• Korean Journal of Plant Taxonomy
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• v.46 no.2
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• pp.247-255
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• 2016

As an attempt to determine the identity of the old trees of flowering cherries planted in the yard of the Catholic Archdiocese of Daegu, we conducted comparative phylogenetic analyses between wild and cultivated Prunus yedoensis Matsum. We generated the phylogeny (MP) and haplotype network (TCS) of 25 individuals, including wild P. yedoensis, from Jeju Island, cultivated P. ${\times}$yedoensis 'Somei-yoshino' from Korea and Japan, and P. spachiana f. ascendens (Makino) Kitam. from Jeju Island and Japan based on highly informative sequences of two cpDNA regions (rpl16 gene and trnS-trnG intergenic spacer). The wild and cultivated P. yedoensis were distinguished from each other in both the phylogeny and haplotype networks, and the old flowering cherry trees in Daegu had a cpDNA haplotype identical to that of the cultivated P. ${\times}$yedoensis 'Someiyoshino'. Compared to the cultivated P. ${\times}$yedoensis 'Somei-yoshino', wild P. yedoensis appears to have greater haplotype diversity, presumably originating from the genetic diversity of P. spachiana f. ascendens that functioned as a maternal parent in the hybrid origin of wild P. yedoensis. A future detailed study requires extensive sampling of P. spachiana f. ascendens from Japan and Korea to determine their precise phylogenetic relationships relative to wild and cultivated P. yedoensis. We concluded that the old flowering cherry trees planted in the yard of the Catholic Archdiocese of Daegu are highly likely to be of cultivated origin rather than wild types from Jeju Island, as previously speculated.

• Journal of Mushroom
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• v.7 no.4
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• pp.150-155
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• 2009

Because the import of Inonotus obliquus have been rapidly increased in Korea, we developed the Inonotus species-specific marker by using various sequences including ITS sequences, PCR-RFLP and STS primers and used this marker to determine both genetic relatedness and strains discrimination of Inonotus spp. Total 17 different Inonotus spp. were examined by using ITS sequences and classified into 2 different groups. One strain, ASI74008 isolated from Kamchaka island of Siberia, showed the high sequence identity (98%) at the nucleotide level to the other I. obliquus DSM strain, indicating the ASI74008 belong to I. obliquus species. Comparison of banding patterns after restriction enzyme digestions with PCR amplicons of ITS region revealed some variations depending on the species and strains. However, PCR products amplified with STS primer showed species specific patterns.Therefore, use of both STS primers and PCR-RFLP could help for better strain identification.

• The Plant Pathology Journal
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• v.24 no.2
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• pp.152-158
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• 2008

A peculiar virus-like disease of tomato showing yellow mosaic and necrotic spots on leaves and necrosis on veins, petioles and stems was observed at the Tomato Experimental Station (TES), Buyeo, Chungcheongnamdo, Korea. The disease incidence at TES fields ranged from 21 to 35% infecting different tomato cultivars. For this reason, to identify the virus infecting tomato and to characterize the virus based on biology, serology, cytology and at molecular level. Here, leaf samples were randomly collected from different infected tomato cultivars at TES fields and greenhouses and tested by ELISA using Pepper mottle virus (PePMoV) and Tomato mosaic virus (ToMV) antisera. Infected saps were mechanically inoculated in different host plants to test for pathogenicity, symptomatology and host ranges. Infected tissues and ultrathin sections were examined by electron microscopy. Finally, putative coat protein and 3'-untranslated region (CP/3'-UTR) fragment was amplified and cloned for sequence determination and analyzed its genetic relationship to existing PepMoV and PVY sequences at the Genbank. Results showed 69% of the samples were positive with PepMoV, 13% with ToMV and 19 % were doubly infected with PepMoV and ToMV. Symptoms greatly varied from different host plants inoculated with tomato leaf sap infected with PepMoV alone and discussed in detailed in this paper. Electron microscopy from infected tissues showed filamentous particles of 720-750nm in length, a typical morphology and size of PepMoV. In addition, cylindrical inclusion bodies, pinwheels, scrolls and laminates with masses of fibrillar inclusions were also found in ultrathin sections. Alignment of the sequences of the CP/3'-UTR revealed >96% sequence identity with PepMoV and only <61% with PVY. Taken together, all these evidences presented clearly indicated that the causal agent infecting tomato at TES was PepMoV and we designated this PepMoV infecting tomato as Tom-sd2 strain in this study.

