• Title, Summary, Keyword: DNA barcodes

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Taxonomy of introduced commercial insect, Zophobas atratus (Coleoptera: Tenebrionidae) and a comparison of DNA barcoding with similar tenebrionids, Promethis valgipes and Tenebrio molitor in Korea (도입된 상업용 거저리(Zophobas atratus)의 분류 및 형태유사종 갈색거저리 (Tenebrio molitor)와 대왕거저리(Promethis valgipes)와의 DNA 바코드 특성 분석)

  • Park, Hae Chul;Jung, Boo Hee;Han, Taeman;Lee, Young Bo;Kim, Seong-Hyun;Kim, Nam Jeong
    • Journal of Sericultural and Entomological Science
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    • v.51 no.2
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    • pp.185-190
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    • 2013
  • The superworm, as known the larva of Zophobas morio, has been officially imported from 2011 and bred commercially in Korea. But it is named as the corrected scientific name, Zophobas atratus by junior synonym throughout traditional taxonomy in this study and newly designated Korean name as 'a-me-ri-ca-wang-geo-jeo-ri' in terms of resource management. Z. atratus was compared with wild native tenebrionids, Promethis valgipes and a commercial reared Tenebrio molitor on the basis of DNA barcode analysis. As the results, the average genetic divergence was 21.4% between Z. atratus and P. valgipes, and 20.9% between Z. atratus and T. molitor. These large divergences imply these tenebrionids species can be easily identified by DNA barcodes. The results of genetic divergences within species also suggest that Korean populations of Z. atratus, having the same haplotype, might be introduced from the same area of foreign country. On the other hand, a population of T. molitor was separated into two distinct intra-specific groups with DNA barcoding gaps ranged from 1.17- 2.19%. We suppose that domestic breeding entities of T. molitor might be introduced and mixed from two different local groups. Through this study, we expect that classification for two tenebrionid introduced from foreign countries can be used for the management of insect resources in Korea.

Development of Molecular Marker for the authentication of Patriniae Radix by the analysis of DNA barcodes (DNA 바코드 분석을 통한 패장 기원종 감별용 분자 마커 개발)

  • Kim, Wook Jin;Ji, Yunui;Lee, Young Mi;Kang, Young Min;Choi, Goya;Kim, Ho Kyoung;Moon, Byeong Cheol
    • The Korea Journal of Herbology
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    • v.29 no.6
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    • pp.45-53
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    • 2014
  • Objectives : Due to the morphological similarity of in the roots of herbal medicine, the official herbal medicine is very difficult to authenticate between the original plants of Patriniae Radix and two adulterant Patrinia species. Therefore, we introduced DNA barcode analysis to establish a powerful tool for the authentication of Patriniae Radix from its adulterants. Methods : To analyze DNA barcode regions, genomic DNA was extracted from twenty-nine specimens of Patrinia scabiosaefolia, Patrinia villosa, Patrinia saniculifolia, and Patrinia rupestris, and internal transcribed spacer 2(ITS2), matK and rbcL genes were amplified. For identification of species specific sequences, a comparative analysis was performed by the ClastalW based on entire sequences of ITS2, matK and rbcL genes, respectively. Results : In comparison of three DNA barcode sequences, we identified 22, 22, and 12 species-specific nucleotides enough to distinguish each four species from ITS2, matK and rbcL gene, respectively. The sequence differences at the corresponding positions were available genetic marker nucleotides to discriminate the correct species among analyzed four species. These results indicated that comparative analysis of ITS2, matK and rbcL genes were useful genetic markers to authenticate Patriniae Radix. Conclusions : The marker nucleotides enough to distinguish P. scabiosaefolia, P. villosa, P. saniculifolia, and P. rupestris, were obtained at 22 SNP marker nucleotides from ITS2 and matK DNA barcode sequences, but they were confirmed at 12 SNP marker nucleotides from rbcL. These differences could be used to authenticate Patriniae Radix from its adulterants as well as discriminating each four species.

Identification of Marker Nucleotides for the Molecular Authentication of Arisaematis Rhizoma Based on the DNA Barcode Sequences (천남성(天南星) 유전자 감별을 위한 DNA 바코드 분석 및 Marker Nucleotide 발굴)

