• Korean Journal of Ichthyology
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• v.33 no.4
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• pp.217-225
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• 2021

The family Platycephalidae is a taxonomic group of economically important demersal flathead fishes that predominantly occupy tropical or temperate estuaries and coastal environments of the Indo-Pacific oceans and the Mediterranean Sea. In this study, we for the first time analyzed the complete mitochondrial genome (mitogenome) of the flathead Platycephalus cultellatus Richardson, 1846 from Vietnam by Next Generation Sequencing method. Its mitogenome was 16,641 bp in total length, comprising 13 protein-coding genes (PCGs), two ribosomal RNA genes, and 22 transfer RNA genes. The gene composition and order of the mitogenome were identical to those of typical vertebrates. The phylogenetic trees were reconstructed based on the concatenated nucleotide sequence matrix of 13 PCGs and the partial sequence of a DNA barcoding marker, cox1 in order to determine its molecular phylogenetic position among the order Scorpaeniformes. The phylogenetic result revealed that P. cultellatus formed a monophyletic group with species belonging to the same family and consistently clustered with one nominal species, P. indicus, and two Platycephalus sp. specimens. Besides, the cox1 tree confirmed the taxonomic validity of our specimen by forming a monophyletic clade with its conspecific specimens. The mitogenome of P. cultellatus analyzed in this study will contribute valuable information for further study on taxonomy and phylogeny of flatheads.

• The Korean Journal of Mycology
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• v.47 no.4
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• pp.329-335
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• 2019

Endophytic fungal strains were isolated from the sterilized roots of a medicinal plant, Ligusticum chuanxiong and identified based on morphological characteristics and molecular analysis of internal transcribed spacer, large subunit rDNA, and beta-tubulin DNA regions. Our results confirmed the presence of Pithomyces chartarum and Plectosphaerella niemeijerarum in the fungal strains. To the best of our knowledge, the fungal strains have not been reported in Korea. In this report, we describe morphological characteristics and phylogenetic trees of these endophytic fungal strains.

• Mycobiology
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• v.44 no.3
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• pp.137-145
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• 2016

Most known species in the Strophariaceae are decomposers and grow on various kind of organic matter. Approximately 18 genera and 1,316 species in the Strophariaceae have been reported worldwide. Through an ongoing survey of indigenous fungi in Korea, 29 specimens belonging to the Strophariaceae were collected from 2012 to 2016. These specimens were identified based on morphological characteristics and molecular analysis of internal transcribed spacer sequences. Fifteen taxa were confirmed, with eight species matching those previously recorded. Seven species in five genera were shown to be new records in Korea: Galerina marginata, Gymnopilus crociphyllus, Gymnopilus picreus, Hebeloma birrus, Hebeloma cavipes, Pholiota multicingulata, and Psilocybe thaizapoteca. In this study, we provide detailed morphological descriptions of these species and investigate their evolutionary relationships by constructing phylogenetic trees.

• ALGAE
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• v.18 no.3
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• pp.191-197
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• 2003

Histones are important proteins that interact with the DNA double helix to form nucleosome. Two putative histone genes, GjH2A-1 and GjH2A-2 were isolated from a red alga Griffithsia japonica. The putative open reading frame of GjH2A-1 and GjH2A-2 shared high similarity with the previously reported amino acid sequences of histone H2As. They have a motif consisting of seven amino acids A-G-L-Q-F-P-V, which matches the histone H2A motif [AC]-G-L-x-F-P-V. Phylogenetic trees were constructed from amino acid sequences of 38 histone H2As. The histone H2As were divided into two groups: major H2As and H2A.F/Z variants. The major histone H2A group consisted of animals, fungi, plants + green algae, and red algae H2A subgroups. The animal histone H2A subgroup was divided into vertebrates, echinoderms, nematodes, insects, and segmented worms H2As. The putative red algal histone genes, GjH2A-1 and GjH2A-2, constituted an independent lineage. This is the first report on red algal histone genes.

• ALGAE
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• v.21 no.3
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• pp.287-294
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• 2006

Neosiphonia japonica is a rhodomelacean red alga that occurs in Korea, Japan, China, far-east Russia, northwest America, and New Zealand. Although it is distinguished by a bush-like habit having four pericental cells with cortication and numerous branches on axes, the taxonomy of N. japonica is still problematic. To investigate the taxonomy and phylogeny of the species, we analyzed rbcL and phycoerythrin (cpeA/B) genes from 19 samples of N. japonica and putative relatives. Phylogenetic trees from both genes show that N. japonica from Korea, Japan, New Zealand, and USA is clearly separated from N. decumbens, N. harlandii, and N. flavimarina from the Pacific Ocean. Instead, N. harveyi from the Atlantic Ocean was more related to N. flavimarina than to N. japonica. This result supports morphological and distributional differences between N. japonica and N. harveyi. However, the close relationship between these species suggests that they might have a recent most common ancestor. This is the second report to use the cpeA/B gene for evaluating species diversity in the Rhodophytes.

