• Journal of Life Science
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• v.22 no.1
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• pp.62-73
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• 2012

This study was carried out to investigate the genetic relationship of Flammulina velutipes with other species. The ribosomal DNA cluster containing 4 rRNA genes from F. velutipes 4154 were sequenced. The length of the rDNA cluster sequence was estimated at 7,403 bp long and consisted of 1,806 bp of SSU rDNA, 245 bp of ITS 1 region, 159 bp of 5.8S rDNA, 308 bp of ITS 2 region, 3,402 bp of LSU rDNA, 1,400 bp of IGS 1 region, and 83 bp of 5S rDNA. The F. velutipes 4154 genes were contained in the rDNA cluster of F. velutipes in the order of SSU rDNA - ITS 1 - 5.8S rDNA - ITS 2 - LSU rDNA - IGS 1 - 5S rDNA. The phylogenetic relationships of 20 strains of Tricholomataceae and Physalacriaceae were analyzed by conducting distance analysis using the Neighbor-joining (NJ) method. The 20 strains used in this study were divided into three groups and the strains of the genus Flammulina were related very closely to strains of Physalacria bambusae.

• Korean Journal of Microbiology
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• v.51 no.1
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• pp.86-95
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• 2015

To study the halobacterial diversity at the rhizospheric soil of coastal plant native to Dokdo islands, several host plant were selected and its rhizospheric soil was sampled. Soil sample was diluted serially and pure isolation was done by sub-culture using marine agar media. 26 halophilic strains cultivable at the marine medium containig concentration of 9.0% sodium chloride were selected among total 161 isolates. Their partial 16S rRNA gene sequences extracted from genomic DNA were analyzed and partially identified. Furthermore, to identify their genetic relationship, phylogenetic tree was deduced. Total 26 strains were belongs to Firmicutes (30.8%), Gamma proteobacteria (53.8%), Bacteroidetes (7.7%), Alpha proteobacteria (7.7%), and Actinobacteria (7.7%). These results showed the specific difference from previous researches which has been reported the microbial flora of soil or sea water around the Dokdo islands. Furthermore, 4 among 26 halophilic strains grew at above 12.0% NaCl concentrated marine broth, and 2 strains Idiomarina abyssalis LM4H23 and Halomonas huangheensis AS4H13 grew at 15.0% concentration. These halophilic strains thought to overcoming the severe stress like high salt concentration or variation derived from Dokdo-specific climate and might have unknown, specific relationship with their host coastal plant native to Dokdo islands.

• Journal of Life Science
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• v.23 no.1
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• pp.24-30
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• 2013

The purpose of this study was to identify genetic polymorphisms of the mitochondrial cytochrome b (mtDNA cyt b) gene in Korean black (KB) cattle breed and to analyze the genetic relationship between the KB and other breeds. We determined the complete sequence of the mtDNA cyt b gene in 38 KB cattle. We also analyzed their genetic diversity, and phylogenetic analysis was performed by comparison with Korean cattle (KC, called Hanwoo) and breeds from China and Japan. A nucleotide substitution was detected in the KB cattle, and two haplotypes were defined. In the neighbor-joining (NJ) tree, the haplotypes of KB were located in Bos taurus lineage with those of KC, Japanese black (JB), Yanbian and Zaosheng breeds. However, the haplotypes of Chinese breeds, excluding Yanbian and Zaosheng, were separated into B. taurus and B. indicus lineages. In the NJ tree of breeds based on Dxy genetic distances, Chinese breeds mixed with B. taurus and B. indicus lineages were located between B. indicus and B. taurus lineages. KB was contained within B. taurus lineage and was determined to be genetically more closely related to two Chinese (Yanbian and Zaosheng) breeds than to KC and JB. The haplotype distribution and the results of the phylogenetic analysis suggest that KB and KC have genetic differences in their mtDNA cyt b gene sequences.

• The Korea Journal of Herbology
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• v.24 no.3
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• pp.59-68
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• 2009

