• The Korean Journal of Mycology
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• v.47 no.1
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• pp.89-94
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• 2019

A rust fungus on Iris domestica (syn. Belamcanda chinensis) from China was previously identified as Puccinia iridis. Accordingly, the identity of the rust fungus on the same host species in Korea needs to be reexamned. Morphological characteristics of the Korean materials matched with P. iridis. Molecular phylogenetic analyses based on internal transcribed spacer and large subunit rDNA sequences of two representative materials confirmed the identification by high sequence similarities of 100% and 99% with the reference sequences available in NCBI GenBank database. Phylogenetic tree inferred from neighbor-joining method proved them to be clustered in P. iridis group. Thus, the rust fungus on I. domestica in Korea was determined as P. iridis. On the other hand, a previous record that Puccinia belamcandae is another rust agent on I. domestica in Korea should be reconfirmed in future.

• Korean Journal of Plant Resources
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• v.35 no.1
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• pp.100-108
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• 2022

We found Urtica dioica L., an unrecorded alien plant, in the Han River basin of Korea. U. dioica is considered to be native to Europe, much of temperate Asia and western North Africa. This plant has been introduced to many other parts of the world. In Particularly, it reported as an invasive species from East Asia (Japan), Oceania and South America. This species is distinguished from related Korean taxa of the genus by its unisexual flower and dioecious plant species. In the Neighbor-Joining tree, U. dioica samples from the Han River Park (Sangam-dong, Mapo-gu, Seoul) and Yangjaecheon Stream (Daechi-dong, Gangnam-gu, Seoul) clustered into a clade consisting of a U. dioica s.s. Here, we provide a precise description, illustrations, a key to the related taxa, and photographs of its habitat.

• Genomics & Informatics
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• v.9 no.4
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• pp.181-188
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• 2011

In planning a model-based phylogenic study for highly related ethnic data, the SNP marker number is an important factor to determine for relationship inferences. Genotype frequency data, utilizing a sub sampling method, from 63 Pan Asian ethnic groups was used for determining the minimum SNP number required to establish such relationships. Bootstrap random sub-samplings were done from 5.6K PASNPi SNP data. DA distance was calculated and neighbour-joining trees were drawn with every re-sampling data set. Consensus trees were made with the same 100 sub-samples and bootstrap proportions were calculated. The tree consistency to the one obtained from the whole marker set, improved with increasing marker numbers. The bootstrap proportions became reliable when more than 7,000 SNPs were used at a time. Within highly related ethnic groups, the minimum SNPs number for a robust neighbor-joining tree inference was about 7,000 for a 95% bootstrap support.

• Animal Systematics, Evolution and Diversity
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• v.29 no.1
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• pp.18-22
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• 2013

A recent study on the mitochondrial genetic variation of the Carassius auratus population in South Korea suggested that there are 3 distinct mitochondrial lineages in the country, and that they are geographically separated between westward rivers and southward rivers, respectively. In this study, the population genetic structure of amplified fragment length polymorphism (AFLP) of Carassius auratus was investigated. The results of analysis of molecular variance (AMOVA) supported the geographic distinction between westward and southward river populations, but only 3.66% of total genetic variance lies among these populations. The panmicticity of the AFLP genetic variation is backed up by the results of the neighbor-joining dendrogram drawn from a linearized pairwise $F_{ST}$ matrix and Bayesian clustering analysis. The discordance of genetic structure between mitochondrial and AFLP genetic variation may come from difference in effective population size between these markers and/or gene flow between westward and southward river populations through river capture events.

• Asian-Australasian Journal of Animal Sciences
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• v.18 no.12
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• pp.1696-1700
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• 2005

Five China native cattle breeds have been characterized by using 10 microsatellite DNA markers. The studied populations can be divided into five groups: Luxi cattle, Nanyang cattle, Jinnan cattle, Qinchuan cattle and Yanbian cattle. Allele frequencies were calculated and used for the characterization of the breeds and the study of their genetic relationships. Heterozygosity, polymorphism information content, the effective number of alleles was calculated. Nei' standard genetic distance (1978) was calculated and used for a neighbor-joining tree construction. NJ tree showed that Luxi cattle, Nanyang cattle, Jinnan cattle and Qinchuan cattle are closely related, whereas Yanbian cattle are clearly distinct from other four populations. The genetic relationship of five breeds corresponds to their history and geographic origins. This work analyzes the recent origin of these populations and contributes to the knowledge and genetic characterization of China native breeds.

