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Zhang X, Armani A, Giusti A, Wen J, Fan S, Ying X. Molecular authentication of crocodile dried food products (meat and feet) and skin sold on the Chinese market: Implication for the European market in the light of the new legislation on reptile meat. Food Control 2021. [DOI: 10.1016/j.foodcont.2021.107884] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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2
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Sinha K, Sharma P, Som Chaudhury S, Das Mukhopadhyay C, Ruidas B. Species detection using probe technology. FOOD TOXICOLOGY AND FORENSICS 2021:313-346. [DOI: 10.1016/b978-0-12-822360-4.00012-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/19/2023]
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3
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Kumazawa Y, Hattori S, Taga Y. Semi-Nondestructive Certification of Crocodilian Leather by LC-MS Detection of Collagen Marker Peptides. Anal Chem 2019; 91:1796-1800. [PMID: 30599131 DOI: 10.1021/acs.analchem.8b05180] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Leather produced from crocodile, alligator, and caiman skin is widely used in the fashion industry. Crocodilian leather is generally more expensive than mammalian leather, and the value greatly differs even between the crocodilian species. However, inappropriate labeling of the animal source on leather products sometimes arises from accidental or fraudulent substitution, which is difficult to unambiguously detect by existing methods. In the present study, animal source identification of crocodilian leather was carried out using type I collagen-derived marker peptides generated after dechroming, heat denaturation, and trypsin digestion. Definitive discrimination between the three crocodilian species and also a related species, lizard, was achieved based on the detection patterns of selected six marker peptides, determined by LC-MS. Furthermore, powdering of the leather samples enabled a reduction in the sample amount required and allowed the elimination of the dechroming step. Approximately 100 μg of powder was taken from commercial leather watch straps by filing, resulting in only slight damage to the undersides of the straps. The animal sources of the crocodilian products and also a crocodile-embossed calf product were successfully identified using a combination of the crocodilian marker peptides and previously established mammalian marker peptides. This semi-nondestructive species identification method is not only useful for certification of leather products but also for monitoring of international trade of leather and skin.
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Affiliation(s)
- Yuki Kumazawa
- Japan Institute of Leather Research , 520-11 Kuwabara , Toride , Ibaraki 302-0017 , Japan.,Nippi Research Institute of Biomatrix , 520-11 Kuwabara , Toride , Ibaraki 302-0017 , Japan
| | - Shunji Hattori
- Japan Institute of Leather Research , 520-11 Kuwabara , Toride , Ibaraki 302-0017 , Japan.,Nippi Research Institute of Biomatrix , 520-11 Kuwabara , Toride , Ibaraki 302-0017 , Japan
| | - Yuki Taga
- Nippi Research Institute of Biomatrix , 520-11 Kuwabara , Toride , Ibaraki 302-0017 , Japan
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Ahmad Nizar NN, Sultana S, Hossain MM, Johan MR, Ali ME. Double gene targeting multiplex PCR-RFLP detects Crocodylus porosus in chicken meatball and traditional medicine. INTERNATIONAL JOURNAL OF FOOD PROPERTIES 2018. [DOI: 10.1080/10942912.2018.1508164] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Affiliation(s)
- Nina Naquiah Ahmad Nizar
- Nanotechnology and Catalysis Research Centre, Institute of Postgraduate Studies, University of Malaya, Kuala Lumpur, Malaysia
| | - Sharmin Sultana
- Nanotechnology and Catalysis Research Centre, Institute of Postgraduate Studies, University of Malaya, Kuala Lumpur, Malaysia
| | - M.A. Motalib Hossain
- Nanotechnology and Catalysis Research Centre, Institute of Postgraduate Studies, University of Malaya, Kuala Lumpur, Malaysia
| | - Mohd Rafie Johan
- Nanotechnology and Catalysis Research Centre, Institute of Postgraduate Studies, University of Malaya, Kuala Lumpur, Malaysia
| | - Md. Eaqub Ali
- Nanotechnology and Catalysis Research Centre, Institute of Postgraduate Studies, University of Malaya, Kuala Lumpur, Malaysia
- Centre for Research in Biotechnology for Agriculture (CEBAR), University of Malaya, Kuala Lumpur, Malaysia
- University of Malaya Halal Research Centre (UMHRC), University of Malaya, Kuala Lumpur, Malaysia
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5
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Ahmad Nizar NN, Ali ME, Hossain MAM, Sultana S, Ahamad MNU. Double gene targeting PCR assay for the detection of Crocodylus porosus in commercial products. Food Addit Contam Part A Chem Anal Control Expo Risk Assess 2018; 35:1038-1051. [PMID: 29447579 DOI: 10.1080/19440049.2018.1440644] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
The demand for crocodile meat is quickly growing because of its exotic and organoleptic appeal and also the low content of cholesterol and lipids. Moreover, crocodile oil and blood have been used in alternative medicines for treating asthma and several other ailments since ancient times. Furthermore, crocodile hides have great demand in leather industries. All of these have collectively contributed to the extensive hunting, illegal trading and consequent decline of crocodiles in most parts of the world. To keep space with the growing demands, some crocodile species such as Crocodylus porosus have been raised in farms and its commercial trades have been legalised. However, demand for wild crocodiles in foods and medicines has continued in high gear. Recently, several DNA-based methods have been proposed for crocodile detection, but those assays are based on single gene and longer-sized amplicon targets that break down during extensive processing. To address this gap, here we developed and validated a highly stable double gene targeted multiplex PCR assay for the identification of C. porosus materials in commercial products. The assay involved two short sites from C. porosus atp6 (77 bp) and cytb (127 bp) genes and a universal internal control (99 bp) for eukaryotes. The PCR primers were cross-tested against 18 species and validated under pure and mixed matrices under extensive boiling, autoclaving and microwave cooking conditions. Finally, it was used to identify five crocodile-based commercial products. The lower limits of detection for atp6 and cytb genes were 0.001 ng and 0.01 ng DNA, respectively, in pure meat and 1% under mixed matrices. Some inherent features, such as 77-127 bp amplicon sizes, exceptional stability and superior sensitivity, suggested the assay could be used for the identification of C. porosus in any forensic specimen.