Objectives : Bupleuri Radix (Siho) is prescribed as the root of different Bupleurum species on the pharmarcopoeia in Korea and China. Moreover, other species and varieties of the genus Bupleurum have been also distributed on the herbal market as Bupleuri Radix. However, due to the morphological similarity and frequent occurrence of intermediate forms, the correct identification of this radix is very difficult. To develop a reliable method for correct identification and improving the quality standards of official Bupleuri Radix, we analyzed sequences of the ribosomal RNA gene and internal transcribed spacer (rDNA-ITS) region. Methods : PCR amplification of rDNA-ITS region was performed using ITS1 and ITS4 primer from 6 Bupleurum species and 1 variety, B. falcatum L. (Siho), an improved breed of B. falcatum L. (Samdo-Siho), B. chinense DC. (Buk-Siho), B. scorzonerifolium Willd. (Nam-Siho), B. longiadiatum Turcz. (Gae-Siho), B. euphorbiodes Nakai (Deungdae-Siho) and B. latissimum Nakai (Seom-Siho), and nucleotide sequence was determined after sub-cloning into the pGEM-Teasy vector. Authentic marker nucleotides were estimated by the analysis of ClastalW using entire rDNA-ITS sequence of three samples per species. Results : In comparative analysis of the rDNA-ITS sequences, we found specific nucleotides to distinguish Korean (B. falcatum L. and its variety) and Chinese official species (B. chinense DC. and B. scorzonerifolium Willd.) from others at positions 411 and 447, and positions 89, 101, 415 and 599, respectively. Futhermore, we also found nucleotide indels (insertion and/or deletion) and substitutions to identify each of different Bupleurum species, 2 positions for B. falcatum L. and its variety, 6 positions for B. chinense DC., 49 positions for B. scorzonerifolium Willd., 8 positions for B. euphorbioides Nakai, 7 positions for B. longiradiatum Nakai and 9 positions for B. latissimum Nakai. These sequence differences at corresponding positions are avaliable nucleotide markers to determine the botanical origins of Bupleuri Radix. Moreover, we confirmed the phylogenetic relationship of B. latissimum Nakai, a Korean endemic speices, among Bupleurum species based on the rDNA-ITS sequence. Conclusions : These marker nucleotides would be useful to identify the official herbal medicines by the providing of definitive information that can identify each plant species and distinguish it from unauthentic adulterant Bupleurum species.

• Asian-Australasian Journal of Animal Sciences
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• v.21 no.12
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• pp.1696-1702
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• 2008

In order to learn the origin of the Chinese Mongolian horse, we analyzed polymorphisms within the mtDNA D-loop variable region in 305 horses of 6 types of 3 different breeds, including one imported breed, one cultivated breed and 4 types of one local breed. We detected 13 different haplotypes, and subsequent sequence analysis showed that all 6 horse types were genetically diverse. By constructing a cladogram of mtDNA D-loop sequences from the 6 horse types along with homologous sequences from several other horse types obtained from GenBank, we showed that Chinese Mongolian horses have a close genetic relationship with other horse types from Mongolia. We also speculate that several Chinese Mongolian horses descended from Przewalskii horse. Additionally, the 13 haplotypes were dispersed throughout the cladogram, suggesting that Chinese Mongolian horses likely originated from multiple female ancestors. A phylogenetic map of the 6 horse types showed that the genetic relationship between the local Wuzhumuqin and Wushen types were the closest. The Xinihe and Baerhu were also closely related to each other, and slightly more distantly related to the cultivated Sanhe breed. All five of the local Chinese horse types had a much more distant relationship with the imported Thoroughbred breed.

• Journal of Species Research
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• v.3 no.1
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• pp.7-16
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• 2014

Many species of Lymantria are important forestry pests, including L. dispar which is well known distributed from Asia to North America as an invasive species. Like of most other genera of moths, the systematic of this genus is still in dispute, especially on the monophyly and the relationship within this genus due to the fact that genus is very large and varied. This genus was morphologically defined only by a single aphomorphy. To clarify the monophyly of the genus Lymantria, to reveal the phylogenetic relationship among the Indonesian species, and to establish the genetic characters of Indonesian Lymantria, we analyzed 9 species of Indonesian Lymantria involving 33 other species distributed around the world based on nucleotide sequence variation across a 516-bp region in the CO I gene. The results showed that the base composition of this region was a high A+T biased (C: 0.3333). The results also showed that the monophyly of Lymantria was not supported by bootstrap tests at any tree building methods. Indonesian species was distributed into four different groups but the relationship among them was still in dispute. It indicates that relationships among the basal nodes (groups) proposed here were least valid due to the fact that the number of species may not be enough to represent the real number of species in the nature. Moreover CO I gene sequences alone were not able to resolve their relationships at the basal nodes. More investigations were needed by including more species and other genes that the more conserved.

