• 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.

• The Plant Pathology Journal
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• v.24 no.3
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• pp.361-364
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• 2008

The complete nucleotide sequences of a Korean isolate of Potato virus X(PVX-Kr) has been determined. Full-length cDNA of PVX-Kr has been directly amplified by long template reverse transcription and polymerase chain reaction(RT-PCR) using virus specific 5'-end primer and 3'-end primer, and then constructed in a plasmid vector. Consecutive subclones of a full-length cDNA clone were constructed to identify whole genome sequence of the virus. Total nucleotide sequences of genome of PVX-Kr were 6,435 excluding one adenine at poly A tail, and genome organization was identical with that of typical PVX species. Comparison of whole genome sequence of PVX-Kr with those of European and South American isolates showed 95.4-96.8% and 77.4-77.9%, in nucleotide similarity, respectively. Sequenced PVX-Kr in this study and twelve isolates already reported could be divided into two subgroups in phylogeny based on their complete nucleotide sequences. Phylogenetic tree analysis demonstrated that PVX-Kr was clustered with European and Asian isolates(Taiwan, os, bs, Kr, S, X3, UK3, ROTH1, Tula) in the same subgroup and South American isolates(CP, CP2, CP4, HB) were clustered in the other subgroup.

• Journal of Life Science
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• v.11 no.5
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• pp.400-404
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• 2001

A new human endogenous retroviral family (HERV-S) has recently been identified from human X chromosome. It is 6.7 kb in length and has a typical retroviral structure with LTR-gag-pol-env-LTR. Using the PCR and sequencing approach, we investigated LTR elements of the HERV-S family from a human genomic DNA. Four LTR elements (HSL-1, HSL-5, HSL-10, HSL-11) were identified and have a high degree of sequence similarity(96-99%) with that of the HERV-S. Phylogenetic analysis from the HERV-S family indicated that the LTR elements were mainly divided into 2- groups through evolutionary divergence in the primate evolution. Further investigation of the HERV-S LTR elements in primates may cast light on the integration timing into the primate genome and understanding of human evolution.

• Journal of Aquaculture
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• v.22 no.1
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• pp.83-91
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• 2009

The Korean doty barbel Hemibarbus mylodon (Cypriniformes; Cyprinidae) is a critically endangered freshwater fish species mainly because of its natural habitat degradation. Three full-length complementary DNA (cDNA) clones representing different muscle actin isoforms were isolated and characterized. The three muscle actin isoforms were 1,294-1,601 bp long with the identical open reading frames of 1,134 bp with the deduced amino acid residues of 377. They showed 83.9-87.2% identities in the coding nucleotide level and 96.8-98.1% identities in the amino acid level. Phylogenetic analysis with the coding nucleotide sequences revealed that three muscle actin isoforms of H. mylodon formed strongly supported monophyletic groups with one of cypriniform skeletal $\alpha$-actin (acta1), cypriniform aortic $\alpha$-actins (acta2), and uncharacterized Danio rerio muscle actin isoform/Salmo trutta slow muscle actin (a novel muscle actin type). Our phylogenetic tree further suggested that cypriniform acta2 only showed the orthologous relationship to tetrapod acta2. Other multiple actin isoforms from diverse teleostean taxa were however clustered to no tetrapod orthologs, i.e., acta1, cardiac $\alpha$-actins (aetc1), acta2, and enteric $\gamma$-actin (actg2). This result strongly suggested that teleostean muscle actins have experienced different and complicated evolutionary history in comparison to mammalian counterparts.

• Journal of Microbiology and Biotechnology
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• v.9 no.6
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• pp.870-872
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• 1999

The ubiquinone and G+C contents of the bioflocculant-producing fungus, a new Aspergillus strain, were detennined using high-perfonnance liquid chromatography. The internal transcribed spacers 1 and 2 (ITS1 and ITS2), and the 5.8S ribosomal DNA (rDNA) of the strain were amplified and sequenced. The strain contained ubiquinone-l0($H_2$)as a major quinone and the G+C content was 49 mol%. A phylogenetic analysis of the ITS regions indicated that the strain belonged to the genus Aspergillus according to its previously classified morphological characteristics. Based on a sequence homology search, the strain was most closely related to Petromyces muricatus (anamorph, A. muricatus; accession number, AJ005674). The sequence of a new Aspergillus strain in ITS1 and ITS2, and 5.8S rDNA showed 97% homology to P. muricatus. Therefore, the strain is believed to be a new bioflocculant-producing Aspergillus strain.

• The Plant Pathology Journal
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• v.27 no.1
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• pp.1-7
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• 2011

Colletotrichum panacicola isolates were obtained from anthracnose lesions of Korean ginseng and compared with four Colletotrichum species in morphology, molecular phylogeny and pathogenicity. Based on morphological characteristics, C. panacicola was easily distinguished from Colletotrichum gloeosporioides but not from Colletotrichum higginsianum, Colletotrichum destructivum and Colletotrichum coccodes. A phylogenetic tree generated from ribosomal DNA-internal transcribed spacer sequences revealed that C. panacicola is remarkably distinguished from C. gloeosporioides and C. coccodes but not from C. higginsianum and C. destructivum. However, molecular sequence analysis of three combined genes (actin + elongation factor-$1{\alpha}$ + glutamine synthatase) provided sufficient variability to distinguish C. panacicola from other Colletotrichum species. Pathogencity tests showed that C. panacicola is pathogenic to Korean ginseng but not to other plants. These results suggest that C. panacicola is an independent taxon distin-zguishable from C. gloeosporioides and other morphologically similar Colletotrichum species.

