Molecular analysis of Taro and Bali cattle using cytochrome oxidase subunit I (COI) in Indonesia
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https://orcid.org/0000-0002-7128-0914
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Abstract. Susari NNW, Suastika P, Agustina KK. 2021. Molecular analysis of Taro and Bali cattle using cytochrome oxidase subunit I (COI) in Indonesia. Biodiversitas 22: 165-172. Cytochrome oxidase subunit I (COI) is one of the molecular markers often used as a differentiator with many advantages in phylogeny analysis, and it thus rarely undergoes substitution. This research was conducted to characterize the genetics of Taro and Bali (Bos javanicus) cattle. Blood from the animals was collected from the jugularis vein and amplified by PCR. The target area was COI with a primer that was successfully amplified, namely the forward BICOIF (5'-TTC-TCAACCAACCATAAAGATATTGG-3') and the reverse BICOIR fragment (5'-TAG-ACTTCGGGGTGTCCAAAGAATCA-3'). The PCR products' sequencing was carried out by phylogeny analysis using MEGA 6 software. The amplicon value that succeeded in electrophoresis was 710bp, while six polymorphic sites were obtained at base positions of 1, 300, 379, 675, 676, and 679. The haplotypes (Hap) obtained were 4, with a genetic distance that ranged from 0.000-0.001. The nitrogenous bases of the amino acid composition from the samples showed no significant difference. The phylogenetic tree (Tamura-Nei) classified the cattle into two clades with a genetic distance of 0.0005.
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References
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Chao Z, Liao J, Liang Z, Huang S, Zhang L, Li J. 2014. Cytochrome C oxidase subunit i barcodes provide an efficient tool for Jinqian Baihua She (Bungarus parvus) authentication. Pharmacog Mag 10 (40): 449–457. https://doi.org/10.4103/0973-1296.141816
Clutterbuck J A. 2011. Genomic evidence of repeat-induced point mutation (RIP) in filamentous ascomycetes. Fung Genet Biol 48 (3): 306–326. https://doi.org/10.1016/j.fgb.2010.09.002
da Silva J M, Creer S, dos Santos A, Costa A C, Cunha M R, Costa F O, Carvalho G R. 2011. Systematic and evolutionary insights derived from mtDNA COI Barcode diversity in the Decapoda (crustacea: Malacostraca). PLoS ONE 6 (5): 1–15. https://doi.org/10.1371/journal.pone.0019449
Dharmawan N S, Damriyasa I M, Mahardika I G, Swastika K, Hartiningsih L P, Agustina K K. 2020. A seroepidemiological study of bovine cysticercosis in Bali and Nusa Tenggara, Indonesia. Vet World 13 (2): 284–289. https://doi.org/10.14202/vetworld.2020.284-289
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Garg R K, Mishra V. 2018. Molecular insights into the genetic and haplotype diversity among four populations of Catla catla from Madhya Pradesh revealed through mtDNA cyto b gene sequences. J Genet Eng Biotechnol 16(1): 169–174. https://doi.org/10.1016/j.jgeb.2017.11.003
Gissi C, Iannelli F, Pesole G. 2008. Evolution of the mitochondrial genome of Metazoa as exemplified by comparison of congeneric species. Heredity 101 (4): 301–320. https://doi.org/10.1038/hdy.2008.62
Gonçalves R, Freitas A I, Jesus J, De la Rúa P, Brehm A. 2015. Structure and genetic variation of the mitochondrial control region in the honey bee Apis mellifera. Apidologie 46 (4): 515–526. https://doi.org/10.1007/s13592-014-0341-y
Griffiths A J F, Gelbart W M, Lewontin R C, Miller J H. 1999. Modern Genetic Analysis. Retrieved from https://www.ncbi.nlm.nih.gov/books/NBK21322/
Hajibabaei M, Janzen D H, Burns J M, Hallwachs W, Hebert P D N. 2006. DNA barcodes distinguish species of tropical Lepidoptera. Proc Nati Acad Sci USA 103 (4): 968–971. https://doi.org/10.1073/pnas.0510466103
Hao M, Qiao J, Qi H. 2020. Current and emerging methods for the synthesis of single?stranded DNA. Genes 11 (2): 1–15. https://doi.org/10.3390/genes11020116
Hashemi-Aghdam S S, Rafie G, Akbari S, Oshaghi M A. 2017. Utility of mtDNA-COI barcode region for phylogenetic relationship and diagnosis of five common pest cockroaches. J Arthropod-Borne Dis 11 (2): 172–183.
