1
|
Feng J, Ren Q, Xie A, Jiang Z, Liu Y. High-resolution melting analysis to authenticate deer-derived materials in processed products in China using a cytochrome oxidase I mini-barcode. JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE 2024. [PMID: 39051761 DOI: 10.1002/jsfa.13761] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2024] [Revised: 06/29/2024] [Accepted: 07/09/2024] [Indexed: 07/27/2024]
Abstract
BACKGROUND Deer-derived materials (antler, venison, fetus, penis, bone, tail, and others) are some of the most valuable traditional animal-based medicinal and food materials in China. In production, processing, and trade, the quality of deer products varies. The market is confusing, and counterfeit and shoddy products are common. There is an urgent need to establish an accurate identification method. RESULTS Two pairs of primers suitable for identifying deer-derived medicinal materials were obtained by screening the cytochrome oxidase I (COI) sequences of 18 species from nine genera of the deer family. The two primers were used to identify the species and adulteration of 22 batches of commercially available deer-derived products with a mini-barcode combining high-resolution melting (HRM) technology and methodical investigation. Deer-derived materials (sika and red deer) were correctly identified by species using varying DNA amounts (1 to 500 ng). The two pairs of primers COI-1FR and COI-2FR yielded melting temperatures (Tm) of 80.55 to 81.00 °C and 82.00 to 82.50 °C for sika deer, and 81.00 to 82.00 °C and 81.40 to 82.00 °C for red deer. Twenty-two batches of commercially available samples were analyzed by HRM analysis and conventional amplification sequencing, and it was found that the species samples had an error rate of species labeling of 31.8%. Four batches of samples were identified as mixed (adulterated) in the HRM analysis. CONCLUSION The combination of DNA mini-barcode with HRM analysis facilitated the accurate identification of species of deer-derived materials, especially the identification of samples in an adulterated mixed state. © 2024 Society of Chemical Industry.
Collapse
Affiliation(s)
- Jian Feng
- Hainan Provincial Key Laboratory of Resources Conservation and Development of Southern Medicine & International Joint Research Center for Quality of Traditional Chinese Medicine, Hainan Branch of the Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Haikou, China
| | - Qiqi Ren
- Hainan Provincial Key Laboratory of Resources Conservation and Development of Southern Medicine & International Joint Research Center for Quality of Traditional Chinese Medicine, Hainan Branch of the Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Haikou, China
| | - Anzhen Xie
- Hainan Provincial Key Laboratory of Resources Conservation and Development of Southern Medicine & International Joint Research Center for Quality of Traditional Chinese Medicine, Hainan Branch of the Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Haikou, China
| | - Zixiao Jiang
- Hainan Provincial Key Laboratory of Resources Conservation and Development of Southern Medicine & International Joint Research Center for Quality of Traditional Chinese Medicine, Hainan Branch of the Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Haikou, China
| | - Yangyang Liu
- Hainan Provincial Key Laboratory of Resources Conservation and Development of Southern Medicine & International Joint Research Center for Quality of Traditional Chinese Medicine, Hainan Branch of the Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Haikou, China
| |
Collapse
|
2
|
Jayasundara SL, Algewatta HR, Jayawardana S, Perera M, Peiris LDC. Molecular Identification and Evolutionary Divergence of the Sri Lankan Sambar Deer, Rusa unicolor (Kerr 1792). Animals (Basel) 2023; 13:2877. [PMID: 37760277 PMCID: PMC10525601 DOI: 10.3390/ani13182877] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Revised: 09/05/2023] [Accepted: 09/08/2023] [Indexed: 09/29/2023] Open
Abstract
The Sambar is one of the largest deer species distributed mainly in Asia, and it has been listed as a vulnerable species. Taxonomy based on morphological characterization has been the gold standard method used to identify the Sambar deer species. Yet, morphological identification is challenging and requires expertise. To conduct species identification and taxonomic decisions, we performed the molecular identification of R. unicolor found in Sri Lanka using DNA barcodes, COI, and Cyt b to compare the Sri Lankan R. unicolor with the Indian R. unicolor and other R. unicolor subspecies. We obtained mitochondrial DNA sequences from COI and Cyt b from blood samples collected from the wet zone in Sri Lanka. A phylogenetic tree was constructed based on the Bayesian analyses using MrBayes 3.2.7. Molecular dating was implemented in Bayesian Evolutionary Analysis Sampling Trees (BEAST v1.8.2) on the concatenated sequence using a log-normal relaxed clock and Yule species tree prior, with four categories. The results showed that the Sri Lankan R. unicolor is genetically different from the Indian R. unicolor and other R. unicolor subspecies. The divergence occurred approximately 1.1 MYA (million years ago) in the Pleistocene era. The results are essential for designing new conservation platforms for these Sambar deer species.
