• Animal Systematics, Evolution and Diversity
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• 제38권2호
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• pp.91-97
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• 2022

Spionid polychaete Prionospio kirrae Wilson, 1990 is newly reported from the Yellow Sea in Korea. This species is characterized by four pairs of branchiae, which are apinnate on chaetigers 2-4 and pinnate on chaetiger 5, a caruncle extending to the posterior end of chaetiger 1, the presence of a distinctly high dorsal crest on chaetiger 11, and the presence of tridentate hooded hooks with rounded apical teeth. Sequences of partial mitochondrial cytochrome c oxidase subunit I (COI), 16S ribosomal DNA(16S rDNA), and the nuclear 18S ribosomal DNA(18S rDNA) of the species are determined from Korean specimens.

• ALGAE
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• 제34권4호
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• pp.253-266
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• 2019

Several species classified to the genus Ulva are primarily responsible for causing green tides all over the world. For almost two decades, green tides have been resulted in numerous ecological problems along the eastern coast of Jeju Island, Korea. In order to characterize the species of Ulva responsible for causing the massive blooms on Jeju Island, we conducted DNA barcoding of tufA and rbcL sequences on 183 specimens of Ulva from eight sites on Jeju Island. The concatenated analysis identified five bloom-forming species: U. australis, U. lactuca, U. laetevirens, U. ohnoi and a novel species, U. pseudo-ohnoi sp. nov. Among them, U. australis, U. lactuca, and U. laetevirens caused to the blooms coming mainly from the substratum. U. ohnoi and U. pseudo-ohnoi sp. nov. were causative the free-floating blooms. Four species, except U. australis, are characterized by marginal teeth. A novel species, U. pseudo-ohnoi sp. nov., is clearly diverged from the U. lactuca, U. laetevirens, and U. ohnoi clade in the concatenated maximum likelihood analysis. Accurate species delimitation will contribute to a management of massive Ulva blooms based on this more comprehensive knowledge.

• Mycobiology
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• 제44권1호
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• pp.1-6
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• 2016

Ganoderma lucidum has a long history of use as a traditional medicine in Asian countries. However, the taxonomy of Ganoderma species remains controversial, since they were initially classified on the basis of their morphological characteristics. Recently, it was proposed that G. lucidum from China be renamed as G. sichuanense or G. lingzhi. In the present study, phylogenetic analysis using the internal transcribed spacer region rDNA sequences of the Ganoderma species indicated that all strains of the Korean 'G. lucidum' clustered into one group together with G. sichuanense and G. lingzhi from China. However, strains from Europe and North American, which were regarded as true G. lucidum, were positioned in a clearly different group. In addition, the average size of the basidiospores from the Korean cultivated Yeongji strains was similar to that of G. lingzhi. Based on these results, we propose that the Korean cultivated Yeongji strains of 'G. lucidum' should be renamed as G. lingzhi.

• 한국균학회소식:학술대회논문집
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• 한국균학회 2015년도 추계학술대회 및 정기총회
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• pp.41-41
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• 2015

