• Research in Plant Disease
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• v.28 no.2
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• pp.57-60
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• 2022

Leaves of Chionanthus retusus were found to be damaged by leaf spot disease associated with a fungus in Iksan, Korea. Leaf spots were angular to irregular, vein-limited, scattered, 1-8 mm diameter, brownish-gray to dark brown when dry, with heavy fructification. The pathogen causes premature defoliation of C. retusus plant and was identified as Pseudocercospora chionanthi-retusi based on morphological and molecular-phylogenetic analyses. The phylogenetic tree was constructed using multi-locus DNA sequence data of partial actin (actA), partial translation elongation factor 1-alfa (tef1), partial DNA-directed RNA polymerase II second largest subunit (rpb2) genes, and internal transcribed spacer regions. Current study provides detail morphological description of P. chionanthi-retusi on C. retusus in Korea, with supports of phylogenetic analysis and pathogenicity test.

• Proceedings of the Microbiological Society of Korea Conference
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• 1997.04a
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• pp.54.2-54.2
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• 1997

• Korean Journal of Medicinal Crop Science
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• v.18 no.6
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• pp.379-388
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• 2010

Adenophora racemosa is recently reported as a new Korean endemic plant species. However, the phylogenetic relationship of this genus has been controversial due to the morphological similarity and frequent morphological change of aerial parts. To verify the phylogenetic position of Adenophora racemosa and phylogenetic relationship of genus Adenophora, we analyzed the internal transcribed spacer (ITS) sequence of nuclear ribosomal DNA (nrDNA) and random amplified polymorphic DNA (RAPD) using 21 individual of 6 Adenophora species, A. verticillata, A. divaricata, A. racemosa, A. remotiflora, A. stricata and A. tetraphylla. In comparative analysis of the nrDNA-ITS sequences, we could not found not only any species specific nucleotide sequence but also could not estimated their inter or intra species. In the phylogenic analysis based on the RAPD derived DNA polymorphism, Adenophora species were classified into four groups by clustering analysis of the UPGMA. These results suggest that the DNA fingerprinting based on RAPD is more suitable than nrDNA-ITS sequence for the phylogenetic analysis of Adenophora species.

• Parasites, Hosts and Diseases
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• v.60 no.4
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• pp.273-279
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• 2022

Laelapinae mites are involved in transmission of microbial diseases between wildlife and humans, with an impact on public health. In this study, 5 mite members in the subfamily Laelapinae (laelapin mites; LM) were morphologically identified by light microscopy, and the phylogenetic relationship of LM was analyzed in combination with the sequence information of part of the LM cytochrome oxidase subunit I (cox1) gene. The morphological identification revealed that 5 mites belonged to the genera Laelaps and Haemolaelaps, respectively. Sequence analysis showed that the ratio of nonsynonymous mutation rate to synonymous mutation rate of LM was less than 1, indicating that the LM cox1 gene had undergone purifying selection. Phylogenetic analysis showed that the Laelapinae is a monophyletic group. The genera Haemolaelaps and Hyperlaelaps did not separated into distinct clades but clustered together with species of the genus Laelaps. Our morphological and molecular analyses to describe the phylogenetic relationships among different genera and species of Laelapinae provide a reference for the improvement and revision of the LM taxonomy system.

• Korean Journal of Plant Taxonomy
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• v.50 no.1
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• pp.8-16
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• 2020

Complete chloroplast genome sequences provide detailed information about any structural changes of the genome, instances of phylogenetic reconstruction, and molecular markers for fine-scale analyses. Recent developments of next-generation sequencing (NGS) tools have led to the rapid accumulation of genomic data, especially data pertaining to chloroplasts. Short reads deposited in public databases such as the Sequence Read Archive of the NCBI are open resources, and the corresponding chloroplast genomes are yet to be completed. The V. dilatatum complex in Korea consists of four morphologically similar species: V. dilatatum, V. erosum, V. japonicum, and V. wrightii. Previous molecular phylogenetic analyses based on several DNA regions did not resolve the relationship at the species level. In order to examine the level of variation of the chloroplast genome in the V. dilatatum complex, raw reads of V. dilatatum deposited in the NCBI database were used to reconstruct the whole chloroplast genome, with these results compared to the genomes of V. erosum, V. japonicum, and three other species in Viburnum. These comparative genomics results found no significant structural changes in Viburnum. The degree of interspecific variation among the species in the V. dilatatum complex is very low, suggesting that the species of the complex may have been differentiated recently. The species of the V. dilatatum complex share large unique deletions, providing evidence of close relationships among the species. A phylogenetic analysis of the entire genome of the Viburnum showed that V. dilatatum is a sister to one of two accessions of V. erosum, making V. erosum paraphyletic. Given that the overall degree of variation among the species in the V. dilatatum complex is low, the chloroplast genome may not provide a phylogenetic signal pertaining to relationships among the species.

