HYBRID DE NOVO ASSEMBLY AND ANONATION ANALYSIS OF SCALLOPED SPINY LOBSTER (PANULIRUS HOMARUS) DRAFT SEQUENCE GENOME

• Main Author: Salsabila Hendratno, Putri
• Format: Final Project
• Language: Indonesia
• Subjects: Ilmu hayati ; Biologi
• Online Access: https://digilib.itb.ac.id/gdl/view/82238
• Institution: Institut Teknologi Bandung

Lobster has economic importance due to its high price and demand in the international market which always increases from year to year. Even though Indonesia has high potential for lobster cultivation, disease problems in collectively cultivated lobsters cause large losses in the lobster production sector every year. Whole genome sequencing can be useful for understanding the basic genetic characteristics of lobsters. There is limited information on genomic research for Indonesian lobster species, therefore, this research aims to assemble the genome of the sand lobster (Panulirus homarus) which is expected to be able to support the basic research and cultivation sector of sand lobsters in Indonesia in the near future. In this research, an assembly experiment was carried out by combining short read sequencing and long-read sequencing technology or commonly called hybrid read sequencing to produce a more comprehensive and complete genome. Long read sequencing was carried out using Oxford Nanopore with 20GB and 10x coverage, while short read sequencing used Illumina NextSeq 500 with 65GB and 20x coverage. The assembly flow in this study consists of quality control and filtering processes, genome profile estimation, and genome assembly using the hybrid scaffolding method. After obtaining the genome results, annotation analysis was carried out on the genome results and the sand lobster genome reference NCBI GCA_032361405.1. Assembly data processing uses CyVerse computing resources and the Geneious program is used for the annotation process of the draft genome sequence. The estimated genome size of Panulirus homarus was 2.21 Gbp. After mapping, the genome mapping precision rate was 95.6%. The results of the sand lobster draft genome assembly using the short-reads, long-reads, and hybrid-reads methods have N50 sizes of 1,728 bp, 9,436 bp, and 11,485 bp respectively with a completeness level of the ortholog genome for each method of 28.8%. 44.8%, and 55.4%. The annotation results from the draft genome show a total of 705 annotations, while the number of annotations for the NCBI reference genome GCA_032361405.1 is a total of 354 annotations. The annotations consist of AttB, AttL, AttP, AttR, CDS, D-Loop, Gene, rRNA, and tRNa.