Oomycetes belong to the kingdom Straminipila, a remarkably diverse group which includes brown algae and planktonic diatoms, although they have previously been classified under the kingdom Fungi. These organisms have evolved both saprophytic and pathogenic lifestyles, and more than 60% of the known species are pathogens on plants, the majority of which are classified into the order Peronosporales (includes downy mildews, Phytophthora, and Pythium). Recent phylogenetic investigations based on DNA sequences have revealed that the diversity of oomycetes has been largely underestimated. Although morphology is the most valuable criterion for their identification and diversity, morphological species identification is time-consuming and in some groups very difficult, especially for non-taxonomists. DNA barcoding is a fast and reliable tool for identification of species, enabling us to unravel the diversity and distribution of oomycetes. Accurate species determination of plant pathogens is a prerequisite for their control and quarantine, and further for assessing their potential threat to crops. The mitochondrial cox2 gene has been widely used for identification, taxonomy and phylogeny of various oomycete groups. However, recently the cox1 gene was proposed as a DNA barcode marker instead, together with ITS rDNA. To determine which out of cox1 or cox2 is best suited as universal oomycete barcode, we compared these two genes in terms of (1) PCR efficiency for 31 representative genera, as well as for historic herbarium specimens, and (2) in terms of sequence polymorphism, intra- and interspecific divergence. The primer sets for cox2 successfully amplified all oomycete genera tested, while cox1 failed to amplify three genera. In addition, cox2 exhibited higher PCR efficiency for historic herbarium specimens, providing easier access to barcoding type material. In addition, cox2 yielded higher species identification success, with higher interspecific and lower intraspecific divergences than cox1. Therefore, cox2 is suggested as a partner DNA barcode along with ITS rDNA instead of cox1. Including the two barcoding markers, ITS rDNA and cox2 mtDNA, the multi-locus phylogenetic analyses were performed to resolve two complex clades, Bremia lactucae (lettuce downy mildew) and Peronospora effuse (spinach downy mildew) at the species level and to infer evolutionary relationships within them. The approaches discriminated all currently accepted species and revealed several previously unrecognized lineages, which are specific to a host genus or species. The sequence polymorphisms were useful to develop a real-time quantitative PCR (qPCR) assay for detection of airborne inoculum of B. lactucae and P. effusa. Specificity tests revealed that the qPCR assay is specific for detection of each species. This assay is sensitive, enabling detection of very low levels of inoculum that may be present in the field. Early detection of the pathogen, coupled with knowledge of other factors that favor downy mildew outbreaks, may enable disease forecasting for judicious timing of fungicide applications.

• Animal Systematics, Evolution and Diversity
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• 제36권2호
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• pp.182-184
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• 2020

Isaacsicalanus paucisetus Fleminger, 1983, a monotypic species of the family Spinocalanidae Vervoort, 1951, was first reported from a hydrothermal vent field in the East Pacific Rise off the mouth of the Gulf of California. The mitochondrial cytochrome oxidase I(mtCOI) DNA barcodes are considered a useful tool to assist traditional taxonomy and species discrimination in calanoid copepods. However, the mtCOI DNA barcodes of I. paucisetus have not been reported due to the species rarity and the difficulty of sampling. In this study, we firstly determined the mtCOI DNA barcodes of the I. paucisetus newly collected from a hydrothermal vent in the North Fiji Basin of the southwestern Pacific. All mtCOI DNA barcodes of I. paucisetus were identical and intraspecies variations of spinocalanid species were 0.0-3.0%. Interspecies and intergeneric variations were 13.4-25.2% and 16.7-24.1%, respectively. The DNA barcodes of I. paucisetus obtained in the present study would be helpful for understanding taxonomic relationships of widespread spinocalanid species.

• Animal Systematics, Evolution and Diversity
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• 제26권3호
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• pp.183-186
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• 2010

To identify Korean red-backed voles (Myodes regulus) from Korea by mitochondrial DNA (mtDNA) sequencing, we obtained mtDNA control region sequences of 17 red-backed voles from Korea and northeast China, and these sequences were compared with the corresponding haplotypes of Myodes obtained from GenBank. We identified five red-backed voles from Mt. Changbai and Harbin as M. rufocanus and another three redbacked voles from Harbin as M. rutilus, respectively. Moreover, nine red-backed voles from Korea, showing the average nucleotide distance of 0.66% among nine haplotypes, were different from other species of Myodes, and the average distance between nine haplotypes of red-backed voles from Korea and seven haplotypes of M. rufocanus was 6.41%, whereas the average distance between nine haplotypes of red-backed voles from Korea and five haplotypes of M. rutilus was 14.8%. We identified the red-backed voles from Korea as M. regulus, and found that M. regulus is distinct in its mtDNA control region sequences as well, although we propose further analyses with additional specimens from East Asia using nuclear and mtDNA markers to confirm the distinctness of M. regulus.

• Journal of Microbiology and Biotechnology
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• 제17권6호
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• pp.945-951
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• 2007

DNA-DNA hybridization has been established as an important technology in bacterial species taxonomy and phylogenetic analysis. In this study, we analyzed how the efficiency with which the genomic DNA from one species hybridizes to the genomic DNA of another species (DNA-DNA hybridization) in microarray analysis relates to the similarity between two genomes. We found that the predicted DNA-DNA hybridization based on genome sequence similarity correlated well with the experimentally determined microarray hybridization. Between closely related strains, significant numbers of highly divergent genes (>55% identity) and/or the accumulation of mismatches between conserved genes lowered the DNA-DNA hybridization signal, and this reduced the hybridization signals to below 70% for even bacterial strains with over 97% 16S rRNA gene identity. In addition, our results also suggest that a DNA-DNA hybridization signal intensity of over 40% indicates that two genomes at least shared 30% conserved genes (>60% gene identity). This study may expand our knowledge of DNA-DNA hybridization based on genomic sequence similarity comparison and further provide insights for bacterial phylogeny analyses.

