• Journal of Life Science
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• v.21 no.7
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• pp.939-946
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• 2011

Sequence data of Cytochrome Oxidase Subunit I (COI) gene of mitochondria were used to elucidate the taxonomy and phylogenetic relationships of the terrestrial planarian taxa in Korea. Published COI gene sequences from Family Bipaliidae in GenBank were also included in the phylogenetic analysis. The aligned data sets for Terricola ranged from 387 to 444 nucleotides (bp) as a result of differences in insert nucleotides. The phylogeny based on COI analysis was not congruenced with the morphological traits. Bipalium nobile included the remainder taxa (Bipalium adventitium, Bipalium venosum, Bipalium kewense, and Bipalium multilineatum). Internal nodes were strongly supported (>91%). The phylogenetic tree on COI analysis showed that most identified species were well separated from each other. The main phylogenetic analysis formed monophyletic groups. COI gene of mitochondria could have the resolving power for taxonomy information for the terrestrial planarian taxa in Korea.

• International Journal of Industrial Entomology and Biomaterials
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• v.33 no.2
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• pp.121-131
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• 2016

Ten microsporidian isolates from Samia cynthia ricini, and Antheraea assamensis in India along with a Nosema reference strain (NIK-1s_mys) from B. mori India were characterised morphologically and molecular based tools. The test isolates observed elongated oval in shape while reference strain was oval and ranging from 3.80 to 4.90 m in length and 2.60 to 3.05 m in width. The ribosomal DNA region 'IGS' of test isolates assessed by PCR amplification, followed by cloning and sequencing. IGS sequence and phylogenetic analysis of test microsporidian isolates showed very close relationship with three Nosema references species: N. philosamia, N. antheraea isolated from Philosamia cynthia ricini and Antheraea perny in China respectively and N. disstriae from Malacosma disstriae in Canada. The clustering pattern of dendogram reveals all test isolates appear distinct from Nosema std. (NIK-1s_mys) India used as reference strain in the study. The result suggests IGS indeed a suitable and highly applicable molecular tool for identifying and characterise the microsporidian isolates in similar population.

• Animal Systematics, Evolution and Diversity
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• v.24 no.3
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• pp.327-332
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• 2008

Soft coral Dendronephthya gigantea (Verrill, 1864) is a conspicuous species dominating shallow sea waters of Jejudo Island, Korea. Recently its whole mitochondrial genome sequencing was completed by us and the sequence information provided an opportunity to test the age of Octocorallia and time of evolutionary separation between some representative orders of the subclass Octocorallia. Molecular phylogenetic analyses based on 13 mitochondrial protein encoding genes revealed a polyphyletic relationship among octocorallians representing two orders (Alcyonacea and Gorgonacea) and four families (Alcyoniidae, Nephtheidae, Briareidae, and Gorgoniidae). Estimates of divergence times among octocorallians indicate that the first splitting might occur around end of or after Cretaceous period (50-79 million years ago (Ma)). The age is relatively young compared to the long history of stony sea corals (>240 Ma). Taken together our result suggests a possible relatively recent radiating evolution at least in the order Alcyonacea and Gorgonacea. Molecular dating and phylogenetic analysis based on much broader taxon sampling and many genes might give an insight into this interesting hypothesis.

• Parasites, Hosts and Diseases
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• v.41 no.4
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• pp.209-219
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• 2003

The evolutionary course of the CsRn1 long-terminal-repeat (LTR) retrotransposon was predicted by conducting a phylogenetic analysis with its paralog LTR sequences. Based on the clustering patterns in the phylogenetic tree, multiple CsRn1 copies could be grouped into four subsets, which were shown to have different integration times. Their differential sequence divergences and heterogeneous integration patterns strongly suggested that these subsets appeared sequentially in the genome of C. sinensis. Members of recently expanding subset showed the lowest level of divergence in their L TR and reverse transcriptase gene sequences. They were also shown to be highly polymorphic among individual genomes of the trematode. The CsRn1 element exhibited a preference for repetitive, agenic chromosomal regions in terms of selecting integration targets. Our results suggested that CsRn1 might induce a considerable degree of intergenomic variation and, thereby, have influenced the evolution of the C. sinensis genome.

