Sequencing and Characterization of Complete Mitogenome DNA for Rasbora spp. with Phylogenetic Consideration

Rasbora are freshwater fishes that belongs to Cyprinidae family. Rasbora species share similar morphology and are closely related which makes them difficult to be differentiated between species. In this study, the morphometry analysis and mitochondrial DNA were used to distinguish the species and ab...

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Main Author:	Cynthia Keranti, Kamar
Format:	Thesis
Language:	English
Published:	2019
Subjects:	Q Science (General) QR Microbiology
Online Access:	http://ir.unimas.my/id/eprint/26222/1/Cynthia%20Keranti%20Anak%20Kamar%20ft.pdf
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institution	Universiti Malaysia Sarawak
collection	UNIMAS Institutional Repository
language	English
topic	Q Science (General) QR Microbiology
spellingShingle	Q Science (General) QR Microbiology Cynthia Keranti, Kamar Sequencing and Characterization of Complete Mitogenome DNA for Rasbora spp. with Phylogenetic Consideration
description	Rasbora are freshwater fishes that belongs to Cyprinidae family. Rasbora species share similar morphology and are closely related which makes them difficult to be differentiated between species. In this study, the morphometry analysis and mitochondrial DNA were used to distinguish the species and able to resolve the phylogenetic relationship between these species. A total of 58 rasbora specimens from four species (Rasbora sumatrana (20), Rasbora hobelmani (11), Rasbora tornieri (20), and Rasbora borapetensis (7)) were individually identified using morphometric analysis. The mitochondrial DNA were amplified by using the long polymerase chain reaction (PCR). Four sets of primer were designed for partial fragment of mitochondrial genome. The newly paired primer were made from these 4 sets of primer for complete fragments of mitochondrial genome. The complete mitochondrial DNA of 4 Rasbora species consists of 22 tRNA genes, 13 protein coding genes, and 2 rRNA genes with sequence full length of 16,539 bp (Rasbora sumatrana), 16,541 bp (Rasbora hobelmani), 16,573 bp (Rasbora tornieri), and 16,520 bp (Rasbora borapetensis) respectively. The phylogenetic position of these 4 Rasbora species was evaluated by using concatenated 13 protein coding genes of complete mitochondrial sequence. The morphometry and mitochondrial DNA study has successfully correlated these 4 Rasbora species by using discriminant function analysis and sequencing respectively. In conclusions, the molecular work produce more reliable results than morphometric study in identifying the species as the resolution of the species phylogeny can be observed.
format	Thesis
qualification_level	Master's degree
author	Cynthia Keranti, Kamar
author_facet	Cynthia Keranti, Kamar
author_sort	Cynthia Keranti, Kamar
title	Sequencing and Characterization of Complete Mitogenome DNA for Rasbora spp. with Phylogenetic Consideration
title_short	Sequencing and Characterization of Complete Mitogenome DNA for Rasbora spp. with Phylogenetic Consideration
title_full	Sequencing and Characterization of Complete Mitogenome DNA for Rasbora spp. with Phylogenetic Consideration
title_fullStr	Sequencing and Characterization of Complete Mitogenome DNA for Rasbora spp. with Phylogenetic Consideration
title_full_unstemmed	Sequencing and Characterization of Complete Mitogenome DNA for Rasbora spp. with Phylogenetic Consideration
title_sort	sequencing and characterization of complete mitogenome dna for rasbora spp. with phylogenetic consideration
granting_institution	Universiti Malaysia Sarawak (UNIMAS)
granting_department	Faculty of Resource Science and Technology
publishDate	2019
url	http://ir.unimas.my/id/eprint/26222/1/Cynthia%20Keranti%20Anak%20Kamar%20ft.pdf
_version_	1783728306916425728