• Animal cells and systems
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• v.4 no.1
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• pp.77-85
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• 2000

This study has demonstrated the molecular variation of 5S rRNA genes in 15 Allium subgenus Rhizirideum and 1 Allium subg. Allium. For cloning of the 5S rRNA genes, PCR products were obtained from amplification with oligonucleotide primers which were derived from the conserved coding region of 5S rRNA genes. These amplified PCR products were cloned and identified by FISH and sequence analysis. The 5S rRNA loci were primarily located on chromosomes 5 and/or 7 in diploid species and various chromosomes in alloploid species. The size of the coding region of 5S rRNA genes was 120 bp in all the species and the sequences were highly conserved within Allium species. The sizes of nontranscribed spacer (NTS) region were varied from 194 bp (A. dektiude-fustykisum, 2n=16) to 483 bp (A. sativum). Two kinds of NTS regions were observed in A. victorialis var. platyphyllum a diploid, A. wakegi an amphihaploid, A. sacculiferum, A. grayi, A. deltoide-fistulosum and A. wenescens all allotetraploids, while most diploid species showed only one NTS region. The species containing two components of NTS region were grouped with different diploid species in a phylogenetic tree analysis using the sequences of 5S rRNA genes and adjacent non-coding regions.

• Genomics & Informatics
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• v.7 no.1
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• pp.26-31
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• 2009

Heat shock proteins are a class of molecular chaperones that can be found in nearly all organisms from Bacteria, Archaea and Eukarya domains. Heat shock proteins experience increased transcription during periods of heat induced osmotic stress and are involved in protein disaggregation and refolding as part of a cell's danger signaling cascade. Heat shock protein, Hsp20 is a small molecular chaperone that is approximately 20kDa in weight and is hypothesized to prevent aggregation and denaturation. Hsp20 can be found in several strains of Proteobacteria, which comprises the largest phyla of the Bacteria domain and also contains several medically significant bacterial strains. Genomic analyses were performed to determine a common evolutionary pattern among Hsp20 sequences in Proteobacteria. It was found that Hsp20 shared a common ancestor within and among the five subclasses of Proteobacteria. This is readily apparent from the amount of sequence similarities within and between Hsp20 protein sequences as well as phylogenetic analysis of sequences from proteobacterial and non-proteobacterial species.

• Journal of fish pathology
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• v.35 no.1
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• pp.135-140
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• 2022

In this study, we determined the cause of a disease outbreak in small yellow croaker(Larimichthys polyactis) in Jeju island. The major external signs in the dead fish were hemorrhage of the skin. Vibrio harveyi were isolated from a few fishes and viruses were not detected from the diseased fish. However, flukes were confirmed on the skin and we conducted molecular identification and phylogenetic analysis of the isolated parasites. The obtained 28S rRNA sequence of our specimen(Accession No. OM333244) showed the highest homology with Neobenedenia girellae, while the COI sequence of our specimen showed the highest homology with N. melleni. Further sequence analysis with other genes and morphological observation are necessary for accurate identification.

• Mycobiology
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• v.49 no.2
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• pp.188-195
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• 2021

The genus Pseudoperonospora, an obligate biotrophic group of Oomycota, causes the most destructive foliar downy mildew disease on many economically important crops and wild plants. A previously unreported disease by Pseudoperonospora was found on oriental pickling melon (Cucumis melo var. conomon) in Korea, which is a minor crop cultivated in the temperate climate zone of East Asia, including China, Korea, and Japan. Based on molecular phylogenetic and morphological analyses, the causal agent was identified as Pseudoperonospora cubensis, and its pathogenicity has been proven. Importantly, two phylogenetic clades of P. cubensis, harboring probably two distinct species, were detected within the same plots, suggesting simultaneous coexistence of the two clades. This is the first report of P. cubensis causing downy mildew on oriental pickling melon in Korea, and the confirmation of presence of two phylogenetic clades of this pathogen in Korea. Given the high incidence of P. cubensis and high susceptibility of oriental pickling melon to this disease, phytosanitary measures, including rapid diagnosis and effective control management, are urgently required.

• Journal of Species Research
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• v.8 no.3
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• pp.313-317
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• 2019

Bats influence overall ecosystem health by regulating species diversity and being a major source of zoonotic viruses. Hence, there is a need to elucidate their migration, population structure, and phylogenetic relationship. The complete mitochondrial genome is widely used for studying the genome-level characteristics and phylogenetic relationship of various animals due to its high mutation rate, simple structure, and maternal inheritance. In this study, we determined the complete mitogenome sequence of the bird-like noctule (Nyctalus aviator) by Illumina next-generation sequencing. The sequences obtained were used to reconstruct a phylogenic tree of Vespertilionidae to elucidate the phylogenetic relationship among its members. The mitogenome of N. aviator is 16,863-bp long with a typical vertebrate gene arrangement, consisting of 13 protein-coding genes (PCGs), 22 transfer RNA genes, 2 ribosomal RNA genes, and 1 putative control region. Overall, the nucleotide composition is as follows: 32.3% A, 24.2% C, 14.3% G, and 29.2% T, with a slight AT bias (61.5%). The base composition of the 13 PCGs is as follows: 30.3% A, 13.4% G, 31.0% T, and 25.2% C. The phylogenetic analysis, based on 13 concatenated PCG sequences, infers that N. aviator is closely related to N. noctula with a high bootstrap value (100%).