• Korean Journal of Plant Resources
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• v.31 no.1
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• pp.37-51
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• 2018

Molecular phylogenetic analysis was conducted to evaluate the taxonomic relationships of genus Arisaema L. distributed in Korea and the molecular phylogenetic characteristics of three authentic Arisaema species for the herbal medicine Arisaematis Rhizoma (the rhizomes of A. amurense, A. heterophyllum, and A. erubescens). The sequences of three DNA barcodes (rDNA-ITS, matK, and rbcL) were analyzed using 50 samples of nine taxa consisted of eight Korean and one Chinese Arisaema with one outgroup (Dracunculus vulgaris). Both individual and combined phylogenetic analyses of three DNA barcode sequences revealed that the treated nine taxa are independently classified into six distinct clades (Clade I, A. amurense f. amurense and A. amurense f. serratum; Clade II, A. serratum and A. takesimense; Clade III, A. ringens; Clade IV, A. erubescens; Clade V, A. heterophyllum; Clade VI, A. thunbergii subsp. thunbergii and A. thunbergii subsp. geomundoense). These six clades were reasonably divided into three individual sections, Pedatisecta, Sinarisaema, and Tortuosa. Futhermore, the results of comparative DNA barcode sequences analyses provided a significant information for the taxonomic reconsideration of Arisaema L. at the specific and intraspecific level. However, we could not confirm the taxonomic characteristics or identity among the three authentic medicinal species through the molecular phylogenetic analyses of genus Arisaema L. for Arisaematis Rhizoma.

• Korean Journal of Plant Taxonomy
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• v.37 no.1
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• pp.1-15
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• 2007

Phylogenetic studies were conducted for 42 populations of Korean viola based on matK gene and atpB-rbcL intergenic spacer region of chloroplast DNA. In the matK tree, section Chamaemelanium and Dischidium were formed as a distinct group. Five subsections of section Nomimium were paraphyletic. In atpB-rbcL intergenic spacer region analysis, two species of sect. Chamaemelanium were monophyletic, and section Dischidium was placed sister to subsection patellares clade except for V. keiskei. Five subsections of section Nomimium were also paraphyletic as matK tree. the separate data analyses were incongruent in the relationships among 42 populations, especially for the position of section Dischidium and V. keiskei. The combined analyses of two chloroplast regions showed three major clades; section Chamaemelanium and Dischidium (x=6) formed a sister to subsections Hypocarpae and Trigonocarpae (x=10) clade; subsections Bilobatae and vaginatae (x=10 or 12) formed a clade with V. keiskei; and 19 populations of subsection patellares (x=12) except for V. keiskei were recognized as an independent clade within section Nomimium. Although combined data suggest three major clades of Korean viola, the origins of each clade from outgroup were discordance with previous ITS and trnL-F data.

• ALGAE
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• v.31 no.3
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• pp.231-241
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• 2016

We examined the genetic diversity and abundance of picocyanobacteria using barcoded amplicon sequencing approaches and flow cytometry in the East Sea and the East China Sea to determine the distribution patterns of diversity during spring in seas adjacent to the Korean Peninsula. Synechococcus clades I and IV, which have been known as cold-adapted ecotypes, dominated at most stations. However, the relative abundances of the two dominant clades differed in their spatial patterns. Clade I was exclusively dominant in the shelf area of the East China Sea and the north East Sea. However, the dominant genotypes belonging to clade I had different spatial distributions in the two areas and responded oppositely to seawater temperature. The dominance of distinct genotypes under the different ecological conditions suggests the presence of ecologically different ecotypes within the clade. Abundances of clade IV were greater than those of clade I at most stations in the southwest East Sea, showing an apparently different pattern from that of the other areas. A warm-water adapted clade II was observed at significant levels only at stations located in the eastern East China Sea affected by a branch of the warm Kuroshio Current. These results suggest that the physicochemical properties of influencing water masses play an important role in determining the distribution of Synechococcus genotypes.

• Journal of Life Science
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• v.18 no.6
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• pp.753-758
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• 2008

Genus Hemerocallis is a herbaceous species and some species among their taxa are very important herbal medicines. We evaluated representative samples of the eight taxa in Korea with inter simple sequence repeats (ISSR) markers to estimate phylogenetic relationships within taxa of this genus. The studied taxa were Hemerocallis fulva L., H. fulva for. kwanso, H. dumortieri Morren, H. coreana Nakai, H. hongdoensis M.G.Chung & S.S.Kang, H. middendorffi Trautv. et Mayer, H. thunbergii Baker, H. minor Miller. In addition, we investigated the genetic variation and structure of Korean populations of these taxa. The mean genetic diversity was 0.098 across species, varying from 0.068 to 0.123. A low level of genetic variation was found in populations of Hemerocallis species. Specially, gene diversity for H. minor was maintained the highest among genus Hemerocallis. An indirect estimate of the number of migrants per generation (Nm=0.218) indicated that gene flow was not extensive among Korean populations of Hemerocallis species. The phylogenic tree showed distinct three clades. One includes H. fulva, H. fulva for. kwanso and H. middendorffi. Another includes three Hemerocallis species, H. dumortieri, H. thunbergii and H. minor. The H. coreana and H. hongdoensis were shown as the sister group to the second clades. Although the size of sampling was not large enough for eight Korean Hemerocallis species, the analyses of ISSRs will certainly provide an enhanced view on the phylogeny of species.