• 한국잠사곤충학회지
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• 제51권2호
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• pp.185-190
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• 2013

2011년부터 수입되어 사육 유통되는 슈퍼밀웜의 국내 샘플들은 형태 분류학적 검토를 통하여 Zophobas atratus란 종으로 밝혀졌고, Z. morio란 학명은 이 종의 동물이 명임이 확인되었다. 이 외래종은 자원 관리측면에서 국명을 '아메리카왕거저리'로 신칭하였다. 이 종과 형태적으로 유사한 자생종 P. valgipes 및 사육종 T. molitor와 DNA 바코드 분석 결과, Zophobas atratus와 P. valgipes는 평균 21.4%, Zophobas atratus와 Z. morio는 20.9%의 염기분화율을 보여 DNA 바코드로 쉽게 종 동정할 수 있음을 확인하였다. Z. atratus의 국내집단은 모두 동일 일배체형을 갖고 있어 국외의 동일 지역 개체군이 국내로 유입된 것으로 추정된 반면에 Z. molitor는 동일 사육집단 내에서도 두 개의 종내 집단이 뚜렷이 구분되고 서로의 염기 분화율이 1.17 ~ 2.19%로 갭을 형성한 것으로 보아 국내 Z. molitor 사육개체들은 서로 다른 지역 집단이 혼입되어 대량 사육에 이용되어진 것으로 추정된다. 이번 연구를 통하여 분석된 상업적으로 도입, 이용되는 2종의 거저리류의 분류학적 기초 정보가 국내 곤충자원 관리를 위하여 유용하게 이용될 것으로 판단된다.

• 식물분류학회지
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• 제50권4호
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• pp.403-412
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• 2020

Colonies of three independent gametophytes (one that is filamentous and two that are ribbon-like) without sporophytes occur in Gyeonggi-do, Gangwon-do, Gyeongsang-do, and Jeju-do, Korea. They have a moss-like appearance at first sight, with tiny plantlets and gemmae, and grow in cool, shaded, relatively deep dint places of large rocks, such as the small caves in high mountains, close to valleys. The gametophytes were identified based on morphological and molecular data by chloroplast DNA (cpDNA) sequence data (rbcL, rps4 gene and rps4-trnS intergenic spacer). Here, rbcL, rps4 gene and rps4-trnS intergenic spacer data of one independent gametophyte distributed in Korea have the same morphology, DNA sequence and monophyletic group as Crepidomanes intricatum from the eastern United States. They also share the same cpDNA data with Crepidomanes schmidtianum recently reported from Korea. The other independent gametophyte should be Hymenophyllum wrightii based on cpDNA data. The last one was presumed to be Pleurosoriopsis makinoi based on molecular data. The taxonomic status was confirmed to be the forma of Hymenophyllum wrightii through a revision of Hymenophyllum wrightii f. serratum based on molecular data.

• 한국균학회소식:학술대회논문집
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• 한국균학회 2014년도 춘계학술대회 및 임시총회
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• pp.45-45
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• 2014

Individualities of precious health mushroom called Zhenghonggu@ from respective protections scattered among all main mountains of Fujian China were collected and recognized locally, then compared with Russula griseocarnosa. Their internal transcribed spacer (ITS) region (ITS1, ITS2 and 5.8S rDNA) of the nuclear rDNA were amplified, AMOVA analyzed, nested clade analyzed and then compared with the ITS sequences of relative Russula species from other regions of China to confirm the taxonomic status of Zhenghonggu$^@$ and its population structure. Total 23 haplotypes from different protections of Fujian can be clustered into three clades similar to the three lineages of Dahongjun$^@$ from southeastern China reported by Li et al. The geographic distribution characteristic of these three phylogeny clades may be closely coupled with the vegetation regionalization and/or the differences of coenosium construction of Fagaceae that is the host of Russula griseocarnosa. The correlation of taxonomy, phylogeny and geographical distribution of Russula are discussed.