• Journal of Mushroom
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• v.10 no.2
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• pp.93-99
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• 2012

This study was carried to identify a correct species and asses genetic diversity within the same species of Grifola spp. preserved in Division of applied Microbiology. Contaminated isolates showed different growth rates, morphology and color of hyphae. We have reconstructed the phylogenetic tree of a select group of Grifola spp. using nucleotide sequences of the internal transcribed spacer region(ITS) region. The phylogenetic tree was constructed by using the neighbor-joining method. PELF primers of 20-mer were used to assess genetic diversity of preserved isolates. Sequence analysis showed that four strains were identified completely different nomenclature. According to the analysis of ITS sequences, the genus Grifola clustered into one group, most of which correlated with species-groups identified by RAPD method. Eight isolates included strain GM01 showed high similarity with Grifola frondosa. All isolates were collected in the Japan(GM01, GM02, GM03) was identified as Grifola frondosa and isolates of the China(GM05, GM06, GM08) was identified as Bjerkandera fumosa, Grifola frondosa and Dichomitus squalens, respectively. RAPD analysis of genetic polymorphisms of genus Grifola showed a very different band patterns on the isolat. As the result of RAPD and ITS region sequences analysis for preserved isolates, it seems likely that 4 isolates of Grifola spp. may be need to reclassify or eliminate from preserved catalogue.

• Journal of Mushroom
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• v.9 no.1
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• pp.27-33
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• 2011

This study was carried to identify a correct species and asses genetic diversity within the same species of Trametes spp. preserved in Division of applied Microbiology The morphological and cultural characteristics of preserved strains were observed through microscope and investigated on PDA, respectively. Contaminated isolates showed different growth rates, morphology and color of hyphae. We have reconstructed the phylogenetic tree of a select group of Trametes spp. using nucleotide sequences of the internal transcribed spacer region(ITS) region. The phylogenetic tree was constructed by using the neighbor-joining method. PELF primers of 20-mer were used to assess genetic diversity of preserved isolates. Sequence analysis showed that five strains were different species and six strains were identified completely different nomenclature. According to the analysis of ITS sequences, the genus Trametes clustered into four distinct group, most of which correlated with species-groups identified by RAPD method. Seven isolates included TM 01 strain showed high similarity with Trametes versicolr, TM 07 and TM 10 high similarity with Trametes gibbosa, and TM 05 high similarity with Trametes elegans. But isolates collected in the United States was identified as T. junipericola. T. gibbosa and T. versicolor by RAPD analysis of genetic polymorphisms showed a very different band patterns and these strains showed different band patterns on areas. As the result of RAPD and ITS region sequences analysis for preserved isolates, it seems likely that 11 isolates of Trametes spp. may be need to reclassify or eliminate from preserved catalogue.

• Journal of Mushroom
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• v.10 no.1
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• pp.37-43
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• 2012

This study was carried to identify a correct species and asses genetic diversity within the same species of Polyporus spp. preserved in Division of applied Microbiology. Contaminated isolates showed different growth rates, morphology and color of hyphae. We have reconstructed the phylogenetic tree of a select group of Polyporus spp. using nucleotide sequences of the internal transcribed spacer region(ITS) region. The phylogenetic tree was constructed by using the neighbor-joining method. PELF primers of 20-mer were used to assess genetic diversity of preserved isolates. Sequence analysis showed that three strains were different species and four strains were identified completely different nomenclature. According to the analysis of ITS sequences, the genus Polyporus clustered into five distinct group, most of which correlated with species-groups identified by RAPD method. Four isolates included strain PM02 showed high similarity with P. arcularius, four isolates included strain PM03 high similarity with P. alveolaris, three isolates included strain PM01 high similarity with P. tuberaster, and PM 06 and PM04 high similarity with P. brumalis and P. squamossus. Isolates were collected in the United States(PM10, PM11) was identified as P. alveolarius and P. arcularius. RAPD analysis of genetic polymorphisms of genus Polyporus showed a very different band patterns. As the result of RAPD and ITS region sequences analysis for preserved isolates, it seems likely that 6 isolates of Polyporus spp. may be need to reclassify or eliminate from preserved catalogue.