  • Kim, Wook Jin;Lee, Young Mi;Ji, Yunui;Kang, Young Min;Choi, Goya;Kim, Ho Kyoung;Moon, Byeong Cheol
    • The Korea Journal of Herbology
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    • v.29 no.6
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    • pp.35-43
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    • 2014
  • Objectives : Official Arisaematis Rhizoma is described only three species, Arisaema amurnse, Arisaema erubescens, and Arisaema heterophyllum, in national Pharmacopoeia. However, other Arisaema species, Arisaema ringens, Arisaema takesimense and Arisaema serratum, also have been distributed as an inauthentic Arisaematis Rhizoma in the herbal market. To develop a reliable molecular authentication method for Arisaematis Rhizoma in species level, we analyzed DNA barcode regions using six Arisaema species. Methods : Thirty-eight samples of six Arisaema plants species (A. amurense, A. amurense f. serratum, A. heterophyllum, A. takesimense, and A. serratum) were collected from different habitate and nucleotide sequences of DNA barcode regions (rDNA-ITS, matK, and rbcL gene) were analyzed after PCR amplification. The species-specific sequences and phylogenetic relations were estimated using entire sequences of three DNA barcodes based on the analysis of ClastalW and UPGMA, respectively. Results : The comparative analysis of DNA barcode sequences were revealed inter-species specific nucleotides to distinguish the medicinal plant of Arisaema Rhizoma in species levels excluding between A. amurense and its subspecies (A. amurense f. serratum) and A. takesimense and A. serratum, respectively. However, we obtained sequence differences enough to discriminate authentic and inauthentic Arisaematis Rhizoma. Therefore, we suggest that these SNP type molecular genetic markers were an reliable method avaliable to identify official herbal medicines. Conclusions : These marker nucleotides could be useful to identify the official herbal medicines by providing definitive information that can identify original medicinal plant and distinguish from inauthentic adulterants and substitutes.

Korea Barcode of Life Database System (KBOL)

  • Kim, Sung-Min;Kim, Chang-Bae;Min, Gi-Sik;Suh, Young-Bae;Bhak, Jong;Woo, Tae-Ha;Koo, Hye-Young;Choi, Jun-Kil;Shin, Mann-Kyoon;Jung, Jong-Woo;Song, Kyo-Hong;Ree, Han-Il;Hwang, Ui-Wook;Park, Yung-Chul;Eo, Hae-Seok;Kim, Joo-Pil;Yoon, Seong-Myeong;Rho, Hyun-Soo;Kim, Sa-Heung;Lee, Hang;Min, Mi-Sook
    • Animal cells and systems
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    • v.16 no.1
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    • pp.11-19
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    • 2012
  • A major concern regarding the collection and storage of biodiversity information is the inefficiency of conventional taxonomic approaches in dealing with a large number of species. This inefficiency has increased the demand for automated, rapid, and reliable molecular identification systems and large-scale biological databases. DNA-based taxonomic approaches are now arguably a necessity in biodiversity studies. In particular, DNA barcoding using short DNA sequences provides an effective molecular tool for species identification. We constructed a large-scale database system that holds a collection of 5531 barcode sequences from 2429 Korean species. The Korea Barcode of Life database (KBOL, http://koreabarcode.org) is a web-based database system that is used for compiling a high volume of DNA barcode data and identifying unknown biological specimens. With the KBOL system, users can not only link DNA barcodes and biological information but can also undertake conservation activities, including environmental management, monitoring, and detecting significant organisms.

Monitoring of Raw Materials for Commercial Home Meal Replacement Products Using DNA Barcode Information (DNA 바코드를 이용한 가정간편식 제품의 원재료 모니터링 연구)

  • Yu, Yeon-Cheol;Hong, Yewon;Kim, Jung Ju;Lee, Dong Ho;Kim, Hyung Soo;Moon, Guiim;Park, Eun Mi
    • Journal of Food Hygiene and Safety
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    • v.35 no.3
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    • pp.234-242
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    • 2020
  • In this study, we monitored the raw materials in home-meal replacement (HMR) products, which have shown more than 63% growth in market size for two years. A total of 89 HMR products were purchased and the DNA barcodes of 112 raw materials in the product samples were analyzed. In order to identify the raw material species, a primer set specific for the 16S ribosomal RNA region of each raw material species was amplified. The amplicon was purified and sequenced, and then used to perform a BLAST search provided by the National Institutes of Health (NIH). The species of the raw material was determined by comparing the nucleotide sequences of the species registered in GenBank with identity and match score. Twenty-four species and three genera were identified from 112 raw materials. Three genera were identified at the genus level because a large number of species belonging to the same genus exist within 98% of the identity criteria. The results of the determination were compared with the available raw materials suggested in the Korea Food Code to determine the Korean name and availability of the foods. Six non-listed species were determined to be edible according to information provided by influential domestic and foreign organizations.

DNA barcode and phylogenetic study of the tribe Desmodieae (Fabaceae) in Korea (한국산 도둑놈의갈고리족(콩과)의 DNA 바코드 및 계통학적 연구)

