Bioinformatic Analysis of the Cytb Gene to Estimate the Domestication Potential of Mahseer Fish Genus Tor spp.
DOI:
https://doi.org/10.52046/agrikan.v16i1.1531Keywords:
Cytb, domestikasi, haplotype, IUCN, TorAbstract
The purpose of this study is to estimate the population of fish of the genus Tor as a source of proper domestication. Bioinformatic analysis was carried out by extracting data from the NCBI gene bank and alignment of the Cytb gene sequences using the ClustalW program to further analyze the nucleotide characteristics using MEGA software, determining genetic variation using the dnasp5 software, and using median joining analysis to reveal the relationship between Tor fish haplotypes from different locations. The results obtained from this study show that the haplotype diversity values of fish of the genus Tor spp. in the domesticated farm population and the natural population are still high, namely 0.9 and 0.8, respectively, as well as the occurrence of haplotype groupings based on other population origins. Domestication of Tor genus fish can be sourced from domesticated farms, and the wild is still ideal because the haplotype diversity is still high.
References
Berry, E. A., Guergova-Kuras, M., Huang, L. S., & Crofts, A. R. (2000). Structure and function of cytochrome bc complexes. Annual review of biochemistry, 69(1), 1005-1075.
Chew, P. C., Christianus, A., Zudaidy, J. M., Ina-Salwany, M. Y., Chong, C. M., & Tan, S. G. (2021). Microsatellite Characterization of Malaysian Mahseer (Tor spp.) for Improvement of Broodstock Management and Utilization. Animals, 11(9), 2633.
Clark-Walker, G. D., Rittenberg, B., & Lascelles, J. (1967). Cytochrome synthesis and its regulation in Spirillum itersonii. Journal of Bacteriology, 94(5), 1648-1655.
Das,G., Das,S.P., Bit,A., Sahoo,L., Channaveer,R., Swain,S.K., Sundaray,J.K., Sahoo,S.K., Jayasankar,P. and Das,P.2016. Complete Mitochondrion of Thor khudree. https://www.ncbi.nlm.nih.gov/nuccore/KX950700. (diakses pada 27/12/2021).
Fan, P., Fjeldså, J., Liu, X., Dong, Y., Chang, Y., Qu, Y., G. song and Lei, F. (2021). An approach for estimating haplotype diversity from sequences with unequal lengths. Methods in Ecology and Evolution, 12(9), 1658-1667.
Godet, L., & Devictor, V. (2018). What conservation does. Trends in ecology & evolution, 33(10), 720-730.
Irwanto, D. 2017. Tenggelamnya Sundalandia Dan Penelusuran Cikal Bakalnya Peradaban. Prosiding Seminar Nasional Kelautan dan Perikanan III 2017 Universitas Trunojoyo Madura, 7 September 2017.
Haryono, H., dan Subagja, J. 2007. Pertumbnhan Ikan Tambra (Tor tambroides) dan Kancera (Tor soro) Pada Proses Domestikasi dengan Jenis Pakan yang Berbeda. JURNAL BIOLOGI INDONESIA. Vol 4, No 3.
Jaafar, F., Na-Nakorn, U., Srisapoome, P., Amornsakun, T., Duong, T. Y., Gonzales-Plasus, M. M., Hoang, D. H and Parhar, I. S. (2021). A current update on the distribution, morphological features, and genetic identity of the Southeast Asian mahseers, Tor species. Biology, 10(4), 286.
Kottelat, M., Pinder, A. & Harrison, A. 2018. Tor tambra. The IUCN Red List of Threatened Species 2018: e.T188012A89801879. https://dx.doi.org/10.2305/IUCN.UK.2018-2.RLTS.T188012A89801879.en. (diakses pada 16/12/2021).
Librado, P., & Rozas, J. (2009). DnaSP v5: a software for comprehensive analysis of DNA polymorphism data. Bioinformatics, 25(11), 1451-1452.
Lim, L. W. K., Chung, H. H., Lau, M. M. L., Aziz, F., & Gan, H. M. (2021). Improving the phylogenetic resolution of Malaysian and Javan mahseer (Cyprinidae), Tor tambroides and Tor tambra: Whole mitogenomes sequencing, phylogeny and potential mitogenome markers. Gene, 791, 145708.
Nguyen, T. T., Na-Nakorn, U., Sukmanomon, S., & ZiMing, C. (2008). A study on phylogeny and biogeography of mahseer species (Pisces: Cyprinidae) using sequences of three mitochondrial DNA gene regions. Molecular Phylogenetics and Evolution, 48(3), 1223-1231.
Radhi, M. R. M., Zulfahm, I., & Akmal, Y. (2021). Komperatif Osteocranium Tor tambra (Valenciennes 1842) dan Tor tambroides (Bleeker 1854) di Perairan Aceh. Prosiding Biotik, 8(1).
Rahayu, D. A., & Nugroho, E. D. (2015). DNA Barcode Dan Haplotype Network Ikan Lokal Dari Telaga Banyu Biru Kabupaten Pasuruan. In Seminar Nasional Ikan Ke-8; Masyarakat Iktiologi Indonesia: Bogor, Indonesia (Vol. 2, pp. 67-75).
