• 한국균학회소식:학술대회논문집
• /
• 한국균학회 2014년도 춘계학술대회 및 임시총회
• /
• pp.17-17
• /
• 2014

Over five thousand higher fungal specimens were collected from 32 forest areas of Chungcheong and Gyeongsang province from 2012 to 2013. We obtained 513 strains and 3,120 ITS sequences. Mushrooms were first identified with macro- and micro-scopic characters, and their identification was confirmed on the basis of ITS sequences. Voucher specimens were designated for each species found in Korea. Construction of DNA barcoding Database is currently underway with sequences of 409 species. During the development of the database, some new species were recognized, along with several Korean new records. When the system has been completed, it will provide essential molecular information for metagenomic and phylogenetic researches for higher fungi.

• 식물분류학회지
• /
• 제46권3호
• /
• pp.273-282
• /
• 2016

The establishment of a DNA barcode database at the regional scale and assessments of the utility of DNA barcodes are crucial for conservation biology and for the sustainable utilization of biological resources. Schisandraceae is a small family consisting of ca. 45 species. It contains many economically important species, such as Schisandra chinensis, which is widely used as a source in tonic beverages and in oriental medicine. In Korea, three species, S. chinensis, S. repanda, and Kadsura japonica, are distributed. We evaluated the level of variation of the DNA sequences of rbcL, matK, and the ITS regions from 13 accessions representing the distributional range of the three species. The three DNA barcode regions were easily amplified and sequenced. The minimum values of the interspecific genetic distances among S. chinensis, S. repanda, and K. japonica either separately or in combination are 4- to 23-fold higher than the maximum value of the intraspecific distance, showing that there is a clear DNA barcoding gap in the regions for Korean Schisandraceae. Phylogenetic analyses of the three DNA barcode regions, separately and simultaneously, indicate that all of the DNA barcode regions are useful for identifying a species of Schisandraceae in Korea. The distinctiveness of the three species of Schisandraceae was also supported at the species level when Chinese and Japanese populations were added. The results of this study indicate that three concatenated regions constitute the best option for DNA barcoding in Schisandraceae in Korea.

• ALGAE
• /
• 제35권3호
• /
• pp.293-301
• /
• 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.

• 한국자원식물학회지
• /
• 제35권2호
• /
• pp.346-361
• /
• 2022

독성 식물로 인한 식중독 사고는 매년 발생하고 있으며, 일부 독성 식물은 식용 식물로 오인 섭취되어 식중독을 유발하기 때문에 독성 식물의 정확한 종 식별이 요구되고 있다. 이러한 요구에 따라 감정기관에서는 독성 식물의 종 식별에 적합한 DNA 바코드를 찾아 신속하고 정확한 종 식별에 활용할 수 있는 데이터베이스를 구축하는 것이 필요한 실정이다. 따라서 본 연구는 다양한 독성 식물에서 DNA 바코드 구간의 염기서열을 확보하고, 각각에 적합한 DNA 바코드를 확인하여 데이터베이스를 구축하고자 하였으며, 기초 연구로써 제주도에 자생하는 독성식물 19종을 선정하여 7개의 DNA 바코드 (trnH-psbA, trnL-trnF, trnL intron, rbcL, matK, ITS1-ITS4, 18S rRNA)를 이용한 종식별을 수행하였다. 종 식별 결과 trnL-trnF 바코드와 ITS1-ITS4 바코드가 PCR 증폭 및 염기서열 획득에 가장 용이하였으며, 두 개의 바코드를 조합하여 사용하면 19종 중 18종의 식물에서 단일 종 식별이 가능하였다. 따라서 미지의 독성 식물에 대한 감정이 의뢰되었을 때 trnL-trnF 바코드와 ITS1-ITS4 바코드를 조합하여 사용하면 신속한 종 식별에 도움이 될 것으로 사료된다. 본 연구에서 제시된 독성식물 19종의 염기서열 및 DNA 바코드 데이터베이스는 더욱 신속하고 정확한 독성 식물의 종 식별 감정에 도움이 될 것이다.

• Animal Systematics, Evolution and Diversity
• /
• 제35권1호
• /
• pp.33-36
• /
• 2019

The marine interstitial annelid Pharyngocirrus uchidai(Sasaki, 1981) has been only known from Japan. In this study, we report the occurrence of P. uchidai for the first time in four localities along the eastern coast of Korea: Bukmyeon, Gamchu, Gase, and Oeongchi. Species identification was confirmed by comparison of DNA barcoding sequences with morphological examination from the type locality, Oshoro, Japan. We generated a total of 25 sequences of a partial segment (580 bp) of the cytochrome c oxidase subunit I gene (COI), representing five specimens from each locality. Maximum intra-specific variation was 1.2% in terms of Kimura two-parameter (K2P) distance, observed between two individuals each from Gamchu (i.e., between two specimens from the single locality), Gamchu and Oeongchi, Gamchu and Oshoro, and Oeongchi and Oshoro. On the other hand, an identical haplotype was found in all the five localities, substantiating our species identification for the Korean populations. Inter-specific K2P distance between P. uchidai and an unidentified Saccocirrus sp. from Canada (based on public database entries) was 22.4-23.4%.

• Animal cells and systems
• /
• 제16권1호
• /
• pp.11-19
• /
• 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.

