CYPERUS clade in the phylogenetic analysis. Within the CYPERUS clade, C4 plants were monophyletic but their phylogenetic relationships were unclear. The genera Kyllinga and Lipocarpha were not supported as an independent genus in either case because they were nested by the Cyperus species in the molecular phylogenetic trees in the present and in previous studies. To determine the classification within the CYPERUS clade, a detailed morphological study and a molecular phylogenetic analysis at a high resolution will be necessary.

• Journal of Life Science
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• v.30 no.11
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• pp.947-955
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• 2020

The foot-and-mouth disease virus (FMDV), a member of the Aphthovirus genus in the Picornaviridae family, affects wild and domesticated ruminants and pigs. During replication of the FMDV RNA (ribonucleic acid) genome, FMDV-encoding RNA polymerase 3D acts in a highly location-specific manner. This suggests that specific RNA structures recognized by 3D polymerase within non-coding regions of the FMDV genome assist with binding during replication. One such region is the cis-acting replication element (CRE), which functions as a template for RNA replication. The FMDV CRE adopts a stem-loop conformation with an extended duplex stem, supporting a novel 15-17 nucleotide loop that derives stability from base-stacking interactions, with the exact RNA nucleotide sequence of the CRE producing different RNA secondary structures. Here, we show that CRE sequences of FMDVs isolated in Korea from 2010 to 2017 exhibit A and O genotypes. Interestingly, variations in the RNA secondary structure of the Korean FMDVs are consistent with the phylogenetic relationships between these viruses and reveal the specificity of FMDV infections for particular host species. Therefore, we conclude that each genetic clade of Korean FMDV is characterized by a unique functional CRE and that the evolutionary success of new genetic lineages may be associated with the invention of a novel CRE motif. Therefore, we propose that the specific RNA structure of a CRE is an additional criterion for FMDV classification dependent on the host species. These findings will help correctly analyze CRE sequences and indicate the specificity of host species for future FMDV epidemics.

• Economic and Environmental Geology
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• v.52 no.2
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• pp.159-168
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• 2019

The western Gyeonggi Massif, where records evidence of Phanerozoic subduction/collision tectonics, is an important area to understand the crustal evolutionary history of the Korean Peninsula. This study presents geometric and kinematic characteristics of the geological structures of the Taean Formation in the Gomseom area, southwestern Gyeonggi Massif. We interpreted the geometric relationships between structural elements, and conducted stereographic and down-plunge projections for structural domains. As a result, at least three different deformational events ($D_1$, $D_2$ and $D_3$) are recognized in the study area. In the first deformational event ($D_1$), regional foliations being well defined by the preferred orientation of muscovite and biotite were formed. In the second deformational event ($D_2$), NNE-trending low-angle contractional faults and related crenulation lineations/cleavages were formed. The crenulation lineations shallowly plunge toward SSW~SSE or NNW~NNE. In the third deformational event ($D_3$), SE-plunging folds and NE-trending high-angle faults were formed as 'fault-related fold' and 'fold-accommodation fault', indicating that the $D_3$ folds and faults are genetically linked to each other. This contribution provides important insights into the structural evolution of the Taean Formation along western Gyeonggi Massif, where had evolved as subduction/collisional orogenic belts in the East Asia.

• Korean Journal of Ichthyology
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• v.33 no.4
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• pp.226-239
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• 2021

Sebastes minor, Sebastes trivittatus, Sebastes owstoni, and Sebastes steindachneri are indigenous fish species inhabiting the central part of the East Sea, Korea. In order to understand the molecular evolution of these four rockfishes, we sequenced the complete mitochondrial genomes (mitogenomes) of S. minor and S. trivittatus. To further analyze the phylogeny of Sebastes species, the mitogenomes of 16 rockfishes were comparatively investigated. The complete mitochondrial DNA (mtDNA) nucleotide sequences of S. minor and S. trivittatus were 16,408 bp and 16,409 bp in length, respectively. A total of 37 genes were found in mtDNA of S. minor and S. trivittatus, including 13 protein-coding genes, 2 ribosomal RNA genes, and 22 transfer RNA genes, which exhibited similar characters with other Sebastes species in the East Sea, Korea. In addition, we detected a conserved motif "ATGTA" in the control region of the four Sebastes species, but no tandem repeat units. Comparative analyses of the congeneric mitochondrial genomes were performed, which showed that control regions were more variable than the concatenated protein-coding genes. As a result of analysing phylogenetic relationships of four Sebastes species by using concatenated nucleotide sequences of 13 protein-coding genes, S. minor, S. trivittatus, S. owstoni and S. steindachneri were clustered into three clades. The phylogenetic tree exhibited that S. minor and S. steindachneri shared a closer relationship, whereas S. trivittatus and S. vulpes formed another distinct clade. Our results contribute to a better understanding of evolutionary patterns of Sebastes species inhabiting the middle East Sea, Korea.