Genetic diversity and phylogenetic relationship among Anabantoidei fish (Anabantiformes) in South Kalimantan, Indonesia based on SDS-PAGE analysis
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Abstract. Sasmita R, Mabrur, Rahmy USA, Badruzsaufari. 2019. Genetic diversity and phylogenetic relationship among Anabantoidei fish (Anabantiformes) in South Kalimantan, Indonesia based on SDS-PAGE analysis. Biodiversitas 20: 2519-2527. Protein profile is a molecular marker for diversity and phylogenetic analysis of germplasm, including Anabantoidei fish which is abundant in freshwater ecosystem of South Kalimantan. The aim of this research was to analyze genetic diversity and construct phylogenetic relationship among Anabantoidei fish based on SDS PAGE analysis. Protein was extracted from muscle tissue of six species of Anabantoidei fish and precipitated using Ammonium sulfate salt. Soluble protein content was determined using Bradford assay and then separated based on SDS-PAGE method. Genetic diversity and phylogenetic relationship were constructed using PAST software based on UPGMA method. The results showed that the soluble protein of fish muscle can be precipitated optimally in different ammonium sulfate concentration. Based on SDS-PAGE analysis, 59 different protein bands have been separated from gels with molecular weight ranging from 28.15 to 181.61 kDa. On the protein level, the Anabantoidei fish showed high genetic polymorphism (greater than 90%) with 3, 2 and 5 monomorphic bands on non-precipitated, AS-precipitated and combination between non- and AS-precipitated proteins, respectively. The phylogenetic reconstruction also exhibited that the Anabantoidei fish has the unique phylogenetic trees, especially for the combined protein datasets. This information would be useful for freshwater fish conservation and breeding programs.
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References
Betancur-R R, Wiley EO, Arrataria G, Aceros A, Bailly N, Miya M, Lecointre G, and Orti G. 2017. Phylogenetic Classification of Bony Fishes. BMC Eolutionary Biology. 17 (162): 1-40.
Bone Q, and Moore RH. 2008. Biology of Fishes. 3rd Edition. Taylor and Francis Group, New York USA.
Bradford MM. 1976. A rapid and sensitive method for the Quantitation of Microgram Quantities of Protein Utilizing the Principle of Protein-Dye Binding. Anal Biochem. 72: 248-254.
Burgess RR. 2009. Protein Precipitation Techniques. In. Methods in Enzymology. USA: University of Wisconsin-Madison, Elsvier.
Crick, RHC., 1963. On the genetic code. Science New York. 139: 461-464.
Datovo A, de Pinna MCC, and Johnson GD. 2014. The Infrabranchial Musculature and Its Bearing on the Phylogeny of Percomorph Fishes (Osteichthyes, Teleostei). PLOS ONE. 9 (10): 1-20.
Dekic R, Friscic J, Ivanc A, and Kukavica B. 2016. Characterization of Proteins From Popovo minnow (Delminichthys Ghetaldii Steindachner, 1882) Muscle. Turkish J Fisher Aqua Sci. 16: 637-642.
Ebied ABM, Aly FM, Abu-AlMaaty AH, and Allam M. Assesment of Genetic variation and Changes in Protein Subunits induced by Petroleum Oil in the Three Species of Red Sea Fishses using SDS-PAGE and ISSRs markers. IOSR-J. Pharm. Biol Sci. 9(6): 16-22.
Elghobashy HA, Rahman AA, Ibrahem LH, and Rashed MA. 2005. Phylogenetic Relationships for Some Tilapia Species Using Electrophorhesis. Egypt. J. Exp. Biol. 1: 57-63.
Fenselstein J. 1985. Confidence-limits on Phylogenies – An Approach using the bootstrap. Evolution. 39: 783-791.
Fishbase. 2017. List of Freshwater Fishes Reported from Indonesia. http://www.fishbase.org.
