• Animal Systematics, Evolution and Diversity
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• v.11 no.2
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• pp.291-299
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• 1995

Sampels of Korean field mice (apodemus peninsulae peninsulae Thomas ) from six localities in Korea were used for the analyses of mitochondrial DNa (Mt DNA) fragment patterns resulted from the digestion with eight restriction enzymes. A total of 29 fragments were recognized and seven mtDNA clones were revealed. The nucleotide-sequence divergences (p) among the seven mtDNA clones ranged from 0.42% to 2.01%. Moreover, the seven clones were grouped into three major subgroups with the mean divergence value of 1.52% among them. One subgroup was composed of three clones of 18 sample from three localities (16, Cheongu: 1, Mt. Sobaek : 1, Mt. weolak) L another subgroup, three clones of eight samples from four localities (2, Cheongju ; 2 , Mt. Weolak ; 2, Mt. Gaya ; 2, haenam) ; and the last subgroup, one clone of two samples from Cheongju. Three subgroups were also distinct with one another in their mtDNA genotypes of Stu I and the former two subgroups differed from the last subgroup in their genotypes with Pvu II. Further analyses with additional samples from various localities in Korea appeared to be necessary in order to clarify the taxonomic status of the distinct mtDNA subgroups.

• Animal cells and systems
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• v.3 no.2
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• pp.199-205
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• 1999

The nucleotide sequences of a 504 bp segment of the mitochondrial cytochrome b gene were analyzed to survey the intraspecific variation of the brown frog, Rana dybowskii, collected from nine populations in South Korea. Comparisons of sequence divergence of the cytochrome b gene suggest that the populations examined are clearly classified into two types (type 1 and type 2), diverged from each other by a high value of 14.3-15.9% sequence divergence. The two types are distributed allopatrically in most populations, but only one population occurs sympatrically. In the Tonghae population, their spawning grounds differ in that type 1 spawns in the puddle and type 2 spawns in the mountain creek. Based on the genetic divergences of the cytochrome b gene sequences, the phylogenetic status of Korean R. dybowskii is elucidated by comparing it with related brown frogs distributed in an area adjacent to the Korean Peninsula. Interspecific sequence divergences among type 1, type 2 and other related brown frog species (Russian R. dybowskii, R. pirica, R. ornativentris, R. chensinensis: 2n=24 chromosomes) used in this study ranged from 11.7 to 16.3%. R. dybowskii in Tsushima is very similar to our type 1 (sequence divergence＝0-1.6%) and R. chensinensis in western China is closest to our type 2 (sequence divergence＝6.8-7.5%).

• International Journal of Industrial Entomology and Biomaterials
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• v.6 no.1
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• pp.63-68
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• 2003

We investigated the sequence divergence of the geographic samples of the queen bumble bee (Bombus ardens) in Korea. A portion of mitochondrial COI gene sequences (423 bp) was analyzed for 44 individuals collected from seven localities. Sequence analysis resulted in four COI haplotypes with the maximum nucleotide divergence of only 0.5% (two bp). One haplotype (BA1) was dominant in all localities surveyed (86.4%). The finding of low sequence divergence and dominance of one haplotype appear to reflect, although limited, the life history of the B. ardens queens subjected to active dispersal and seasonal fluctuation in queen number.

• Animal Systematics, Evolution and Diversity
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• v.28 no.4
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• pp.269-278
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• 2012

Gobiids are hyperdiverse compared with other teleost groups, with about 2,000 species occurring in marine, freshwater, and blackish habitats, and they show a remarkable variety of morphologies and ecology. Testing the effectiveness of DNA barcodes on species that have emerged as a result of radiation remains a major challenge in evolutionary biology. Here, we used the cytochrome c oxidase subunit 1 (COI) sequences from 144 species of gobies and related species to evaluate the performance of distance-based DNA barcoding and to conduct a phylogenetic analysis. The average intra-genus genetic distance was considerably higher than that obtained in previous studies. Additionally, the interspecific divergence at higher taxonomic levels was not significantly different from that at the intragenus level, suggesting that congeneric gobies possess substantial interspecific sequence divergence in their COI gene. However, levels of intragenus divergence varied greatly among genera, and we do not provide sufficient evidence for using COI for cryptic species delimitation. Significantly more nucleotide changes were observed at the third codon position than that at the first and the second codons, revealing that extensive variation in COI reflects synonymous changes and little protein level variation. Despite clear signatures in several genera, the COI sequences did resolve genealogical relationships in the phylogenetic analysis well. Our results support the validity of COI barcoding for gobiid species identification, but the utilization of more gene regions will assist to offer a more robust gobiid species phylogeny.

• Genomics & Informatics
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• v.19 no.2
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• pp.15.1-15.7
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• 2021

The direction of evolution can estimate based on the variation among nonsynonymous to synonymous substitution. The simulative study investigated the nucleotide sequence of closely related strains of respiratory syndrome viruses, codon-by-codon with maximum likelihood analysis, z selection, and the divergence time. The simulated results, dN/dS > 1 signify that an entire substitution model tends towards the hypothesis's positive evolution. The effect of transition/transversion proportion, Z-test of selection, and the evolution associated with these respiratory syndromes, are also analyzed. Z-test of selection for neutral and positive evolution indicates lower to positive values of dN-dS (0.012, 0.019) due to multiple substitutions in a short span. Modified Nei-Gojobori (P) statistical technique results also favor multiple substitutions with the transition/transversion rate from 1 to 7. The divergence time analysis also supports the result of dN/dS and imparts substantiating proof of evolution. Results conclude that a positive evolution model, higher dN-dS, and transition/transversion ratio significantly analyzes the evolution trend of severe acute respiratory syndrome coronavirus 2, severe acute respiratory syndrome coronavirus, and Middle East respiratory syndrome coronavirus.

