Related Experiment Video
Updated: Dec 29, 2025
The Barnacle Balanus improvisus as a Marine Model - Culturing and Gene Expression
Published on: August 8, 2018
Improved genomic resources for the black tiger prawn (Penaeus monodon)
Dong Van Quyen1, Han Ming Gan2, Yin Peng Lee2
1Laboratory of Molecular Microbiology, Institute of Biotechnology, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet, Cau Giay, Hanoi, Viet Nam; University of Science and Technology of Hanoi, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet, Cau Giay, Hanoi, Viet Nam.
This study significantly improved the tiger prawn genome assembly using advanced sequencing and assembly methods. The enhanced genome resource will advance functional genomics and breeding programs for this valuable aquaculture species.
Area of Science:
- Aquaculture Genomics
- Marine Biology
- Bioinformatics
Background:
- Farmed crustaceans, particularly shrimp, are high-value aquaculture species crucial for export income, with tiger prawn (Penaeus monodon) being a major commodity.
- Existing genomic resources for shrimp are limited, with the current P. monodon genome assembly being highly fragmented and incomplete (<35% BUSCO completeness).
- Challenges in crustacean genomics include large, repetitive genomes and limitations of standard sequencing and assembly methods.
Purpose of the Study:
- To improve the genome assembly and completeness of the tiger prawn (Penaeus monodon).
- To generate a more robust genomic resource for supporting functional genomics and molecular breeding studies in Vietnam.
- To overcome limitations of previous assemblies by employing PCR-free sequencing and advanced assembly algorithms.
Main Methods:
- Generated Illumina PCR-free pair-end sequencing reads to minimize PCR bias and improve gap filling.
- Performed de novo assembly using the MaSuRCA assembler.
- Scaffolded the assembly with Nanopore long reads and existing transcriptome data.
Main Results:
- Produced a significantly improved P. monodon genome assembly of 1.6 Gbp with 1,211,364 scaffolds and an N50 length of 1982 bp.
- Achieved high BUSCO (Biopython Orthologous Universal Single-Copy Orthologs) completeness of 96.8% for Arthropoda, representing a ~20% increase over previous assemblies.
- The revised genome assembly (NCBI Accession Code: VIGR01) demonstrates over 90% completeness of Arthropod BUSCO single-copy genes.
Conclusions:
- The enhanced tiger prawn genome assembly provides a valuable and significantly more complete genomic resource.
- This improved resource will facilitate advanced functional genomics research and molecular-based breeding strategies for Penaeus monodon.
- The study highlights the effectiveness of combining PCR-free sequencing, advanced assemblers, and long-read data for improving complex genomes.
