Molecular Identification Of Fish Larvae In Merbok River Through Dna Metabarcoding

This study aimed to elucidate the diversity and distribution of fish larvae in Merbok River through molecular identification by the DNA metabarcoding approach. In the first phase of this study, a molecular database for the fish species of Merbok River was completed through the expansion of the exist...

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التفاصيل البيبلوغرافية
المؤلف الرئيسي:	Alshari, Norli Fauzani Mohd Abu Hassan
التنسيق:	أطروحة
اللغة:	English
منشور في:	2020
الموضوعات:	QH1 Natural history (General - Including nature conservation geographical distribution)
الوصول للمادة أونلاين:	http://eprints.usm.my/55143/1/NORLI%20FAUZANI%20BINTI%20MOHD%20ABU%20HASSAN%20ALSHARI%20-%20TESIS%20cut.pdf
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id	my-usm-ep.55143
record_format	uketd_dc
spelling	my-usm-ep.551432022-10-05T04:24:32Z Molecular Identification Of Fish Larvae In Merbok River Through Dna Metabarcoding 2020-07 Alshari, Norli Fauzani Mohd Abu Hassan QH1 Natural history (General - Including nature conservation, geographical distribution) This study aimed to elucidate the diversity and distribution of fish larvae in Merbok River through molecular identification by the DNA metabarcoding approach. In the first phase of this study, a molecular database for the fish species of Merbok River was completed through the expansion of the existing reference database of 12S ribosomal RNA (rRNA) gene for the 120 documented species morphologically identified in previous studies in combination with existing Cytochrome Oxidase Subunit 1 (COI) database. In the second phase, a metabarcoding study of fish larvae samples obtained from four stations (St1, St2, St3 and St4), representing the upper to lower zone of a lower to higher salinity gradient was conducted. The genomic DNA of the fish larvae were extracted, amplified and enriched by using REPLI-g Mitochondrial DNA kit. Next generation sequencing (NGS) of this whole genome was done using the Illumina MiSeq platform, followed by bioinformatics analysis. A BLAST analysis on the de novo assembled scaffolds of the four samples detected a total of 89 fish larvae species, 65 genera and 41 families from 1071 and 943 total genome scaffolds belonging to COI and 12S rRNA genes, respectively. From the total number of scaffolds, Oryzias javanicus and Oryzias dancena showed the highest abundance and followed by other estuarine species commonly found such as Lutjanus argentimaculatus, Lutjanus malabaricus and others. Considerable non-overlapping of species identity between the metabarcoding and morphological data is suggested to be due to variation in spawning season and sampling biasness (commercial compared to wild species) among other factors. 2020-07 Thesis http://eprints.usm.my/55143/ http://eprints.usm.my/55143/1/NORLI%20FAUZANI%20BINTI%20MOHD%20ABU%20HASSAN%20ALSHARI%20-%20TESIS%20cut.pdf application/pdf en public masters Universiti Sains Malaysia Pusat Pengajian Sains Kajihayat
institution	Universiti Sains Malaysia
collection	USM Institutional Repository
language	English
topic	QH1 Natural history (General - Including nature conservation geographical distribution)
spellingShingle	QH1 Natural history (General - Including nature conservation geographical distribution) Alshari, Norli Fauzani Mohd Abu Hassan Molecular Identification Of Fish Larvae In Merbok River Through Dna Metabarcoding
description	This study aimed to elucidate the diversity and distribution of fish larvae in Merbok River through molecular identification by the DNA metabarcoding approach. In the first phase of this study, a molecular database for the fish species of Merbok River was completed through the expansion of the existing reference database of 12S ribosomal RNA (rRNA) gene for the 120 documented species morphologically identified in previous studies in combination with existing Cytochrome Oxidase Subunit 1 (COI) database. In the second phase, a metabarcoding study of fish larvae samples obtained from four stations (St1, St2, St3 and St4), representing the upper to lower zone of a lower to higher salinity gradient was conducted. The genomic DNA of the fish larvae were extracted, amplified and enriched by using REPLI-g Mitochondrial DNA kit. Next generation sequencing (NGS) of this whole genome was done using the Illumina MiSeq platform, followed by bioinformatics analysis. A BLAST analysis on the de novo assembled scaffolds of the four samples detected a total of 89 fish larvae species, 65 genera and 41 families from 1071 and 943 total genome scaffolds belonging to COI and 12S rRNA genes, respectively. From the total number of scaffolds, Oryzias javanicus and Oryzias dancena showed the highest abundance and followed by other estuarine species commonly found such as Lutjanus argentimaculatus, Lutjanus malabaricus and others. Considerable non-overlapping of species identity between the metabarcoding and morphological data is suggested to be due to variation in spawning season and sampling biasness (commercial compared to wild species) among other factors.
format	Thesis
qualification_level	Master's degree
author	Alshari, Norli Fauzani Mohd Abu Hassan
author_facet	Alshari, Norli Fauzani Mohd Abu Hassan
author_sort	Alshari, Norli Fauzani Mohd Abu Hassan
title	Molecular Identification Of Fish Larvae In Merbok River Through Dna Metabarcoding
title_short	Molecular Identification Of Fish Larvae In Merbok River Through Dna Metabarcoding
title_full	Molecular Identification Of Fish Larvae In Merbok River Through Dna Metabarcoding
title_fullStr	Molecular Identification Of Fish Larvae In Merbok River Through Dna Metabarcoding
title_full_unstemmed	Molecular Identification Of Fish Larvae In Merbok River Through Dna Metabarcoding
title_sort	molecular identification of fish larvae in merbok river through dna metabarcoding
granting_institution	Universiti Sains Malaysia
granting_department	Pusat Pengajian Sains Kajihayat
publishDate	2020
url	http://eprints.usm.my/55143/1/NORLI%20FAUZANI%20BINTI%20MOHD%20ABU%20HASSAN%20ALSHARI%20-%20TESIS%20cut.pdf
_version_	1747822315467440128

Molecular Identification Of Fish Larvae In Merbok River Through Dna Metabarcoding

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