spelling	my-unimas-ir.262222023-04-25T08:55:18Z Sequencing and Characterization of Complete Mitogenome DNA for Rasbora spp. with Phylogenetic Consideration 2019-07-31 Cynthia Keranti, Kamar Q Science (General) QR Microbiology Rasbora are freshwater fishes that belongs to Cyprinidae family. Rasbora species share similar morphology and are closely related which makes them difficult to be differentiated between species. In this study, the morphometry analysis and mitochondrial DNA were used to distinguish the species and able to resolve the phylogenetic relationship between these species. A total of 58 rasbora specimens from four species (Rasbora sumatrana (20), Rasbora hobelmani (11), Rasbora tornieri (20), and Rasbora borapetensis (7)) were individually identified using morphometric analysis. The mitochondrial DNA were amplified by using the long polymerase chain reaction (PCR). Four sets of primer were designed for partial fragment of mitochondrial genome. The newly paired primer were made from these 4 sets of primer for complete fragments of mitochondrial genome. The complete mitochondrial DNA of 4 Rasbora species consists of 22 tRNA genes, 13 protein coding genes, and 2 rRNA genes with sequence full length of 16,539 bp (Rasbora sumatrana), 16,541 bp (Rasbora hobelmani), 16,573 bp (Rasbora tornieri), and 16,520 bp (Rasbora borapetensis) respectively. The phylogenetic position of these 4 Rasbora species was evaluated by using concatenated 13 protein coding genes of complete mitochondrial sequence. The morphometry and mitochondrial DNA study has successfully correlated these 4 Rasbora species by using discriminant function analysis and sequencing respectively. In conclusions, the molecular work produce more reliable results than morphometric study in identifying the species as the resolution of the species phylogeny can be observed. Universiti Malaysia Sarawak (UNIMAS) 2019-07 Thesis http://ir.unimas.my/id/eprint/26222/ http://ir.unimas.my/id/eprint/26222/1/Cynthia%20Keranti%20Anak%20Kamar%20ft.pdf text en validuser masters Universiti Malaysia Sarawak (UNIMAS) Faculty of Resource Science and Technology Aprilian, E., Roesma, D. I., & Tjong, D. H. (2016). Morphological variation of Bada fish (Rasbora maninjau, Lumbantobing) in Maninjau Lake, West Sumatra. Journal of Entomology and Zoology Studies, 4(2), 541-544. Bankevich, A., Nurk, S., Antipov, D., Gurevich, A. A., Dvorkin, M., Kulikov, A. S., Lesin, V. M., Nikolenko, S. I., Pham, S., Prjibelski, A. D., Pyshkin, A. V., Sirotkin, A. V., Vyahhi, N., Tesler, G., Alekseyev, M. A., & Pevzner, P. A. (2012). SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. Journal of Computational Biology, 19(5), 455-477. Barlow, G. W. (1961). Causes and Significance of Morphological Variation in Fishes. Systematic Zoology, 10(3), 105-117. Berbel-Filho, W. M., Jacobina, U. P., & Martinez, P. A. (2013). Preservation effects in geometric morphometric approaches: Freezing and alcohol in a freshwater fish. Ichthyological Research, 60(3), 268-271. Bíró, R. K. (2015). Constructing Phylogenetic Trees (Unpublished bachelor's thesis). Eötvös Loránd University, Budapest, Hungary. Brittan, M. R. (1954). The cyprinid fish genus Rasbora in Malaya. The Raffles Bulletin of Zoology, 25, 129-156. Chandra, R., & Prusty, B. A. K. (2011). A new record of a fish species, Rasbora daniconius, in the wetlands of Keoladeo National Park, Bharatpur, India, and conservation concerns. Environmental Research Journal, 4(5-6), 499-514. Chang, C., Tsai, C., & Jang-Liaw, N. (2013). Complete mitochondrial genome of the Chinese rasbora Rasbora steineri (Teleostei, Cyprinidae). Mitochondrial DNA, 24(3), 183-185. 