  • JIN, Dong-Pil;PARK, Jong-Won;PARK, Jong-Soo;CHOI, Byoung-Hee
    • Korean Journal of Plant Taxonomy
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    • v.49 no.3
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    • pp.224-239
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    • 2019
  • Species identification for the Korean tribe Desmodieae was conducted using the DNA barcoding genes rbcL, matK (from chloroplast DNA) and ITS (from nuclear ribosomal DNA). A total of 25 taxa (n = 75) in five genera were sequenced, and neighbor-joining trees were constructed using different combinations of DNA barcodes. When comparing these phylogenetic trees, a tree with all loci combined (rbcL + matK + ITS) showed the highest rate of identification success (72%). On this tree, two subtribes and five genera within the tribe were supported as monophyletic. In the Desmodiinae clade, Desmodium and Hylodesmum were more closely related to each other than to Ohwia. In the Hylodesmum clade, H. oldhamii was found to be a sister to H. podocarpum complex, and all taxa within the complex were identified successfully. Subsp. fallax, regarded as a variety of subsp. oxyphyllum, is closely clustered with subsp. podocarpum. Although var. mandshuricum has been regarded as a synonym of var. oxyphyllum, this taxon is supported as a distinct variety. For the Lespedezinae clade, all species of Kummerowia were monophyletic, while nine of 16 Lespedeza taxa were identified successfully. In particular, the resolution of Macrolespedeza (28.5%) was lower than that of Junceae (77.8%). Among the Lespedeza taxa, L. cuneata was distinguishable from L. lichiyuniae, despite morphological similarities. It has been suggested that both L. maritima and L. inschanica are hybrids. The former is thought to be an independent species. While it is difficult to determine whether the latter originated via hybridization, this study showed that it is closely related to L. juncea.

On Schmarda's lost earthworm and some newly found New Zealand species (Oligochaeta: Megadrilacea: Lumbricidae, Acanthodrilidae, Octochaetidae, & Megascolecidae s. stricto)

  • Blakemore, Robert J.
    • Journal of Species Research
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    • v.1 no.2
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    • pp.105-132
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    • 2012
  • The saga of Megascolides orthostichon (Schmarda, 1861)-the first native worm described from Australasia-continues as its type-locality is unequivocally returned from Hobart, Tasmania to Mt Wellington, Auckland where a brief survey failed to unearth it. Since it has not been seen for 150 yrs, it may qualify under NZTCS or IUCN classification as 'Nationally Critical' if not 'Extinct'. New reports are for exotic Megascolecidae Anisochaeta kiwi sp. nov. and A. kiwi mihi sub-sp. nov. plus addition to the NZ faunal list of Australian Anisochaeta macleayi (Fletcher, 1889) that, due to its wide distribution in Australia and now New Zealand, may be a candidate model-species suitably resilient for eco-toxicological culture and monitoring. For holarctic Lumbricidae, new records are of Dendrobaena attemsi (Michaelsen, 1903) and the Murchieona muldali (Omodeo, 1956) morph or subspecies of M. minuscula (Rosa, 1906), neither lumbricid previously uncovered in Asia/Australasia. Also found for the first time outside its East Asian homeland is Eisenia japonica (Michaelsen, 1892) (which is compared to Japanese E. japonica hiramoto sub-sp. nov. and to E. anzac Blakemore, 2011). Records of these exotics plus recent new native species described by the author-including two, Rhododrilus mangamingi and Deinodrilus orcus spp. novae, herein-raise the numbers of megadriles known from New Zealand to 228 (sub-)species in five families. Preliminary mtDNA COI sequence barcodes are presented. Genus Tokea Benham, 1904 is revived on its lack of dorsal pores, losing or gaining some species with Megascolides M'Coy, 1878. An updated checklist of all 228 New Zealand taxa is appended.

Reports of Drawida (Oligochaeta: Moniligastridae) from far East Asia

  • Blakemore, Robert J.;Lee, Seunghan;Seo, Hong-Yul
    • Journal of Species Research
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    • v.3 no.2
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    • pp.127-166
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    • 2014
  • Moniligastrids are an important yet often ignored earthworm group commonly found in cultivated soils, especially paddy, in the tropical East. Seven new taxa are: Drawida koreana austri, D. koreana nanjiro, D. koreana shindo, D. odaesan, D. jeombongsan, D. companio and D. csuzdii Blakemore spp. or sub-spp. nov. from Korea. Drawida csuzdii is the first new species from North Korea since Lumbricidae Eisenia koreana (Zicsi, 1972). Historical East Asian moniligastrids are reviewed chronologically and Drawida barwelli (Beddard, 1886), D. japonica (Michaelsen, 1892) and D. siemsseni Michaelsen, 1910 are compared on their museum types. These three taxa were thought similar and related to D. nepalensis Michaelsen, 1907 and its possible synonym D. burchardi Michaelsen, 1903 (priority!) and both of these to prior D. uniqua (Bourne, 1887). Indian Drawida calebi Gates, 1945 is compared to new material of D. japonica from Japan, and D. willsi Michaelsen, 1907 to the new sub-species of D. koreana Kobayashi, 1938 from Korea. Where available, mtDNA COI gene barcodes are provided to help objective determinations and a phylogram is provided with outgroup Ocnerodrilidae Eukerria saltensis (Beddard, 1895) itself found in rice paddy/irrigation. The challenge now is comparison of all early taxa in their various homelands in order to assess the genetic variability and taxonomic boundaries acceptable, especially for unpigmented D. barwelli and also for pink/grey D. japonica and blue/grey D. koreana. A checklist of moniligastrids is appended showing 22 species from China (including Hainan and Taiwan), 21 from Korea, nine from Japan and the Drawida ghilarovi Gates, 1969 species-complex from far eastern Russian (Siberia). Recent Drawida dandongensis Zhang & Sun, 2014 from Sino-Korean border is misdescribed and cannot be meaningfully compared to any other Drawidas.