• Journal of Life Science
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• v.24 no.6
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• pp.626-632
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• 2014

The genetic structure and phylogenetic relationship were investigated in Korean red spotted grouper populations using the nucleotide sequence polymorphisms of the mitochondrial DNA (mtDNA) cytochrome c oxidase subunit I (COI) gene. The COI gene was sequenced showed 99.1-99.8% identity with the EF607565 sequence previously reported. A total of twenty haplotypes were found, and the Korean population showed nineteen haplotypes. Among those, Hap_03 and Hap_08 showed Jeju-do and China-specific COI sequences, respectively. However, Hap_07 had twelve COI sequences from South Korea and records from Hong Kong and Taiwan. Neighbor-joining (NJ) trees constructed from the phylogenetic analyses based on the polymorphisms of the COI haplotypes showed a monophyletic branching pattern within the genus Epinephelus. This indicated that the red spotted grouper populations had evolved from common maternal ancestors. In addition, the Hap_08, which had the COI sequence recorded only from China Sea, was found in the middle of the NJ tree nearby Hap_07 and showed a close relationship with Hap_07. This indicates that Chinese red spotted grouper is also maternally related to other populations in East Asia. Consequently, East Asian red spotted grouper populations are maternally related, as well as sharing the same evolutionary history, and are still affected by the East Asian ocean current (Kuroshio). These findings help to explain the genetic structure and phylogenetic relationship of red spotted grouper and also contribute to research on artificial breeding and industrialization.

• Animal cells and systems
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• v.3 no.3
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• pp.303-309
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• 1999

Inter- and intraspecific genetic relationships between Rana amurensis from Korea and Russia and other brown frogs were investigated by nucleotide sequence of a 504 base pair (bp) fragment of the mitochondrial cytochrome b gene. Nucleotide sequence similarities among Korean populations of R. amurensis ranged from 99.6% to 97.6% and 98.8% within Russian populations. The nucleotide sequence similarity between Korean and Russian R. amurensis ranged from 86.9% to 85.5%. Based on Kimura-2-parameter distance, the sequence divergence between R. amurensis from Korea and Russia was 16.18% and 18.04% among other related brown frogs. interspecific sequence divergences among R. amurensis and other related brown frogs diverged by 20.3%. Using an estimate of 2-4% mitochondrial DNA sequence divergence per million years, Korean and Russian R. amurensis diverged about 8 to 4 million years ago (Mya) and other brown frogs diverged about 9 to 5 Mya from ancestral frogs and distributed from North Asia to Sakhalin in a short time. In the neighbor-joining and UPGMA tree R. amurensis was clustered into two groups with Korean and Russian populations and the other brown frogs were grouped separately with diverged trichotomous clusters (R. dybowskii and R. pirica, R. okinavana and R. tsushimensis, and R. japonica and R. longicrus).

• Asian-Australasian Journal of Animal Sciences
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• v.21 no.7
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• pp.947-953
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• 2008

We studied genetic diversity and relationships among Mongolian goat populations on the basis of microsatellite DNA polymorphisms. DNA samples from eight populations (Bayandelger, Ulgii Red, Zavkhan Buural, Sumber, Zalaajinst White, Erchim Black, Dorgon, and Gobi Gurvan Saikhan) from geographically distinct areas of Mongolia were analyzed by using 10 microsatellite DNA markers. Since the 10 markers were highly polymorphic, the genetic characteristics of these native goat populations could be estimated. Genetic diversity within populations, as estimated by the expected heterozygosities, was high, ranging from 0.719 to 0.746, but genetic differentiation between populations was low, representing only 1.7% of the total genetic variation. The results suggest that Mongolian native goat populations still have a semi-wild genetic structure reflecting traditional Mongolian nomadism and the short history of artificial selection. The genetic relationships among the populations were not clear in the neighbor-joining tree generated from the modified Cavalli-Sforza chord genetic distances. By using principal components analysis, the five core populations of Mongolian native goats (Bayandelger, Ulgii Red, Zavkhan Buural, Sumber, and Dorgon) and the populations crossed with Russian breeds (Zalaajinst White, Erchim Black, and Gobi Gurvan Saikhan) were distinguished. There was no correlation between genetic relationships among the populations and the geographical distribution of the populations.

• Journal of the Korean Society of Fisheries and Ocean Technology
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• v.51 no.1
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• pp.79-85
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• 2015

Three specimens of larvae (5.2~7.8 mm in standard length (SL)), of the family Scombridae, were collected from the southeastern waters off Jeju Island in August, 2014. These specimens were identified to Katsuwonus pelamis have melanophores distributed on the 1st dorsal-fin spines and post ventral margin on caudal peduncle. An analysis of the cytochrome oxidase submit I (COI) sequences (652 base pairs) of mitochondrial DNA showed that our specimens must be K. pelamis, because their sequences were concordant with those of the adult K. pelamis (genetic distance= 0.000~0.002), followed by Auxis rochei (genetic distance= 0.061~0.063) and Euthynnus affinis (genetic distance= 0.077~0.079). During the larval stage, K. pelamis differed from Thunnus spp. species in melanophores distribution period of 1st dorsal-fin spines, lower jaws and ventral margin on caudal peduncle. In conclusion, occurrence of K. pelamis larvae means Korean waters are potential spawning ground of K. pelamis.

