A vertebrate-specific qPCR assay as an endogenous internal control for robust species identification

Forensic Science International: Genetics - Tập 56 - Trang 102628 - 2022
Kei Taniguchi1, Tomoko Akutsu1, Ken Watanabe1, Yoshinori Ogawa1, Kazuhiko Imaizumi1
1National Research Institute of Police Science, 6-3-1 Kashiwanoha, Kashiwa, Chiba 277-0882, Japan

Tài liệu tham khảo

T. O'Connor, The archaeology of animal bones, Texas A&M University Press 2008. Newman, 2002, Identification of archaeological animal bone by PCR/DNA analysis, J. Archaeol. Sci., 29, 77, 10.1006/jasc.2001.0688 Yang, 2004, DNA species identification of archaeological salmon bone from the Pacific Northwest Coast of North America, J. Archaeol. Sci., 31, 619, 10.1016/j.jas.2003.10.008 Wong, 2008, DNA barcoding detects market substitution in North American seafood, Food Res. Int., 41, 828, 10.1016/j.foodres.2008.07.005 Ballin, 2010, Authentication of meat and meat products, Meat Sci., 86, 577, 10.1016/j.meatsci.2010.06.001 Baker, 2002, Effect of British hunting ban on fox numbers, Nature, 419, 34, 10.1038/419034a Dalén, 2004, Identifying species from pieces of faeces, Conserv. Genet., 5, 109, 10.1023/B:COGE.0000014060.54070.45 Meyer, 1995, Polymerase chain reaction-restriction fragment length polymorphism analysis: a simple method for species identification in food, J. AOAC Int, 78, 1542, 10.1093/jaoac/78.6.1542 Asensio, 2008, Determination of food authenticity by enzyme-linked immunosorbent assay (ELISA), Food Control, 19, 1, 10.1016/j.foodcont.2007.02.010 Tobe, 2008, A multiplex assay to identify 18 European mammal species from mixtures using the mitochondrial cytochrome b gene, Electrophoresis, 29, 340, 10.1002/elps.200700706 Pereira, 2010, Identification of species by multiplex analysis of variable-length sequences, Nucleic Acids Res, 38, 10.1093/nar/gkq865 Hebert, 2003, Biological identifications through DNA barcodes, Proc. Biol. Sci., 270, 313, 10.1098/rspb.2002.2218 Dawnay, 2007, Validation of the barcoding gene COI for use in forensic genetic species identification, Forensic Sci. Int, 173, 1, 10.1016/j.forsciint.2006.09.013 Taberlet, 2007, Power and limitations of the chloroplast trnL (UAA) intron for plant DNA barcoding, Nucleic Acids Res, 35, 10.1093/nar/gkl938 Armstrong, 2005, DNA barcodes for biosecurity: invasive species identification, Philos. Trans. R. Soc. Lond. B Biol. Sci., 360, 1813, 10.1098/rstb.2005.1713 Ward, 2005, DNA barcoding Australia’s fish species, Philos. Trans. R. Soc. Lond. B Biol. Sci., 360, 1847, 10.1098/rstb.2005.1716 Hebert, 2004, Identification of Birds through DNA Barcodes, PLoS Biol., 2, 10.1371/journal.pbio.0020312 Bradley, 2001, A test of the genetic species concept: cytochrome-b sequences and mammals, J. Mammal., 82, 960, 10.1644/1545-1542(2001)082<0960:ATOTGS>2.0.CO;2 Imaizumi, 2007, Development of species identification tests targeting the 16S ribosomal RNA coding region in mitochondrial DNA, Int J. Leg. Med, 121, 184, 10.1007/s00414-006-0127-5 Heid, 1996, Real time quantitative PCR, Genome Res, 6, 986, 10.1101/gr.6.10.986 Terio, 2010, Identification of tuna species in commercial cans by minor groove binder probe real-time polymerase chain reaction analysis of mitochondrial DNA sequences, Mol. Cell. Probes, 24, 352, 10.1016/j.mcp.2010.07.006 Hird, 2012, Development of real-time PCR assays for the detection of Atlantic cod (Gadus morhua), Atlantic salmon (Salmo salar) and European plaice (Pleuronectes platessa) in complex food samples, Eur. Food Res. Technol., 234, 127, 10.1007/s00217-011-1596-4 Hulley, 2019, Development and validation of probe-based multiplex real-time PCR assays for the rapid and accurate detection of freshwater fish species, PLoS One, 14, 10.1371/journal.pone.0210165 Watanabe, 2004, A quick method for species identification of Japanese eel (Anguilla japonica) using real-time PCR: an onboard application for use during sampling surveys, Mar. Biotechnol. (NY), 6, 566, 10.1007/s10126-004-1000-5 Taylor, 2002, Species-specific TaqMan probes for simultaneous identification of (Gadus morhua L.), haddock (Melanogrammus aeglefinus L.) and whiting (Merlangius