• Parasites, Hosts and Diseases
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• v.52 no.3
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• pp.299-304
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• 2014

This study aimed to identify the assemblages (or subassemblages) of Giardia duodenalis by using normal or nested PCR based on 4 genetic loci: glutamate dehydrogenase (gdh), triose phosphate isomerase (tpi), ${\beta}$-giardin (bg), and small subunit ribosomal DNA (18S rRNA) genes. For this work, a total of 216 dogs' fecal samples were collected in Guangdong, China. The phylogenetic trees were constructed with MEGA5.2 by using the neighbor-joining method. Results showed that 9.7% (21/216) samples were found to be positive; moreover, 10 samples were single infection (7 isolates assemblage A, 2 isolates assemblage C, and 1 isolate assemblage D) and 11 samples were mixed infections where assemblage A was predominant, which was potentially zoonotic. These findings showed that most of the dogs in Guangdong were infected or mixed-infected with assemblage A, and multi-locus sequence typing could be the best selection for the genotype analysis of dog-derived Giardia isolates.

• Molecules and Cells
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• v.22 no.1
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• pp.78-88
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• 2006

The phylogeny of the subfamily Tephritinae (Diptera: Tephritidae) was reconstructed from mitochondrial 16S ribosomal RNA gene sequences using 53 species representing 11 currently recognized tribes of the Tephritinae and 10 outgroup species. The minimum evolution and Bayesian trees suggested the following phylogenetic relationships: (1) monophyly of the Tephritinae was strongly supported; (2) a sister group relationship between the Tephritinae and Plioreocepta was supported by the Bayesian tree; (3) the tribes Tephrellini, Myopitini, and Terelliini (excluding Neaspilota) were supported as monophyletic groups; (4) the non-monophyletic nature of the tribes Dithrycini, Eutretini, Noeetini, Tephritini, Cecidocharini, and Xyphosiini; and (5) recognition of 10 putative tribal groups, most of which were supported strongly by the statistical tests of the interior branches. Our results, therefore, convincingly suggest that an extensive rearrangement of the tribal classification of the Tephritinae is necessary. Since our sampling of taxa heavily relied on the current accepted classification, some lineages identified by the present study were severely under-sampled and other possible major lineages of the Tephritinae were probably not even represented in our dataset. We believe that our results provide baseline information for a more rigorous sampling of additional taxa representing all possible major lineages of the subfamily, which is essential for a comprehensive revision of the tephritine tribal classification.

• Journal of Species Research
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• v.5 no.2
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• pp.235-240
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• 2016

To investigate the indigenous prokaryotic species diversity in Korea, various environmental samples from diverse ecosystems were examined taxonomically. The isolated bacterial strains were identified based on 16S rRNA gene sequences, and those exhibiting at least 98.7% sequence similarity with known bacterial species but never reported in Korea were selected as unrecorded species. As an outcome of this study, 10 unrecorded bacterial species belonging to the phylum Firmicutes were discovered from various sources such as soil, tidal flat, fresh water, sea water, kimchi and gut of Fulvia mutica. The unrecorded species were assigned to 7 different genera of 5 families, namely Bacillus and Ornithinibacillus of Bacillaceae, Exiguobacterium of Exiguobacteriaceae, Brevibacillus and Paenibacillus of Paenibacillaceae, Staphylococcus of Staphylococcaceae, and Lactococcus of Streptococcaceae. The selected isolates were subjected to further taxonomic characterization including the analysis of Gram reaction, cellular and colonial morphology, biochemical activities, and phylogenetic trees. The descriptive information on the 10 unrecorded species are provided.

• Journal of Ecology and Environment
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• v.29 no.4
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• pp.353-360
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• 2006

Ecological correlates of flowering times often are examined to infer evolutionary mechanisms for flowering time diversities. We examined ecological characteristic associations such as growth habits and pollination modes with flowering times among 3,037 Korean angiosperms experiencing strong climatic seasonalities. We first examined taxonomic membership effects on flowering times across diverse taxonomic levels. Phylogeny constrained flowering times at all levels down to the genus level. We then analyzed the effects of ecological characteristics using subset data consisting of species randomly selected from each genus to control phylogenetic effects. The commonly observed patterns of early flowering of woody species in temperate regions existed. Spring flowering shrubs and trees, however, both being woody, were involved with biotic and abiotic vectors, respectively. In two herbaceous groups of annuals and perennials, annuals flowered later in the growing season than perennials although both herbs tended to be associated with abiotic vectors when flowering in autumn. These results support our hypothesis that species able to decouple vegetative and reproductive growth flower in spring's dry season, but species with different habits, even when they flower within the same season, are subjected to different selective pressures for efficient pollination.

• Molecules and Cells
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• v.21 no.1
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• pp.89-103
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• 2006

Population structure was investigated in Reticulitermes speratus populations in the Korean Peninsula and the Japanese Archipelago. All trees derived from analyses of the combined sequence dataset of two mitochondrial genes, COII and COIII, showed that R. speratus populations cluster into two major clades comprising the Korean/southern Japanese populations and the northern Japanese populations. Analysis of population genetic structure showed strong genetic partitioning between populations of the two clades. To understand historical migration routes and current distributions, the phylogeographic history of R. speratus was inferred from intra-/interspecific phylogeny and divergence times estimated between the clades of the phylogenetic tree. The estimated migration route and divergence time of ancestral R. speratus are congruent with recent paleogeographic hypotheses involving land-bridge connections between the Asian continent and the Japanese Archipelago. We suggest that ancestral R. speratus separated into northern and southern Japanese populations after its migration into the Japanese main islands from East China during the early Pleistocene via the East China Sea basin, which may have been exposed during that period. The Korean populations seem to have diverged recently from southern Japanese populations; this may explain the current distribution of R. speratus in the Japanese Arachipelago, and account for why it is restricted to northern areas of the Tokara Strait.