• Genomics & Informatics
• /
• 제21권3호
• /
• pp.39.1-39.15
• /
• 2023

DNA barcoding without assessing reliability and validity causes taxonomic errors of species identification, which is responsible for disruptions of their conservation and aquaculture industry. Although DNA barcoding facilitates molecular identification and phylogenetic analysis of species, its availability in clariid catfish lineage remains uncertain. In this study, DNA barcoding was developed and validated for clariid catfish. 2,970 barcode sequences from mitochondrial cytochrome c oxidase I (COI) and cytochrome b (Cytb) genes and D-loop sequences were analyzed for 37 clariid catfish species. The highest intraspecific nearest neighbor distances were 85.47%, 98.03%, and 89.10% for COI, Cytb, and D-loop sequences, respectively. This suggests that the Cytb gene is the most appropriate for identifying clariid catfish and can serve as a standard region for DNA barcoding. A positive barcoding gap between interspecific and intraspecific sequence divergence was observed in the Cytb dataset but not in the COI and D-loop datasets. Intraspecific variation was typically less than 4.4%, whereas interspecific variation was generally more than 66.9%. However, a species complex was detected in walking catfish and significant intraspecific sequence divergence was observed in North African catfish. These findings suggest the need to focus on developing a DNA barcoding system for classifying clariid catfish properly and to validate its efficacy for a wider range of clariid catfish. With an enriched database of multiple sequences from a target species and its genus, species identification can be more accurate and biodiversity assessment of the species can be facilitated.

• The Plant Pathology Journal
• /
• 제40권2호
• /
• pp.171-191
• /
• 2024

Identification of Helicotylenchus species is very challenging due to phenotypic plasticity and existence of cryptic species complexes. Recently, the use of rDNA barcodes has proven to be useful for identification of Helicotylenchus. Molecular markers are a quick diagnostic tool and are crucial for discriminating related species and resolving cryptic species complexes within this speciose genus. However, DNA barcoding is not an error-free approach. The public databases appear to be marred by incorrect sequences, arising from sequencing errors, mislabeling, and misidentifications. Herein, we provide a comprehensive analysis of the newly obtained, and published DNA sequences of Helicotylenchus, revealing the potential faults in the available DNA barcodes. A total of 97 sequences (25 nearly full-length 18S-rRNA, 12 partial 28S-rRNA, 16 partial internal transcribed spacer [ITS]-rRNA, and 44 partial cytochrome c oxidase subunit I [COI] gene sequences) were newly obtained in the present study. Phylogenetic relationships between species are given as inferred from the analyses of 103 sequences of 18S-rRNA, 469 sequences of 28S-rRNA, 183 sequences of ITS-rRNA, and 63 sequences of COI. Remarks on suggested corrections of published accessions in GenBank database are given. Additionally, COI gene sequences of H. dihystera, H. asiaticus and the contentious H. microlobus are provided herein for the first time. Similar to rDNA gene analyses, the COI sequences support the genetic distinctness and validity of H. microlobus. DNA barcodes from type material are needed for resolving the taxonomic status of the unresolved taxonomic groups within the genus.

• Weed & Turfgrass Science
• /
• 제4권1호
• /
• pp.18-25
• /
• 2015

DNA 바코드는 게놈 DNA의 단편을 이용해 형태적 지식없이 종을 동정하는 방법으로 전 세계적으로 최근에 많이 이용하고 있으며 고등식물에서는 엽록체 rbcL과 matK 유전자를 이용하고 있다. 본 연구에서는 표준 식물 바코드마커와 핵 ITS 부위를 이용하여 국내 포아풀아과 잡초 16속 29종 163생태형의 바코드 데이터를 생산하는 것을 목적으로 하였다. 더불어 포아풀아과의 바코드에서 각 마커의 효율성도 조사하였다. 바코드 결과 PCR 증폭과 염기서열 분석성공률은 rbcL에서 가장 높았으며 matK에서 가장 낮았다. 반대로 바코드 갭은 matK에서 가장 높은 반면 rbcL에서 가장 낮았으며, 종 식별 해상력은 matK에서 가장 높고, ITS에서 가장 낮았다. 그러나 바코드 갭과 종 식별 해상력이 가장 높은 matK를 포아풀아과에서 바코드 마커로 이용하는 것은 너무 낮은 PCR 증폭과 염기서열 분석성공률(58.3%) 때문에 고려해야할 것으로 생각된다. 단일마커로 rbcL과 ITS는 포아풀아과의 바코드에 적절하게 이용될 수 있으며, 두 마커를 조합으로 이용하면 공통으로 분석된 샘플에 따라 바코드 갭과 종 식별 해상력을 높일 수 있었다. 포아풀아과의 바코드데이터는 미국의 국립생물공학정보센터에 기탁하여 genbank 번호를 부여받아 공개하였다.

• 환경생물
• /
• 제41권2호
• /
• pp.145-166
• /
• 2023

Parrots have been threatened by global trade to meet their high demand as pets. Controlling parrot trade is essential because parrots play a vital role in the ecosystem. Accurate species identification is crucial for controlling parrot trade. Parrots have been traded as eggs due to their advantages of lower mortality rates and more accessible transport than live parrots. A molecular method is required to identify parrot eggs because it is difficult to perform identification using morphological features. In this study, DNAs were obtained from 43 unidentified parrot eggs using a non-destructive sampling method. Partial cytochrome b (CYTB) gene was then successfully amplified using polymerase chain reaction (PCR) and sequenced. Sequences newly obtained in the present study were compared to those available in the GenBank by database searching. In addition, phylogenetic analysis was conducted to identify species using available sequences in GenBank along with sequences reported in previous studies. Finally, the 43 parrot eggs were successfully identified as seven species belonging to two families and seven genera. This non-destructive sampling method for obtaining DNA and molecular identification might help control the trade of parrot eggs and prevent their illegal trade.