• Journal of Ginseng Research
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• 제41권3호
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• pp.339-346
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• 2017

Background: In this study, we investigated how to convert the Panax ginseng DNA sequence code and chemical fingerprints into a two-dimensional code. In order to improve the compression efficiency, GATC2Bytes and digital merger compression algorithms are proposed. Methods: HPLC chemical fingerprint data of 10 groups of P. ginseng from Northeast China and the internal transcribed spacer 2 (ITS2) sequence code as the DNA sequence code were ready for conversion. In order to convert such data into a two-dimensional code, the following six steps were performed: First, the chemical fingerprint characteristic data sets were obtained through the inflection filtering algorithm. Second, precompression processing of such data sets is undertaken. Third, precompression processing was undertaken with the P. ginseng DNA (ITS2) sequence codes. Fourth, the precompressed chemical fingerprint data and the DNA (ITS2) sequence code were combined in accordance with the set data format. Such combined data can be compressed by Zlib, an open source data compression algorithm. Finally, the compressed data generated a two-dimensional code called a quick response code (QR code). Results: Through the abovementioned converting process, it can be found that the number of bytes needed for storing P. ginseng chemical fingerprints and its DNA (ITS2) sequence code can be greatly reduced. After GTCA2Bytes algorithm processing, the ITS2 compression rate reaches 75% and the chemical fingerprint compression rate exceeds 99.65% via filtration and digital merger compression algorithm processing. Therefore, the overall compression ratio even exceeds 99.36%. The capacity of the formed QR code is around 0.5k, which can easily and successfully be read and identified by any smartphone. Conclusion: P. ginseng chemical fingerprints and its DNA (ITS2) sequence code can form a QR code after data processing, and therefore the QR code can be a perfect carrier of the authenticity and quality of P. ginseng information. This study provides a theoretical basis for the development of a quality traceability system of traditional Chinese medicine based on a two-dimensional code.

• 원예과학기술지
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• 제35권3호
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• pp.344-360
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• 2017

Zoysia 속 잔디는 학교운동장 및 공원, 골프장, 스포츠경기장과 같이 다양한 장소에 식재되고 있는 중요한 잔디이다. 해안가에서 자생하는 Zoysia 속 들잔디와 갯잔디는 외부 형태적 특성이 유사하여 외부 형태적 분류 뿐 만 아니라 분자생물학적 분류도 필요하다. 본 연구에서는 nrDNA-ITS(Internal Transcribed Spacer)의 DNA 바코드 분석을 통해서 자생하는 들잔디와 갯잔디의 분자생물학적 신속한 분류체계를 확립하고자 하였다. 이를 위해 난지형 잔디인 Zoysia 속 들잔디(Z. japonica) 및 갯잔디(Z. sinica)와 한지형 대표 잔디인 크리핑 벤트그라스(A. stolonifera) 및 켄터키 블루그라스(P. pratensis)의 nrDNA-ITS 염기서열을 확보하였다. 확보된 들잔디및 갯잔디, 크리핑 벤트그라스, 켄터키 블루그라스의 ITS 염기서열 전체 구간은 각 686bp와 687bp, 683bp, 681bp으로 확인되었으며, nrDNA-ITS 내부 염기서열구간 분석 결과, ITS1의 크기는 248-249bp, ITS2는 270̵-274bp, 5.8S rDNA는 163-164bp의 차이로, 각 4종의 잔디가 ITS 염기서열을 이용하여 식별되었다. 특히, 들잔디와 갯잔디 nrDNA-ITS 염기서열은 19 염기(2.8%) 차이를 나타냈으며, ITS1과 ITS2의 G + C 함량은 55.4-63.3% 임을 확인하였다. 이러한 들잔디와 갯잔디의 ITS 염기서열 차이를 바탕으로 CAPS 마커로 전환하여 대조구 및 수집된 자생 Zoysia 속 잔디 영양체 62개체를 분석한 결과, 외부형태학적 분류법으로 들잔디 개체, 갯잔디 개체로 동정되었지만, ITSCAPS 마커를 이용한 분자생물학적 분류법으로 들잔디 36개체와 갯잔디 22개체 뿐만 아니라 들잔디와 갯잔디간의 자연교배종 4개체도 식별하였다. 이상의 결과에서 들잔디와 갯잔디는 ITS 염기서열 및 ITS 기반 CAPS를 통하여 식별할 수 있을 것으로 판단된다.

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