Mitochondrial genome analysis and genetic charaterization of endangered humphead wrasse, cheilinus undulatus (rüppell, 1835) from Sabah, Malaysia

Mitochondrial (mt) Deoxyribonucleic acid (DNA) loci have been employed in various marine taxa, including reef fishes with the objective of resolving phylogeny, assigning parentage and delineating haplotypes. In this study, complete mtDNA genome was sequenced and the D-Loop locus was applied to estim...

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Main Author:	Pressly Anak Matthew
Format:	Thesis
Language:	English English
Published:	2019
Subjects:	QL614-639.8 Fishes
Online Access:	https://eprints.ums.edu.my/id/eprint/41255/1/24%20PAGES.pdf https://eprints.ums.edu.my/id/eprint/41255/2/FULLTEXT.pdf
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spelling	my-ums-ep.412552024-10-18T07:18:29Z Mitochondrial genome analysis and genetic charaterization of endangered humphead wrasse, cheilinus undulatus (rüppell, 1835) from Sabah, Malaysia 2019 Pressly Anak Matthew QL614-639.8 Fishes Mitochondrial (mt) Deoxyribonucleic acid (DNA) loci have been employed in various marine taxa, including reef fishes with the objective of resolving phylogeny, assigning parentage and delineating haplotypes. In this study, complete mtDNA genome was sequenced and the D-Loop locus was applied to estimate the population status of the Humphead Wrasse (HHW) Cheilinus undulatus. The Humphead Wrasse (HHW) is a long-lived reef-associated fish and the largest member of wrasses (family Labridae). However, it is endangered throughout its natural distributional range, primarily due to being a target in the Live Reef Fish for Food Trade. Specimens tissue were collected from three localities in Sabah, i.e. Kota Kinabalu, Sandakan and Semporna. The objectives of this study are 1) to sequence the mtDNA of the HHW, and 2) to identify population structure using D-LOOP of the HHW. The result of the sequencing data assemblies yielded six mitochondrial genomes and deposited into the National Center for Biotechnology Information (NCBI) with the accession number MH675879, MH675880, MH688049, MH688050, MH688051, MH688052. The result from AMOVA and overall Fst (-0.02914) showed that all three population absent from population structuring despite geographical distinct. The AMOVA showed a variation (100%) arise within the population instead among population. The neutrality test from Tajima`D (Kota Kinabalu: -1.825 and Sandakan: -1.009), and more sensitive Fu’s Fs Statistic (Kota Kinabalu: -3.9844 and Sandakan-1.149), and mismatch distribution showed unimodal graph pattern suggested as C. undulatus undergoes recent population expansion. Haplotype frequency analysis produce a total 25 haplotypes whereas unique 11 haplotype is detected from three local population. High haplotypic diversity encountered in the Kota Kinabalu (0.682), Sandakan (0.902) and Sempona (1.000) and low nucleotide diversity in Kota Kinabalu (0.003), Sandakan (0.004), and Semporna (0.002), and starburst pattern of common haplotypes median joining network support C. undulatus population expansion. The first genetic characterization data from mtDNA and all three populations structure analysis of C. undulatus from Sabah study provide a new insight for conservation attention. 2019 Thesis https://eprints.ums.edu.my/id/eprint/41255/ https://eprints.ums.edu.my/id/eprint/41255/1/24%20PAGES.pdf text en public https://eprints.ums.edu.my/id/eprint/41255/2/FULLTEXT.pdf text en validuser masters Universiti Malaysia Sabah Borneo Marine Research Institute
institution	Universiti Malaysia Sabah
collection	UMS Institutional Repository
language	English English
topic	QL614-639.8 Fishes
spellingShingle	QL614-639.8 Fishes Pressly Anak Matthew Mitochondrial genome analysis and genetic charaterization of endangered humphead wrasse, cheilinus undulatus (rüppell, 1835) from Sabah, Malaysia
description	Mitochondrial (mt) Deoxyribonucleic acid (DNA) loci have been employed in various marine taxa, including reef fishes with the objective of resolving phylogeny, assigning parentage and delineating haplotypes. In this study, complete mtDNA genome was sequenced and the D-Loop locus was applied to estimate the population status of the Humphead Wrasse (HHW) Cheilinus undulatus. The Humphead Wrasse (HHW) is a long-lived reef-associated fish and the largest member of wrasses (family Labridae). However, it is endangered throughout its natural distributional range, primarily due to being a target in the Live Reef Fish for Food Trade. Specimens tissue were collected from three localities in Sabah, i.e. Kota Kinabalu, Sandakan and Semporna. The objectives of this study are 1) to sequence the mtDNA of the HHW, and 2) to identify population structure using D-LOOP of the HHW. The result of the sequencing data assemblies yielded six mitochondrial genomes and deposited into the National Center for Biotechnology Information (NCBI) with the accession number MH675879, MH675880, MH688049, MH688050, MH688051, MH688052. The result from AMOVA and overall Fst (-0.02914) showed that all three population absent from population structuring despite geographical distinct. The AMOVA showed a variation (100%) arise within the population instead among population. The neutrality test from Tajima`D (Kota Kinabalu: -1.825 and Sandakan: -1.009), and more sensitive Fu’s Fs Statistic (Kota Kinabalu: -3.9844 and Sandakan-1.149), and mismatch distribution showed unimodal graph pattern suggested as C. undulatus undergoes recent population expansion. Haplotype frequency analysis produce a total 25 haplotypes whereas unique 11 haplotype is detected from three local population. High haplotypic diversity encountered in the Kota Kinabalu (0.682), Sandakan (0.902) and Sempona (1.000) and low nucleotide diversity in Kota Kinabalu (0.003), Sandakan (0.004), and Semporna (0.002), and starburst pattern of common haplotypes median joining network support C. undulatus population expansion. The first genetic characterization data from mtDNA and all three populations structure analysis of C. undulatus from Sabah study provide a new insight for conservation attention.
format	Thesis
qualification_level	Master's degree
author	Pressly Anak Matthew
author_facet	Pressly Anak Matthew
author_sort	Pressly Anak Matthew
title	Mitochondrial genome analysis and genetic charaterization of endangered humphead wrasse, cheilinus undulatus (rüppell, 1835) from Sabah, Malaysia
title_short	Mitochondrial genome analysis and genetic charaterization of endangered humphead wrasse, cheilinus undulatus (rüppell, 1835) from Sabah, Malaysia
title_full	Mitochondrial genome analysis and genetic charaterization of endangered humphead wrasse, cheilinus undulatus (rüppell, 1835) from Sabah, Malaysia
title_fullStr	Mitochondrial genome analysis and genetic charaterization of endangered humphead wrasse, cheilinus undulatus (rüppell, 1835) from Sabah, Malaysia
title_full_unstemmed	Mitochondrial genome analysis and genetic charaterization of endangered humphead wrasse, cheilinus undulatus (rüppell, 1835) from Sabah, Malaysia
title_sort	mitochondrial genome analysis and genetic charaterization of endangered humphead wrasse, cheilinus undulatus (rüppell, 1835) from sabah, malaysia
granting_institution	Universiti Malaysia Sabah
granting_department	Borneo Marine Research Institute
publishDate	2019
url	https://eprints.ums.edu.my/id/eprint/41255/1/24%20PAGES.pdf https://eprints.ums.edu.my/id/eprint/41255/2/FULLTEXT.pdf
_version_	1818611385554173952

Mitochondrial genome analysis and genetic charaterization of endangered humphead wrasse, cheilinus undulatus (rüppell, 1835) from Sabah, Malaysia

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