• Journal of Species Research
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• 제11권4호
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• pp.266-277
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• 2022

The current surveys of Ulva in the subtidal area around Jeju Island give a chance to discover unrecorded green algal species of the Korean macroalgal flora. As a result of this investigation, we found Ulva adhaerens Matusmoto & Shimada, inhabiting the subtidal regions, up to 15 m deep, and conducted the DNA barcoding on plastid rbcL-3P and tufA regions with describing the morphological characteristics. Our specimens of U. adhaerens forms a monophyletic clade with the Japanese type specimen and U. piritoka Ngāti Kuri, Heesch & W.A. Nelson from New Zealand exhibiting each 0.3% sequence divergences, respectively, in the plastid rbcL-3P. The genetic variation of U. adhaerens clade is 1.0-3.9% in rbcL-3P and 4.8-9.8% in tufA to each Ulva species, including the generic type, U. lactuca Linneaus. The morphology of Korean U. adhaerens specimens is identical to the type specimens of U. adhaerens from Japan having the development of rhizoidal filaments from both of the cell layers of the distromatic blade and the extension of rhizoidal clumps with adhesive trait between blades by extended rhizoidal clumps at the basal blades. The thallus attachment to substrate is by numerous minute discoidal plates made up of rhizoids originating from the inner part of distromatic blades in basal. Although there are still some problems to resolve the relationship between U. adhaerens and U. piritoka in the rbcL dataset and the phylogenetic pattern of the Group II intron of rbcL, we propose the new record of U. adhaerens in Korean macroalgal flora based on the morphological characteristics of Korean specimens. Continued study of the genus Ulva by morphological and molecular assessment will delimit the species of Ulva, elucidate the relationships between them, and uncover the species diversity.

• 한국응용곤충학회지
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• 제55권4호
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• pp.471-475
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• 2016

버섯파리는 국내 양송이 균상 재배지에서 발생하여 버섯 균사와 자실체를 가해하고 간접적으로는 병을 매개하여 피해는 해마다 증가하고 있다. 부여군 세도면, 보령시 성주면, 용인시 남사면, 칠곡군 약목면 등 총 4개 지역의 버섯 재배사에서 끈끈이트랩을 이용하여 채집한 버섯파리 성충을 DNA barcoding 방법으로 Cytochrome Oxidase I (COI)의 염기서열 분석을 통해 종 동정을 실시하였다. 그 결과 4개 조사지역의 양송이에서 발생하는 버섯파리는 모두 긴수염버섯파리(Lycoriella ingenua)로 동정되었다.

• ALGAE
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• 제33권1호
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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.

• Molecules and Cells
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• 제23권2호
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• pp.220-227
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• 2007

The development of suitable genetic markers would be useful for defining species and delineating the species boundaries of morphologically indistinguishable sponges. In this study, genetic variation in the sequences of nuclear rDNA and the mitochondrial cytochrome c oxidase subunit 1 and 3 (CO1 and CO3) regions were compared in morphologically indistinguishable Korean Halichondriidae sponges in order to determine the most suitable species-specific molecular marker region. The maximal congeneric nucleotide divergences of Halichondriidae sponges in CO1 and CO3 are similar to those found among anthozoan cnidarians, but they are 2- to 8-fold lower than those found among genera of other triploblastic metazoans. Ribosomal internal transcribed spacer regions (ITS: ITS1 + ITS2) showed higher congeneric variation (17.28% in ITS1 and 10.29% in ITS2) than those of CO1 and CO3. Use of the guidelines for species thresholds suggested in the recent literature indicates that the mtDNA regions are not appropriate for use as species-specific DNA markers for the Halichondriidae sponges, whereas the rDNA ITS regions are suitable because ITS exhibits a low level of intraspecific variation and a relatively high level of interspecific variation. In addition, to test the reliability of the ITS regions for identifying Halichondriidae sponges by PCR, a species-specific multiplex PCR primer set was developed.

• 한국균학회지
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• 제46권4호
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• pp.375-382
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• 2018

Members of the genus Mortierella (Mortierellales) are filamentous fungi, which are found on nearly all substrates, but more frequently in soil. Till date, 7 species of Mortierella have been reported in Korea, but being a ubiquitous group with high species diversity in temperate zones, this number is still low. During a survey of fungal biodiversity in Korea, we collected many isolates of Mortierella, and through morphological and molecular phylogenetic analyses, identified them to be 3 previously unrecorded species, namely, M. chienii, M. epicladia, and M. gamsii. A total of 10 Mortierella species in Korea, including the 3 species reported in the present study, are widely distributed in 5 out of 7 phylogenetic groups of this genus. This indicates that the diversity of Mortierella was so far underestimated in Korea. Multi-locus sequence analysis is required to provide a more reliable backbone for some uncertain phylogenetic groupings and to more clearly define a species of Mortierella, which would encourage deeper research in the diversity and ecological roles of Mortierella and allied genera.

