• Korean Journal of Pharmacognosy
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• v.53 no.4
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• pp.226-233
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• 2022

Ephedra herbs are defined as stem of Ephedra sinica , Ephedra intermedia and Ephedra equisetina in the Korean Pharmacopoeia. It is important to use pure herbs to derive the safety and efficacy of herbal medicine. However, the identification of these herbs by conventional taxonomic methods is difficult. Recently, many studies have applied these DNA barcoding for the identification of herbal medicinal species using standard DNA markers. In this study, we report a case study in which the identification of Ephedra species was done by DNA barcoding. For identification of Ephedra species, 17 samples were collected, and a reference DNA barcode library was developed using 6 markers (rbcL, matK, ITS2, ycf1, ycf3, and rpoC2). To develop KASP-SNP markers, we selected 4 markers (ycf1, ycf3, rpl2, and rbcL), which were able to distinguish three Ephedra species. In the result, the specific markers for each of the three Ephedra were clustered into FAM-positive section, whereas non-targeted plants were clustered either HEX-positive or negative section. Therefore, we have developed KASP assay that allow rapid and easy Ephedra species identification using three KASP markers.

• Journal of Marine Life Science
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• v.8 no.1
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• pp.43-49
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• 2023

This study applied a metagenomic analysis of the penguins' gut microbiome from fecal samples of Adélie Penguin (Pygoscelis adeliae) and Emperor Penguin (Aptenodytes forsteri) living along the Ross Sea, Antarctica. As a result of taxonomic analysis, 7 phyla and 18 families were mainly present in the gut microbiome of Adélie and Emperor penguins. To assess microbial diversity, we performed alpha diversity and OTU abundance analyses. It was confirmed that the Adélie Penguin's gut microbial species had a higher diversity than Emperor Penguin's. Based on the Beta diversity analysis using PCoA, differences were observed in the clustering between Adélie and Emperor penguins, respectively. Through the KEGG pathway analysis using PICRUSt, the nucleoside and nucleotide biosynthesis pathway was the most prevalent in Adélie and Emperor penguins. This study enabled a comparison and analysis of the composition and diversity of the gut microbiome in Adélie and Emperor Penguins. It could be utilized for future research related to penguin feeding habits and could serve as a foundation for analyzing the gut microbiomes of various other Antarctic organisms.

• Journal of Animal Science and Technology
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• v.65 no.5
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• pp.951-970
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• 2023

This study utilized Italian ryegrass silage (IRGS) - based total mixed ration (TMR) as feedstuff and evaluated its effects on rumen fermentation, growth performance, blood parameters, and bacterial community in growing Hanwoo heifers. Twenty-seven Hanwoo heifers (body weight [BW], 225.11 ± 10.57 kg) were randomly allocated to three experimental diets. Heifers were fed 1 of 3 treatments as follows: TMR with oat, timothy, and alfalfa hay (CON), TMR with 19% of IRGS (L-IRGS), and TMR with 36% of IRGS (H-IRGS). Feeding high levels of IRGS (H-IRGS) and CON TMR to heifers resulted in a greater molar proportion of propionate in the rumen. The impact of different TMR diets on the BW, average daily gain, dry matter intake, and feed conversion ratio of Hanwoo heifers during the growing period did not differ (p > 0.05). Furthermore, the blood metabolites, total protein, albumin, aspartate aminotransferase, glucose, and total cholesterol of the heifers were not affected by the different TMR diets (p > 0.05). In terms of rumen bacterial community composition, 264 operational taxonomic units (OTUs) were observed across the three TMR diets with 240, 239, and 220 OTUs in CON, L-IRGS, and H-IRGS, respectively. IRGS-based diets increased the relative abundances of genera belonging to phylum Bacteroidetes but decreased the abundances of genus belonging to phylum Firmicutes compared with the control. Data showed that Bacteroidetes was the most dominant phylum, while Prevotella ruminicola was the dominant species across the three TMR groups. The relative abundance of Ruminococcus bromii in the rumen increased in heifers fed with high inclusion of IRGS in the TMR (H-IRGS TMR). The relative abundance of R. bromii in the rumen significantly increased when heifers were fed H-IRGS TMR while P. ruminicola increased in both L-IRGS and H-IRGS TMR groups. Results from the current study demonstrate that the inclusion of IRGS in the TMR is comparable with the TMR containing high-quality forage (CON). Thus, a high level of IRGS can be used as a replacement forage ingredient in TMR feeding and had a beneficial effect of possibly modulating the rumen bacterial community toward mainly propionate-producing microorganisms.

