• ALGAE
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• v.34 no.1
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• pp.57-70
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• 2019

DNA metabarcoding is currently used for large-scale taxonomic identification to understand the community composition in various marine ecosystems. However, before being widely used in this emerging field, this experimental and analytic approach still has several technical challenges to overcome, such as polymerase chain reaction (PCR) bias, and lack of well-established metabarcoding markers, a task which is difficult but not impossible to achieve. In this study, we present an adapted PCR-free small-organelles enriched metagenomics (SoEM) method for marine biodiversity assessment. To avoid PCR bias and random artefacts, we extracted target DNA sequences without PCR amplification from marine environmental samples enriched with small organelles including mitochondria and plastids because their genome sequences provide a valuable source of molecular markers for phylogenetic analysis. To experimentally enrich small organelles, we performed subcellular fractionation using modified differential centrifugation for marine environmental DNA samples. To validate our SoEM method, two marine environmental samples from the coastal waters were tested the taxonomic capturing capacity against that of traditional DNA metabarcoding method. Results showed that, regardless of taxonomic levels, at least 3-fold greater numbers of taxa were identified in our SoEM method, compared to those identified by the conventional multi-locus DNA metabarcoding method. The SoEM method is thus effective and accurate for identifying taxonomic diversity and presents a useful alternative approach for evaluating biodiversity in the marine environment.

• 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.

• ALGAE
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• v.35 no.3
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• pp.293-301
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• 2020

The applications of DNA barcoding have a wide range of uses, such as in taxonomic studies to help elucidate cryptic species and phylogenetic relationships and analyzing environmental samples for biodiversity monitoring and conservation assessments of species. After obtaining the DNA barcode sequences, sequence similarity-based homology analysis is commonly used. This means that the obtained barcode sequences are compared to the DNA barcode reference databases. This bioinformatic analysis necessarily implies that the overall quantity and quality of the reference databases must be stringently monitored to not have an adverse impact on the accuracy of species identification. With the development of next-generation sequencing techniques, a noticeably large number of DNA barcode sequences have been produced and are stored in online databases, but their degree of validity, accuracy, and reliability have not been extensively investigated. In this study, we investigated the extent to which the amount and types of erroneous barcode sequences were deposited in publicly accessible databases. Over 4.1 million sequences were investigated in three largescale DNA barcode databases (NCBI GenBank, Barcode of Life Data System [BOLD], and Protist Ribosomal Reference database [PR2]) for four major DNA barcodes (cytochrome c oxidase subunit 1 [COI], internal transcribed spacer [ITS], ribulose bisphosphate carboxylase large chain [rbcL], and 18S ribosomal RNA [18S rRNA]); approximately 2% of erroneous barcode sequences were found and their taxonomic distributions were uneven. Consequently, our present findings provide compelling evidence of data quality problems along with insufficient and unreliable annotation of taxonomic data in DNA barcode databases. Therefore, we suggest that if ambiguous taxa are presented during barcoding analysis, further validation with other DNA barcode loci or morphological characters should be mandated.

• Korean Journal of Ichthyology
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• v.27 no.3
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• pp.165-182
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• 2015

The snailfishes (Scorpaenoidei: Liparidae) is a large group requiring taxonomic reviews because of a potential taxonomic confusion due to its great similarity in external morphology between species and a variation of its body color with size. Molecular phylogeny and taxonomic review were conducted for 10 species in 3 genera reported around the Korean waters, which facilitate understanding interrelationship within its family, and further management of fisheries resources. Molecular phylogeny using mitochondrial COI (mtCOI) and nuclear RAG2 (nRAG2) sequences indicates that the reciprocal monophyly of the three genera (Careproctus, Crystallichthys, and Liparis) were supported except Crystallichthys matsushimae, being closely related to Careproctus notosaikaiensis in only mtDNA COI topology. Liparis ingens Gilbert and Burke (1912) was reported as a distinct species differing from L. ochotensis. However, in the present study, comparing L. ingens from Korea with L. ochotensis from Japan and Russia, the two species were well corresponded in their morphology and molecule, therefore, we suggest L. ingens to be treated as a junior synonym of L. ochotensis.