• ALGAE
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• v.33 no.1
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• pp.1-19
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• 2018

Members of the family Parviluciferaceae (Alveolata, Perkinsozoa) are the well-known dinoflagellate parasitoids along with Amoebophrya ceratii species complex and parasitic chytrid Dinomyces arenysensis and contain six species across three genera (i.e., Parvilucifera infectans, P. sinerae, P. rostrata, and P. corolla, Dinovorax pyriformis, and Snorkelia prorocentri) so far. Among Parvilucifera species, the two species, P. infectans and P. sinerae, are very similar or almost identical each other morphologically and genetically, thereby make it difficult to distinguish between the two. The only main difference between the two species known so far is the number of sporangium wall (i.e., 2 layers in P. infectans vs. 3 layers in P. sinerae). During sampling in Masan bay, Korea during the spring season of 2015, the dinoflagellate Akashiwo sanguinea cells infected by the parasite Parvilucifera were observed and this host-parasite system was established in culture. Using this culture, its morphological and ultrastructural features with special emphasis on the variation in the number of sporangium wall over developmental times, were investigated. In addition, the sequences of rDNA regions and ${\beta}-tubulin$ genes were determined. The result clearly demonstrated that the trophocyte at 36 h was covered with 4 layers, and then outer layer of the sporocyte gradually degraded over time, resulting in wall structure consisting of two layers, with even processes being detached from 7-day-old sporangium with smooth surface, indicating that the difference in the number of layers seems not to be an appropriate ultrastructural character for distinguishing P. infectans and P. sinerae. While pairwise comparison of the large subunit rDNA sequences showed 100% identity among P. infectans / P. sinerae species complex, genetic differences were found in the small subunit (SSU) rDNA sequences but the differences were relatively small (11-13 nucleotides) compared with those (190-272 nucleotides) found among the rest of Parvilucifera species (P. rostrata and P. corolla). Those small differences in SSU rDNA sequences of P. infectans / P. sinerae species complex may reflect the variations within inter- strains of the same species from different geographical areas. Taken together, all morphological, ultrastructural, and molecular data from the present study suggest that they are the same species.

• Journal of Microbiology and Biotechnology
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• v.27 no.1
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• pp.179-188
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• 2017

White-rot basidiomycetes are the organisms that decompose lignin most efficiently, and Trametes villosa is a promising species for ligninolytic enzyme production. There are several publications on T. villosa applications for lignin degradation regarding the expression and secretion of laccase and manganese peroxidase (MnP) but no reports on the identification and characterization of lignin peroxidase (LiP), a relevant enzyme for the efficient breakdown of lignin. The object of this study was to identify and partially characterize, for the first time, gDNA, mRNA, and the corresponding lignin peroxidase (TvLiP) protein from T. villosa strain CCMB561 from the Brazilian semiarid region. The presence of ligninolytic enzymes produced by this strain grown in inducer media was qualitatively and quantitatively analyzed by spectrophotometry, qPCR, and dye fading using Remazol Brilliant Blue R. The spectrophotometric analysis showed that LiP activity was higher than that of MnP. The greatest LiP expression as measured by qPCR occurred on the $7^{th}$ day, and the ABSA medium (agar, sugarcane bagasse, and ammonium sulfate) was the best that favored LiP expression. The amplification of the TvLiP gene median region covering approximately 50% of the T. versicolor LPGIV gene (87% identity); the presence of Trp199, Leu115, Asp193, Trp199, and Ala203 in the translated amplicon of the T. villosa mRNA; and the close phylogenetic relationship between TvLiP and T. versicolor LiP all indicate that the target enzyme is a lignin peroxidase. Therefore, T. villosa CCMB561 has great potential for use as a LiP, MnP, and Lac producer for industrial applications.