Frankham R, Ballou JD, Briscoe, DA. 2004. A Primer of Conservation Genetics; Cambridge University Press: New York, NY, USA, Volume 39.
Gam LH, Leow CW, Baie S. 2006. Proteomic analysis of snakehead fish (Channa striata) muscle tissue. Malaysian J Biochem Mol Biol 14: 25-32.
Hammer Ø, Harper DAT and Ryan PD. 2001. PAST: Paleontological Statistic Software Package for Education and Data Analysis. Paleontologia Electronica. 4(1): 1-9.
Haniffa MA, Sheela PJ, Milton JM., and Kavitha K. 2017. Protein Profiling for Phylogenetic Relationship in Snakehead Species. Iranian J. of Fisheries Sci. 16 (4): 1178-1186.
Hidayati D, Abdulgani N, Setiyawan H, Trisnawati I, Ashuri NM, Nailis N. 2016. Analysis of protein profiles in diabetic rat blood plasma induced by alloxan. AIP Conf Proc 1854: 020016.1-020016.6.
Hidayaturrahmah, Mabrur, Santoso HB, Sasmita R, Rahmy USA, and Badruzsaufari. 2019. Protein profiles of Giant Mudskipper and its potential use as biomarker candidate for heavy metal contamination in Barito Estuary, Indonesia. Biodiversitas 20 (3): 745-753.
Karp A, Kresovich S, Bhat KV, Ayad WG, and Hodgkin T. 1997. Molecular Tool in Plant Genetic Resources Conservation: A Guide To The Technologies. IPGRI Technology Bulletin. No. 2.
Kottelat M, & Whitten T. 1996. Freshwater biodiversity in Asia with special reference to fish. World Bank Technical Paper. 343; 1-59.
Laemmli UK. 1970. Cleavege of Structural Proteins During The Assembly of The Head of Bacteriophage T4. Nature. 227: 680-685.
Low BW and Lim KKP. 2012. Gouramies of the genus Trichopodus in Singapore (Actinopterygii: Perciformes: Osphronemidae). Nature in Singapore. 5: 83-93.
Mabrur, Rahmy USA, Sasmita R, Badruzsaufari. 2018. Protein Profiles of Haruan Fish (Channa striata) from South Kalimantan. In: Soendjoto MA, Dharmono, Riefani MK, Ansari ML, Septiyan RA, Syahdi N. (eds.) The Potency, Opportunity and Challenges in Wetland Management; Proceeding of National Seminar on Wetland Environment 3 (1): 39-45. Universitas Lambung Mangkurat, Banjarmasin, 11 November 2017. [Indonesian]
Mahboob S, Farooq M, Mahmood S, Nasir N, Sultana S, Chaudhry AS, Al-Akel AS, Al-Balawi HFA, Al-Minsed F, and Al-Ghanim KA. 2012. Phylogenetic Relationship of Cultured and Wild Labeo rohita and Cirrhinus mrigala Based on Muscle Protein profile in DifferentWeight Groups: A New Tool in Phylogenetic Analysis. Int. J. Food properties. 15(5): 949-960.
Maidie A, Sumoharjo, Asra SW, Ramadhan M, and Hidayanto DN. 2015. Development of Betok Fish Tiller (Anabas testudineus) for Household Industry. Media Akuakultur. 10(1): 31-37.
Mursyidin DH, Purnomo P, Sumardi I, Daryono BS. 2018. Molecular Diversity of Tidal Swamp Rice (Oryza sativa L.) in South Kalimantan, Indonesia. Diversity. 10 (22). 1-10
Nei M, and Li. WM. 1979. Mathematical Model for Studying Genetic Variation in Terms of Restriction Endonuclease. PNAS. 76: 5269-5273.
Nelson JS. 2016. Fishes of The World. 5th Edition. John Wiley & Sons, Inc., New Jersey, USA.
Nirenberg MW, Mathaei JH, Jones OW, Martin RG. and Burondes, SH. 1963. Approximation of genetic code via, cell free protein synthesis detected by template RNA. Federation Proceedings. 22: 55-61.