• Journal of Ecology and Environment
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• 제46권2호
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• pp.126-135
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• 2022

Background: Pollinators are important ecological elements due to their role in the maintenance of ecosystem health, wild plant reproduction, crop production and food security. The pollinator-plant interaction supports the preservation of plant and animal populations and it also improves the yield in pollination dependent crops. Having knowledge about the plant-pollinator interaction is necessary for development of pesticide risk assessment of pollinators and conservation of endangering species. Results: Traditional methods to discover the relatedness of insects and plants are based on tracing the visiting pollinators by field observations as well as palynology. These methods are time-consuming and needs expert taxonomists to identify different groups of pollinators such as insects or identify flowering plants through palynology. With pace of technology, using molecular methods become popular in identification and classification of organisms. DNA metabarcoding, which is the combination of DNA barcoding and high throughput sequencing, can be applied as an alternative method in identification of mixed origin environmental samples such as pollen loads attached to the body of insects and has been used in DNA-based discovery of plant-pollinator relationship. Conclusions: DNA metabarcoding is practical for plant-pollinator studies, however, lack of reference sequence in online databases, taxonomic resolution, universality of primers are the most crucial limitations. Using multiple molecular markers is preferable due to the limitations of developed universal primers, which improves taxa richness and taxonomic resolution of the studied community.

• Mycobiology
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• 제50권4호
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• pp.219-230
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• 2022

Agaricales species form pileate-stipitate fruiting bodies and play important roles in maintaining the terrestrial ecosystem as decomposers, symbionts, and pathogens. Approximately 23,000 Agaricales species have been known worldwide, and 937 species have been recorded in the Republic of Korea. However, most of them were identified solely based on morphological characteristics that often led to misidentifications. The specimens collected from 2018 to 2020 in the Republic of Korea were identified based on phylogenetic analysis of the internal transcribed spacer (ITS) sequences. Their identities were confirmed by microscopic characteristics. As a result, 14 Agaricales species were discovered for the first time in the Republic of Korea. They belonged to nine genera: Agaricus, Calocybe, Cortinarius, Hygrocybe, Inocybe, Lepista, Leucoagaricus, Marasmius, and Psathyrella. Detailed macroscopic and microscopic descriptions were provided to help distinguish these species. The morphological and molecular data provided in this study will serve as reliable references for the identification of Agaricales species.

• Animal Systematics, Evolution and Diversity
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• 제39권3호
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• pp.99-113
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• 2023

The nudibranch is one of the most colorful gastropod species found in oceans worldwide. Unlike many other gastropod groups, the nudibranch loses an external shell in the adult stage, but instead develops various chemical defense systems. More than 2,500 nudibranch species have been reported worldwide, and 73 species are currently recorded in Korean waters. In this study, we present morphological descriptions, DNA barcode information of mtDNA cox1 sequence, and taxonomic review for five nudibranch species: Apata pricei (MacFarland, 1966), Doto rosacea Baba, 1949, Janolus toyamensis Baba and Abe, 1970, Polycera abei (Baba, 1960), and Trinchesia sibogae (Bergh, 1905). Of these, we also provide in-depth discussion of taxonomic issue of A. pricei that was previously subdivided into two subspecies, A. pricei pricei and A. pricei komandorica. Our morphological examination and molecular analyses of the mtDNA cox1 sequences indicate that these two subspecies are not taxonomically warranted. The phylogenetic information for the other nudibranch species from mtDNA cox1 sequence analysis is also included, providing a molecular basis for species identification and inferring their local phylogenies within each of the species groups discussed herein.

• 한국패류학회지
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• 제32권3호
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• pp.221-229
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• 2016

Fifty-five specimens of Octopus longispadiceus, belonging to the family Octopodidae, were collected for the first time from the East Sea of Korea and identified by DNA barcoding. This species is characterized by its long right third arm and ligula, the presence of enlarged suckers in the mature male, small white spots on the mantle, head, and arms, and no cirrus above the eye. A molecular analysis of the partial cytochrome c oxidase subunit I gene showed that these specimens are all the same species and have the smallest genetic distance with O. longispadiceus (Kimura- two-parameter distance = 0.002-0.003). A new Korean name, "Bal-mun-eo" is proposed for this species.

• Molecules and Cells
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• 제43권7호
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• pp.591-599
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• 2020

Complex cell-to-cell communication underlies the basic processes essential for homeostasis in the given tissue architecture. Obtaining quantitative gene-expression of cells in their native context has significantly advanced through single-cell RNA sequencing technologies along with mechanical and enzymatic tissue manipulation. This approach, however, is largely reliant on the physical dissociation of individual cells from the tissue, thus, resulting in a library with unaccounted positional information. To overcome this, positional information can be obtained by integrating imaging and positional barcoding. Collectively, spatial transcriptomics strategies provide tissue architecture-dependent as well as position-dependent cellular functions. This review discusses the current technologies for spatial transcriptomics ranging from the methods combining mechanical dissociation and single-cell RNA sequencing to computational spatial re-mapping.