Evaluasi Primer Gen COI sebagai Biomarker Ketertelusuran Ikan menggunakan Bioinformatika Evaluation of COI Gene Primer as a Biomarker Traceability using Bioinformatics
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Accepted
18 March 2022
Published
12 April 2022
Keywords:
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DNA barcoding, in silico, traceability, primer
Abstract
Traceability is carried out to provide information for tracking fish species, especially of high economic value and vulnerable to extinction. Bioinformatics can predict biomarker for fish traceability. This study was aimed to evaluate widely used primer sequences of COI gene for fish traceability and identify new universal primer sequences. Primers used in previous researches were evaluated and aligned with 33 fish species sequences from the NCBI GenBank. The relationship of those 33 fish species was evaluated using Percent Identity Matrix (PIM) and phylogenetic trees. The results showed not all primers have a good quality. CO1shark25 and CO1shark315 primer can be aligned to 31-32 fish sequences but did not fulfilled the ideal primer parameters. Therefore, several new universal primers were designed that fit the ideal criteria. The primer was designed and evaluated by using PerlPrimer and OligoEvaluator software. Fish universal mini-barcode primers from Lagocephalus lagocephalus, Takifugu vermicularis, Arothron hispidus, Hypanus americanus, Isurus oxyrhyncus, and Katsuwonus pelamis sequences successfully designed and evaluated for alternative biomarkers.
References
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Ozturk AR, Can T. 2017. A multiplex primer design algortihm for target amplifaction of continouous genomic regions. BMC Bioinformatics. 18(306):1-9.
Panprommin D, Soontomprasit K, Tuncharoen S, Pithakpol S, Keerelang J. 2019. DNA barcodes for the identification of species diversity in fish from Kwan Phayao, Thailand. Journal of Asia-Pacific Biodiversity. 12: 382-289.
Parks SL, Goldman N. 2014. Maximum likelihood inference of small trees in the presence of long branches. Systematic Biology. 63(5):798-811.
Spencer ET, Bruno JF. 2019. Fishy business: red snapper mislabeling along the coastline of the Southeastern United States. Frontiers in Marine Science. 6(513):1-7.
Sultana S, Ali ME, Hossain MAM, Asing, Naquiah N, Zaidul ISM. 2017. Universal mini COI barcode for the identification of fish species in processed products. Food Research International. 105:19-28.
Sunarno, Novriani H. 2016. Desain primer PCR secara manual untuk amplifikasi gen dtx bakteri penyebab difteri dengan masalah homologi sekuens DNA. The Biomedical and Basic Health Tecnology, Health Research and Development Centre. 66(12): 544-550.
Tamura K, Nei M, dan Kumar S. 2004. Prospects for inferring very large phylogenies by using the neighbr-joining method. The Proceedings of the National Academy of Sciences. 101:11030-11035.
Vallone PM, Butler JM. 2004. AutoDimer: a screening tool for primer-dimer and hairpin structures. Biotechniques. 37(2):226-231.
Wallace L, Boilard SMAL, Eagle SHC, Spall J. 2012. DNA Barcodes for everyday life: routine authentication of natural health products. Food Research International. 49(1):446-452.
Ward RD, Zemlak TS, Innes BH, Last PR, Hebert PD. 2005. DNA barcoding Australia’s fish species. Philosophical Transactions of the Royal Society B. 360(1462):1847-1857.
Wen J, Zeng L, Chen Z, Zhou Y, Xu Y, Xhen D, Sun Y, Zhao J, Zhang W, Li H. 2017. Species identification of dried scallop adductor muscle (yao zhu) products sold on the market. Food Control 71:83-87.
Wu JS, Lee C, Wu CC, Shiue YL. 2004. Primer design using genetic algorithm. Bioinformatics. 20(11):1710-1717.
Ajitama Y. 2017. Autentikasi Kerupuk Udang Dengan Metode DNA Barcoding. [skripsi]. Bogor (ID): Institut Pertanian Bogor.
Ataman C, Çelik U, Rehbein H. 2006. Identification of some Aegean fish species by native isoelectric focussing. European Food Research and Technology. 222(1-2):99-104.