Collapse
Affiliation(s)
- Subodha Lakruwani Jayasundara
- Department of Zoology, Faculty of Applied Sciences, University of Sri Jayewardenepura, Nugegoda 10250, Sri Lanka; (S.L.J.); (M.P.)
| | - Hirusha Randimal Algewatta
- Department of Zoology, Faculty of Applied Sciences, University of Sri Jayewardenepura, Nugegoda 10250, Sri Lanka; (S.L.J.); (M.P.)
| | - Suhada Jayawardana
- Wildlife Rehabilitation Center, Department of Wildlife Conservation, 811A, Jayanthipura, Btataramulla 10120, Sri Lanka;
| | - Minoli Perera
- Department of Zoology, Faculty of Applied Sciences, University of Sri Jayewardenepura, Nugegoda 10250, Sri Lanka; (S.L.J.); (M.P.)
| | - L. Dinithi C. Peiris
- Genetics & Molecular Biology Unit/Department of Zoology, Faculty of Applied Sciences, University of Sri Jayewardenepura, Nugegoda 10250, Sri Lanka
| |
Collapse
|
3
|
Filip E, Strzała T, Stępień E, Cembrowska-Lech D. Universal mtDNA fragment for Cervidae barcoding species identification using phylogeny and preliminary analysis of machine learning approach. Sci Rep 2023; 13:9133. [PMID: 37277428 DOI: 10.1038/s41598-023-35637-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Accepted: 05/21/2023] [Indexed: 06/07/2023] Open
Abstract
The aim of the study was to use total DNA obtained from bone material to identify species of free-living animals based on the analysis of mtDNA fragments by molecular methods using accurate bioinformatics tools Bayesian approach and the machine learning approach. In our research, we present a case study of successful species identification based on degraded samples of bone, with the use of short mtDNA fragments. For better barcoding, we used molecular and bioinformatics methods. We obtained a partial sequence of the mitochondrial cytochrome b (Cytb) gene for Capreolus capreolus, Dama dama, and Cervus elaphus, that can be used for species affiliation. The new sequences have been deposited in GenBank, enriching the existing Cervidae mtDNA base. We have also analysed the effect of barcodes on species identification from the perspective of the machine learning approach. Machine learning approaches of BLOG and WEKA were compared with distance-based (TaxonDNA) and tree-based (NJ tree) methods based on the discrimination accuracy of the single barcodes. The results indicated that BLOG and WEKAs SMO classifier and NJ tree performed better than TaxonDNA in discriminating Cervidae species, with BLOG and WEKAs SMO classifier performing the best.
Collapse
Affiliation(s)
- Ewa Filip
- Institute of Biology, University of Szczecin, Wąska 13, 71-415, Szczecin, Poland.
- The Centre for Molecular Biology and Biotechnology, University of Szczecin, Szczecin, Poland.
| | - Tomasz Strzała
- Department of Genetics, Faculty of Biology and Animal Science, Wrocław University of Environmental and Life Sciences, Wrocław, Poland
| | - Edyta Stępień
- Institute of Marine and Environmental Sciences, University of Szczecin, Adama Mickiewicza 16, 70-383, Szczecin, Poland
| | - Danuta Cembrowska-Lech
- Institute of Biology, University of Szczecin, Wąska 13, 71-415, Szczecin, Poland
- Sanprobi Sp. z o. o. Sp. k., Kurza Stopka 5C, 70-535, Szczecin, Poland
| |
Collapse
|
4
|
Harding LE. Available names for Rangifer (Mammalia, Artiodactyla, Cervidae) species and subspecies. Zookeys 2022; 1119:117-151. [PMID: 36762356 PMCID: PMC9848878 DOI: 10.3897/zookeys.1119.80233] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2022] [Accepted: 07/19/2022] [Indexed: 11/12/2022] Open
Abstract
Advancements in molecular and phylogenetic analysis have revealed the need for greater taxonomic resolution since Rangifer (Reindeer and caribou: Cervidae) was last revised in 1961. Recent literature shows that many of the subspecies and several species synonymised out of existence are, in fact, valid, some names have been misapplied, and new subspecies-level clades are in need of description. This paper reviews available names for recently defined ecotypes of reindeer and caribou in compliance with ICZN rules for zoological nomenclature.