• Journal of Animal Science and Technology
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• v.60 no.12
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• pp.32.1-32.10
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• 2018

Background: Necdin (NDN), a member of the melanoma antigen family showing imprinted pattern of expression, has been implicated as causing Prader-Willi symptoms, and known to participate in cellular growth, cellular migration and differentiation. The region where NDN is located has been associated to QTLs affecting reproduction and early growth in cattle, but location and functional analysis of the molecular mechanisms have not been established. Methods: Here we report the sequence variation of the entire coding sequence from 72 samples of cattle, yak, buffalo, goat and sheep, and discuss its variation in Bovidae. Median-joining network analysis was used to analyze the variation found in the species. Synonymous and non-synonymous substitution rates were determined for the analysis of all the polymorphic sites. Phylogenetic analysis were carried out among the species of Bovidae to reconstruct their relationships. Results: From the phylogenetic analysis with the consensus sequences of the studied Bovidae species, we found that only 11 of the 26 nucleotide changes that differentiate them produced amino acid changes. All the SNPs found in the cattle breeds were novel and showed similar percentages of nucleotides with non-synonymous substitutions at the N-terminal, MHD and C-terminal (12.3, 12.8 and 12.5%, respectively), and were much higher than the percentage of synonymous substitutions (2.5, 2.6 and 4.9%, respectively). Three mutations in cattle and one in sheep, detected in heterozygous individuals were predicted to be deleterious. Additionally, the analysis of the biochemical characteristics in the most common form of the proteins in each species show very little difference in molecular weight, pI, net charge, instability index, aliphatic index and GRAVY (Table 4) in the Bovidae species, except for sheep, which had a higher molecular weight, instability index and GRAVY. Conclusions: There is sufficient variation in this gene within and among the studied species, and because NDN carry key functions in the organism, it can have effects in economically important traits in the production of these species. NDN sequence is phylogenetically informative in this group, thus we propose this gene as a phylogenetic marker to study the evolution and conservation in Bovidae.

• Korean Journal of Ichthyology
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• v.36 no.2
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• pp.139-155
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• 2024

Using the cytb gene region of the mitochondrial DNA of eight populations of Sarcocheilichthys nigripinnis morii and five populations of S. variegatus wakiyae, which belong to the genus Sarcocheilichthys from Korea, the genetic diversity and molecular phylogenetic relationships of each population were examined. As a result of the analysis, it was confirmed that the S. variegatus wakiyae population had higher genetic diversity than the S. nigripinnis morii population. In the phylogenetic tree of genus Sarcocheilichthys fish in Korea based on the cytb gene, the Yeongsan River (YSR) population of S. variegatus wakiyae forms a clade with the Tamjin River (TJR), Yeongsan River (YSR), and Seomjin River (SJR) population of S. nigripinnis morii, and genetic relationships that do not align with the current classification system were observed. Meanwhile, on the nuclear DNA phylogenetic tree, S. variegatus wakiyae and S. nigripinnis morii could be clearly distinguished, showing mitonuclear inconsistency where mitochondrial and nuclear DNA conflicted on the phylogenetic tree. The Seomjin River (SJR) population of S. nigripinnis morii was translocated to the Dongjin River (DJR) population, haplotype from which crossbreeding was presumed to have occurred was confirmed. Among the rivers flowing into the East Sea, the S. nigripinnis morii population is known to have been introduced and inhabit only the Hyeongsan River (HSR), and it is presumed to be a population formed by translocation from the Han River (HR) population, with a haplotype representing a unique genetic group also confirmed. The Han River (HR), Geum River (GR), and Mangyeong River (MGR) populations of S. nigripinnis morii formed a genetically identical population with S. czerskii and S. soldatovi distributed north of the Yalu River, and accordingly, a taxonomic reexamination was required through morphological and molecular phylogenetic studies by securing various specimens.

