• Proceedings of the National Institute of Ecology of the Republic of Korea
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• v.2 no.1
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• pp.32-41
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• 2021

South Korea presently harbors less than 800 long-tailed gorals (Naemorhedus caudatus), an endangered species. I report for the first time on the taxonomic status and genetic diversity of the Korean species using non-invasive fecal sampling based on mitochondrial cytochrome b gene sequence analyses. To determine the taxonomic status of this species, I reconstructed a consensus neighbor-joining tree and generated a minimum spanning network combining haplotype sequences obtained from feces with a new goral-specific primer set developed using known sequences of the Korean goral and related species (e.g., Russian goral, Chinese goral, Himalayan goral, Japanese serow, etc.). I also examined the genetic diversity of this species. The Korean goral showed only three different haplotypes. The phylogenetic tree and parsimony haplotype network revealed a single cluster of Korean and Russian gorals, separate from related species. Generally, the Korean goral has a relatively low genetic diversity compared with that of other ungulate species (e.g., moose and red deer). I preliminarily showcased the application of non-invasive fecal sampling to the study of genetic characteristics, including the taxonomic status and genetic diversity of gorals, based on mitochondrial DNA. More phylogenetic studies are necessary to ensure the conservation of goral populations throughout South Korea.

• Korean Journal of Microbiology
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• v.49 no.3
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• pp.282-285
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• 2013

Microbial diversities in the 300 m and 500 m deep seawaters near Goseong, Gangwon Province (South Korea), were investigated. Pyrosequencing of 16S rRNA genes of marine microbes resulted in 19,474 reads from the 300 m deep seawaters, which consisted of Alphaproteobacteria (57.41%) and Gammaproteobacteria (38.85%), and 82,806 reads from the 500 m deep seawaters, which consisted of Gammaproteobacteria (99.64%) mostly. Rhodobacterales (57.31%) were dominant in the 300 m deep seawaters, but Alteromonadales (45.65%) and Oceanospirillales (34.61%) were dominant in the 500 m deep seawaters. On the bases of operational taxonomic units and diversity indexes (Shannon and Simpson), biodiversity of marine bacteria in the 500 m deep seawaters was shown to be higher than that in the 300 m deep seawaters.

• Journal of Species Research
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• v.5 no.3
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• pp.333-342
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• 2016

Based on the taxonomic survey to uncover the ciliate diversity in the eastern Kangwon-province, twenty-six species were identified from moss-covered soils and assigned to 5 classes, 9 orders, 12 families, and 15 genera. Of these, fifteen species are first records from Korea, and brief remarks with photographs were provided.

• Mycobiology
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• v.41 no.3
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• pp.121-125
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• 2013

Arbuscular mycorrhizal fungi (AMF) have mutualistic relationships with more than 80% of terrestrial plant species. This symbiotic relationship is ancient and would have had important roles in establishment of plants on land. Despite their abundance and wide range of relationship with plant species, AMF have shown low species diversity. However, molecular studies have suggested that diversity of these fungi may be much higher, and genetic variation of AMF is very high within a species and even within a single spore. Despite low diversity and lack of host specificity, various functions have been associated with plant growth responses to arbuscular mycorrhizal fungal colonization. In addition, different community composition of AMF affects plants differently, and plays a potential role in ecosystem variability and productivity. AMF have high functional diversity because different combinations of host plants and AMF have different effects on the various aspects of symbiosis. Consequently, recent studies have focused on the different functions of AMF according to their genetic resource and their roles in ecosystem functioning. This review summarizes taxonomic, genetic, and functional diversities of AMF and their roles in natural ecosystems.