• Parasites, Hosts and Diseases
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• v.59 no.1
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• pp.89-95
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• 2021

Microcotyle sebastis is a gill monogenean ectoparasite that causes serious problems in the mariculture of the Korean rockfish, Sebastes schlegelii. In this study, we isolated the parasite from fish farms along the coasts of Tongyeong, South Korea in 2016, and characterized its infection, morphology and molecular phylogeny. The prevalence of M. sebastis infection during the study period ranged from 46.7% to 96.7%, and the mean intensity was 2.3 to 31.4 ind./fish, indicating that the fish was constantly exposed to parasitic infections throughout the year. Morphological observations under light and scanning electron microscopes of the M. sebastis isolates in this study showed the typical characteristics of the anterior prohaptor and posterior opisthaptor of monogenean parasites. In phylogenetic trees reconstructed using the nuclear 28S ribosomal RNA gene and the mitochondrial cytochrome c oxidase I gene (cox1), they consistently clustered together with their congeneric species, and showed the closest phylogenetic relationships to M. caudata and M. kasago in the cox1 tree.

• The Plant Pathology Journal
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• v.37 no.1
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• pp.1-23
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• 2021

Resistance to diseases caused by turnip mosaic virus (TuMV) in crop species of the family Brassicaceae has been studied extensively, especially in members of the genus Brassica. The variation in response observed on resistant and susceptible plants inoculated with different isolates of TuMV is due to a combination of the variation in the plant resistome and the variation in the virus genome. Here, we review the breadth of this variation, both at the level of variation in TuMV sequences, with one eye towards the phylogeny and evolution of the virus, and another eye towards the nature of the various responses observed in susceptible vs. different types of resistance responses. The analyses of the viral genomes allowed comparisons of pathotyped viruses on particular indicator hosts to produce clusters of host types, while the inclusion of phylogeny data and geographic location allowed the formation of the host/geographic cluster groups, the derivation of both of which are presented here. Various studies on resistance determination in particular brassica crops sometimes led to further genetic studies, in many cases to include the mapping of genes, and in some cases to the actual identification of the genes. In addition to summarizing the results from such studies done in brassica crops, as well as in radish and Arabidopsis (the latter as a potential source of candidate genes for brassica and radish), we also summarize work done using nonconventional approaches to obtaining resistance to TuMV.

• Research in Plant Disease
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• v.28 no.3
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• pp.132-142
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• 2022

Plantation forests are established by planting Eucalyptus tree species to provide timber and pulp for the construction industries and to meet the energy needs in Ethiopia. Besides the extensive Eucalyptus plantations in the country, fungal pathogen-related diseases are the main challenges to successful production and management. The disease survey was conducted in the Eucalyptus growing areas of Ethiopia during 2019/2020 and 2020/2021. The objective of this research was to assess the diseases associated with Eucalyptus plant species and identify the causal fungal species. Plants of E. camaldulensis were the dominant species in the survey fields and were severely associated with stem and branch canker diseases. Diseased samples were collected and fungal species were identified as Didymellaceae according to culture morphology and affirmed by internal transcribed spacer sequence analysis. In phylogeny, isolates in the study and a reference strain formed supportive monophyletic clades with strong 90% and 95% support with Didymella coffeae-arabicae and Didymella pinodella respectively. Pathogenicity tests revealed that Didymellaceae could infect E. camaldulensis. The findings are the first reports of Eucalyptus stem canker disease caused by Didymellaceae in Ethiopia.

• Mycobiology
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• v.49 no.6
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• pp.559-581
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• 2021

The coastal marine ecosystems of Vietnam are one of the global biodiversity hotspots, but the biodiversity of marine fungi is not well known. To fill this major gap of knowledge, we assessed the genetic diversity (ITS sequence) of 75 fungal strains isolated from 11 surface coastal marine and deeper waters in Nha Trang Bay and Van Phong Bay using a culture-dependent approach and 5 OTUs (Operational Taxonomic Units) of fungi in three representative sampling sites using next-generation sequencing. The results from both approaches shared similar fungal taxonomy to the most abundant phylum (Ascomycota), genera (Candida and Aspergillus) and species (Candida blankii) but were different at less common taxa. Culturable fungal strains in this study belong to 3 phyla, 5 subdivisions, 7 classes, 12 orders, 17 families, 22 genera and at least 40 species, of which 29 species have been identified and several species are likely novel. Among identified species, 12 and 28 are new records in global and Vietnamese marine areas, respectively. The analysis of enzyme activity and the checklist of trophic mode and guild assignment provided valuable additional biological information and suggested the ecological function of planktonic fungi in the marine food web. This is the largest dataset of marine fungal biodiversity on morphology, phylogeny and enzyme activity in the tropical coastal ecosystems of Vietnam and Southeast Asia. Biogeographic aspects, ecological factors and human impact may structure mycoplankton communities in such aquatic habitats.