• Korean Journal of Veterinary Service
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• v.36 no.1
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• pp.23-30
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• 2013

An avian rotavirus (AvRV-2) was isolated from feces of broilers suffering from acute gastroenteritis in 2011. It was the first avian rotavirus isolated in Korea. To investigate the molecular characteristics of AvRV-2, the VP4, VP6, VP7 and NSP4 gene nucleotide sequences were determined and compared with those of rotavirus strains available in the GenBank database. The phylogenetic tree of VP7 gene showed that AvRV-2 had a high degree of nucleotide sequence homology (93.4% to 94.7%) with those of rotaviruses belonging to genotype G19 cluster. The phylogenetic tree of the VP4 gene revealed a high degree of nucleotide sequence homology (95.8% to 95.9%) with genotype P[30] rotaviruses isolated from chickens. The VP6 and NSP4 gene nucleotide sequences showed the highest identities with those of avian strains with 95.3% to 96.4% and 90.3% to 92.2%, respectively. Genetic characterization of the VP4, VP6, VP7 and NSP4 showed that AvRV-2 strain was most closely related to chicken rotavirus strains from Germany and Japan. Comparative nucleotide sequences and phylogenetic analysis indicated that avian rotavirus isolated from broilers belonged to genotype G19P[30] and it was the first report on avian rotavirus infection in Korea.

• ALGAE
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• v.31 no.4
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• pp.303-315
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• 2016

Compsopogon specimens collected in China were examined based on morphology and DNA sequences. Five molecular markers from different genome compartments including rbcL, COI, 18S rDNA, psbA, and UPA were identified and used to construct a phylogenetic relationship. Phylogenetic analyses indicated that two different morphological types from China clustered into an independent clade with Compsopogon specimens when compared to other global samples. The Compsopogon clade exhibited robust support values, revealing the affiliation of the samples to Compsopogon caeruleus. Although the samples were distributed in a close geographical area, unexpected sequence divergences between the Chinese samples implied that they were introduced by different dispersal events and from varied origins. It was speculated that Compsopogon originated in North America, a portion of the Laurentia landmass situated in the Rodinia supercontinent at approximately 573.89-1,701.50 million years ago during the Proterozoic era.Although Compsopogonhad evolved for a rather long time, genetic conservation had limited its variability and rate of evolution, resulting in the current monospecific global distribution. Additional global specimens and sequence information were required to increase our understanding of the evolutionary history of this ancient red algal lineage.

• The Korean Journal of Mycology
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• v.46 no.4
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• pp.375-382
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• 2018

Members of the genus Mortierella (Mortierellales) are filamentous fungi, which are found on nearly all substrates, but more frequently in soil. Till date, 7 species of Mortierella have been reported in Korea, but being a ubiquitous group with high species diversity in temperate zones, this number is still low. During a survey of fungal biodiversity in Korea, we collected many isolates of Mortierella, and through morphological and molecular phylogenetic analyses, identified them to be 3 previously unrecorded species, namely, M. chienii, M. epicladia, and M. gamsii. A total of 10 Mortierella species in Korea, including the 3 species reported in the present study, are widely distributed in 5 out of 7 phylogenetic groups of this genus. This indicates that the diversity of Mortierella was so far underestimated in Korea. Multi-locus sequence analysis is required to provide a more reliable backbone for some uncertain phylogenetic groupings and to more clearly define a species of Mortierella, which would encourage deeper research in the diversity and ecological roles of Mortierella and allied genera.

• Korean Journal of Plant Resources
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• v.29 no.5
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• pp.547-554
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• 2016

The genus Tilia is characterized by linear form bracts of which the lower part is attached to the peduncle of a cyme. This character is distinguished from the others genus of Malvaceae. The purpose of this study is verifying the phylogenetic relationship of genus Tilia. Phylogenetic analyses were conducted to evaluate relationships of 10 taxa of Tilia in Korea and Japan including one outgroup (Gossypium hirsutum). The molecular phylogenetic analyses were conducted with sequences based on ITS, trnL-F and rpl32-trnL region. The combined data result of ITS, trnL-F and rpl32-trnL was formed by 6 clades. T. kiusiana situated as the most basal clade. T. amurensis, T. taquetii and T. rufa are composed a clade. T. koreana, T. insularis and T. japonica was formed independent clade. T. insularis has the closest relationship with T. japonica. T. miqueliana, T. mandshurica, and T. megaphylla are composed a clade and showed a sister relationship than other species.