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

Jill Sela Roja, Anak Entalai (2020) Complete Mitochondrial DNA Sequence of Rasbora : Mitogenome Characterization and Phylogenetic Implications. Masters thesis, Universiti Malaysia Sarawak (UNIMAS).

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Abstract

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.

Item Type: Thesis (Masters)
Additional Information: Thesis (MSc.) - Universiti Malaysia Sarawak , 2020.
Uncontrolled Keywords: Rasbora argyrotaenia, Rasbora myersi, Rasbora sarawakensis, mitochondrial DNA, phylogenetic analysis, unimas, university, universiti, Borneo, Malaysia, Sarawak, Kuching, Samarahan, ipta, education, Postgraduate, research, Universiti Malaysia Sarawak.
Subjects: Q Science > QH Natural history > QH301 Biology
Q Science > QH Natural history > QH426 Genetics
Divisions: Academic Faculties, Institutes and Centres > Faculty of Resource Science and Technology
Depositing User: JILL SELA ROJA ANAK ENTALAI
Date Deposited: 05 Mar 2020 06:16
Last Modified: 05 Mar 2020 06:16
URI: http://ir.unimas.my/id/eprint/29315

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