• Korean Journal of Agricultural Science
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• v.48 no.4
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• pp.693-702
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• 2021

The aim of this study was to analyze the genetic diversity and distance of the Korean native black goat line. Thus far, this Korean native black goat line has not been studied intensively, especially in genetic diversity and relationship studies in comparison with other breeds. In total, eleven microsatellite (MS) markers were used to evaluate alleles from 391 Korean native black goats and foreign hybrid animals. The genetic diversity index was evaluated based on the allele distributions. Four Korean native black goat lines showed expected ranges of observed heterozygosity, expected heterozygosity, and polymorphism information content (PIC) values for use in genetic diversity research (0.509 - 0.643, 0.434 - 0.623 and 0.356 - 0.567). Lines from the Korean native black goat and foreign hybrid were clearly separated according to principal coordinates analysis (PCoA), phylogenetic tree and tended to be clustered in each Korean native black goat line. Thus, this study can be used for analyzing the genetic relationships between Korean native black goats and foreign breeds for line preservation and for fundamental information to determine breed improvement strategies.

• Journal of Plant Biotechnology
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• v.43 no.1
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• pp.82-90
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• 2016

Most Araliaceae plant species distributed in Korea are economically important because of their high medicinal values. This study was conducted to develop barcode markers from sequence analysis of chloroplast DNA in 14 taxa of Araliaceae species grown in South Korea. Sequencing of seven chloroplast DNA regions was performed to establish the DNA barcode markers, as suggested by the Consortium for the Barcode of Life (CBOL). From the sequence analysis of chloroplast DNA, we identified specific sequences and nucleotides that allowed us to discriminate among each other 14 Korean Araliaceae species. The sequence in the region of psbA-trnH revealed the most frequent DNA indels and substitutions of all 7 regions studied. This psbA-trnH marker alone can discriminate among all 14 species. There are no differences between Korean and Chinese Panax ginseng in all seven sequenced chloroplast DNA regions. A phylogenetic tree constructed using the seven chloroplast DNA regions revealed that Tetrapanax papyriferus should be classified as an independent clade. The Aralia and Panax genera showed a close phylogenetic relationship. Five species in the Eleutherococcus genus were more closely related to Kalopanax septemlobus than to any Panax species.

• Korean Journal of Microbiology
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• v.32 no.4
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• pp.245-251
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• 1994

Ten strains of 7 species from the genus Ganoderma, G. lucidum ATCC 64251, FP-103561-T, and ES70701, G. applanatum ATCC 44053 and FP-57035-T. G. lobatum ATCC 42985, G. resinaceum ATCC 52416, G. subamboinense var. laevisporum ATCC 52420, G. meredithae ATCC 64492, and G. microsporum ATCC 76024, were studied to discuss their phylogenetic relationships by utilizing restriction fragment length polymorphisms (RFLPs) of mitochondrial DNAs (mtDNAs). Six restriction enzymes, BamHI, BglII, EcoRI, HindIII, PvuII, and XbaI which digested mtDNAs into adequate numbers of restriction fragments for cluster analysis, were used in this study. Restriction profiles of strains for each restriction enzyme were treated as analysis characters to calculate similarity coefficients, which were converted into nucleotide sequence divergence values whose mean values were then arranged in a matrix table. This table was utilized for a phylogenetic analysis using the Neighborjoining method of the PHYLIP package to construct phylogenetic tree. Three strains of G. lucidum and two strains of G. applanatum exhibited different lineages each but one of G. applanatum strains showed a close relationship with G. lobatum, which reflected the species complexity of these species whose strains were phenotypically indistinguishable but genetically distinct. The present results suggest that the natural classification of Ganoderma needs to be considered from the viewpoints of molecular biology-based systematics as well as morphological classifications and cultural identifications for better phylogenetic conclusions.

• Korean Journal of Plant Resources
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• v.34 no.1
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• pp.1-16
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• 2021

The phylogenetic relationships among thirty-two strains (P1~P32; including Cordyceps sp., Paecilomyces sp., Beauveria sp., Aranthomyces sp., Isaria sp. and Himenostilbe sp.) in Miryang region located in the southern part of Korea, were investigated based on internal transcribed spacer (ITS) sequences of ribosomal DNA. A fragment of ITS region was amplified by polymerase chain reaction (PCR) using the specific primer pairs ITS1 and ITS4. After obtained same size of PCR products from various strains, we cloned them into a pGEM-T easy vector to determine their sequences. BLAST analyses of the nucleotide sequence ITS1, 5.8S and ITS2 gene fragments revealed the identity and their phylogenetic relationship. Among 32 strains isolated from Miryang region, Cordyceps militaris was shared 100% sequences with Genbank (AY49191, EU825999, AY491992), while some species are not shared perfectly with reported sequences. For example, strain P17 (P. tenuipes in Ulju-gun Gaji Mountain) has some differences among the other strains of P. tenuipes (Miryang-si Jocheon-eup, Miryang-si Gaji Mountain) and those of gene bank. We conclude that ITS analyses with strains in the suburbs of Miryang in this study can be effectively used as a tool for classification, evaluation and collection of the natural eco-type genetic resources.