Porto JIR, Gomes JAA, Farias IP, and Feldber E. 2015. Using Molecular Biology Techniques to Characterize the Diversity of Amazonian Ornamental Fish. Molecular Biology Techniques: 227-244
Quyen VDH, Phuong TTL, Oanh TT, Thuoc TL, and Binh DT. 2015. Phylogenetic Relationship of Freshwater Fish in Vietnamese Mekong. International Conference on Biological, Enviroment and Food Engineering (BEFE). Singapore: 58-61
Rath A, Cunningham F, Deber CM. 2013. Acrylamide concentration determines the direction magnitude of helical membrane protein gel shifts. Proc Nat Acad Sci USA. 110 (39): 15668-15673
Regan CT. 1909. The classification of teleostean fishes. Ann Mag Nat Hist 8: 75–86.
Roy S, and Kumar V. 2014. A Practical Approach on SDS PAGE for Separation of Protein. Int. J. Sci. Research. 3(8): 955-960.
Ruber L. 2009. Labyrinth Fishes (Anabantoidei). In. S.B. Hodges., & S. Kumar. The Timetree of Life. Oxford University Press, London.
Sabullah MK, Ahmad SA, Shukor MY, Gansau AJ, Syed MA, Sulaiman MR, Shamaan NA. 2015. Heavy metal biomarker: Fish behavior, cellular alteration, enzymatic reaction and proteomics approaches. Intl Food Res J 22 (2): 435-454.
Sasmita R, Susilawati IO, Rahmy USA, Mabrur. 2018. Protein profiles from Catfish (Pangasius hypophthalmus) and Baung Fish (Hemibagrus nemurus) Muscle from South Kalimantan. Appl Sci Technol. 2 (1): 230-234.
Saxena A, and Soranganba N. 2014. Proteins Diversity in Various Tissue of the Body of Carps. Biol. Chem. Research. 1: 108-122.
Thada V, and Jaglan DV. 2013 Comparison of Jaccard, Dice, Cosine Similarity Coeffecient to Find Best Fitness Value for Web Retrieved Documents Using Genetic Algorithm. IJIET. 2(4): 202-205.
Velamala GR, Babu KR, and Naranji MK. 2017. Genetic information of Snappers (Family: Lutjanidae) from Indian Waters Using SDS-PAGE Technique. Gen Aqua. 1: 49-55.
Wiley EO and Johnson GD. 2010.A teleost classification based on monophyletic groups. In: Nelson JS, Schultze H-P, Wilson MVH, editors. Origin and Phylogenetic Interrelationships of Teleosts. Mu¨nchen: Verlag Dr. Friedrich Pfeil. 123–182.
Zhou H, and Guo XY. 2015. Soil Heavy Metal Pollution Evaluation around Mine Area with Traditional and Ecological Assessment Methods. J. of Geosci. Environ Protect.. 3: 28-33.
Bone Q, and Moore RH. 2008. Biology of Fishes. 3rd Edition. Taylor and Francis Group, New York USA.
Bradford MM. 1976. A rapid and sensitive method for the Quantitation of Microgram Quantities of Protein Utilizing the Principle of Protein-Dye Binding. Anal Biochem. 72: 248-254.
Burgess RR. 2009. Protein Precipitation Techniques. In. Methods in Enzymology. USA: University of Wisconsin-Madison, Elsvier.
Crick, RHC., 1963. On the genetic code. Science New York. 139: 461-464.
Datovo A, de Pinna MCC, and Johnson GD. 2014. The Infrabranchial Musculature and Its Bearing on the Phylogeny of Percomorph Fishes (Osteichthyes, Teleostei). PLOS ONE. 9 (10): 1-20.
Dekic R, Friscic J, Ivanc A, and Kukavica B. 2016. Characterization of Proteins From Popovo minnow (Delminichthys Ghetaldii Steindachner, 1882) Muscle. Turkish J Fisher Aqua Sci. 16: 637-642.