• Asian-Australasian Journal of Animal Sciences
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• v.25 no.2
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• pp.163-169
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• 2012

Interferon regulatory factor 6 (IRF6) gene is a member of the IRF-family, and plays functionally diverse roles in the regulation of the immune system. In this report, the 13,720 bp porcine IRF6 genomic DNA structure was firstly identified with a putative IRF6 protein of 467 amino acids. Alignment and phylogenetic analysis of the porcine IRF6 amino acid sequences with their homologies to other species showed high identity (over 96%). Tissues expression of IRF6 mRNA was observed by RT-PCR, the results revealed IRF6 expressed widely in eight tissues. One SNP (HQ026023:1383 G>C) in exon7 and two SNPs (HQ026023:130 G>A; 232 C>T) in the 5′ promoter region of porcine IRF6 gene were demonstrated by DNA sequencing analysis. A further analysis of SNP genotypes associated with immune traits including IFN-${\gamma}$ and IL10 concentrations in serum was carried out in three pig populations including Large White, Landraces and Songliao Black pig (a Chinese indigenous breed). The results showed that the SNP (HQ026023:1383 G>C) was significantly associated with the level of IFN-${\gamma}$ (d 20) in serum (p = 0.038) and the ratio of IFN-${\gamma}$ to IL10 (d 20) in serum (p = 0.041); The other two SNPs (HQ026023:130 G>A; 232 C>T) were highly significantly associated with IL10 level in serum both at the day 20 (p = 0.005; p = 0.001) and the day 35 (p = 0.004; p = 0.006). Identification of the porcine IRF6 gene will help our further understanding of the molecular basis of the IFN regulation pathway in the porcine immune response. All these results should indicate that the IRF6 gene can be regarded as a molecular marker associated with the IL10 level in serum and used for genetic selection in the pig breeding.

• Development and Reproduction
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• v.10 no.2
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• pp.127-133
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• 2006

[ $17\;{\alpha}-hydroxylase/17,20-lyase(P450_{C17})$ ] is the key enzyme mediating the conversion of progesterone to $17\;{\alpha}-hydroxyprogesterone$, ultimately to androstenedione during steroidogenesis. R. dybowskii's ovarian $P450_{C17}$ cDNA was cloned to understand the regulatory mechanism of ovarian steroidogenic pathway at the molecular level in amphibian. A 2.5kb cDNA clone encoding a single open-reading frame with a 519 deduced amino acid was isolated with the screening of ovarian cDNA library. This sequence contained the three highly conserved domains as seen in $P450_{C17}$ of other species. The comparison of amino acid sequence of Rana $P450_{C17}$ with other animal's $P450_{C17}$ showed relatively high identity with 76% in Xenopus, 63% in chicken, 60% in rainbow trout, and 45% in human. Phylogenic analysis also indicated that Rana $P450_{C17}$ gene was evolutionary well conserved among vertebrate. Northern analysis indicated that the two different sizes of $P450_{C17}$ transcripts with approximately 2.5 and 3.6kb were detected in ovary tissue, but not in other tissues. The expression vector of Rana $P450_{C17}$ clearly showed the $17\;{\alpha}-hydroxylase$ activity converting the exogenous progesterone into $17\;{\alpha}-hydroxyprogesterone$ in the nonsteroidogenic COS-1 cells. Therefore, Rana $P450_{C17}$ cDNA is very useful to investigate the molecular mechanism of the ovarian steroidogenesis in amphibian.

