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Omics Strategies in Aquatic Animal Research

Aquatic animals encompass fish, mollusks, crustaceans, benthic invertebrates, and marine vertebrates. They are characterized by remarkable species diversity, unique genomic features, and strong phenotypic plasticity in response to environmental changes. As powerful analytical tools, multi-omics technologies have been widely applied to decode the molecular mechanisms underlying aquaculture breeding, immune adaptation, developmental regulation, toxicological responses, and biological evolution in aquatic animals.

1. Current Status of Aquatic Animal Omics Resources

Aquatic animals can be broadly categorized into five major taxonomic groups with unevenly distributed omics resources: fish, including commercial cultured species and deep-sea fish; mollusks, including bivalves, gastropods, and cephalopods; crustaceans, such as shrimps and crabs; other benthic invertebrates, including corals, sea cucumbers, and sea urchins; and higher marine vertebrates, such as cetaceans and sea turtles.

Public databases such as iFish, FishSED, MolluscDB, and CrustyBase generally cover six core omics research dimensions: genomics, transcriptomics, epigenomics, single-cell/spatial omics, proteomics, and metabolomics. Nevertheless, current aquatic omics resources still face two key limitations.

First, species coverage is extremely unbalanced. Fish omics resources are far more abundant than those available for mollusks, crustaceans, and other marine invertebrates. For instance, the Fish10K Project has yielded 464 high-quality reference genomes in its first phase, whereas most marine invertebrate species still have only dozens of genomic records available.

Second, omics data remain insufficient, and most existing analytical platforms only support single-layer omics analysis, lacking integrated tools for cross-omics comparison and collaborative research.

We systematically sorted and analyzed relevant publications from PubMed using the search keyword combination “Fish + diverse omics” and summarized three developmental stages of aquatic omics research. Genomics and transcriptomics have formed mature technical systems and have served as fundamental research tools since the 2000s. Proteomics and metabolomics are undergoing gradual application expansion and are well suited for functional verification of aquatic phenotypic traits. Single-cell and spatial transcriptomics have emerged as cutting-edge research fields with rapid publication growth after 2020, although their development is still restricted by immature sample pretreatment systems.

In general, omics dataset reserves for most aquatic animal species remain insufficient, and targeted efforts are still needed to further advance aquatic omics research.

2. Core Research Fields of Aquatic Animal Omics

Multi-omics technologies support multiple mainstream research directions applicable to aquatic animal taxa, covering the full research chain from germplasm innovation to ecological adaptation.

• Genetic germplasm breeding: Identifies loci associated with economically important traits, develops functional molecular markers, and provides theoretical guidance for selective breeding of high-yield and stress-resistant aquatic varieties.
• Immunity and environmental stress adaptation: Reveals the molecular regulatory mechanisms by which aquatic animals respond to biotic stress, such as pathogen infection, and abiotic stress, such as salinity fluctuation, temperature change, and hypoxia.
• Nutrition and flesh quality regulation: Clarifies the core pathways regulating flavor formation, feed utilization efficiency, and individual growth of aquatic products.
• Developmental biology: Uncovers the molecular networks controlling embryogenesis, organ differentiation, and larval metamorphosis in aquatic animals.
• Aquatic environmental toxicology: Analyzes the toxic effects of heavy metals, microplastics, and other pollutants on aquatic organisms and assesses potential marine ecological risks.
• Evolution and ecological adaptation: Decodes evolutionary patterns and unique adaptive strategies that enable aquatic animals to survive in extreme marine and freshwater habitats.

3. Key Technical Barriers in Aquatic Omics Experiments

Aquatic omics research faces universal technical bottlenecks, mainly arising from complex sample characteristics and the intrinsic genomic complexity of aquatic species. These factors bring major challenges to sample pretreatment and bioinformatics analysis.

Aquatic animal tissues contain large amounts of interfering substances, such as high-concentration salts, polysaccharides, polyphenols, pigments, and proteins, which can seriously affect the extraction of high-purity nucleic acids and proteins. In addition, tissue-colonized symbiotic microorganisms, together with severe DNA/RNA degradation and contamination in deep-sea, rare, or tiny species, can further compromise sample quality. Meanwhile, small-sized aquatic individuals often cannot provide sufficient biological material for long-read sequencing and single-cell sequencing experiments.

At the genomic level, many aquatic animals exhibit high heterozygosity, extensive polyploidy, massive repetitive sequences, and ultra-large genome sizes. These characteristics greatly increase the difficulty of genome assembly, sequence alignment, and variant detection. Notably, most mollusk and crustacean species still lack high-quality chromosome-level reference genomes, which has become a major bottleneck restricting downstream omics analyses.

4. BMKGENE Customized Omics Solutions for Aquatic Animals

Chromosome-Level Whole Genome Assembly

High-quality reference genomes are the foundational prerequisite for multi-omics research. BMKGENE has established a mature assembly pipeline and targeted sequencing strategy for aquatic species, integrating 50× NGS short reads for genome survey, 30× PacBio HiFi long reads for preliminary genome assembly, 100× Hi-C data for chromosome-level scaffolding, and 12G RNA-seq data for accurate gene annotation.