• Journal of the Korean Society of Marine Environment & Safety
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• v.27 no.7
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• pp.924-942
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• 2021

The expansion of the Changjiang Diluted Water (CDW) plume during summer is known to be a major factor influencing phytoplankton diversity, community structure, and the regional marine environment of the northern East China Sea (ECS). The discharge of the CDW plume was very high in the summer of 2020, and cruise surveys and stationary monitoring were conducted to understand the dynamics of changes in environmental characteristics and the impact on phytoplankton diversity and community structure. A cruise survey was conducted from August 16 to 17, 2020, using R/V Eardo, and a stay survey at the Ieodo Ocean Research Station (IORS) from August 15 to 21, 2020, to analyze phytoplankton diversity and community structure. The southwestern part of the survey area exhibited low salinity and high chlorophyll a fluorescence under the influence of the CDW plume, whereas the southeastern part of the survey area presented high salinity and low chlorophyll a fluorescence under the influence of the Tsushima Warm Current (TWC). The total chlorophyll a concentrations of surface water samples from 12 sampling stations indicated that nano-phytoplankton (20-3 ㎛) and micro-phytoplankton (> 20 ㎛) were the dominant groups during the survey period. Only stations strongly influenced by the TWC presented approximately 50% of the biomass contributed by pico-phytoplankton (< 3 ㎛). The size distribution of phytoplankton in the surface water samples is related to nutrient supplies, and areas where high nutrient (nitrate) supplies were provided by the CDW plume displayed higher biomass contribution by micro-phytoplankton groups. A total of 45 genera of nano- and micro-phytoplankton groups were classified using morphological analysis. Among them, the dominant taxa were the diatoms Guinardia flaccida and Nitzschia spp. and the dinoflagellates Gonyaulax monacantha, Noctiluca scintillans, Gymnodinium spirale, Heterocapsa spp., Prorocentrum micans, and Tripos furca. The sampling stations affected by the TWC and low in nitrate concentrations presented high concentrations of photosynthetic pico-eukaryotes (PPE) and photosynthetic pico-prokaryotes (PPP). Most sampling stations had phosphate-limited conditions. Higher Synechococcus concentrations were enumerated for the sampling stations influenced by low-nutrient water of the TWC using flow cytometry. The NGS analysis revealed 29 clades of Synechococcus among PPP, and 11 clades displayed a dominance rate of 1% or more at least once in one sample. Clade II was the dominant group in the surface water, whereas various clades (Clades I, IV, etc.) were found to be the next dominant groups in the SCM layers. The Prochlorococcus group, belonging to the PPP, observed in the warm water region, presented a high-light-adapted ecotype and did not appear in the northern part of the survey region. PPE analysis resulted in 163 operational taxonomic units (OTUs), indicating very high diversity. Among them, 11 major taxa showed dominant OTUs with more than 5% in at least one sample, while Amphidinium testudo was the dominant taxon in the surface water in the low-salinity region affected by the CDW plume, and the chlorophyta was dominant in the SCM layer. In the warm water region affected by the TWC, various groups of haptophytes were dominant. Observations from the IORS also presented similar results to the cruise survey results for biomass, size distribution, and diversity of phytoplankton. The results revealed the various dynamic responses of phytoplankton influenced by the CDW plume. By comparing the results from the IORS and research cruise studies, the study confirmed that the IORS is an important observational station to monitor the dynamic impact of the CDW plume. In future research, it is necessary to establish an effective use of IORS in preparation for changes in the ECS summer environment and ecosystem due to climate change.

• ALGAE
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• v.34 no.4
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• pp.289-301
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• 2019

Mixotrophy in marine organisms is an important aspect of ecology and evolution. The discovery of mixotrophic abilities in phototrophic dinoflagellates alters our understanding of the dynamics of red tides. In the phototrophic dinoflagellate genus Alexandrium, some species are mixotrophic, but others are exclusively autotrophic. There are differences in the ecological roles of autotrophic and mixotrophic Alexandrium in marine food webs. However, of the 34 known Alexandrium species, the mixotrophic ability of >20 species has yet to be explored. In this study, the mixotrophic capabilities of Alexandrium insuetum CCMP2082, Alexandrium mediterraneum CCMP3433, Alexandrium pacificum CCMP3434, Alexandrium tamutum ATSH1609, and Alexandrium margalefii CAWD10 were investigated by providing each species with 22 diverse prey items including bacterium-sized microbeads (1 ㎛), the cyanobacterium Synechococcus sp., algal prey species, and the ciliate Mesodinium rubrum. None of the 5 Alexandrium species fed on any of the prey items. These results increase the number of Alexandrium species lacking mixotrophic abilities to 9, compared to the 7 known mixotrophic Alexandrium species. Furthermore, the Alexandrium phylogenetic tree based on the large subunit ribosomal DNA contained 3 large clades, each of which had species with and without mixotrophic abilities. Thus, the acquisition or loss of mixotrophic abilities in Alexandrium might readily occur.