Baldwin CC, Mounts JH, Smith DG, Weigt LA. 2009. Genetic identification and color descriptions of early life-history stages of Belizean Phaeoptyx and Astrapogon (Teleostei: Apogonidae) with Comments on identification of adult Phaeoptyx. Zootaxa. 1-22.
Bingpeng X, Heshan L, Zhilan Z, Chunguang W, Yanguo W, Jianjun W. 2018. DNA barcoding for identification of fish species in the Taiwan Strait. PLoS ONE. 13(6): e0198109.
Borah P. 2009. Primer designing for PCR. Science Vision. 11(3):134-136.
Chin TC, Adibah A, Hariz ZD, Azizah MS. 2016. Detection of mislabelled seafood products in Malaysia by DNA barcoding: Improving transparency in food market. Food Control. 64:247-256.
Chuang LY, Cheng YH, Yang CH. 2013. Specific primer design for the polymerase chain reaction. Biotechnology Letters. 35(10): 1-9.
Costa H, Mafra I, Oliveira MBPP, Amaral JS. 2016. Encyclopedia of food and health. RMFS. 177-183.
Davidovic RS, Bozovic AM, Mandusic VL, Krajnovic MM. 2014. Methylation-specific PCR: four steps in primer design. Central European Journal of Biology. 9(12): 1127-1139.
Diss T. 2003. Molecular Biology in Cellular Pathology. United Kingdom (UK): John Willey and Sons.
Fernández A, García T, Asensio L, Rodríguez MÁ, González I, Lobo E, Hernández PE, Martín R. 2002. Identification of the clam species Ruditapes decussatus (grooved carpet shell), Venerupis rhomboides (yellow carpet shell) and Venerupis pullastra (pullet carpet shell) by ELISA. Food and Agricultural Immunology. 14(1): 65-71.
Fotedar S, Lukehurst S, Jackson G, Snow M. 2019. Molecular tools for identification of shark species involved in depredation incidents in Western Australian fisheries. PLOS ONE 14(1): e0210500.
Govender A, Groeneveld J, Singh S, Willows-Munro S. 2019. The design and testing of mini-barcode markers in marine lobsters. PLOS ONE. 14(1): e0210492.
Green SJ, Venkatramanan R, Naqib A. 2015. Deconstructing the polymerase chain reaction: understanding and correcting bias associated with primer degeneracies and primer-template mismatches. PLOS ONE. 10(5):e0128122.
Hebert PDN, Ratnasingham S, deWaard JR. 2003a. Barcoding animal life: cytochrome c oxidase subunit 1 divergences among closely related species. Proceedings of the Royal Society of London. 270: 96-99.
Hebert PDN, Cywinska A, Ball SL, deWaard JR. 2003b. Biological identifications through DNA barcodes. Proceedings of the Royal Society of London. 270:313–321.
Horstkotte B, Rehbein H. 2003. Fish species identification by means of restriction fragment length polymorphism and high‐performance liquid chromatography. Food Science. 68(9):2658-2666.
Jennings WB, Ruschi PA, Ferraro G, Quijada CC, Silva-Malanski ACG, Prosdicimi F, Buckup PA. 2019. Barcoding the Neotropical freshwater fish fauna using a new pair of universal COI primers with a discussion of primer dimers and M13 primer tails. Genome. 0:1-7.
Kumar S, Stecher G, Li M, Knyaz C, Tamura K. 2018. MEGA X: molecular evolutionary genetics analysis across computing platforms. Molecular Biology and Evolution. 35(6):1547-1549.
Li WH, Graur D. 1991. Fundamentals of Molecular Evolution Second Edition. Dallas (USA): Sinauer.
Lorenz TC. 2012. Polymerase Chain Reaction: basic protocol plus troubleshooting and optimization strategies. Journal of Visualized Experiments. 63(3998):1-15.
Mammedov TG, Pienaar E, Whitney SE, TerMaat JR, Carvill G, Goliath R,Subramanian A, Vilijoen HJ. 2008. A fundamental study of the PCR amplification of GC-rich DNA templates. Computational Biology and Chemistry. 32(6): 452-457.