97 Chen, F., Ma, H., Ma, C., Zhang, H., Zhao, M., Meng, Y., Wei, H. & Ma, L. (2016). Sequencing and characterization of mitochondrial DNA genome for Brama japonica (Perciformes: Bramidae) with phylogenetic consideration. Biochemical Systematics and Ecology, 68, 109-118. Chung, H. H. (2013). Ontogenic expression and functional characterization of FADS2, an enzyme for long-chained unsaturated fatty acid desaturation in zebrafish (Ph.D dissertation). Universiti Sains Malaysia, Pulau Pinang, Malaysia. Elliott, N. G., Haskard, K. & Koslow, J. A. (1995). Morphometric analysis of orange roughy (Hoplostethus atlanticus) off the continental slope of southern Australia. Journal of Fish Biology, 46(2), 202-220. Fang, F., Norï, N., M., Liao, T. Y., Källersjö, M., & Kullander, S. O. (2009). Molecular phylogenetic interrelationships of the south Asian cyprinid genera Danio, Devario and Microrasbora (Teleostei, Cyprinidae, Danioninae). Zoologica Scripta, 38(3), 237-256. Gilpin, D. (2011). The complete illustrated guide to animals, birds & fish of the British Isles. Anness Publishing, London, United Kingdom. Hadiaty, R. K. (2009). Rasbora lacrimula, a new species of cyprinid fish from eastern Borneo (Teleostei: Cyprinidae). Ichthyological Exploration of Freshwaters, 20(2), 105-109. Hair, J. F., Tatham, R. L., Anderson, R. E. & Black, W. (1998). Multivariate Data Analysis (5th Ed.). Upper Saddle River, USA: Prentice Hall. Ho, C., Liu, M. & Chen, M. (2014). Complete mitochondrial genome of Rasbora trilineata (Cypriniformes, Cyprinidae). Mitochondrial DNA, 1-3. Hrbek, T., & Farias, I. P. (2008). The complete mitochondrial genome of the pirarucu (Arapaima gigas, Arapaimidae, Osteoglossiformes). Genetics and Molecular Biology, 31(1), 293-302. 98 Hubert, N., Wibowo, A., Busson, F., Caruso, D., Sulandari, S., Nafiqoh, N., Pouyaud, L., Ruber, L., Avarre, J., Herder, F., Hanner, R., Keith, P., Hadiaty, R. K. & Kadarusman. (2015). DNA Barcoding Indonesian freshwater fishes: challenges and prospects. DNA Barcodes, 3(1), 144-169. Inger, R. F. & Chin, P. K. (1990). The freshwater fishes of North Borneo (Vol. 45). Sabah, Malaysia, Kota Kinabalu: Sabah Zoological Society. Jang-Liaw, N., Tsai, C., Chang, C., & Watanabe, K. (2013). Complete mitochondrial genome of the Moltrechts minnow, Aphyocypris moltrechti (Teleostei, Cyprinidae), in comparison with A. kikuchii. Mitochondrial DNA, 24(2), 117-119. Jiang, M., Yang, C., & Wen, H. (2014). The complete mitochondrial genome of Aspiorhynchus laticeps and its phylogenetic analysis. Meta Gene, 2, 218-225. Kannan, L., & Wheeler, W. C. (2012). Maximum Parsimony on Phylogenetic networks. Algorithms for Molecular Biology, 7(9), 1-10. Kashyap, A., Awasthi, M. & Serajuddin, M. (2015). Intraspecific Diversity of Freshwater Murrel, Channa punctatus. International Journal of Fisheries and Aquatic Studies, 3(2), 166–173. Kocher, T. D. & Stepien, C. A. (1997). Molecular systematics of fishes. San Diego, CA: Academic Press. Kottelat, M. (1984). A new Rasbora s.l. (Pisces: Cyprinidae) from Northern Thailand. Revue Suisse de Zoologie., 91, 717–723. Kottelat, M., Whitten, A. J., Kartikasari, S. N. & Wirjoatmodjo, S. (1993). Freshwater fishes of western Indonesia and Sulawesi. Hong Kong: Periplus Editions. Kottelat, M. & Tan, H. H. (2011). Identity of Rasbora beauforti, a cyprinid fish from Borneo (Teleostei: Cyprinidae). Ichthyological Exploration of Freshwaters, 22(4), 319-326. 