Ebied ABM, Aly FM, Abu-AlMaaty AH, and Allam M. Assesment of Genetic variation and Changes in Protein Subunits induced by Petroleum Oil in the Three Species of Red Sea Fishses using SDS-PAGE and ISSRs markers. IOSR-J. Pharm. Biol Sci. 9(6): 16-22.
Elghobashy HA, Rahman AA, Ibrahem LH, and Rashed MA. 2005. Phylogenetic Relationships for Some Tilapia Species Using Electrophorhesis. Egypt. J. Exp. Biol. 1: 57-63.
Fenselstein J. 1985. Confidence-limits on Phylogenies – An Approach using the bootstrap. Evolution. 39: 783-791.
Fishbase. 2017. List of Freshwater Fishes Reported from Indonesia. http://www.fishbase.org.
Frankham R, Ballou JD, Briscoe, DA. 2004. A Primer of Conservation Genetics; Cambridge University Press: New York, NY, USA, Volume 39.
Gam LH, Leow CW, Baie S. 2006. Proteomic analysis of snakehead fish (Channa striata) muscle tissue. Malaysian J Biochem Mol Biol 14: 25-32.
Hammer Ø, Harper DAT and Ryan PD. 2001. PAST: Paleontological Statistic Software Package for Education and Data Analysis. Paleontologia Electronica. 4(1): 1-9.
Haniffa MA, Sheela PJ, Milton JM., and Kavitha K. 2017. Protein Profiling for Phylogenetic Relationship in Snakehead Species. Iranian J. of Fisheries Sci. 16 (4): 1178-1186.
Hidayati D, Abdulgani N, Setiyawan H, Trisnawati I, Ashuri NM, Nailis N. 2016. Analysis of protein profiles in diabetic rat blood plasma induced by alloxan. AIP Conf Proc 1854: 020016.1-020016.6.
Hidayaturrahmah, Mabrur, Santoso HB, Sasmita R, Rahmy USA, and Badruzsaufari. 2019. Protein profiles of Giant Mudskipper and its potential use as biomarker candidate for heavy metal contamination in Barito Estuary, Indonesia. Biodiversitas 20 (3): 745-753.
Karp A, Kresovich S, Bhat KV, Ayad WG, and Hodgkin T. 1997. Molecular Tool in Plant Genetic Resources Conservation: A Guide To The Technologies. IPGRI Technology Bulletin. No. 2.
Kottelat M, & Whitten T. 1996. Freshwater biodiversity in Asia with special reference to fish. World Bank Technical Paper. 343; 1-59.
Laemmli UK. 1970. Cleavege of Structural Proteins During The Assembly of The Head of Bacteriophage T4. Nature. 227: 680-685.
Low BW and Lim KKP. 2012. Gouramies of the genus Trichopodus in Singapore (Actinopterygii: Perciformes: Osphronemidae). Nature in Singapore. 5: 83-93.
Mabrur, Rahmy USA, Sasmita R, Badruzsaufari. 2018. Protein Profiles of Haruan Fish (Channa striata) from South Kalimantan. In: Soendjoto MA, Dharmono, Riefani MK, Ansari ML, Septiyan RA, Syahdi N. (eds.) The Potency, Opportunity and Challenges in Wetland Management; Proceeding of National Seminar on Wetland Environment 3 (1): 39-45. Universitas Lambung Mangkurat, Banjarmasin, 11 November 2017. [Indonesian]
Mahboob S, Farooq M, Mahmood S, Nasir N, Sultana S, Chaudhry AS, Al-Akel AS, Al-Balawi HFA, Al-Minsed F, and Al-Ghanim KA. 2012. Phylogenetic Relationship of Cultured and Wild Labeo rohita and Cirrhinus mrigala Based on Muscle Protein profile in DifferentWeight Groups: A New Tool in Phylogenetic Analysis. Int. J. Food properties. 15(5): 949-960.