• Proceedings of the Korean Society for Bioinformatics Conference
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• 2003.10a
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• pp.26-51
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• 2003

Large scale protein interaction maps provide a new, global perspective with which to analyse protein function. PSIMAP, the Protein Structural Interactome Map, is a database of all the structurally observed interactions between superfamilies of protein domains with known three-dimensional structure in thePDB. PSIMAP incorporates both functional and evolutionary information into a single network. It makes it possible to age protein domains in terms of taxonomic diversity, interaction and function. One consequence of it is to predict the most important protein domain structure in evolution. We present a global analysis of PSIMAP using several distinct network measures relating to centrality, interactivity, fault-tolerance, and taxonomic diversity. We found the following results: ${\bullet}$ Centrality: we show that the center and barycenter of PSIMAP do not coincide, and that the superfamilies forming the barycenter relate to very general functions, while those constituting the center relate to enzymatic activity. ${\bullet}$ Interactivity: we identify the P-loop and immunoglobulin superfamilies as the most highly interactive. We successfully use connectivity and cluster index, which characterise the connectivity of a superfamily's neighbourhood, to discover superfamilies of complex I and II. This is particularly significant as the structure of complex I is not yet solved. ${\bullet}$ Taxonomic diversity: we found that highly interactive superfamilies are in general taxonomically very diverse and are thus amongst the oldest. This led to the prediction of the oldest and most important protein domain in evolution of lift. ${\bullet}$ Fault-tolerance: we found that the network is very robust as for the majority of superfamilies removal from the network will not break up the network. Overall, we can single out the P-loop containing nucleotide triphosphate hydrolases superfamily as it is the most highly connected and has the highest taxonomic diversity. In addition, this superfamily has the highest interaction rank, is the barycenter of the network (it has the shortest average path to every other superfamily in the network), and is an articulation vertex, whose removal will disconnect the network. More generally, we conclude that the graph-theoretic and taxonomic analysis of PSIMAP is an important step towards the understanding of protein function and could be an important tool for tracing the evolution of life at the molecular level.

• Mycobiology
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• v.50 no.1
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• pp.55-65
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• 2022

Lichen is a symbiotic mutualism of mycobiont and photobiont that harbors diverse organisms including endolichenic fungi (ELF). Despite the taxonomic and ecological significance of ELF, no comparative investigation of an ELF community involving isolation of a pure culture and high-throughput sequencing has been conducted. Thus, we analyzed the ELF community in Parmotrema tinctorum by culture and metabarcoding. Alpha diversity of the ELF community was notably greater in metabarcoding than in culture-based analysis. Taxonomic proportions of the ELF community estimated by metabarcoding and by culture analyses showed remarkable differences: Sordariomycetes was the most dominant fungal class in culture-based analysis, while Dothideomycetes was the most abundant in metabarcoding analysis. Thirty-seven operational taxonomic units (OTUs) were commonly observed by culture-and metabarcoding-based analyses but relative abundances differed: most of common OTUs were underrepresented in metabarcoding. The ELF community differed in lichen segments and thalli in metabarcoding analysis. Dissimilarity of ELF community intra lichen thallus increased with thallus segment distance; inter-thallus ELF community dissimilarity was significantly greater than intra-thallus ELF community dissimilarity. Finally, we tested how many fungal sequence reads would be needed to ELF diversity with relationship assays between numbers of lichen segments and saturation patterns of OTU richness and sample coverage. At least 6000 sequence reads per lichen thallus were sufficient for prediction of overall ELF community diversity and 50,000 reads per thallus were enough to observe rare taxa of ELF.

• Animal Systematics, Evolution and Diversity
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• v.25 no.1
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• pp.65-80
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• 2009

Pyrgotidae is a small acalyptrate family including about 370 species worldwide and little attention has been given to their systematics until recently. Latest changes in taxonomic status of some of the Korean species made this review inevitable. In the present study, the Korean pyrgotid species are reviewed with discussion of their taxonomic status. We also provide a revised key to all 14 Korean species (seven Adapsilia, three Eupyrgota, two Parageloemyia, one Porpomastix, and one Tephritopyrgota species) supplemented by digital images to facilitate accurate identification.