99 Kottelat, M. & Tan, H. H. (2011). Rasbora atranus, a new species of fish from central Borneo (Teleostei: Cyprinidae). Ichthyological Exploration of Freshwaters, 22(3), 215-220. Kottelat, M. & Tan, H. H. (2012). Rasbora cryptica, a new species of fish from Sarawak, Borneo (Teleostei: Cyprinidae). Ichthyological Exploration of Freshwaters, 23(1), 37-44. Kottelat, M. (2005). Rasbora notura, a new species of cyprinid fish from Malay Peninsula (Teleostei: Cyprinidae). Ichthyological Exploration of Freshwaters, 16(3), 265-270. Kottelat, M. (2007). Rasbora dies, a new species of cyprinid fish from eastern Borneo (Teleostei: Cyprinidae). Ichthyological Exploration of Freshwaters, 18(4), 301-305. Kottelat, M. (2012). Rasbora rheophila, a new species of fish from northern Borneo (Teleostei: Cyprinidae). Revue Suisse De Zoologie., 119(1), 77-87. Kumar, R., Singh, P. J., Nagpure, N. S., Kushwaha, B., Srivastava, S. K. & Lakra, W. S. (2007). A non-invasive technique for rapid extraction of DNA from fish scales. Indian Journal of Experimental Biology, 45, 992-997. Kusuma, W. E. & Kumazawa, Y. (2015). Complete mitochondrial genome sequences of two Indonesian rasboras (Rasbora aprotaenia and Rasbora lateristriata). Mitochondrial DNA Part A, 27(6), 4222-4223. Kusuma, W. E., Ratmuangkhwang, S. & Kumazawa, Y. (2016). Molecular phylogeny and historical biogeography of the Indonesian freshwater fish Rasbora lateristriata species complex (Actinopterygii: Cyprinidae): Cryptic species and west-to-east divergences. Molecular Phylogenetics and Evolution, 105, 212–223. Kusuma, W. E., Samuel, P. D., Wiadnya, D. G., Hariati, A. M. & Kumazawa, Y. (2017). Complete mitogenome sequence of Rasbora argyrotaenia (Actinopterygii: Cyprinidae). Mitochondrial DNA Part B, 2(2), 373-374. 100 Liao, T. Y., Kullander, S. O. & Fang, F. (2010). Phylogenetic analysis of the genus Rasbora (Teleostei: Cyprinidae). Zoologica Sripta, 39, 155-176. Lowe, T.M. and Chan, P.P. (2016) tRNAscan-SE On-line: Search and Contextual Analysis of Transfer RNA Genes. Nucleic Acids Research, 44, W54-57. Lumbantobing, D. N. (2010). Four New Species of the Rasbora trifasciata-Group (Teleostei: Cyprinidae) from Northwestern Sumatra, Indonesia. Copeia, 2010(4), 644-670. Lumbantobing, D. N. (2014). Four new species of Rasbora of the Sumatrana group (Teleostei: Cyprinidae) from northern Sumatra, Indonesia. Zootaxa, 3764(1), 1-25. Mahapatro, G., Mishra, D., Shaw, K., Mishra, S., & Jena, T. (2012). Phylogenetic Tree Construction for DNA Sequences using Clustering Methods. Procedia Engineering, 38, 1362-1366. Martin, M. (2011). Cutadapt removes adapter sequences from high-throughput sequencing reads. EMBnet Journal, 17(1), 10-12. Matthews, W. J. (1998). Patterns in Freshwater Fish Ecology. New York, USA: Chapman & Hall. Meyer, A., Biermann, C. H., & Orti, G. (1993). The phylogenetic position of the zebrafish (Danio rerio), a model system in developmental biology: An invitation to the comparative method. Proceedings of the Royal Society of London. Series B: Biological Sciences, 252(1335), 231-236. Mollah, M., Yeasmine, S., Hossen, M. B. & Ahammad, A. K. (2012). Landmark-based morphometric and meristic variations of Glossogobius giuris in three stocks. Journal of the Bangladesh Agricultural University, 10(2), 375-384. Moreira, D. A., Buckup, P. A., Britto, M. R., Magalhães, M. G., Andrade, P. C., Furtado, C., & Parente, T. E. (2016). The complete mitochondrial genome of Corydoras nattereri (Callichthyidae: Corydoradinae). Neotropical Ichthyology, 14(1), e150167. 101 Moyle, P. B., & Cech, J. J., Jr. (2004). Fishes: An Introduction to Ichthyology (5th ed.). USA: Prentice Hall. Muchlisin, Z. A. (2013). Morphometric Variations of Rasbora Group (Pisces: Cyprinidae) in Lake Laut Tawar, Aceh Province, Indonesia, Based on Truss Character Analysis. HAYATI Journal of Biosciences, 20(3), 138-143. Ng, H. H. & Kottelat, M. (2013). The identity of the cyprinid fishes Rasbora dusonensis and R. tornieri (Teleostei: Cyprinidae). Zootaxa, 3635(1), 62-70. Parenti, L. R. & Lim, K. K. (2005). Fishes of the Rajang Basin, Sarawak, Malaysia. The Raffles Bulletin of Zoology, (13), 175-208. Peng, Z., Wang, J., & He, S. (2006). The complete mitochondrial genome of the helmet catfish Cranoglanis bouderius (Siluriformes: Cranoglanididae) and the phylogeny of otophysan fishes. Gene, 376(2), 290-297. Prosdocimi, F., Carvalho, D. C., Almeida, R. N., & Beheregaray, L. B. (2011). The complete mitochondrial genome of two recently derived species of the fish genus Nannoperca (Perciformes, Percichthyidae). Molecular Biology Reports, 39(3), 2767-2772. Rainboth, W. J. & Kottelat, M. (1987). Rasbora spilocerca, a New Cyprinid from the Mekong River. Copeia, 1987(2), 417-423. Roberts, T. R. (1989). The freshwater fishes of Western Borneo (Kalimantan Barat, Indonesia). San Francisco: California Academy of Sciences. 