merlangus L.), Mol. Ecol. Notes, 2, 599, 10.1046/j.1471-8286.2002.00269.x Rojas, 2010, Novel TaqMan real-time polymerase chain reaction assay for verifying the authenticity of meat and commercial meat products from game birds, Food Addit. Contam. Part A Chem. Anal. Control Expo. Risk Assess., 27, 749, 10.1080/19440040903503070 Natonek-Wiśniewska, 2019, Development of a sensitive and specific qPCR method to detect duck and goose DNA in meat and feathers, Eur. Food Res. Technol., 245, 335, 10.1007/s00217-018-3165-6 Kesmen, 2012, Detection of chicken and turkey meat in meat mixtures by using real-time PCR assays, J. Food Sci., 77, C167, 10.1111/j.1750-3841.2011.02536.x Ji, 2011, A method for quantifying mixed goat cashmere and sheep wool, Forensic Sci. Int 208(, 208, 139, 10.1016/j.forsciint.2010.11.017 Wozney, 2012, Real-time PCR detection and quantification of elephantid DNA: species identification for highly processed samples associated with the ivory trade, Forensic Sci. Int, 219, 106, 10.1016/j.forsciint.2011.12.006 O’Neill, 2013, Development of novel real-time TaqMan® PCR assays for the species and sex identification of otter (Lutra lutra) and their application to noninvasive genetic monitoring, Mol. Ecol. Resour., 13, 877, 10.1111/1755-0998.12141 Knapp, 2016, Development of a real-time PCR for a sensitive one-step coprodiagnosis allowing both the identification of carnivore feces and the detection of toxocara spp. and echinococcus multilocularis, Appl. Environ. Microbiol, 82, 2950, 10.1128/AEM.03467-15 O'Leary, 2016, Reference sequence (RefSeq) database at NCBI: current status, taxonomic expansion, and functional annotation, Nucleic Acids Res, 44, D733, 10.1093/nar/gkv1189 Edgar, 2004, MUSCLE: multiple sequence alignment with high accuracy and high throughput, Nucleic Acids Res, 32, 1792, 10.1093/nar/gkh340 Kavlick, 2011, Quantification of human mitochondrial DNA using synthesized DNA standards, J. Forensic Sci., 56, 1457, 10.1111/j.1556-4029.2011.01871.x Tanabe, 2007, A real-time quantitative PCR detection method for pork, chicken, beef, mutton, and horseflesh in foods, Biosci., Biotechnol., Biochem., 71, 3131, 10.1271/bbb.70683 Conte, 2018, Using synthetic oligonucleotides as standards in probe-based qPCR, Biotechniques, 64, 177, 10.2144/btn-2018-2000 Bustin, 2009, The MIQE guidelines: minimum information for publication of quantitative real-time PCR experiments, Clin. Chem., 55, 611, 10.1373/clinchem.2008.112797 Ye, 2012, Primer-BLAST: a tool to design target-specific primers for polymerase chain reaction, BMC Bioinforma., 13, 134, 10.1186/1471-2105-13-134 Delsuc, 2006, Tunicates and not cephalochordates are the closest living relatives of vertebrates, Nature, 439, 965, 10.1038/nature04336 Putnam, 2008, The amphioxus genome and the evolution of the chordate karyotype, Nature, 453, 1064, 10.1038/nature06967 Kavlick, 2018, Development of a universal internal positive control, Biotechniques, 65, 275, 10.2144/btn-2018-0034 Cammà, 2012, Development and validation of fast Real-Time PCR assays for species identification in raw and cooked meat mixtures, Food Control, 23, 400, 10.1016/j.foodcont.2011.08.007 Tobe, 2008, A technique for the quantification of human and non-human mammalian mitochondrial DNA copy number in forensic and other mixtures, Forensic Sci. Int Genet, 2, 249, 10.1016/j.fsigen.2008.03.002 Pegels, 2012, Evaluation of a TaqMan real-time PCR assay for detection of chicken, turkey, duck, and goose material in highly processed industrial feed samples, Poult. Sci., 91, 1709, 10.3382/ps.2011-01954 2021, RNAcentral 2021: secondary structure integration, improved sequence search and new member databases, Nucleic Acids Res, 49, D212, 10.1093/nar/gkaa921 2015, New Products, Science, 349, 1125, 10.1126/science.349.6252.1125-a Kitpipit, 2014, Forensic animal DNA analysis using economical two-step direct PCR, Forensic Sci. Med Pathol., 10, 29, 10.1007/s12024-013-9521-8 Marx, 2015, PCR heads into the field, Nat. Methods, 12, 393, 10.1038/nmeth.3369 Thomas, 2020, A system for rapid eDNA detection of aquatic invasive species, Environ. DNA, 2, 261, 10.1002/edn3.25