Maidie A, Sumoharjo, Asra SW, Ramadhan M, and Hidayanto DN. 2015. Development of Betok Fish Tiller (Anabas testudineus) for Household Industry. Media Akuakultur. 10(1): 31-37.
Mursyidin DH, Purnomo P, Sumardi I, Daryono BS. 2018. Molecular Diversity of Tidal Swamp Rice (Oryza sativa L.) in South Kalimantan, Indonesia. Diversity. 10 (22). 1-10
Nei M, and Li. WM. 1979. Mathematical Model for Studying Genetic Variation in Terms of Restriction Endonuclease. PNAS. 76: 5269-5273.
Nelson JS. 2016. Fishes of The World. 5th Edition. John Wiley & Sons, Inc., New Jersey, USA.
Nirenberg MW, Mathaei JH, Jones OW, Martin RG. and Burondes, SH. 1963. Approximation of genetic code via, cell free protein synthesis detected by template RNA. Federation Proceedings. 22: 55-61.
Porto JIR, Gomes JAA, Farias IP, and Feldber E. 2015. Using Molecular Biology Techniques to Characterize the Diversity of Amazonian Ornamental Fish. Molecular Biology Techniques: 227-244
Quyen VDH, Phuong TTL, Oanh TT, Thuoc TL, and Binh DT. 2015. Phylogenetic Relationship of Freshwater Fish in Vietnamese Mekong. International Conference on Biological, Enviroment and Food Engineering (BEFE). Singapore: 58-61
Rath A, Cunningham F, Deber CM. 2013. Acrylamide concentration determines the direction magnitude of helical membrane protein gel shifts. Proc Nat Acad Sci USA. 110 (39): 15668-15673
Regan CT. 1909. The classification of teleostean fishes. Ann Mag Nat Hist 8: 75–86.
Roy S, and Kumar V. 2014. A Practical Approach on SDS PAGE for Separation of Protein. Int. J. Sci. Research. 3(8): 955-960.
Ruber L. 2009. Labyrinth Fishes (Anabantoidei). In. S.B. Hodges., & S. Kumar. The Timetree of Life. Oxford University Press, London.
Sabullah MK, Ahmad SA, Shukor MY, Gansau AJ, Syed MA, Sulaiman MR, Shamaan NA. 2015. Heavy metal biomarker: Fish behavior, cellular alteration, enzymatic reaction and proteomics approaches. Intl Food Res J 22 (2): 435-454.
Sasmita R, Susilawati IO, Rahmy USA, Mabrur. 2018. Protein profiles from Catfish (Pangasius hypophthalmus) and Baung Fish (Hemibagrus nemurus) Muscle from South Kalimantan. Appl Sci Technol. 2 (1): 230-234.
Saxena A, and Soranganba N. 2014. Proteins Diversity in Various Tissue of the Body of Carps. Biol. Chem. Research. 1: 108-122.
Thada V, and Jaglan DV. 2013 Comparison of Jaccard, Dice, Cosine Similarity Coeffecient to Find Best Fitness Value for Web Retrieved Documents Using Genetic Algorithm. IJIET. 2(4): 202-205.
Velamala GR, Babu KR, and Naranji MK. 2017. Genetic information of Snappers (Family: Lutjanidae) from Indian Waters Using SDS-PAGE Technique. Gen Aqua. 1: 49-55.
Wiley EO and Johnson GD. 2010.A teleost classification based on monophyletic groups. In: Nelson JS, Schultze H-P, Wilson MVH, editors. Origin and Phylogenetic Interrelationships of Teleosts. Mu¨nchen: Verlag Dr. Friedrich Pfeil. 123–182.
Zhou H, and Guo XY. 2015. Soil Heavy Metal Pollution Evaluation around Mine Area with Traditional and Ecological Assessment Methods. J. of Geosci. Environ Protect.. 3: 28-33.
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