• Parasites, Hosts and Diseases
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• v.55 no.1
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• pp.47-54
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• 2017

The prevalence of cercarial infection in freshwater snails and their evolutionary trends were studied in Nakhon Nayok province, Thailand. A total of 2,869 individual snails were examined for parasitic infections. The results showed that 12 snail species were found to host larval stages of trematodes with an overall prevalence of 4.7%. The infected specimens included 7 types at the cercarial stage; cercariae, megalurous cercariae, echinostome cercariae, furcocercous cercariae, parapleurolophocercous cercariae, virgulate cercariae, and xiphidiocercariae. Regarding molecular identification, ITS2 sequence data of each larval trematode were analyzed, and a dendrogram was constructed using the neighbor-joining method with 10,000 replicates. The dendrogram was separated into 6 clades (order/family), including Echinostomatida/Echinostomatidae, Echinostomatida/Philophthalmidae, Opisthorchiida/Heterophyidae, Plagiorchiida/Prosthogonimidae, Plagiorchiida/Lecithodendriidae, and Strigeatida/Cyathocotylidae. These findings were used to confirm morphological characteristics and evolutionary trends of each type of cercariae discovered in Nakhon Nayok province. Furthermore, this investigation confirmed that the ITS2 data of cercariae could be used to study on phylogenetic relationships or to determine classification of this species at order and/or family level when possible.

• Korean Journal of Oriental Medicine
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• v.14 no.1
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• pp.129-135
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• 2008

Phylogenetic relationship and DNA polymorphism among local populations of the Asparagus cochinchinensis have been investigated based on nuclear ribosomal DNA ITS sequences and RAPD analysis in Korea. In result, two genetically distinct groups of local populations except Geoje were recognized by the phylogenetic tree both in rDNA-ITS and RAPD. One was called 'western coast group' that includes the Buan 1, 2 and Taean and the other was 'southern coast group' that includes Haenam, Yeosu and Namhae. Thus, the geographical relationship of Asparagus cochinchinensis was two well-typified clades. These results suggest that the geographical genetic variation of Asparagus cochinchinensis is closely connected with the slow and long period of propagation via the coast in Korean Peninsula.

• ALGAE
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• v.33 no.1
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• pp.69-84
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• 2018

We examined the species diversity of Herposiphonia on Korean coasts, based on a combination of morphology and molecular analyses of the mitochondrial COI-5P DNA barcode marker and plastid rbcL gene. We report the presence of eight species including three novel species: H. donghaensis sp. nov., H. jejuinsula sp. nov., H. sparsa sp. nov., H. caespitosa, H. fissidentoides, H. insidiosa, H. parca, and H. subdisticha. Specimens were separated into eight clades in both the COI-5P and rbcL gene analyses, with 1.3-19.6 and 6.6-15% interspecific sequence divergence, respectively. These eight species are also distinguishable by several morphological characteristics such as: branching pattern (d/i pattern in H. donghaensis sp. nov. and H. sparsa sp. nov.; d/d/d/i pattern in others), shape of determinate branch (ligulate in H. fissidentoides; terete in others), number of vegetative trichoblasts (1-2 in H. insidiosa and H. sparsa sp. nov.; 3-4 in H. caespitosa; absent in others), and number of segments and pericentral cells in determinate branches. About three novel species revealed by our analyses, H. donghaensis sp. nov. is newly discovered, and H. jejuinsula sp. nov. and H. sparsa sp. nov. were previously reported in Korea as H. nuda and H. secunda, respectively. Our results show that DNA barcoding and rbcL analyses are useful for delimiting species boundaries and discovering cryptic species diversity in the genus Herposiphonia.

• Journal of Microbiology and Biotechnology
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• v.13 no.6
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• pp.846-852
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• 2003

rpoB DNAs (279 bp) from 34 species of 5 actinomycete genera were sequenced and a phylogenetic tree was constructed based on the sequences obtained. The genera were clearly differentiated in the rpoB tree, forming clades specific to their respective genus. In addition, 2 signature amino acid residues specific to Streptomyces were found in a multiple alignment of the deduced amino acid sequences. To empirically confirm that this rpoB gene analysis system could be used to differentiate actinomycete isolates, the proposed system was used to identify 16 actinomycete isolates from Jeju Island. All isolates were successfully differentiated into the genera Streptomyces and Micromonospora. Accordingly, this is the first report that an rpoB sequence analysis has been effectively used to differentiate actinomycete strains at the genus level.