DETECTION OF VARIATION IN THE COMPLETE GENOME DRAFT OF SAND LOBSTER (PANULIRUS HOMARUS, LINNAEUS 1758) THROUGH HYBRID DE NOVO ASSEMBLY

• Main Author: Halim, Junius
• Format: Final Project
• Language: Indonesia
• Online Access: https://digilib.itb.ac.id/gdl/view/79032
• Institution: Institut Teknologi Bandung

Indonesia is one of the longest coastlines country in the world, harboring a high potential of marine commodities, one of which is lobster, a marine commodity with high economic value. However, despite an international market demand of 200,000 tons per year, Indonesia was only able to export 2,200 tons in 2020. The sand lobster (Panulirus homarus) is one of the most common lobster species in Indonesian waters, yet genetic research at the molecular level has not been conducted to enhance its production. De novo assembly is a method used to generate complete genome drafts of organisms without reference, utilizing short reads, long reads, or hybrid-reads sequencing data. Genome assembly was performed using the de Bruijn graph concept and k-mer theory. Genetic variation represents the phenomenon of changes in an organism's genetic material, which can be caused by events such as substitutions, deletions, insertions, transitions, transversions, and other genetic material alterations.Samples of sand lobster tissue were processed using Illumina NextSeq 500 with an input of 65 Gb for generating short reads sequences and Oxford Nanopore Technology (ONT) with an input of 20.2 Gb for generating long reads sequences. The genome assembly process mainly consists of quality control and filtering, genome profile estimation, genome assembly with short-reads, and hybrid scaffolding. Subsequently, detected types of variations in the samples were compared to the reference genome of related species. Computational and data processing resources were provided by CyVerse (www.cyverse.org). Short reads sequencing data were filtered to address overexpression sequence content and adapters problems, while long reads sequencing data were filtered to improve the average quality and increase the average size along with N50 of sequences. The estimated size of the sand lobster (Panulirus homarus) genome is about 2.21 Gbp with a high level of heterozygosity. The mapping accuracy between the short-reads and long-reads assembly results reached up to 95.6%. The draft genome assembly of the sand lobster (Panulirus homarus) using short-reads, long-reads, and hybrid-reads approaches had N50 sizes of 1,728; 9,436; and 11,485 bp, respectively, with genome completeness levels of 28.8; 44.8; and 55.4% for orthologous genes. Detected variations in the draft genome of the sand lobster (Panulirus homarus) using the hybrid-reads approach included Multiple-Nucleotide Polymorphism (MNP) variations, insertions, and combined variations.