Collapse
Affiliation(s)
- Lee E. Harding
- 2339 Sumpter Drive, Coquitlam, BC, V3J 6Y3, Coquitlam, CanadaunaffiliatedCoquitlamCanada
| |
Collapse
|
5
|
Yang F, Ding F, Chen H, He M, Zhu S, Ma X, Jiang L, Li H. DNA Barcoding for the Identification and Authentication of Animal Species in Traditional Medicine. EVIDENCE-BASED COMPLEMENTARY AND ALTERNATIVE MEDICINE : ECAM 2018; 2018:5160254. [PMID: 29849709 PMCID: PMC5937547 DOI: 10.1155/2018/5160254] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/19/2017] [Accepted: 03/11/2018] [Indexed: 02/06/2023]
Abstract
Animal-based traditional medicine not only plays a significant role in therapeutic practices worldwide but also provides a potential compound library for drug discovery. However, persistent hunting and illegal trade markedly threaten numerous medicinal animal species, and increasing demand further provokes the emergence of various adulterants. As the conventional methods are difficult and time-consuming to detect processed products or identify animal species with similar morphology, developing novel authentication methods for animal-based traditional medicine represents an urgent need. During the last decade, DNA barcoding offers an accurate and efficient strategy that can identify existing species and discover unknown species via analysis of sequence variation in a standardized region of DNA. Recent studies have shown that DNA barcoding as well as minibarcoding and metabarcoding is capable of identifying animal species and discriminating the authentics from the adulterants in various types of traditional medicines, including raw materials, processed products, and complex preparations. These techniques can also be used to detect the unlabelled and threatened animal species in traditional medicine. Here, we review the recent progress of DNA barcoding for the identification and authentication of animal species used in traditional medicine, which provides a reference for quality control and trade supervision of animal-based traditional medicine.
Collapse
Affiliation(s)
- Fan Yang
- Institute of Forensic Science, Ministry of Public Security, Beijing 100038, China
- Beijing Engineering Research Center of Crime Scene Evidence Examination, Institute of Forensic Science, Beijing 100038, China
| | - Fei Ding
- Center for Bioresources & Drug Discovery and School of Biosciences & Biopharmaceutics, Guangdong Pharmaceutical University, Guangzhou, Guangdong 510006, China
| | - Hong Chen
- Center for Bioresources & Drug Discovery and School of Biosciences & Biopharmaceutics, Guangdong Pharmaceutical University, Guangzhou, Guangdong 510006, China
| | - Mingqi He
- Center for Bioresources & Drug Discovery and School of Biosciences & Biopharmaceutics, Guangdong Pharmaceutical University, Guangzhou, Guangdong 510006, China
| | - Shixin Zhu
- Center for Bioresources & Drug Discovery and School of Biosciences & Biopharmaceutics, Guangdong Pharmaceutical University, Guangzhou, Guangdong 510006, China
| | - Xin Ma
- Institute of Forensic Science, Ministry of Public Security, Beijing 100038, China
- Beijing Engineering Research Center of Crime Scene Evidence Examination, Institute of Forensic Science, Beijing 100038, China
| | - Li Jiang
- Institute of Forensic Science, Ministry of Public Security, Beijing 100038, China
- Beijing Engineering Research Center of Crime Scene Evidence Examination, Institute of Forensic Science, Beijing 100038, China
| | - Haifeng Li
- Center for Bioresources & Drug Discovery and School of Biosciences & Biopharmaceutics, Guangdong Pharmaceutical University, Guangzhou, Guangdong 510006, China
| |
Collapse
|
6
|
Gaikwad S, Warudkar A, Shouche Y. Efficacy of DNA barcoding for the species identification of spiders from Western Ghats of India. Mitochondrial DNA A DNA Mapp Seq Anal 2016; 28:638-644. [PMID: 27159727 DOI: 10.3109/24701394.2016.1166219] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
DNA barcoding has emerged as an additional tool for taxonomy and as an aid to taxonomic impediments. Due to their extensive morphological variation, spiders are taxonomically challenging. Therefore, all over the world, attempts are being made to DNA barcode species of spiders. Till now no attempts were made to DNA barcode Indian spiders despite their rich diversity. We have generated DNA barcodes for 60 species (n = 112) of spiders for the first time from India. Although only 17 species were correctly identified at the species level, DNA barcoding correctly discriminated 99% of the species studied here. We have also found high intraspecies nucleotide divergence in Plexippus paykulli suggesting cryptic diversity that needs to be studied in detail. Our study also showed non-specific amplification of the Cytochrome Oxidase I (COI) gene of endosymbiont bacteria Wolbachia. However, these cases are very rare and could be resolved by the use of modified or group specific primers.
Collapse
Affiliation(s)
- Swapnil Gaikwad
- a Microbial Culture Collection (MCC) , Pune , Maharashtra , India
| | - Ashwin Warudkar
- a Microbial Culture Collection (MCC) , Pune , Maharashtra , India
| | - Yogesh Shouche
- a Microbial Culture Collection (MCC) , Pune , Maharashtra , India
| |
Collapse
|