Complete Mitochondrial DNA Sequence of Rasbora : Mitogenome Characterization and Phylogenetic Implications

Rasbora are freshwater fishes that belongs to Cyprinidae family whereby most of its member share similar morphology which makes them difficult to be differentiated between species. In this study, both the morphometry analysis and mitochondrial DNA approach were used to resolve the phylogenetic relat...

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Main Author:	Jill Sela Roja, Anak Entalai
Format:	Thesis
Language:	English
Published:	2020
Subjects:	QH301 Biology QH426 Genetics
Online Access:	http://ir.unimas.my/id/eprint/29315/1/Jill.pdf
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spelling	my-unimas-ir.293152023-05-19T02:31:43Z Complete Mitochondrial DNA Sequence of Rasbora : Mitogenome Characterization and Phylogenetic Implications 2020-03-05 Jill Sela Roja, Anak Entalai QH301 Biology QH426 Genetics Rasbora are freshwater fishes that belongs to Cyprinidae family whereby most of its member share similar morphology which makes them difficult to be differentiated between species. In this study, both the morphometry analysis and mitochondrial DNA approach were used to resolve the phylogenetic relationship between these species. The complete sequence of mt-genome for R. argyrotaenia, R. myersi, R. sarawakensis and Rasbora sp. were 16,574 bp, 16,581 bp, 16,709 bp and 16,518 bp respectively. The structure of all study species mtDNA was characterized using bioinformatics analysis. Rasbora mt-genome comprises of a standard set of 22 tRNAs, two rRNAs, 13 PCGs and two typical non-coding regions. The AT-skew and GC-skew values in the whole genome of Rasbora were 0.141 and -0.268 respectively, revealing that the H-strand had the amount of C and A were more prevalent. All the tRNA genes could be folded into cloverleaf secondary structures, while the secondary structure of Ser (AGY) lacked a D arm (DHU stem). By comparing Rasbora genome sequence with the recognition sites in teleost species, five conserved sequence blocks were identified in the control region. The common conserved motif sequence of origin of L-strand replication were also identified. The phylogenetic analyses were based on the concatenated of nucleotide sequence and amino acid sequence from 13 PCGs. The phylogenetic position of R. argyrotaenia, R. myersi, R. sarawakensis and Rasbora sp. were evaluated from the Maximum likelihood trees. Overall, this study enriches the knowledge of Rasbora mt-genomes while partially resolving the ambiguity of the phylogenetic relationships of Rasbora taxonomy. Universiti Malaysia Sarawak (UNIMAS) 2020-03 Thesis http://ir.unimas.my/id/eprint/29315/ http://ir.unimas.my/id/eprint/29315/1/Jill.pdf text en validuser masters Universiti Malaysia Sarawak (UNIMAS) Faculty of Science and Resource Technology
institution	Universiti Malaysia Sarawak
collection	UNIMAS Institutional Repository
language	English
topic	QH301 Biology QH426 Genetics
spellingShingle	QH301 Biology QH426 Genetics Jill Sela Roja, Anak Entalai Complete Mitochondrial DNA Sequence of Rasbora : Mitogenome Characterization and Phylogenetic Implications
description	Rasbora are freshwater fishes that belongs to Cyprinidae family whereby most of its member share similar morphology which makes them difficult to be differentiated between species. In this study, both the morphometry analysis and mitochondrial DNA approach were used to resolve the phylogenetic relationship between these species. The complete sequence of mt-genome for R. argyrotaenia, R. myersi, R. sarawakensis and Rasbora sp. were 16,574 bp, 16,581 bp, 16,709 bp and 16,518 bp respectively. The structure of all study species mtDNA was characterized using bioinformatics analysis. Rasbora mt-genome comprises of a standard set of 22 tRNAs, two rRNAs, 13 PCGs and two typical non-coding regions. The AT-skew and GC-skew values in the whole genome of Rasbora were 0.141 and -0.268 respectively, revealing that the H-strand had the amount of C and A were more prevalent. All the tRNA genes could be folded into cloverleaf secondary structures, while the secondary structure of Ser (AGY) lacked a D arm (DHU stem). By comparing Rasbora genome sequence with the recognition sites in teleost species, five conserved sequence blocks were identified in the control region. The common conserved motif sequence of origin of L-strand replication were also identified. The phylogenetic analyses were based on the concatenated of nucleotide sequence and amino acid sequence from 13 PCGs. The phylogenetic position of R. argyrotaenia, R. myersi, R. sarawakensis and Rasbora sp. were evaluated from the Maximum likelihood trees. Overall, this study enriches the knowledge of Rasbora mt-genomes while partially resolving the ambiguity of the phylogenetic relationships of Rasbora taxonomy.
format	Thesis
qualification_level	Master's degree
author	Jill Sela Roja, Anak Entalai
author_facet	Jill Sela Roja, Anak Entalai
author_sort	Jill Sela Roja, Anak Entalai
title	Complete Mitochondrial DNA Sequence of Rasbora : Mitogenome Characterization and Phylogenetic Implications
title_short	Complete Mitochondrial DNA Sequence of Rasbora : Mitogenome Characterization and Phylogenetic Implications
title_full	Complete Mitochondrial DNA Sequence of Rasbora : Mitogenome Characterization and Phylogenetic Implications
title_fullStr	Complete Mitochondrial DNA Sequence of Rasbora : Mitogenome Characterization and Phylogenetic Implications
title_full_unstemmed	Complete Mitochondrial DNA Sequence of Rasbora : Mitogenome Characterization and Phylogenetic Implications
title_sort	complete mitochondrial dna sequence of rasbora : mitogenome characterization and phylogenetic implications
granting_institution	Universiti Malaysia Sarawak (UNIMAS)
granting_department	Faculty of Science and Resource Technology
publishDate	2020
url	http://ir.unimas.my/id/eprint/29315/1/Jill.pdf
_version_	1783728369859297280

Complete Mitochondrial DNA Sequence of Rasbora : Mitogenome Characterization and Phylogenetic Implications

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