Capture fisheries and aquaculture account for more than 15% of the animal protein consumed by humans. Aquaculture is an agricultural field that has developed rapidly in recent years and has important economic and cultural significance. However, the long-term sustainability of fisheries and aquaculture faces many challenges, including overfishing, climate change, germplasm degradation, and disease. Developments in sequencing technologies and advances in genomics can help address some of these challenges and benefit sustainable fisheries and aquaculture. The draft whole-genome sequence provides better insights for improving yields and quality in various agricultural sectors. Whole genome sequencing has been done for oysters, shrimp, tilapia, rainbow trout, catfish, Atlantic salmon, and striped bass.

CD Genomics is a leading service provider for agricultural genomics research, offering reliable aquaculture genome sequencing services to support research and breeding efforts in the field of aquaculture genomics for clients worldwide. Our services help improve aquaculture production efficiency, sustainability, product quality, and profitability to support the commercial sector and benefit consumers.

Our aquaculture genome sequencing service

The genome is the complete collection of all functional and non-functional DNA sequences in an organism, thus providing insights into the uniqueness of species in aquaculture and/or fisheries. CD Genomics offers comprehensive and customizable genome sequencing services for aquaculture. We utilize advanced next-generation sequencing and long-read sequencing technology platforms, as well as bioinformatics tools to perform whole genome sequencing of major fish species in aquaculture and fisheries, providing reliable data to support genomic and other studies on fish genome structure, organization, and function.

Our services cover all stages of the sequencing process, from library preparation to data analysis, ensuring high-quality and accurate results. We offer several whole genome sequencing programs for aquaculture species, including but not limited to:

What we offer

Our sequencing data supports aquaculture genomics studies for dozens of fish and shellfish species, including genetic linkage mapping, physical mapping, microarrays, single nucleotide polymorphism (SNP) arrays, transcriptome databases, and development of genomic reference sequences at all stages.

• SNP genotyping

SNPs are key genetic markers for phenotypic variation in aquaculture species. Our advanced SNP genotyping service identifies and characterizes SNPs associated with desired traits, providing valuable insights for selective breeding programs.

• Genome-wide assembly and annotation

We provide comprehensive genome assembly and annotation services to ensure accurate reconstruction and annotation of aquaculture genomes. By utilizing sophisticated bioinformatics tools and processes, we carefully analyze sequencing data to identify genes and annotate their functional elements.

• Linkage mapping and physical mapping

We can construct genetic linkage maps for most major aquaculture species to facilitate genetic enhancement in aquaculture. We ensure that most genomic sequences are anchored to aquaculture linkage maps.

• Transcriptome characterization

A vast resource of expressed sequence tags (ESTs) exists for major aquaculture species. We use RNA-seq to more efficiently characterize differentially expressed genes in response to disease or stress in several important aquaculture species and to identify markers associated with growth, heat stress, disease, and tissue specificity in aquaculture species.

• Non-coding transcripts, genomic expression regulation, and epigenomics analysis

Based on high-quality reference genome sequences, we work to identify microRNAs and long non-coding RNAs in aquaculture species. In addition, we can perform genome-scale analysis of epigenetic regulation in oysters, Atlantic salmon, rainbow trout, tilapia, yellow perch, and bluegill.

• Performance traits, phenotypic variation, and QTL analysis

Many aquaculture phenotypes are inherently complex and quantitative. We provide QTL mapping and GWAS analysis for aquaculture species to correlate genetic and phenotypic variation. We aim to help you uncover the genetic basis of aquaculture performance and production traits and use this information in genetic enhancement programs.

Applications of aquaculture genome sequencing

• Selective breeding for performance

Sequencing the aquaculture genome enables the identification of genes associated with desired production traits such as growth rate, feed conversion efficiency and stress tolerance. By utilizing gene-assisted selection, breeders can make informed decisions to selectively breed individuals carrying superior genetic variation.

• Disease resistance and health management

Sequencing the aquaculture genome helps identify genes and molecular pathways involved in immune responses and disease resistance. This knowledge can help develop targeted approaches, such as selective breeding to improve disease resistance or developing vaccines against specific pathogens.

• Conservation and sustainable fisheries

By analyzing the genetic diversity and population structure of wild species, we can gain insight into their evolutionary history and inform conservation efforts. In addition, genome sequencing can help identify genes associated with population adaptation and resilience, which is critical for sustainably managing fisheries and mitigating the effects of environmental change.

Case study of aquaculture genome sequencing

There are roughly 4,100 species in the order of Siluriformes (catfish), which comprise 12% of all fish species and 6.3% of all vertebrate species. Catfish are valuable for comparative biological studies because their basal phylogenetic position places them closer to a common fish ancestor than most bony fish (infraclass Teleostei). Catfish are also valuable worldwide as an important source of dietary protein. Channel catfish (Ictalurus punctatus, family Ictaluridae) is a highly adaptive species as reflected by its broad geographic distribution, tolerance of low water quality and resistance against various infectious agents despite the lack of scales.

Fig. 1. Characteristics of duplicated genes in the channel catfish genome. (Liu et al., 2016)

• Researchers used Illumina sequencing to sequence and assemble a high-quality reference genome sequence for the channel catfish, a major aquaculture species in the United States.
• The reference genome sequence was validated by a genetic map of 54,000 SNPs and annotated with 26,661 predicted protein-coding genes.
• Through comparative analysis of the genomes and transcriptomes of scaly and scaleless fish, as well as scale regeneration experiments, researchers address the genomic basis for the evolutionary loss of scales, the catfish's most striking physical feature, and provide insights into the lack of secreted calcium-binding phosphate Evidence for the evolutionary loss of catfish scales.
• The channel catfish reference genome sequence, along with two other scaly catfish genome sequences and transcriptomes, provide important resources for evolutionary and biological studies.

CD Genomics has complete genomes sequenced for dozens of important aquaculture and fisheries species for analysis, comparison, and knowledge discovery. By leveraging the knowledge gained from genome sequencing, aquaculture stakeholders can make informed decisions to optimize breeding programs, improve disease resistance, and promote sustainable fisheries. If you are interested, please feel free to contact us.

Reference

1. Liu, Zhanjiang, et al. The channel catfish genome sequence provides insights into the evolution of scale formation in teleosts. Nature communications. 7.1 (2016): 11757.