Maralit BA, Roselyn D, Aguila A, Minerva Fatimae H, Ventolero A, Sweedy Kay L, Perez A, Demian A. Willette B, Mudjekeewis D, Santos. 2013. Detection of mislabeled commercial fishery by-products in the Philippines using DNA barcodes and its implications to food traceability and safety. Food Control. 33:119-125
Mikkelsen PM, Bieler R, Kappner I, Rawlings TA. 2006. Phylogeny of Veneroidea (Mollusca: Bivalvia) based on morphology and molecules. Zoological Journal of the Linnean Society. 148:439-521.
Minoudi S, Karaiskou N, Avgeris M, Gkagkavouzis K, Tarantili P, Triantafyllidou D. 2020. Seafood mislabeling in Greek market using DNA barcoding. Food Control. 113:107213.
Mopay M, Wullur S, Kaligis E. 2017. Identifikasi molekuler sirip ikan hiu yang didapat dari pengumpul sirip di Minahasa. Jurnal Pesisir dan Laut Tropis.1(2):1-7.
Muttaqin E, Abdullah A, Nurilmala M, Ichsan M, Simeone BM, Yulianto I, Booth H. 2019. DNA-barcoding as molecular marker for seafood forensics: Species identification of locally consumed shark fish products in the world’s largest shark fishery. IOP Conference Series: Earth and Environmental Science. 278:1-11.
Ozturk AR, Can T. 2017. A multiplex primer design algortihm for target amplifaction of continouous genomic regions. BMC Bioinformatics. 18(306):1-9.
Panprommin D, Soontomprasit K, Tuncharoen S, Pithakpol S, Keerelang J. 2019. DNA barcodes for the identification of species diversity in fish from Kwan Phayao, Thailand. Journal of Asia-Pacific Biodiversity. 12: 382-289.
Parks SL, Goldman N. 2014. Maximum likelihood inference of small trees in the presence of long branches. Systematic Biology. 63(5):798-811.
Spencer ET, Bruno JF. 2019. Fishy business: red snapper mislabeling along the coastline of the Southeastern United States. Frontiers in Marine Science. 6(513):1-7.
Sultana S, Ali ME, Hossain MAM, Asing, Naquiah N, Zaidul ISM. 2017. Universal mini COI barcode for the identification of fish species in processed products. Food Research International. 105:19-28.
Sunarno, Novriani H. 2016. Desain primer PCR secara manual untuk amplifikasi gen dtx bakteri penyebab difteri dengan masalah homologi sekuens DNA. The Biomedical and Basic Health Tecnology, Health Research and Development Centre. 66(12): 544-550.
Tamura K, Nei M, dan Kumar S. 2004. Prospects for inferring very large phylogenies by using the neighbr-joining method. The Proceedings of the National Academy of Sciences. 101:11030-11035.
Vallone PM, Butler JM. 2004. AutoDimer: a screening tool for primer-dimer and hairpin structures. Biotechniques. 37(2):226-231.
Wallace L, Boilard SMAL, Eagle SHC, Spall J. 2012. DNA Barcodes for everyday life: routine authentication of natural health products. Food Research International. 49(1):446-452.
Ward RD, Zemlak TS, Innes BH, Last PR, Hebert PD. 2005. DNA barcoding Australia’s fish species. Philosophical Transactions of the Royal Society B. 360(1462):1847-1857.
Wen J, Zeng L, Chen Z, Zhou Y, Xu Y, Xhen D, Sun Y, Zhao J, Zhang W, Li H. 2017. Species identification of dried scallop adductor muscle (yao zhu) products sold on the market. Food Control 71:83-87.
Wu JS, Lee C, Wu CC, Shiue YL. 2004. Primer design using genetic algorithm. Bioinformatics. 20(11):1710-1717.
Authors
NugrahaR., DewiP. S., & NurilmalaM. (2022). Evaluasi Primer Gen COI sebagai Biomarker Ketertelusuran Ikan menggunakan Bioinformatika: Evaluation of COI Gene Primer as a Biomarker Traceability using Bioinformatics. Jurnal Pengolahan Hasil Perikanan Indonesia, 25(1), 67-79. https://doi.org/10.17844/jphpi.v25i1.36501
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