Raman, S., Pavan-Kumar, A., Koringa, P. G., Patel, N., Shah, T., Singh, R. K., Krishna,G., Joshi,C.G., Gireesh-Babu,P., Chaudhari,A and Lakra, W. S. (2016). Ion Torrent Next-Generation Sequencing Reveals The Complete Mitochondrial Genome Of Endangered Mahseer Tor khudree (Sykes, 1839). Mitochondrial DNA Part A, 27(4), 2949-2950.
Rozas, J., A. Ferrer-Mata, J.C. Sánches-Delbarrio, S. Girao-Rico, P. Librado, S.E. Ramos-Onsins, and A. Sánchez-Gracia. 2017. DnaSP 6: DNA sequence polymorphism analysis of large datasets. Mol. Biol. Evol. 34:3299-3302. doi:10.1093/molbev/msx248.
Rozas, J., Sánchez-DelBarrio, J. C., Messeguer, X., & Rozas, R. (2003). DnaSP, DNA polymorphism analyses by the coalescent and other methods. Bioinformatics, 19(18), 2496-2497.
Shubra,S., Pavan-Kumar,A., Archana,M. and Nagpure,N.S.2019.Molecular Phylogeny of Mahseers (Direct Submission ton NCBI). https://www.ncbi.nlm.nih.gov/nuccore/NC_056296. (diakses pada 27/12/2021).
Thompson, J. D., Gibson, T. J., & Higgins, D. G. (2003). Multiple sequence alignment using ClustalW and ClustalX. Current protocols in bioinformatics, (1), 2-3.
Turvey, S. T., & Crees, J. J. (2019). Extinction in the Anthropocene. Current Biology, 29(19), R982-R986.
Wibowo, A., & Kaban, S. (2015). Genetic Variation Of Tor tambroides (Bleeker, 1854) Along Batang Tarusan River, West Sumatera: Implications For Stock Identification. Indonesian Fisheries Research Journal, 21(2), 61-66.
Wong, Y. T., Meier, R., & Tan, K. S. (2011). High haplotype variability in established Asian populations of the invasive Caribbean bivalve Mytilopsis sallei (Dreissenidae). Biological Invasions, 13, 341-348.
Zhang, Q., Sun, C., Zhu, Y., Xu, N., & Liu, H. (2020). Genetic diversity and structure of the round-tailed paradise fish (Macropodus ocellatus): Implications for population management. Global Ecology and Conservation, 21, e00876.
Zheng, L. P., Yang, J. X., & Chen, X. Y. (2016). Molecular phylogeny and systematics of the Barbinae (Teleostei: Cyprinidae) in China inferred from mitochondrial DNA sequences. Biochemical Systematics and Ecology, 68, 250-259.
Chew, P. C., Christianus, A., Zudaidy, J. M., Ina-Salwany, M. Y., Chong, C. M., & Tan, S. G. (2021). Microsatellite Characterization of Malaysian Mahseer (Tor spp.) for Improvement of Broodstock Management and Utilization. Animals, 11(9), 2633.
Clark-Walker, G. D., Rittenberg, B., & Lascelles, J. (1967). Cytochrome synthesis and its regulation in Spirillum itersonii. Journal of Bacteriology, 94(5), 1648-1655.
Das,G., Das,S.P., Bit,A., Sahoo,L., Channaveer,R., Swain,S.K., Sundaray,J.K., Sahoo,S.K., Jayasankar,P. and Das,P.2016. Complete Mitochondrion of Thor khudree. https://www.ncbi.nlm.nih.gov/nuccore/KX950700. (diakses pada 27/12/2021).
Fan, P., Fjeldså, J., Liu, X., Dong, Y., Chang, Y., Qu, Y., G. song and Lei, F. (2021). An approach for estimating haplotype diversity from sequences with unequal lengths. Methods in Ecology and Evolution, 12(9), 1658-1667.
Godet, L., & Devictor, V. (2018). What conservation does. Trends in ecology & evolution, 33(10), 720-730.
Irwanto, D. 2017. Tenggelamnya Sundalandia Dan Penelusuran Cikal Bakalnya Peradaban. Prosiding Seminar Nasional Kelautan dan Perikanan III 2017 Universitas Trunojoyo Madura, 7 September 2017.
Haryono, H., dan Subagja, J. 2007. Pertumbnhan Ikan Tambra (Tor tambroides) dan Kancera (Tor soro) Pada Proses Domestikasi dengan Jenis Pakan yang Berbeda. JURNAL BIOLOGI INDONESIA. Vol 4, No 3.
Jaafar, F., Na-Nakorn, U., Srisapoome, P., Amornsakun, T., Duong, T. Y., Gonzales-Plasus, M. M., Hoang, D. H and Parhar, I. S. (2021). A current update on the distribution, morphological features, and genetic identity of the Southeast Asian mahseers, Tor species. Biology, 10(4), 286.