• Journal of Life Science
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• v.8 no.4
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• pp.360-365
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• 1998

The genetic of a recently described virus, hepatitis G virus(HGV) was investigated. HGV envelope 1 (E1) nucleotide sequences isolated from six Korean hepatitis b virus-positive patients by using a reverse transcription-poly-merase chain reaction procedure, were analysed and compared to the seven previously reported HGV isolates. Sequence homology among the Korean isolates was 88-97% whereas among the isolates from different geographic areas was 80-92%, indicating geographical divergence of HGV. Nucleotide substitutions spread uniformly throughiut the E1 fragment. Furthermore, compared to the prototype HGV sequence, frameshift mutations were observed in most of the Korean isolating that a different translating initiation site for the polyprotein exists in the Korean type HGV.

• The Plant Pathology Journal
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• v.19 no.1
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• pp.57-63
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• 2003

An insertion sequence identified as a solo long terminal repeat (LTR) of a new rice copia-like retrotransposon was detected in the ORE of the Pi-b gene from the rice cv. Nipponbare, and was designated as Osr1. Osr1 consists of a 6386 bp nucleotide sequence including 965 bp LTRs on both ends with an 82％ nucleotide sequence identity to the wheat Tarl retrotransposon on reverse transcriptase. Nucleotide divergence was noted among the individual LTRs, as well as the coding region of Osr1. Various restriction fragment length polymorphism (RFLP) of LTR were detected in indica cultivars, whereas, only a few could be detected in the japonica cultivars. The population of Osr1 is lower in the wild-type rice compared with that in the domesticated cultivars. The insertion of LTR sequence in the h-b gene in the susceptible cultivar suggested that retro-tyansposon-mediated insertional mutation might play an important role in the resistance breakdown, as well as in the evolution of resistance genes in rice.

• Fisheries and Aquatic Sciences
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• v.12 no.1
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• pp.44-48
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• 2009

Nucleotide sequences of about 500 bp from the 5' end of mitochondrial (mt) DNA Cytochrome Oxidase I (COI) were analyzed to estimate the genetic variation between wild and cultured populations of the ascidian Halocynthia roretzi from two sites along the coast of Korea. A total of 25 haplotypes were defined by 21 variable nucleotide sites in the examined COI region. Genetic diversity (haplotype diversity and nucleotide divergence) of wild populations was higher than that of the cultured population. These data suggest that reduced genetic variation in the cultured population may have results from bottleneck effect caused by the use of a limited number of parental stock and pooling of gametes for fertilization. Pairwise population $F_{ST}$ estimates inferred that wild and cultured populations were genetically distinct. The combined results suggest that sequence polymorphism in the COI region would be preferable for estimating the genetic diversity of ascidian populations.

• Journal of Plant Biology
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• v.38 no.1
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• pp.107-113
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• 1995

pRLYS1 containing intact rbcL gene of maize (Zea mays L. cv Golden X Bantam T-51; Zm-A) was digested with several restriction enzymes to construct subcones carrying promoter region of rbcL. The DNA fragments of 0.20, 0.19, 0.92 and 1.55 kb among the EcoRI digests, the EcoRI-DdeI digests, the AvaI digests and the EcoRI-BamHI digests of pRLYS1 were subcloned into pBluscriptSK＋and named pRLPS2, pRLPS3, pRLPS14 and pRLPS35, respectively. Four subclones contain the 1.92 kb portion from 136 nucleotide downstream to 1780 nucleotide upstream from the ATG initiation codon of rbcL gene. pRLPS2 (-29 to -229) and pRLPS3 (-239 to -420 from the ATG) were sequenced. When nucleotide sequence of Zm-A was compared with sequence of rbcL promoter region of a different cultivar of maize (Zea mays L. cv WFG TMS X BS7; Zm-B), the difference rate between two cultivars was 4.3%. The mean of sequence divergence between Zm-A and three grass species in the same tribe, Andropogoneae, in the upstream region from 29 to 420 of ATG was 1.8%, whereas between Zm-B and above-mentioned three species was 5.4%. Therefore, Zm-A seems to evolutionarily closer to three other species in Andropogoneae tribe than Zm-B is.

• Mycobiology
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• v.51 no.6
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• pp.388-392
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• 2023

A yeast strain, designated as JAF-11^T, was isolated from flower of Prunus mume Sieb. et Zucc. in Gwangyang, Republic of Korea. Phylogenetic analysis showed that strain JAF-11^T was closely related to Neodothiora populina CPC 39399^T with 2.07 % sequence divergence (12 nucleotide substitutions and three gaps in 581 nucleotides) in the D1/D2 domain of the large subunit (LSU) rRNA gene, and Rhizosphaera macrospora CBS 208.79^T with 4.66 % sequence divergence (25 nucleotide substitutions and five gaps in 535 nucleotides) in the internal transcribed spacer (ITS) region. Further analysis based on the concatenated sequences of the D1/D2 domain of the LSU rRNA gene and the ITS region confirmed that strain JAF-11^T was well-separated from Neodothiora populina CPC 39399^T. In addition to the phylogenetic differences, strain JAF-11^T was distinguished from its closest species, Neodothiora populina CPC 39399^T and Rhizosphaera macrospora CBS 208.79^T belonging to the family Dothioraceae by its phenotypic characteristics, such as assimilation of carbon sources. Hence, the name Neodothiora pruni sp. nov. is proposed with type strain JAF-11^T (KACC 48808^T; MB 850034).