Ferdaus, Fatin Soleha
(2015)
Molecular Characterization of Fish Species Using Mitochondrial
DNA 12S rRNA.
Project Report.
Universiti Sains Malaysia.
(Submitted)
Abstract
This study was undertaken to study the capability of a set of new primers
(unpublished) to amplify partial sequence of mitochondrial DNA (mtDNA) 12S
rRNA gene of marine and freshwater fish species. The primers namely Forward:
5’ - CAA ACT GGG ATT AGA TAC CCC AC - 3’, and Reverse: 5’ - TAC RCT
TAC CAT GTT ACG ACT T - 3’ were able to amplify the seventeen fish species
chosen for this study. Pairwise comparison of the sequence data of the 17 fish
species were undertaken to study the intra-species variations in the partial
sequence of mtDNA 12S rRNA gene. The Thunnus tonggol and Scomberomorus
commerson showed the highest similarity that is 89.37%. Diagramma pictum and
Siganus canaliculatus showed the second highest similarity with 86.26%. The
lowest similarity seen between Leptobarbus hoevenii and Nemipterus bathybius
with 67.77%.
A total of 1354 nucleotide positional polymorphisms were recorded. The
transition (T<->C and A<->G) 628 out of 1354 and the number of transversion
was 514. The lowest number of nucleotide polymorphism was observed in
Siganus canaliculatus 8.3% and Nemipterus bathybius has showed the highest
nucleotide polymorphism with 26.81%. An unrooted neighbor joining tree (NJ) was
constructed to study their genetic relationship.
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