• Asian-Australasian Journal of Animal Sciences
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• v.25 no.8
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• pp.1089-1095
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• 2012

Neonatal Fc receptor (FcRn) gene encodes a receptor that binds the Fc region of monomeric immunoglobulin G (IgG) and is responsible for IgG transport and stabilization. In this report, the 8,900 bp porcine FcRn genomic DNA structure was identified and putative FcRn protein included 356 amino acids. Alignment and phylogenetic analysis of the porcine FcRn amino acid sequences with their homologies of other species showed high identity. Tissues expression of FcRn mRNA was detected by real time quantitative polymerase chain reaction (Q-PCR), the results revealed FcRn expressed widely in ten analyzed tissues. One single nucleotide polymorphism (SNP) (HQ026019:g.8526 C>T) in exon6 region of porcine FcRn gene was demonstrated by DNA sequencing analysis. A further analysis of SNP genotypes associated with serum Classical Swine Fever Virus antibody (anti-CSFV) concentration was performed in three pig populations including Large White, Landrace and Songliao Black pig (a Chinese indigenous breed). Our results of statistical analysis showed that the SNP had a highly significant association with the level of anti-CSFV antibody (At d 20; At d 35) in serum (p = 0.008; p = 0.0001). Investigation of expression and polymorphisms of the porcine FcRn gene will help us in further understanding the molecular basis of the antibody regulation pathway in the porcine immune response. All these results indicate that FcRn gene might be regarded as a molecular marker for genetic selection of anti-CSFV antibody level in pig disease resistance breeding programmes.

• Asian-Australasian Journal of Animal Sciences
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• v.30 no.7
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• pp.912-919
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• 2017

Objective: Identification of the candidate genes that play key roles in phenotypic variations can provide new information about evolution and positive selection. Interleukin (IL)-32 is involved in many biological processes, however, its role for the immune response against various diseases in mammals is poorly understood. Therefore, the current investigation was performed for the better understanding of the molecular evolution and the positive selection of single nucleotide polymorphisms in IL-32 gene. Methods: By using fixation index ($F_{ST}$) based method, IL-32 (9375) gene was found to be outlier and under significant positive selection with the provisional combined allocation of mean heterozygosity and $F_{ST}$. Using nucleotide sequences of 11 mammalian species from National Center for Biotechnology Information database, the evolutionary selection of IL-32 gene was determined using Maximum likelihood model method, through four models (M1a, M2a, M7, and M8) in Codeml program of phylogenetic analysis by maximum liklihood. Results: IL-32 is detected under positive selection using the $F_{ST}$ simulations method. The phylogenetic tree revealed that goat IL-32 was in close resemblance with sheep IL-32. The coding nucleotide sequences were compared among 11 species and it was found that the goat IL-32 gene shared identity with sheep (96.54%), bison (91.97%), camel (58.39%), cat (56.59%), buffalo (56.50%), human (56.13%), dog (50.97%), horse (54.04%), and rabbit (53.41%) respectively. Conclusion: This study provides evidence for IL-32 gene as under significant positive selection in goat.

• The Korean Journal of Mycology
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• v.28 no.2
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• pp.112-117
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• 2000

A similarity coefficient were analyzed by RFLP of fourteen species of entomopathogenic fungi, isolated from inhabiting pupa and adult insect at forest. Each rDNA ITS I and ITS II with primers of ITS 1 and ITS 4 was amplified by PCR. The amplified products were conserved to 500 bp were not demarcated between genus and species. Four Paeciliomyces tenuipes, two Beauveria bassiana and six Cordyceps militaris were treated by seven restriction enzymes and confirmed in species except JB3 by electrophoresis band. However, the band of C. scarabaeicola showed the identity with B. bassiana. The result of this experiment indicated that the teleomorph of C. scarabaeicola was the same as that of B. bassiana. CfoI and HpaII of seven restricted enzymes were easily discriminating in the genus between Paecilomyees and Cordyceps. Especially, CfoI was more effective to classify the genera of Paecilomyees, Cordyceps and Beauveria than other restriction enzymes. The band patterns of RFLP of P. tenuipes, C. militaris, C. scarabaeicola and B. bassiana were also analyzed by UPGMA program of NTSYS-pc and showed 100% significance. Thus, the similarity coefficient tended to be lower between genera by RFLP analysis, but was higher between species.