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Affiliation(s)
- Nina Naquiah Ahmad Nizar
- a Nanotechnology and Catalysis Research Centre (NANOCAT) , University of Malaya , Kuala Lumpur , Malaysia
| | - Md Eaqub Ali
- a Nanotechnology and Catalysis Research Centre (NANOCAT) , University of Malaya , Kuala Lumpur , Malaysia.,b Centre for Research in Biotechnology for Agriculture (CEBAR) , University of Malaya , Kuala Lumpur , Malaysia.,c Institute of Halal Research (IHRUM) , University of Malaya , Kuala Lumpur , Malaysia
| | - M A Motalib Hossain
- a Nanotechnology and Catalysis Research Centre (NANOCAT) , University of Malaya , Kuala Lumpur , Malaysia
| | - Sharmin Sultana
- a Nanotechnology and Catalysis Research Centre (NANOCAT) , University of Malaya , Kuala Lumpur , Malaysia
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Shirley MH, Villanova VL, Vliet KA, Austin JD. Genetic barcoding facilitates captive and wild management of three cryptic African crocodile species complexes. Anim Conserv 2014. [DOI: 10.1111/acv.12176] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Affiliation(s)
- M. H. Shirley
- Wildlife Ecology and Conservation; University of Florida; Gainesville FL USA
| | - V. L. Villanova
- Department of Biology; University of Florida; Gainesville FL USA
| | - K. A. Vliet
- Department of Biology; University of Florida; Gainesville FL USA
| | - J. D. Austin
- Wildlife Ecology and Conservation; University of Florida; Gainesville FL USA
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7
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Wang Y, Feng D, Xue H, Nie C, Li E, Wu X. Universal DNA primers for amplification of complete mitochondrial protein-coding genes and ribosomal RNA genes from Crocodilia. CONSERV GENET RESOUR 2013. [DOI: 10.1007/s12686-013-9899-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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8
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Meganathan PR, Dubey B, Jogayya KN, Haque I. Identification of Indian crocodile species through DNA barcodes. J Forensic Sci 2013; 58:993-8. [PMID: 23718785 DOI: 10.1111/1556-4029.12129] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2011] [Revised: 03/06/2012] [Accepted: 05/06/2012] [Indexed: 12/27/2022]
Abstract
The biodiversity of India includes three crocodile species, Crocodylus palustris, Crocodylus porosus, and Gavialis gangeticus, whose status is threatened due to bushmeat crisis and illegal hunting. The crocodilian conservation management requires novel techniques to help forensic analysts to reveal species identity. DNA barcoding is a species identification technique, where a partial cytochrome c oxidase subunit 1 gene is used as a marker for species identification. Herein, the DNA barcoding technique is evaluated for three Indian crocodiles by analyzing an approximately 750-bp barcode region. The alignment result shows interspecific variations between sequences for discrimination of the three Indian crocodiles leading to species identification. The phylogenetic analyses also substantiate the established crocodilian relationships, which add further advantage to use this DNA barcoding approach for Indian crocodiles. This study provides preliminary evidences for the use of DNA barcoding technique in the identification of Indian crocodile species.