• Journal of Life Science
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• v.11 no.4
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• pp.379-384
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• 2001

Long terminal repeats(LTRs) of the human endogenous retrovirus(HERV) heve been found to be coexpresed with genes located nearby. It has been suggested that the LTR elements have contributed to the genetic variation of human genome connected to various diseases. Recently, HERV-W family was identified in the cerebrospinal fluids and brains of individuals with schizophrenia. Using cHNA library derived from human fetal brain, we performed PCR amplification and identified seven new HERV-W LTR elements. Those LTR elements showed a high degree of sequence similarity(98∼99%) with HERV-W (AF072500). A phylogentic tree obtained by the neighbor-joining method revealed that seven new HERV-W LTR elements(FB-1, 2, 4, 8, 9, 10, 12) were closely related to the AX000960, AF072504, and AF072506 from Gen Bank database. Our data suggest that several copy numbers of the HERV-W LTR elements are expressed in human feta brain and may contribute to an understanding of biological function connected to neuropsychiatric diseases.

• Journal of Veterinary Clinics
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• v.25 no.3
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• pp.139-145
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• 2008

To investigate the genotypic diversity of the porcine reproductive and respiratory syndrome viruses (PRRSV) in Korea, we examined 92 clinical samples from three provinces by RT-PCR and a nested PCR, and the complete open-reading frame 7 (ORF 7) sequences of 15 samples selected from 72 PCR-positive specimens were analyzed. When we compared nucleotide (amino acid) sequences of 80 isolates from Korea and overseas countries, the sequences of 7 samples belonged to North American (NA)-genotype, and those of 8 samples, to European (EU)-genotype. The nucleotide (amino acid) identities between two genotypes were 63.7% (59.8%) to 65.1% (63.1%). When compared with NA prototype VR-2332, the 7 strains of NA-genotype shared 89.8% (93.6%) to 91.2% (96.0%) identity of nucleotide (amino acid) sequence. The 8 strains of EU-type shared 93.6% (92.3%) to 94.3% (93.8%) identity of nucleotide (amino acid) sequence as compared to EU prototype Lelystad. In phylogenetic tree analysis by neighbor-joining method, all of the 8 EU-type strains were clustered into group 4 distinct from ED-prototype Lelystad (group 1). In NA-genotype, 24 domestic isolates reported previously and the 7 strains of NA-type determined in this study were clustered into group 1, while US prototype VR 2332 was classified into different group (group 2). These results suggest that emergence of EU-genotype and the dual-infection of NA- and EU-genotypes may be prevalent in the pig farms in Korea. The high degree of genetic diversity of field PRRSVs should be taken into consideration for control and preventive measures.

• Journal of Animal Science and Technology
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• v.54 no.6
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• pp.401-409
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• 2012

The objective of this study was to determine genetic variation of five Korean native chicken lines using 30 microsatellite (MS) markers, which were previously recommended by ISAG (International Society for Animal Genetics). The initial study indicated that two microsatellite markers, MCW0284 and LEI0192, were not amplified in these lines and excluded for further analysis. Twenty eight microsatellite markers were investigated in 83 birds from five Korean native chicken lines. The identified mean number of alleles was 4.57. Also, the expected, observed heterozygosity (He, Ho) and polymorphism information content (PIC) values were estimated in these markers and they ranged from 0.31~0.868, 0.145~0.699, and 0.268~0.847, respectively. The results were used for the discrimination of five chicken lines using genetic distance values and also neighbor-joining phylogenetic tree was constructed. Based on the He and PIC values, eighteen markers are enough for the discrimination of these Korean native chicken lines for the expected probability of identity values among genotypes of random individuals (PI), random half sibs ($PI_{half-sibs}$) and random sibs ($PI_{sibs}$). Taken together, these results will help the decision of conservation strategies and establishment of traceability system in this native chicken breed. Also, the use of ISAG-recommended microsatellite markers may indicate that the global comparison with other chicken breeds is possible.