Genome assembly of acropora tenuis from short read sequencing data

Sarah Hanisah Mohd Zaifullizan (2018) Genome assembly of acropora tenuis from short read sequencing data. Masters thesis, Universiti Malaysia Sabah.

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Abstract

Acropora tenuis is staghorn coral that is important globally to marine diversity as it makes up the majority of coral reefs in the world. Though much studies have been done to the species in particular, genomic studies are still lacking. The coral (branching fragment) specimen where DNA was extracted from for sequencing was a direct environmental sample. This in itself presents problems as though morphologically identified as A. tenuis, there is still the possibility of hybridization between other species of Acropora corals as they known to mass spawn and this produces problems such as the hybrid formation of the members of the same genus, as well as their symbionts such as dinoflagellate algae Symbiodinium spp. To address these unknowns, this project aimed to broaden the understanding of this species and to enrich the public genomic data available for future research by assembling a draft of A. tenuisgenome de novofrom reads generated from Illumina HiSeq3000. Quality control and trimming of low quality reads were performed using FastQC and Trimmomatic. Sequence reads that have passed quality control were binned and classified taxonomically against NCBI's GenBank genome database. Sequence reads were binned using the software Kraken, followed by de novo assembly using CLC Genomics Workbench 11.0. The binning results found no sequences belonging to the Symbiodinium spp. The assembled genome size was 340,895,668 bp, which was lower than the expected 400 Mbp genome size. The number of contigs and scaffolds produced from the genome assembly was 347,155. Further downstream analysis is needed to annotate the genome and to screen for genes that can be of commercial value.

Item Type:	Thesis (Masters)
Keyword:	Acropora tenuis, Coral genome, De novo genome assembly, Marine biodiversity, Illumina HiSeq
Subjects:	Q Science > QL Zoology > QL1-991 Zoology > QL360-599.82 Invertebrates
Department:	INSTITUTE > Biotechnology Research Institute (BRI)
Depositing User:	DG MASNIAH AHMAD -
Date Deposited:	13 Jun 2025 14:54
Last Modified:	13 Jun 2025 14:54
URI:	https://eprints.ums.edu.my/id/eprint/44030

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