• Korean Journal of Environmental Biology
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• v.39 no.1
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• pp.119-135
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• 2021

Korea has stepped up efforts to investigate and catalog its flora and fauna to conserve the biodiversity of the Korean Peninsula and secure biological resources since the ratification of the Convention on Biological Diversity (CBD) in 1992 and the Nagoya Protocol on Access to Genetic Resources and the Fair and Equitable Sharing of Benefits (ABS) in 2010. Thus, after its establishment in 2007, the National Institute of Biological Resources (NIBR) of the Ministry of Environment of Korea initiated a project called the Korean Indigenous Species Investigation Project to investigate indigenous species on the Korean Peninsula. For 15 years since its beginning in 2006, this project has been carried out in five phases, Phase 1 from 2006-2008, Phase 2 from 2009-2011, Phase 3 from 2012-2014, Phase 4 from 2015-2017, and Phase 5 from 2018-2020. Before this project, in 2006, the number of indigenous species surveyed was 29,916. The figure was cumulatively aggregated at the end of each phase as 33,253 species for Phase 1 (2008), 38,011 species for Phase 2 (2011), 42,756 species for Phase 3 (2014), 49,027 species for Phase 4 (2017), and 54,428 species for Phase 5(2020). The number of indigenous species surveyed grew rapidly, showing an approximately 1.8-fold increase as the project progressed. These statistics showed an annual average of 2,320 newly recorded species during the project period. Among the recorded species, a total of 5,242 new species were reported in scientific publications, a great scientific achievement. During this project period, newly recorded species on the Korean Peninsula were identified using the recent taxonomic classifications as follows: 4,440 insect species (including 988 new species), 4,333 invertebrate species except for insects (including 1,492 new species), 98 vertebrate species (fish) (including nine new species), 309 plant species (including 176 vascular plant species, 133 bryophyte species, and 39 new species), 1,916 algae species (including 178 new species), 1,716 fungi and lichen species(including 309 new species), and 4,812 prokaryotic species (including 2,226 new species). The number of collected biological specimens in each phase was aggregated as follows: 247,226 for Phase 1 (2008), 207,827 for Phase 2 (2011), 287,133 for Phase 3 (2014), 244,920 for Phase 4(2017), and 144,333 for Phase 5(2020). A total of 1,131,439 specimens were obtained with an annual average of 75,429. More specifically, 281,054 insect specimens, 194,667 invertebrate specimens (except for insects), 40,100 fish specimens, 378,251 plant specimens, 140,490 algae specimens, 61,695 fungi specimens, and 35,182 prokaryotic specimens were collected. The cumulative number of researchers, which were nearly all professional taxonomists and graduate students majoring in taxonomy across the country, involved in this project was around 5,000, with an annual average of 395. The number of researchers/assistant researchers or mainly graduate students participating in Phase 1 was 597/268; 522/191 in Phase 2; 939/292 in Phase 3; 575/852 in Phase 4; and 601/1,097 in Phase 5. During this project period, 3,488 papers were published in major scientific journals. Of these, 2,320 papers were published in domestic journals and 1,168 papers were published in Science Citation Index(SCI) journals. During the project period, a total of 83.3 billion won (annual average of 5.5 billion won) or approximately US $75 million (annual average of US $5 million) was invested in investigating indigenous species and collecting specimens. This project was a large-scale research study led by the Korean government. It is considered to be a successful example of Korea's compressed development as it attracted almost all of the taxonomists in Korea and made remarkable achievements with a massive budget in a short time. The results from this project led to the National List of Species of Korea, where all species were organized by taxonomic classification. Information regarding the National List of Species of Korea is available to experts, students, and the general public (https://species.nibr.go.kr/index.do). The information, including descriptions, DNA sequences, habitats, distributions, ecological aspects, images, and multimedia, has been digitized, making contributions to scientific advancement in research fields such as phylogenetics and evolution. The species information also serves as a basis for projects aimed at species distribution and biological monitoring such as climate-sensitive biological indicator species. Moreover, the species information helps bio-industries search for useful biological resources. The most meaningful achievement of this project can be in providing support for nurturing young taxonomists like graduate students. This project has continued for the past 15 years and is still ongoing. Efforts to address issues, including species misidentification and invalid synonyms, still have to be made to enhance taxonomic research. Research needs to be conducted to investigate another 50,000 species out of the estimated 100,000 indigenous species on the Korean Peninsula.