To adapt to the unique properties of aquatic muscle tissues, BMKGENE has optimized SDS-based high-molecular-weight (HMW) DNA extraction methods and upgraded Hi-C crosslinking protocols. We also recommend reserving backup samples to optimize experimental parameters and ensure successful assembly when initial experiments fail.

Population Genomics: WGS vs. SLAF Sequencing

Two mature technical schemes are available for aquatic population genomics research to meet different research scenarios. Whole-genome sequencing (WGS) is suitable for species with small genomes and complete reference genome resources, enabling high-resolution screening of genomic variants.

Developed independently by BMKGENE, Specific-Locus Amplified Fragment (SLAF) sequencing is a cost-effective reduced-representation sequencing strategy for species with large genomes or no reference genomes. Relying on independent clustering algorithms, this technology is widely applied in genetic map construction, GWAS analysis, and population evolutionary research in aquatic animals.

Transcriptomics

Transcriptomics is an indispensable core tool for aquatic biological research. It dynamically captures global gene expression changes, revealing the physiological regulatory mechanisms of aquatic animals under environmental stress, pathogen invasion, and different nutritional conditions, while clarifying key molecular pathways related to immune response, individual development, and economic trait formation. Meanwhile, transcriptomic data provide critical support for gene structure annotation and cross-omics joint analysis.

Based on extensive practical experience in aquatic omics projects, BMKGENE provides comprehensive transcriptomic solutions covering short-read NGS and long-read third-generation sequencing platforms. We also offer transcriptomic solutions for different RNA types, including mRNA, lncRNA, circRNA, and small RNA, to meet diverse research needs.

Single-Cell and Spatial Transcriptomics

Compared with traditional bulk RNA sequencing, single-cell RNA-seq enables gene expression detection at single-cell resolution, identifying cellular heterogeneity that may be masked in mixed tissue samples. However, this technology still has clear limitations in aquatic research, including the lack of species-specific cell markers, osmotic pressure imbalance during cell suspension preparation, and low median gene expression levels in muscle tissue. Single-nucleus RNA-seq serves as an effective alternative and is especially suitable for sequencing frozen aquatic tissue samples.

Spatial transcriptomics provides a higher experimental success rate for aquatic tissues and enables in situ visualization of gene expression in unique aquatic organs, such as gills and hepatopancreas. BMKGENE’s independently developed spatial transcriptomics platform, BMKMANU S3000, has accumulated extensive practical experience in aquatic research. We have also developed patented embedding protocols for high-moisture shellfish samples, effectively addressing the problem of tissue slice fragmentation.

Proteomics and Metabolomics Mass Spectrometry

For aquatic proteomics detection, we recommend Astral DIA mass spectrometry, which delivers broad peptide coverage and stable quantitative results. For metabolomics research, UPLC-QTOF-based non-targeted metabolomics is used to profile global metabolic changes associated with aquatic nutrition regulation, disease occurrence, and pollutant exposure.

Considering the high natural variability of aquatic metabolites, we stipulate no fewer than three biological replicates for differential analysis, while six replicates are recommended to ensure result robustness. Wide-targeted metabolomics can be adopted as a supplementary approach to achieve precise quantification of specific metabolic pathways.

Multi-Omics Integration: A Dominant Research Paradigm

Each omics layer has distinct functional positioning in biological research: genomics provides the basic genomic reference framework of species; transcriptomics acts as the intermediate regulatory link connecting genotype and phenotype; proteomics serves as the direct functional executor of biological traits; and metabolomics reflects the terminal physiological phenotypic characteristics of organisms.

Single-omics technologies can only capture fragmented molecular information, whereas multi-omics integration systematically correlates genomic variation, transcriptional regulation, protein function, and metabolic phenotypes, enabling multi-dimensional interpretation of biological mechanisms.

Common multi-omics integration strategies include transcriptome–proteome correlation analysis for post-transcriptional mechanism exploration, transcriptome–metabolome joint pathway analysis, proteome–metabolome effector molecule screening, microbiota–metabolite–host interaction analysis, and epigenome–transcriptome regulatory axis mining.

The standardized integration workflow includes sample matching, independent single-omics analysis, cross-dimensional correlation mining, and core hub molecule identification. Strict consistency of sample sources and unified numbers of biological replicates are essential to reduce analytical bias.

5. Summary

Integrated multi-omics technologies, including genomics, transcriptomics, proteomics, and metabolomics, provide multi-dimensional molecular evidence for analyzing the physiological regulation and environmental adaptation mechanisms of aquatic animals. However, the unique complexity of aquatic samples and the scarcity of public omics resources remain major bottlenecks restricting in-depth research. Targeted aquatic-specific experimental protocols are urgently needed to enrich molecular datasets and improve analytical accuracy.

With extensive practical experience in aquatic omics projects, BMKGENE has continuously optimized and iterated sample pretreatment and sequencing analysis schemes for diverse aquatic species. Given the significant interspecific differences in aquatic tissue characteristics, it remains challenging to achieve optimal experimental results in every project. Nevertheless, by leveraging practical experience accumulated from numerous aquatic omics projects, BMKGENE will continue to refine customized technical pipelines to deliver high-quality, usable multi-omics data support for aquatic animal research.