A chromosome-level assembly of the black tiger shrimp (Penaeus monodon) genome facilitates the identification of novel growth-associated genes

Abstract

The black tiger shrimp (Penaeus monodon) is one of the most prominent farmed crustacean species with an average annual global production of 0.5 million tons in the last decade. To ensure sustainable and profitable production through genetic selective breeding programs, several research groups have attempted to generate a reference genome using short-read sequencing technology. However, the currently available assemblies lack the contiguity and completeness required for accurate genome annotation due to the highly repetitive nature of the genome and technical difficulty in extracting high-quality, high-molecular weight DNA in this species. Here, we report the first chromosome-level whole-genome assembly of P. monodon. The combination of long-read Pacific Biosciences (PacBio) and long-range Chicago and Hi-C technologies enabled a successful assembly of this first high-quality genome sequence. The final assembly covered 2.39 Gb (92.3% of the estimated genome size) and contained 44 pseudomolecules, corresponding to the haploid chromosome number. Repetitive elements occupied a substantial portion of the assembly (62.5%), highest of the figures reported among crustacean species. The availability of this high-quality genome assembly enabled the identification of novel genes associated with rapid growth in the black tiger shrimp through the comparison of hepatopancreas transcriptome of slow-growing and fast-growing shrimps. The results highlighted several gene groups involved in nutrient metabolism pathways and revealed 67 newly identified growth-associated genes. Our high-quality genome assembly provides an invaluable resource for accelerating the development of improved shrimp strain in breeding programs and future studies on gene regulations and comparative genomics.

Comparative Analysis of PacBio and Oxford Nanopore Sequencing Technologies for Transcriptomic Landscape Identification of Penaeus monodon

“…The recently published chromosome-level P. monodon assembly [ 20 ] was used as the reference genome for read alignment using minimap2 [ 28 ]. The alignment rates were 98.8% for the ONT reads and 98.5% for the PacBio reads ( Supplementary Table S3 ), while the average percent identity of the aligned reads to the reference, as calculated by NanoStat [ 22 ], was 90.1% for ONT and 94.5% for PacBio.…”

“…An improved P. monodon genome assembly was released in 2019 [ 19 ], leveraging a hybrid approach using long reads from ONT MinION sequencing and short reads from paired-end Illumina sequencing. Recently, a high-quality chromosome-level P. monodon genome was achieved by our team using a combination of PacBio high-depth sequencing and Illumina sequencing, with the final scaffolding performed using long-range Chicago and Hi-C technologies [ 20 ].…”

Optimization of high molecular weight DNA extraction methods in shrimp for a long-read sequencing platform

“…Full-size DOI: 10.7717/peerj.10340/ fig-3 content, polyphenols and other secondary metabolites which can interfere downstream DNA library preparations (Panova et al, 2016). Some of the genomes of marine organisms such as water flea (Daphnia pulex ) (Ye et al, 2017), Atlantic cod (Gadus morhua) (Star et al, 2016), black tiger shrimp (Penaeus monodon) (Uengwetwanit et al, 2020;Yuan et al, 2018) and Pacific white shrimp (Litopenaeus vannamei) (Zhang et al, 2019) reportedly contain high density of repetitive sequences, which hinder high quality genome sequence assembly. To overcome this challenge, high quality and integrity of the starting DNA must be used to fully exploit the capacity of the long-read sequencing platform.…”

“…With continuing progress of sequencing technology, whole genome assemblies of few marine organisms are now available such as Atlantic salmon (Salmo salar) (Davidson et al, 2010), Atlantic cod (Gadus morhua) (Star et al, 2011), Pacific oyster (Crassostrea gigas) (Zhang et al, 2012), Pacific white shrimp (Litopenaeus vannamei) (Zhang et al, 2019), Black tiger shrimp (Penaeus monodon) (Uengwetwanit et al, 2020) and Rainbow trout (Oncorhynchus mykiss) (Berthelot et al, 2014). Although whole genome sequencing and de novo assembly have become a routine method for functional genomics studies, genome sequencing of non-model organisms with a large proportion of long repetitive sequences such as marine invertebrates remains challenging.…”

Chitin Synthesis and Degradation in Crustaceans: A Genomic View and Application

“…In recent years, the rapid advancement of genomics, transcriptomics, proteomics, and other omics technologies have greatly facilitated molecular biology studies in crustacean. More than a dozen of crustacean genomes have been sequenced, including those of economically relevant decapods, such as the Pacific white shrimp Litopenaeus ( Penaeus ) vannamei [ 5 ], the black tiger shrimp Penaeus monodon [ 6 ], the swimming crab Portunus trituberculatus [ 7 ], and the marbled crayfish Procambarus virginalis [ 8 ], in addition to amphipods (e.g., Parhyale hawaiensis , and Hyalella azteca ) [ 9 , 10 ], cirripeds (e.g., Amphibalanus amphitrite ) [ 11 ], isopods (e.g., Armadillidium vulgare ) [ 12 ], cladocerans (e.g., Daphnia pulex and Daphnia magna ) [ 13 , 14 ] and copepods (e.g., Eurytemora affinis and Tigriopus japonicus ) [ 15 , 16 ], among others. Moreover, a large number of RNA-Seq datasets obtained from crustaceans at different physiological states, environmental conditions, and a variety of chemical treatments can also be obtained in the public database ( Table 1 ).…”