• Asian-Australasian Journal of Animal Sciences
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• v.29 no.5
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• pp.631-639
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• 2016

China has a long history of sheep (Ovis aries [O. aries]) breeding and an abundance of sheep genetic resources. Knowledge of the complete O. aries mitogenome should facilitate the study of the evolutionary history of the species. Therefore, the complete mitogenome of O. aries was sequenced and annotated. In order to characterize the mitogenomes of 3 Chinese sheep breeds (Altay sheep [AL], Shandong large-tailed sheep [SD], and small-tailed Hulun Buir sheep [sHL]), 19 sets of primers were employed to amplify contiguous, overlapping segments of the complete mitochondrial DNA (mtDNA) sequence of each breed. The sizes of the complete mitochondrial genomes of the sHL, AL, and SD breeds were 16,617 bp, 16,613 bp, and 16,613 bp, respectively. The mitochondrial genomes were deposited in the GenBank database with accession numbers KP702285 (AL sheep), KP981378 (SD sheep), and KP981380 (sHL sheep) respectively. The organization of the 3 analyzed sheep mitochondrial genomes was similar, with each consisting of 22 tRNA genes, 2 rRNA genes (12S rRNA and 16S rRNA), 13 protein-coding genes, and 1 control region (D-loop). The NADH dehydrogenase subunit 6 (ND6) and 8 tRNA genes were encoded on the light strand, whereas the rest of the mitochondrial genes were encoded on the heavy strand. The nucleotide skewness of the coding strands of the 3 analyzed mitogenomes was biased toward A and T. We constructed a phylogenetic tree using the complete mitogenomes of each type of sheep to allow us to understand the genetic relationships between Chinese breeds of O. aries and those developed and utilized in other countries. Our findings provide important information regarding the O. aries mitogenome and the evolutionary history of O. aries inside and outside China. In addition, our results provide a foundation for further exploration of the taxonomic status of O. aries.

• Journal of Food Hygiene and Safety
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• v.33 no.4
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• pp.280-288
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• 2018

In this study, an approach for the analysis of the five cephalopod species (octopus, long-arm octopus, squid, wet-foot octopus, beka squid) consumed in the Republic of Korea is developed. The samples were collected from the Southeast Asian countries Thailand, Indonesia, Vietnam, and China. The SYBR-green-based real-time qPCR method, based on the mitochondrial DNA genome of the five cephalopods was developed and validated. The intergroup variations in the mitochondrial DNA are evident in the bioinformatic analysis of the mitochondrial genomic DNA sequences of the five groups. Some of the highly-conserved and slightly-variated regions are identified in the mitochondrial cytochrome-c-oxidase subunit I (COI) gene, 16s ribosomal RNA (16s rRNA) gene, and 12s ribosomal RNA (12s rRNA) gene of these groups. To specify each five cephalopod groups, specific primer sets were designed from the COI, 16s rRNA and 12s rRNA regions. The specific primer sets amplified the DNA using the SYBR-green-based real-time PCR system and 11 commercially secured animal tissues: Octopus vulgaris, Octopus minor, Todarodes pacificus, Dosidicus gigas, Sepia esculenta, Amphioctopus fangsiao, Amphioctopus aegina, Amphioctopus marginatus, Loliolus beka, Loligo edulis, and Loligo chinensis. The results confirmed by a conveient way to calculate relative amplification levels between different samples in that it directly uses the threshold cycles (Ct)-value range generated by the qPCR system from these samples. This genomic DNA-based molecular technique provides a quick, accurate, and reliable method for the taxonomic classification of the animal tissues using the real-time qPCR.

• Korean Journal of Plant Taxonomy
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• v.31 no.3
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• pp.223-251
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• 2001

Morphological characters of section Atratae of the genus Carex (Cyperaceae) were reexamined. The epidermal patterns of perigynium, achene and leaf were investigated using by a scanning electron microscope (SEM) and a light microscope (LM). Morphological characters such as length and width of stem, leaf, bract, spike, scale, perigynium and achene, and shape of cross-sectioned stem, and leaf, spike, scale, apex of scale, perigynium, beak of perigynium and achene, and epidermal pattern of perigynium, achene and leaf (shape of fundamental epidermal cell and cell wall, type of silica body, shape of beak epidermal cell and cell wall in perigynium, subsidiary cell shape, size and frequency of stomatal complex of leaf) were useful for the identifications of the observed seven taxa. C. gmelinii, C. hancokiana and C. peiktusani have been confused each other due to similar morphological characters. Howerever these taxa were distinct with respect to shape of scale, apex of scale, perigynium, type of silica body, frequence of stomatal complex, subsidal cell shape, and epidermal patterns of achene and leaf.