102 Shi, X., Tian, P., Lin, R., Huang, D., & Wang, J. (2016). Characterization of the Complete Mitochondrial Genome Sequence of the Globose Head Whiptail Cetonurus globiceps (Gadiformes: Macrouridae) and Its Phylogenetic Analysis. Plos One, 11(4), 1-17. Siebert, D. J. (1997). The identities of Rasbora paucisqualis Ahl in Schreitmuller, 1935, and Rasbora bankanensis (Bleeker, 1853), with the designation of a lectotype for R. paucisqualis (Teleostei: Cyprinidae). The Raffles Bulletin of Zoology, 45(1), 29-37. Sim, C. H. (2002). A field guide to the fish of Tasik Bera Ramsar Site, Pahang, Malaysia (1st ed.). Wetlands International-Malaysia Programme. Spiller, L., Grierson, P. F., Davies, P. M., Hemmi, J., Collin, S. P., & Kelley, J. L. (2017). Functional diversity of the lateral line system among populations of a native Australian freshwater fish. The Journal of Experimental Biology, 220(12), 2265-2276. Staton, J. L. (2015). Understanding phylogenies: Constructing and Interpreting Phylogenetic trees. Journal of the South Carolina Academy of Science, 13(1), 22-29. Sulaiman, Z. H. & Mayden, R. L. (2012). Cypriniformes of Borneo (Actinopterygii, Otophysi): An Extraordinary Fauna for Integrated Studies on Diversity, Systematics, Evolution, Ecology, and Conservation. Zootaxa, 3586, 359–376. Suvarna, D. S. & Rita, K. S. D. (2014). Morphometric and electrophoretic studies of Rasbora dandia (Valenciennes) (Pisces; Cyprinidae) from varied habitats in Kerala. Journal of Aquatic Biology & Fisheries, 2(1), 290-296. Syaifullah, S., Fajri, H., & Roesma, D. I. (2015). Morphometric variations of halfbeak fish (Zenarchopterus buffonis) from estuary of west Sumatra, Indonesia. Aquaculture, Aquarium, Conservation & Legislation International Journal of the Bioflux Society, 8(2), 168-176. 103 Taanman, J.-W. (1999). The mitochondrial genome: structure, transcription, translation and replication. Biochimica et Biophysica Acta (BBA) - Bioenergetics, 1410(2), 103–123. Talib, Y., Farooqui, A., Fatema, M., & Khan, W. (2016). Phylogenetic tree construction of biosurfactant producing organisms. Journal of Global Bioscience, 5(5), 4105-4108. Tian, F., Zhao, K., & Tang, Y. (2017). Characterization of the complete mitochondrial genome of Gymnocypris scleracanthus (Teleostei: Cyprinidae). Conservation Genetics Resource, 10(3), 467-469. Trontelj, P. & Fišer, C. (2009). Perspectives: Cryptic species diversity should not be trivialised. Systematics and Biodiversity, 7(1), 1-3. Turan, C., Erguden, D., Gurlek, M., Basusta, N. & Turan, F. (2004). Morphometric Structuring of the Anchovy (Engraulis encrasicolus L.) in the Black, Aegean and North eastern Mediterranean Seas. Turkish Journal of Veterinary and Animal Sciences, 28, 865-871. Turan, C., Oral, M., Öztürk, B. & Düzgüneş, E. (2006). Morphometric and meristic variation between stocks of Bluefish (Pomatomus saltatrix) in the Black, Marmara, Aegean and northeastern Mediterranean Seas. Fisheries Research, 79(1-2), 139-147. Zhang, S., Cui, J., Li, C., Mahboob, S., Al-Ghanim, K., Xu, P. & Sun, J. (2014). The complete mitochondrial genome of Rasbora borapetensis (Cypriniformes: Cyprinidae: Rasbora). Mitochondrial DNA, 27(2), 861-862.

Sequencing and Characterization of Complete Mitogenome DNA for Rasbora spp. with Phylogenetic Consideration

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