Improved genomic resources for the black tiger prawn (Penaeus monodon)

• Published in: Marine genomics Vol. 52; p. 100751
• Main Authors: Van Quyen, Dong, Gan, Han Ming, Lee, Yin Peng, Nguyen, Dinh Duy, Nguyen, Thi Hoa, Tran, Xuan Thach, Nguyen, Van Sang, Khang, Dinh Duy, Austin, Christopher M.
• Format: Journal Article
• Language: English
• Published: Netherlands Elsevier B.V 01-08-2020
• Subjects: Aquaculture; Genome; Illumina; Nanopore; Tiger prawn; Nanopore; Genome; Illumina; Tiger prawn; Aquaculture
• ISSN: 1874-7787; 1876-7478
• DOI: 10.1016/j.margen.2020.100751

World production of farmed crustaceans was 7.8 million tons in 2016. While only making up approximately 10% of world aquaculture production, crustaceans are generally high-value species and can earn significant export income for producing countries. Viet Nam is a major seafood producing country earning USD 7.3 billion in 2016 in export income with shrimp as a major commodity. However, there is a general lack of genomic resources available for shrimp species, which is challenging to obtain due to the need to deal with large repetitive genomes, which characterize many decapod crustaceans. The first tiger prawn (P. monodon) genome assembly was assembled in 2016 using the standard Illumina PCR-based pair-end reads and a computationally-efficient but relatively suboptimal assembler, SOAPdenovo v2. As a result, the current P. monodon draft genome is highly fragmented (> 2 million scaffolds with N50 length of <1000 bp), exhibiting only moderate genome completeness (< 35% BUSCO complete single-copy genes). We sought to improve upon the recently published P. monodon genome assembly and completeness by generating Illumina PCR-free pair-end sequencing reads to eliminate genomic gaps associated with PCR-bias and performing de novo assembly using the updated MaSurCA de novo assembler. Furthermore, we scaffolded the assembly with low coverage Nanopore long reads and several recently published deep Illumina transcriptome paired-end sequencing data, producing a final genome assembly of 1.6 Gbp (1,211,364 scaffolds; N50 length of 1982 bp) with an Arthropod BUSCO completeness of 96.8%. Compared to the previously published P. monodon genome assembly from China (NCBI Accession Code: NIUS01), this represents an almost 20% increase in the overall BUSCO genome completeness that now consists of more than 90% of Arthropod BUSCO single-copy genes. The revised P. monodon genome assembly (NCBI Accession Code: VIGR01) will be a valuable resource to support ongoing functional genomics and molecular-based breeding studies in Vietnam.
•We present a revised black tiger prawn genome assembly•The first Nanopore long read dataset for the black tiger prawn was generated•Scaffolding of the initial genome assembly with transcriptome data improved genome completeness•PCR introduced strong read depth bias in low-GC regions