Kottelat, M., Pinder, A. & Harrison, A. 2018. Tor tambra. The IUCN Red List of Threatened Species 2018: e.T188012A89801879. https://dx.doi.org/10.2305/IUCN.UK.2018-2.RLTS.T188012A89801879.en. (diakses pada 16/12/2021).
Librado, P., & Rozas, J. (2009). DnaSP v5: a software for comprehensive analysis of DNA polymorphism data. Bioinformatics, 25(11), 1451-1452.
Lim, L. W. K., Chung, H. H., Lau, M. M. L., Aziz, F., & Gan, H. M. (2021). Improving the phylogenetic resolution of Malaysian and Javan mahseer (Cyprinidae), Tor tambroides and Tor tambra: Whole mitogenomes sequencing, phylogeny and potential mitogenome markers. Gene, 791, 145708.
Nguyen, T. T., Na-Nakorn, U., Sukmanomon, S., & ZiMing, C. (2008). A study on phylogeny and biogeography of mahseer species (Pisces: Cyprinidae) using sequences of three mitochondrial DNA gene regions. Molecular Phylogenetics and Evolution, 48(3), 1223-1231.
Radhi, M. R. M., Zulfahm, I., & Akmal, Y. (2021). Komperatif Osteocranium Tor tambra (Valenciennes 1842) dan Tor tambroides (Bleeker 1854) di Perairan Aceh. Prosiding Biotik, 8(1).
Rahayu, D. A., & Nugroho, E. D. (2015). DNA Barcode Dan Haplotype Network Ikan Lokal Dari Telaga Banyu Biru Kabupaten Pasuruan. In Seminar Nasional Ikan Ke-8; Masyarakat Iktiologi Indonesia: Bogor, Indonesia (Vol. 2, pp. 67-75).
Raman, S., Pavan-Kumar, A., Koringa, P. G., Patel, N., Shah, T., Singh, R. K., Krishna,G., Joshi,C.G., Gireesh-Babu,P., Chaudhari,A and Lakra, W. S. (2016). Ion Torrent Next-Generation Sequencing Reveals The Complete Mitochondrial Genome Of Endangered Mahseer Tor khudree (Sykes, 1839). Mitochondrial DNA Part A, 27(4), 2949-2950.
Rozas, J., A. Ferrer-Mata, J.C. Sánches-Delbarrio, S. Girao-Rico, P. Librado, S.E. Ramos-Onsins, and A. Sánchez-Gracia. 2017. DnaSP 6: DNA sequence polymorphism analysis of large datasets. Mol. Biol. Evol. 34:3299-3302. doi:10.1093/molbev/msx248.
Rozas, J., Sánchez-DelBarrio, J. C., Messeguer, X., & Rozas, R. (2003). DnaSP, DNA polymorphism analyses by the coalescent and other methods. Bioinformatics, 19(18), 2496-2497.
Shubra,S., Pavan-Kumar,A., Archana,M. and Nagpure,N.S.2019.Molecular Phylogeny of Mahseers (Direct Submission ton NCBI). https://www.ncbi.nlm.nih.gov/nuccore/NC_056296. (diakses pada 27/12/2021).
Thompson, J. D., Gibson, T. J., & Higgins, D. G. (2003). Multiple sequence alignment using ClustalW and ClustalX. Current protocols in bioinformatics, (1), 2-3.
Turvey, S. T., & Crees, J. J. (2019). Extinction in the Anthropocene. Current Biology, 29(19), R982-R986.
Wibowo, A., & Kaban, S. (2015). Genetic Variation Of Tor tambroides (Bleeker, 1854) Along Batang Tarusan River, West Sumatera: Implications For Stock Identification. Indonesian Fisheries Research Journal, 21(2), 61-66.
Wong, Y. T., Meier, R., & Tan, K. S. (2011). High haplotype variability in established Asian populations of the invasive Caribbean bivalve Mytilopsis sallei (Dreissenidae). Biological Invasions, 13, 341-348.
Zhang, Q., Sun, C., Zhu, Y., Xu, N., & Liu, H. (2020). Genetic diversity and structure of the round-tailed paradise fish (Macropodus ocellatus): Implications for population management. Global Ecology and Conservation, 21, e00876.
Zheng, L. P., Yang, J. X., & Chen, X. Y. (2016). Molecular phylogeny and systematics of the Barbinae (Teleostei: Cyprinidae) in China inferred from mitochondrial DNA sequences. Biochemical Systematics and Ecology, 68, 250-259.
Downloads
Published
23-05-2023
How to Cite
Permadi, J., Sukmarani, D., & Rahayu, Y. (2023). Bioinformatic Analysis of the Cytb Gene to Estimate the Domestication Potential of Mahseer Fish Genus Tor spp. Agrikan Jurnal Agribisnis Perikanan, 16(1), 146–151. https://doi.org/10.52046/agrikan.v16i1.1531
Issue
Section
Articles
License
Copyright (c) 2023 Jefri Permadi, Dhuta Sukmarani, Yeni Rahayu
This work is licensed under a Creative Commons Attribution 4.0 International License.
This work is licensed under a Creative Commons Attribution 4.0 International License.