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Heryani L G S S, Wandia I N, Suarna I W, Puja I K, Susari N N W, Agustina K K. 2019. Short communication: Molecular characteristic of taro white cattle based on DNA microsatellite markers. Biodiversitas 20 (3): 671–675. https://doi.org/10.13057/biodiv/d200308
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Kim K I, Lee J H, Li K, Zhang Y P, Lee S S, Gongora J, Moran C. 2002. Phylogenetic relationships of Asian and European pig breeds determined by mitochondrial DNA D-loop sequence polymorphism. Anim Gen 33 (1): 19–25. https://doi.org/10.1046/j.1365-2052.2002.00784.x
Kosman E, Jokela J. 2019. Dissimilarity of individual microsatellite profiles under different mutation models: Empirical approach. Ecol Evol 9 (7): 4038–4054. https://doi.org/10.1002/ece3.5032
Lelana N E, Sutarno, Etikawati N. 2003. Identification of polymorphism on ND-5 mitochondrial DNA fragment of Benggala and Madura cattle with PCR-RFLP technique. Biodiversitas 4 (1): 1–6. https://doi.org/10.13057/biodiv/d040101
Li J T, Che J, Bain R H, Zhao E M, Zhang Y P. 2008. Molecular phylogeny of Rhacophoridae (Anura): A framework of taxonomic reassignment of species within the genera Aquixalus, Chiromantis, Rhacophorus, and Philautus. Mol Phylog Evol 48 (1): 302–312. https://doi.org/10.1016/j.ympev.2008.03.023
Li X, Scanlon M J, Yu J. 2015. Evolutionary patterns of DNA base composition and correlation to polymorphisms in DNA repair systems. Nucleic Acids Res 43 (7): 3614–3625. https://doi.org/10.1093/nar/gkv197
Liu Y, Sharp J S, Do D H T, Kahn R A, Schwalbe H, Buhr F, Prestegard J H. 2017. Mistakes in translation: Reflections on mechanism. PLoS ONE 12 (6): 1–13. https://doi.org/10.1371/journal.pone.0180566
Meenakshi K, Suraj T, Bhagwati S S, Sujith V G, Santhoshkumar K, Sanil G. 2010. Molecular resolution of four Fejervarya Species from Western Ghats ( India ) with their intrageneric phylogeny based on COI , Cyt B , 12S and 16S rRNA Genes. Asian J Exp Biol Sci 1 (4): 782–786.
Mitra S, Ray S K, Banerjee R. 2016. Synonymous codons influencing gene expression in organisms. Res Rep Biochem 6 (1): 57–65. https://doi.org/10.2147/rrbc.s83483
Mohamad K, Olsson M, van Tol H T A, et al. 2009. On the origin of Indonesian cattle. PLoS ONE 4 (5): 1–6. https://doi.org/10.1371/journal.pone.0005490
Morlais, Severson D W. 2002. Complete mitochondrial DNA sequence and amino acid analysis of the cytochrome C oxidase subunit i (COI) from Aedes aegypti. DNA Seq 13 (2): 123–127. https://doi.org/10.1080/10425170290030051
Muyle A, Serres-Giardi L, Ressayre A, Escobar J, Glémin S. 2011. GC-biased gene conversion and selection affect GC content in the oryza genus (rice). Mol Biol Evol 28 (9): 2695–2706. https://doi.org/10.1093/molbev/msr104
Naim D M, Kamal N Z M, Mahboob S. 2020. Population structure and genetic diversity of Aedes aegypti and Aedes albopictus in Penang as revealed by mitochondrial DNA cytochrome oxidase I. Saudi J Biol Sci 27 (3): 953–967. https://doi.org/10.1016/j.sjbs.2020.01.021
Pentinsaari M, Salmela H, Mutanen M, Roslin T. 2016. Molecular evolution of a widely- adopted taxonomic marker (COI ) across the animal tree of life. Sci Rep 6 (1): 1–12. https://doi.org/10.1038/srep35275
Phillips J D, Gillis D J, Hanner R H. 2019. Incomplete estimates of genetic diversity within species: Implications for DNA barcoding. Ecol Evol 9 (5): 2996–3010. https://doi.org/10.1002/ece3.4757
Pierron D, Wildman D E, Hüttemann M, Markondapatnaikuni G C, Aras S, Grossman L I. 2014. Cytochrome c oxidase: Evolution of control via nuclear subunit addition. Biochim et Bioph Acta 1817 (4): 590–597. https://doi.org/10.1016/j.bbabio.2011.07.007.Cytochrome
Quax T E F, Claassens N J, Soll D, Oost J V D. 2015. Codon Bias as a Means to Fine-Tune Gene Expression. Mol Cell 59 (2): 149–161. https://doi.org/10.1016/j.molcel.2015.05.035.
Rodrigues M S, Morelli K A, Jensen A M. 2017. Cytochrome c oxidase subunit 1 gene as a DNA barcode for discriminating Trypanosoma cruzi DTUs and closely related species. Parasites Vectors 10 (1): 1–18. https://doi.org/10.1186/s13071-017-2457-1
Sabir J S M, Rabah S, Yacoub H, et al. 2019. Molecular evolution of cytochrome C oxidase-I protein of insects living in Saudi Arabia. PLoS ONE 14 (11): 1–18. https://doi.org/10.1371/journal.pone.0224336
Schenkel L C, Bakovic M. 2014. Formation and Regulation of Mitochondrial Membranes. Int J Cell Biol 2014 (1): 1–13. https://doi.org/10.1155/2014/709828
Senczuk G, Mastrangelo S, Ciani E, et al. 2020. The genetic heritage of Alpine local cattle breeds using genomic SNP data. Genet Select Evol 52 (1): 1–12. https://doi.org/10.1186/s12711-020-00559-1
Skibinski D O F, Ghiselli F, Diz A P, Milani L, Mullins J G L. 2017. Structure-Related Differences between Cytochrome Oxidase I Proteins in a Stable Heteroplasmic Mitochondrial System. Gen Biol Evol 9 (12): 3265–3281. https://doi.org/10.1093/gbe/evx235
Suriana, Nasaruddin. 2017. Characteristics of partial cytochrome c oxidase subunit I (COI) gene of tree frog (Polypedates celebensis) in Tanjung Peropa Wildlife Reserve Moramo, Southeast Sulawesi. J Vet 17 (4): 517–523. https://doi.org/10.19087/jveteriner.2016.17.4.517 [Indonesian]
Susari N N W, Heryani L G S S. 2018. Genetic Analysis of Taro Cattle (White, Black, Red) And Bali Cattle Using Cytochrome B. Proc. Int Symp Vet Sci 2018: 69–72.
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