• Animal cells and systems
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• v.1 no.2
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• pp.305-311
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• 1997

Dermaptera was investigated, examined and reviewed in taxonomy and for distribution in Youngnam region. Based on the data, the local species groups were measured to choose priority-conservation-area by taxonomic root weighting and distribution analysis at 232 geographical conservation units. Eleven species belonging to 4 families and 8 genera were recorded mounting up to 68.75% of species diversity known in Korea. Found remarkably were the rare and endangered Challia fletcheri Burr at Sobaek Mountain National Park, and unusually Anisolabis maritima (Bonelli) in Taegu, Euborellia pallipes (Shiraki) at Island Geoje and E. plebeja (Dohrn) at Hwanho near Pohang. The highest species diversity was found at the temple Huibang area at Sobaek Mountain National Park with 8 species, which was measured also as the primary priority-conservation-area with 83.41 % of accumulated taxonomic root weighting indices in percentage. Geoje and Hwanho both measured as 12.18% of accumulated taxonomic root weighting index in percentage and complimentary to Sobaek Mountain National Park but supporting 5 and 3 species, respectively. The priority goes to the geographical conservation unit supporting higher species richness between two geographical conservation units in comparison. By the rule, the second priority-conservation-area should be Geoje and the third Hwanho. It is, thus, demonstrated how 11 species can be all conserved by choosing 3 priority-conservation-areas out of 232 geographical conservation units to maintain maximum species in minimum areas.

• Journal of Ecology and Environment
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• v.48 no.2
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• pp.144-151
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• 2024

Background: This study focused on the diet of Clithon retropictum, level II endangered species in Korea. Since the development of brackish water zones has led to a decline in the population of this species, to obtain information on the ecology of C. retropictum required for its conservation and restoration. To investigate the actual preys of C. retropictum in south coast of Korea, we conducted high-throughput sequencing and metabarcoding techniques to extract DNA from gut contents and periphyton in their habitats. Results: Total 118 taxonomic groups were detected from periphyton samples. 116 were Chromista and Cyanobacteria dominated in the most samples. In gut contents samples, 98 taxonomic groups were detected. Similar to the results of periphyton, 96 were Chromista and Cyanobacteria dominated in the most samples. In the principal component analysis based on the presence/absence of taxonomic groups, gut content composition showed more clustered patterns corresponding to their habitats. Bryophyta was the most crucial taxonomic group explaining the difference between periphyton and gut contents compositions of C. retropictum. Conclusions: Our finding suggests that C. retropictum may not randomly consume epilithic algae but instead, likely to supplement their diet with Bryophyta.

• Journal of Veterinary Science
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• v.22 no.3
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• pp.37.1-37.14
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• 2021

Background: Ticks are one of the most common external parasites in dogs, and are associated with the transmission of a number of major zoonoses, which result in serious harm to human health and even death. Also, the increasing number of pet dogs and pet owners in China has caused concern regarding human tick-borne illnesses. Accordingly, studies are needed to gain a complete understanding of the bacterial composition and diversity of the ticks that parasitize dogs. Objectives: To date, there have been relatively few reports on the analysis of the bacterial community structure and diversity in ticks that parasitize dogs. The objective of this study was to investigate the microbial composition and diversity of parasitic ticks of dogs, and assessed the effect of tick sex and geographical region on the bacterial composition in two tick genera collected from dogs in China. Methods: A total of 178 whole ticks were subjected to a 16S ribosomal RNA (rRNA) next generation sequencing analysis. The Illumina MiSeq platform targeting the V3-V4 region of the 16S rRNA gene was used to characterize the bacterial communities of the collected ticks. Sequence analysis and taxonomic assignment were performed using QIIME 2 and the GreenGene database, respectively. After clustering the sequences into taxonomic units, the sequences were quality-filtered and rarefied. Results: After pooling 24 tick samples, we identified a total of 2,081 operational taxonomic units, which were assigned to 23 phyla and 328 genera, revealing a diverse bacterial community profile. The high, moderate and low prevalent taxa include 46, 101, and 182 genera, respectively. Among them, dominant taxa include environmental bacterial genera, such as Psychrobacter and Burkholderia. Additionally, some known tick-associated endosymbionts were also detected, including Coxiella, Rickettsia, and Ricketssiella. Also, the potentially pathogenic genera Staphylococcus and Pseudomonas were detected in the tick pools. Moreover, our preliminary study found that the differences in microbial communities are more dependent on the sampling location than tick sex in the tick specimens collected from dogs. Conclusions: The findings of this study support the need for future research on the microbial population present in ticks collected from dogs in China.