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Affiliation(s)
- P R Meganathan
- Biology Division, DNA Unit, Central Forensic Science Laboratory, 30, Gorachand Road, Park Circus, Kolkata 700 014, West Bengal, India
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Mitochondrial 16S ribosomal RNA gene for forensic identification of crocodile species. J Forensic Leg Med 2013; 20:334-8. [DOI: 10.1016/j.jflm.2012.09.018] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2011] [Revised: 07/15/2012] [Accepted: 09/07/2012] [Indexed: 02/07/2023]
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10
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Dubey B, Meganathan PR, Haque I. Complete mitochondrial genome sequence from an endangered Indian snake, Python molurus molurus (Serpentes, Pythonidae). Mol Biol Rep 2012; 39:7403-12. [PMID: 22331485 DOI: 10.1007/s11033-012-1572-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2011] [Accepted: 01/25/2012] [Indexed: 12/18/2022]
Abstract
This paper reports the complete mitochondrial genome sequence of an endangered Indian snake, Python molurus molurus (Indian Rock Python). A typical snake mitochondrial (mt) genome of 17258 bp length comprising of 37 genes including the 13 protein coding genes, 22 tRNA genes, and 2 ribosomal RNA genes along with duplicate control regions is described herein. The P. molurus molurus mt. genome is relatively similar to other snake mt. genomes with respect to gene arrangement, composition, tRNA structures and skews of AT/GC bases. The nucleotide composition of the genome shows that there are more A-C % than T-G% on the positive strand as revealed by positive AT and CG skews. Comparison of individual protein coding genes, with other snake genomes suggests that ATP8 and NADH3 genes have high divergence rates. Codon usage analysis reveals a preference of NNC codons over NNG codons in the mt. genome of P. molurus. Also, the synonymous and non-synonymous substitution rates (ka/ks) suggest that most of the protein coding genes are under purifying selection pressure. The phylogenetic analyses involving the concatenated 13 protein coding genes of P. molurus molurus conformed to the previously established snake phylogeny.
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Affiliation(s)
- Bhawna Dubey
- National DNA Analysis Centre, Central Forensic Science Laboratory, 30-Gorachand Road, Kolkata, 700 014 West Bengal, India
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Meganathan P, Dubey B, Batzer MA, Ray DA, Haque I. Complete mitochondrial genome sequences of three Crocodylus species and their comparison within the Order Crocodylia. Gene 2011; 478:35-41. [DOI: 10.1016/j.gene.2011.01.012] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2010] [Revised: 01/11/2011] [Accepted: 01/13/2011] [Indexed: 02/07/2023]
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Meganathan PR, Dubey B, Jogayya KN, Haque I. Validation of a Multiplex PCR Assay for the Forensic Identification of Indian Crocodiles*. J Forensic Sci 2011; 56:1241-4. [DOI: 10.1111/j.1556-4029.2011.01812.x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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13
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Molecular phylogenetic analyses of genus Crocodylus (Eusuchia, Crocodylia, Crocodylidae) and the taxonomic position of Crocodylus porosus. Mol Phylogenet Evol 2010; 57:393-402. [DOI: 10.1016/j.ympev.2010.06.011] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2010] [Revised: 06/15/2010] [Accepted: 06/15/2010] [Indexed: 12/31/2022]
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Tobe SS, Linacre A. DNA typing in wildlife crime: recent developments in species identification. Forensic Sci Med Pathol 2010; 6:195-206. [PMID: 20526699 DOI: 10.1007/s12024-010-9168-7] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/13/2010] [Indexed: 11/27/2022]
Abstract
Species identification has become a tool in the investigation of acts of alleged wildlife crimes. This review details the steps required in DNA testing in wildlife crime investigations and highlights recent developments where not only can individual species be identified within a mixture of species but multiple species can be identified simultaneously. 'What species is this?' is a question asked frequently in wildlife crime investigations. Depending on the material being examined, DNA analysis may offer the best opportunity to answer this question. Species testing requires the comparison of the DNA type from the unknown sample to DNA types on a database. The areas of DNA tested are on the mitochondria and include predominantly the cytochrome b gene and the cytochrome oxidase I gene. Standard analysis requires the sequencing of part of one of these genes and comparing the sequence to that held on a repository of DNA sequences such as the GenBank database. Much of the DNA sequence of either of these two genes is conserved with only parts being variable. A recent development is to target areas of those sequences that are specific to a species; this can increase the sensitivity of the test with no loss of specificity. The benefit of targeting species specific sequences is that within a mixture of two of more species, the individual species within the mixture can be identified. This identification would not be possible using standard sequencing. These new developments can lead to a greater number of samples being tested in alleged wildlife crimes.
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Affiliation(s)
- Shanan S Tobe
- Centre for Forensic Science, Strathclyde University, WestCHEM, Glasgow, UK
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Meganathan PR, Dubey B, Jogayya KN, Whitaker N, Haque I. A novel multiplex PCR assay for the identification of Indian crocodiles. Mol Ecol Resour 2010; 10:744-7. [PMID: 21565084 DOI: 10.1111/j.1755-0998.2010.02834.x] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Illegal hunting has been a major threat for the survival of wildlife fauna, including the three crocodile species that India harbours: Crocodylus palustris, Crocodylus porosus and Gavialis gangeticus. Although law prevents trade on these species, illicit hunting for trade continues to threaten the survival of these endangered species; conservation strategies therefore require a rapid molecular identification technique for Indian crocodiles. A multiplex polymerase chain reaction (PCR) assay with species-specific primers, considered as one of the most effective molecular techniques, is described herein. The primers were designed to yield species-specific sized amplicons. The assay discriminates the three Indian crocodile species unambiguously within a short time period using only simple agarose gel electrophoresis. We recommend this multiplex PCR assay to be used in the identification of Indian crocodile species.
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Affiliation(s)
- P R Meganathan
- National DNA Analysis Centre, Central Forensic Science Laboratory, 30-Gorachand Road, Kolkata 700 014, West Bengal, India Madras Crocodile Bank Trust, Centre for Herpetology, Mamallapuram 603 104, Tamil Nadu, India
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