Single cell genomics as a transformative approach for aquaculture research and innovation

Abstract

Single cell genomics encompasses a suite of rapidly maturing technologies that measure the molecular profiles of individual cells within target samples. These approaches provide a large up‐step in biological information compared to long‐established ‘bulk’ methods that profile the average molecular profiles of all cells in a sample, and have led to transformative advances in understanding of cellular biology, particularly in humans and model organisms. The application of single cell genomics is fast expanding to non‐model taxa, including aquaculture species, where numerous research applications are underway with many more envisaged. In this review, we highlight the potential transformative applications of single cell genomics in aquaculture research, considering barriers and potential solutions to the broad uptake of these technologies. Focusing on single cell transcriptomics, we outline considerations for experimental design, including the essential requirement to obtain high quality cells/nuclei for sequencing in ectothermic aquatic species. We further outline data analysis and bioinformatics considerations, tailored to studies with the under‐characterized genomes of aquaculture species, where our knowledge of cellular heterogeneity and cell marker genes is immature. Overall, this review offers a useful source of knowledge for researchers aiming to apply single cell genomics to address biological challenges faced by the global aquaculture sector though an improved understanding of cell biology.

Characterisation of mesenchymal stromal cells in the skin of Atlantic salmon

“…The advent of single-cell technologies, such as single-cell RNA sequencing (scRNA-seq), has revolutionized our ability to study individual cells. While the extraction of individual cells can be challenging in certain tissues, such as the skin and fins (11), leading to biases in cell- type composition, this can be addressed through single-nuclei RNA sequencing (snRNA- seq), allowing the dissociation of nuclei from frozen tissue without losing cellular diversity (12,13). While single-cell/nuclear technologies reveal the transcriptome of individual cells, the spatial location of the cells is lost during dissociation.…”

Genetics and Genomics of Infectious Diseases in Key Aquaculture Species

“…Genetics and genomics hold promise for providing sustainable solutions through the development of disease-resistant strains [12,13]. Specifically, quantitative genetic theory [14] provides the framework for systematically improving disease resistance in host populations, both through selective breeding and, more recently, through the integration of genomic data [15,16]. This approach has been successfully applied in various fields, including agriculture and animal breeding, to enhance disease resilience in animal and plant populations [17].…”

A versatile nuclei extraction protocol for single nucleus sequencing in non-model species–Optimization in various Atlantic salmon tissues

“…Extensive work has been performed in mammals to develop a toolbox of protocols for nuclei extraction in a variety of tissues [3][4][5]. A review of the available protocols, including consideration of their performance in non-model species, concluded that mincing the tissue in salt tween (TST) represents the most effective method for nuclear isolation from frozen tissue in terms of the diversity of cell types captured and reducing background noise [7].…”