Genome sequencing and analysis of acropora gemmifera and pleuractics granulosa from Sabah costal waters

Coral are marine invertebrates classified under the Anthozoa class of the Cnidaria phylum. In this study, Acropora gemmifera and Pleuractis granulosa from Sabah were morphologically identified and found to have green fluorescence (A. gemmifera and P. granulosa) and red fluorescence (P. granulosa) wh...

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Main Author:	Lee, Dexter Jiunn Herng
Format:	Thesis
Language:	English English
Published:	2018
Subjects:	QL360-599.82 Invertebrates
Online Access:	https://eprints.ums.edu.my/id/eprint/42100/1/24%20PAGES.pdf https://eprints.ums.edu.my/id/eprint/42100/2/FULLTEXT.pdf
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spelling	my-ums-ep.421002024-12-16T04:05:02Z Genome sequencing and analysis of acropora gemmifera and pleuractics granulosa from Sabah costal waters 2018 Lee, Dexter Jiunn Herng QL360-599.82 Invertebrates Coral are marine invertebrates classified under the Anthozoa class of the Cnidaria phylum. In this study, Acropora gemmifera and Pleuractis granulosa from Sabah were morphologically identified and found to have green fluorescence (A. gemmifera and P. granulosa) and red fluorescence (P. granulosa) when exposed to blue and green wavelength LED lights respectively. The DNA for both A. gemmifera and P. granulosa, as well as the mRNA from A. gemmifera were extracted and sequenced using Illumina (Solexa) sequencers. The reads generated from the genome sequencing were quality filtered, binned and de novo assembled, resulting in assembled genome sizes of 686.45 Mbp (A. gemmifera) and 1.23 Gbp (P. granulosa) with mean coverages in excess of 80X. The assembled genome sizes may be overinflated due to the possible inclusion of contigs from other contaminating organisms, redundant contigs and misassemblies. Nucleotide variant calling and ploidy estimation suggest that both A. gemmifera and P. granulosa are diploid organisms. The mitochondrial genome assemblies for both A. gemmifera and P. granulosa resulted in two mitochondrial genomes with a size of approximately 18 kbp per genome (mean coverage in excess of 1,300X), with BLASTN alignment suggesting a high degree of similarity between both mitochondrial genomes with other mitochondrial genomes from the Acropora genus. Unsupervised rRNA predictions using the assembled genomes and their subsequent annotation suggests that the assembled genomes may contain contigs from non-coral organisms. A total of 131,730 mRNAs were predicted and assembled (reference-guided assembly) for A. gemmifera, while a total of 152,504 mRNAs were predicted for P. granulosa with the aid of mRNA sequencing data from Lobactis scutaria. These transcripts, as well as the pathways from the KEGG pathway analysis, will serve as a starting point for further investigations and possible commercialisation, though these transcripts and pathways would need to be experimentally validated beforehand. 2018 Thesis https://eprints.ums.edu.my/id/eprint/42100/ https://eprints.ums.edu.my/id/eprint/42100/1/24%20PAGES.pdf text en public https://eprints.ums.edu.my/id/eprint/42100/2/FULLTEXT.pdf text en validuser masters Universiti Malaysia Sabah Institut Penyelidikan Bioteknologi
institution	Universiti Malaysia Sabah
collection	UMS Institutional Repository
language	English English
topic	QL360-599.82 Invertebrates
spellingShingle	QL360-599.82 Invertebrates Lee, Dexter Jiunn Herng Genome sequencing and analysis of acropora gemmifera and pleuractics granulosa from Sabah costal waters
description	Coral are marine invertebrates classified under the Anthozoa class of the Cnidaria phylum. In this study, Acropora gemmifera and Pleuractis granulosa from Sabah were morphologically identified and found to have green fluorescence (A. gemmifera and P. granulosa) and red fluorescence (P. granulosa) when exposed to blue and green wavelength LED lights respectively. The DNA for both A. gemmifera and P. granulosa, as well as the mRNA from A. gemmifera were extracted and sequenced using Illumina (Solexa) sequencers. The reads generated from the genome sequencing were quality filtered, binned and de novo assembled, resulting in assembled genome sizes of 686.45 Mbp (A. gemmifera) and 1.23 Gbp (P. granulosa) with mean coverages in excess of 80X. The assembled genome sizes may be overinflated due to the possible inclusion of contigs from other contaminating organisms, redundant contigs and misassemblies. Nucleotide variant calling and ploidy estimation suggest that both A. gemmifera and P. granulosa are diploid organisms. The mitochondrial genome assemblies for both A. gemmifera and P. granulosa resulted in two mitochondrial genomes with a size of approximately 18 kbp per genome (mean coverage in excess of 1,300X), with BLASTN alignment suggesting a high degree of similarity between both mitochondrial genomes with other mitochondrial genomes from the Acropora genus. Unsupervised rRNA predictions using the assembled genomes and their subsequent annotation suggests that the assembled genomes may contain contigs from non-coral organisms. A total of 131,730 mRNAs were predicted and assembled (reference-guided assembly) for A. gemmifera, while a total of 152,504 mRNAs were predicted for P. granulosa with the aid of mRNA sequencing data from Lobactis scutaria. These transcripts, as well as the pathways from the KEGG pathway analysis, will serve as a starting point for further investigations and possible commercialisation, though these transcripts and pathways would need to be experimentally validated beforehand.
format	Thesis
qualification_level	Master's degree
author	Lee, Dexter Jiunn Herng
author_facet	Lee, Dexter Jiunn Herng
author_sort	Lee, Dexter Jiunn Herng
title	Genome sequencing and analysis of acropora gemmifera and pleuractics granulosa from Sabah costal waters
title_short	Genome sequencing and analysis of acropora gemmifera and pleuractics granulosa from Sabah costal waters
title_full	Genome sequencing and analysis of acropora gemmifera and pleuractics granulosa from Sabah costal waters
title_fullStr	Genome sequencing and analysis of acropora gemmifera and pleuractics granulosa from Sabah costal waters
title_full_unstemmed	Genome sequencing and analysis of acropora gemmifera and pleuractics granulosa from Sabah costal waters
title_sort	genome sequencing and analysis of acropora gemmifera and pleuractics granulosa from sabah costal waters
granting_institution	Universiti Malaysia Sabah
granting_department	Institut Penyelidikan Bioteknologi
publishDate	2018
url	https://eprints.ums.edu.my/id/eprint/42100/1/24%20PAGES.pdf https://eprints.ums.edu.my/id/eprint/42100/2/FULLTEXT.pdf
_version_	1818611446297133056

Genome sequencing and analysis of acropora gemmifera and pleuractics granulosa from Sabah costal waters

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