• The Korean Journal of Malacology
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• v.31 no.4
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• pp.279-283
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• 2015

This study investigated spectroscopic characteristics of shell crystals of eight marine bivalve species using X-ray diffraction (XRD) analysis; moreover, the Family level relatedness of shellfish was investigated. In XRD analysis, the shells of Ruditapes philippinarum, Meretrix lusoria, Anadara granosa, and Fulvia mutica were found to have orthorhombic aragonite $CaCO_3$ crystals, while shells of Patinopecten yessoensis and Crassostrea gigas had trigonal-rhombohedral calcite crystals. The shells of Mytilus coruscus and Atrina pectinata were determined to have a mixture of aragonite and calcite crystals. XRD information revealed the Family level-specific characteristics of shellfish; the results agreed with the current taxonomic system. In conclusion, spectroscopic characteristics of shell crystals indicated Family-level characteristics of shellfish and suggested a more intense species-level investigation; this technology may be useful in identifying shellfish species using small quantities of shells.

• Animal Systematics, Evolution and Diversity
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• v.5 no.1
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• pp.77-88
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• 1989

Genetic and morphometric comparison between two species of the genus Agkistrodon were performed to estimate the degree of genic variation and to clarify the taxonomic status of Cheju population, a suspected hybrid form between A. blomhoffii brevicaudus and A u ussuriensis. A sum of 147 specimens representing six populations of A.b. brevicaudus and two populations of A ussuriensis was used in this study. Out of the 21 loci examined, 5 loci (Adh, Ldh-2, Mdh-2, Mpi, Pgi) were monomorphic with identical mobility in both species. O Other Sioci (Aco, Gp, Fum, [po and Xdh in A b. brevicaudus; Est, Got-l, Gp, Mdh-l and 6Pgd in A ussuriensis) were highly poplymorphic. The degree of genic variation of Ab. b brevicaudus and A ussuriensis was A=1.SS, P=42.1%, HD=0.096, HG=O.l1S, and A= 1.4S, P = 31.6%, HD=0.117, HG =0.121, repectively. These values are twofold higher t than those of other reptilian species reported (Selander, 1976) including Korean species of Rhabdophis tigrina and Elaphe dione (Paik and Yang, 1986, 1987). The average values of t the genetic similarities among six populations of A b. brevicaudus and two populations of A ussuriensis were S=0.919 and S=0.962, respectively, whereas the value between species was S = 0.662. Presumed divergent time estimate (Nei, 1975) of these two species was about 1 1.8 million years ago. The analysis of the geographic variations of various morphological c characters was based on Gloyd’s criteria (Gloyd, 1972). Coloration of tongue and tail tip, t the number of ventral scales, and the number of subcaudal scales are good diagnostic c characters to identify these two species. The pattern of cross band is, however, highly variable within and between populations of both species. No hybrid was detected and the s suspected hybrid form of Cheju population falls within the range of A. ussuriensis in the g genetic and morphometric analyses.

• Korean Journal of Plant Resources
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• v.16 no.1
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• pp.89-98
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• 2003

Pollens of six taxa in the genus Atractytis L. confused with Atractylodes DC. were investigated by the light and the scanning electron microscope. Pollen grains of six taxa in this genus were monads, 46.5-66.7$\mu\textrm{m}$ in length of polar axis, 43.6-60.47$\mu\textrm{m}$ in equatorial width. Aperture was tri-colporate, 19.6-29.1 $\mu\textrm{m}$ in colpus length,7.3-11.0$\mu\textrm{m}$ in colpus width and 6.4-10.6$\mu\textrm{m}$ in porus diameter. The exine was composed of three layers(foot layer, columellne, tectum), and 5.2-8.3 $\mu\textrm{m}$ in thickness. The surface sculpturing pattern was echinate, the spines were 1.4-5.8$\mu\textrm{m}$ in length and 6-33 per 20$\mu\textrm{m}$$^2$ in distribution numbers over the surface. Atractylis L. was not distinguished from Atractylodes DC. by pollen morphology, especially the pollens of Atractylis arabica, A. aristata, A. carduus, A. microcephala were very similar to that of Atractylodes. But its taxonomic significance was different, the taxa of Atractylodes DC. were divided into 2 types by only pollen size, but the treated taxa in this study were divided into various types by pollen size, shape of equatorial view, surface sculpturing and spine size. The characteristics of spine size and shape of equatorial view in A. cancellata and A. prolifera were very useful for consideration of evolutionary trends in this genus.