• The Korea Journal of Herbology
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• v.34 no.6
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• pp.63-70
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• 2019

Objective : Arnebiae Radix, the roots of Arnebia euchroma (Royle) Johnst. or A. guttata Bunge, is a well-known traditional herbal medicine in East Asia. In the Korean Pharmacopoeia, three authentic species, including two Arnebia and Lithospermum erythrorhizon Sieb. et Zucc. have recognized as a Lithospermi Radix. But, the morphological and taxonomic information of two authentic Arnebia species lacks date since their distribution and difficulty of accessing the natural habitats. Methods : A full description of the external morphological characteristics of vegetative and reproductive organs in the original plants was carried out using digital calipers and stereoscope. For providing their taxonomic and nomenclatural synonyms, we reviewed various plant checklists and taxonomic literature. Results : This study provides taxonomic information of A. euchroma and A. guttata based on a morphological examination of authentic plant individuals and field observations. Detailed descriptions of the two Arnebia species, major quantitative and qualitative characteristics, nomenclatural reviews, distribution maps, and lists of voucher specimens examined are provided. The shape of leaves, root length, stem number, calyx length and pubescence as well as corolla color were useful characteristics for identification. Moreover, we confirmed that A. euchroma and A. guttata are clearly heterostylous species. Conclusion : Our research provides valuable basic information that could be used as quality control for distinguishing between Arnebiae Radix and its adulterants. These results will help in the understanding of authentic plants and also provide the verified materials and voucher information.

• Animal Systematics, Evolution and Diversity
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• v.36 no.1
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• pp.10-14
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• 2020

Pagurus is the most diverse hermit crab genus in Korea. In this study, the cytochrome c oxidase subunit I (COI) and 16S rRNA of 24 individuals from four Korean Pagurus species (i.e., 7 Pagurus brachiomastus, 8 P. proximus, 8 P. simulans, and 1 P. rectidactylus) were sequenced and analyzed. No genetic difference was found between the COI and 16S rRNA sequences of P. brachiomastus and P. simulans, and the COI sequences of P. rectidactylus and P. quinquelineatus (comparative species from NCBI). Considering the morphological and ecological characteristics together, we assume that P. simulans and P. rectidactylus are subspecies of P. brachiomastus and P. quinquelineatus, respectively. This study should facilitate further research on the taxonomic status of these species.

• Animal Systematics, Evolution and Diversity
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• v.36 no.1
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• pp.60-77
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• 2020

Cecidomyiidae (Diptera) consists of six subfamilies, which are divided into three groups according to larval ecological habits (phytophagous, mycophagous, and zoophagous). The five basal subfamilies of Cecidomyiidae consist entirely of mycophagous species, with approximately 1500 species described worldwide and 29 previously known to occur in Korea. In this study, 37 named species (1 Lestremiinae, 29 Micromyinae, 4 Winnertziinae, and 3 Porricondylinae species) are newly reported from South Korea. We excluded Lestremia yasukunii Shinji from the list of Korean mycophagous cecidomyiids as it is a nomen nudum. Therefore, we herein officially recognize 65 species, 30 genera, and four subfamilies for the Korean mycophagous cecidomyiid fauna. We also provide diagnoses and photographs to aid species identification and discussion on the four years of gall midge taxonomic inventory in South Korea.

• The Korean Journal of Mycology
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• v.27 no.2 s.89
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• pp.147-157
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• 1999

This paper is the eighth contribution towards taxonomic studies on Cercospora and allied genera, and contains ten species of Korean cercosporoid fungi; viz., Cercospora brassicicola, C. flagellaris, C. sesami, C. zinniae, Passalora amurensis, Pseudocercospora balsaminae, P. humuli, P. puderi, P. salicina, and Stenella dianthi. Morphological characteristics of taxonomic value are described and illustrated for these species to contribute towards a mycological monograph of Korean cercosporoid fungi.

• The Korean Journal of Mycology
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• v.27 no.2 s.89
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• pp.138-146
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• 1999

This paper is the seventh contribution towards taxonomic studies on Cercospora and allied genera, and contains ten species of Korean cercosporoid fungi; viz., Cercospora arcti-ambrosiae, C. cichorii, C. kikuchii, C. subhyalina, Neoramularia koreana, Pseudocercospora ligustri, P. oenotherae, P. rubi, P. zelkowae, and Ramularia archangelicae. Morphological characteristics of taxonomic value are described and illustrated for these species to contribute towards a mycological monograph of Korean cercosporoid fungi.

• The Korean Journal of Mycology
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• v.27 no.1 s.88
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• pp.44-53
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• 1999

This paper is the fifth contribution towards taxonomic studies on Cercospora and allied genera, and contains ten species of Korean cercosporoid fungi; viz., Cercospora adusta, C. chrysanthemi, C. ludwigiana, C. zebrina, Passalora depressa, Pseudocercospora destructiva, P. lonicericola, P. nojimai, Pseudocercosporella inconspicua, and Ramularia major. Morphological characteristics of taxonomic value are described and illustrated for these species to contribute towards a mycological monograph of Korean cercosporoid fungi.