• Journal of Life Science
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• v.11 no.1
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• pp.34-38
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• 2001

The cDNA encoding ribosomal protein S4(RPS 4) from an ovary cDNA library of the Japanese monkey (Macaca fuscata) was cloned and sequenced. The RPS4X gene from monkey X chromosome encodes a deduced protein of 263 amino acids and share 99.1% cDNA sequence similarity and 100% amino acid sequence identify with the human RPS4X. Rate of synonymous substitution was higher in RPS4Y than in RPS4X in comparison to the monkey and human. The ratio of synonymous and nonsynonymous substitutions per site indicated that directional selection has nor occurred in RPS4 genes. Phylogenetic analysis using the neighbor-joining method revealed that X and Y-linked RPS4 genes have evolved independently.

• Molecules and Cells
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• v.19 no.2
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• pp.283-288
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• 2005

Complete 18S rDNA sequences were determined for 10 vetigastropods in order to investigate the phylogeny of Vetigastropoda, which is controversial. These sequences were analyzed together with published sequences for nine other vetigastropods and two nerites. With the two nerites as outgroups, the phylogeny was inferred by three analytical methods, neighbor-joining, maximum likelihood, and maximum parsimony. The 18S rDNA sequence data support the monophyly of four vetigastropod superfamilies, the Pleurotomarioidea, the Fissurelloidea, the Haliotoidea, and the Trochoidea. The present results yield the new branching order: (Pleurotomarioidea (Fissurelloidea ((Scissurelloidea, Lepetodriloidea) (Haliotoidea, Trochoidea)))) within the vetigastropod clade.

• Proceedings of the Korean Society for Applied Microbiology Conference
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• 2000.04a
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• pp.128-134
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• 2000

In the course of flora analysis of soil Archaea, we found very strange 16S rDNA clones, which could possibly constitute a sister clade from known two archael, Crenarchaeota and Euryarchaeota, lineages. Overall signature sequences showed that the clones were closely related to domains Archaea and Eucarya. However, at least nine nucleotides distinguished the novel clones from domains Archaea and Eucarya. Phylogenetic trees drawn by maximum parsimony, neighbor joining and maximum likelihood methods also showed unique phylogenetic position of the clones. A very specific primer set was synthesized to detect the presence of the novel group of organisms in terrestrial environments. A specific DNA fragment was amplified from all of paddy soil DNAs, and this fact suggests that the novel organisms inhabit paddy soils.

• Korean Journal of Ichthyology
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• v.21 no.sup1
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• pp.75-75
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• 2009

The previous morphology-based taxonomic frameworks within the family Sygnathidae had emphasized the significance of the male brood pouch and reproductive biology in defining the group. However, several different hypotheses had been proposed by different investigators. This study have beencarried out to determine the phylogenetic relationships among 19 species belonging to the order Syngnathiformes with three Gasterosteiformes species as outgroup taxa by using the mitochondrial cytochrome b and Rag2 nuclear DNA sequences. Phylogenetic analyses based on neighbor-joining distance, maximum parsimony, minimum evolution and maximum likelihood method strongly supported that the family Syngnathidae, the suborder Syngnathoidei and the order Syngnathiformes were all monophyletic group. Much of previous morphological analyses were supported by our molecular data, but some deep relationships were not clearly resolved with regard to members of the suborder Aulostomoidei.

• Animal cells and systems
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• v.6 no.1
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• pp.81-84
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• 2002

SINE-R retroposons have been derived from human endogenous retrovirus HERV-K family and found to be hominoid specific. Both SINE-R retroposons and HERV_K family are potentially capable of affecting the expression of closely located genes. Using the genomic DNA from patients with schizophrenia, we identified 26 SINE-R retroposons and analyzed them with the sequences derived from the hominoid primates. The SINE-R retroposons from schizophrenia showed 89.7-96.6％ sequence similarities with the sequence of the schizo-cDNA clone that derived from postmortem tissue from the frontal cortex of an individual suffering from schizophrenial. Phylogenetic analysis using the neighbor-joining method revealed that the new SINE-R retroposons in schizophrenia have proliferated independently during hominid evolution. Such retroposons have great relevance to genomic change connected to human diseases. The data suggest that new SINE-R retroposons identified in schizophrenia deserve further investigation as potential leads on the understanding of neuropsychiatric diseases.