Abstract
Single-cell sequencing technologies have led to a revolution in our knowledge of the diversity of cell types, connections between biological levels of organization, and relationships between genotype and phenotype. These advances have mainly come from using model organisms; however, using single-cell sequencing in non-model organisms could enable investigations of questions inaccessible with typical model organisms. This primer describes a general workflow for single-cell sequencing studies and considerations for using non-model organisms (limited to multicellular animals). Importantly, single-cell sequencing, when further applied in non-model organisms, will allow for a deeper understanding of the mechanisms between genotype and phenotype and the basis for biological variation.
Highlights
There have been a few examples where single-cell sequencing (scSeq) has already been used in non-model organisms to investigate questions that are inaccessible with typical model organisms
The fast pace of technological advancement in the field, requirement of organismspecific technical knowledge, and cost are all barriers to applying scSeq to non-model organisms
The first challenge for applications of scSeq in non-model organisms is its recency; since the first study published in 2009 [2], the technology has evolved rapidly, and a slower adoption in non-model organisms is to be expected. Another barrier to scSeq in non-model organisms is the need for organism-specific technical knowledge for sample collection and cell isolation protocols
Summary
Cells are the fundamental units of life, varying in form and function within and between individuals, populations, and species. As in most of biology, our knowledge of humans and model organisms (e.g., Drosophila) far exceeds that of non-model or wild species, which remains a barrier to resolving how organisms function in nature At present, this remains the case for scSeq; scSeq is a promising and proven method, its use has been limited and its potential applications in non-model systems have yet to be realized. Organism-specific protocols for mechanical and enzymatic digestion of intra- and extra-cellular structures are often required [3] Another barrier to scSeq is cost; scSeq is significantly cheaper since it became commercially available, it can be prohibitively expensive compared to bulk sequencing (approximately a 10-fold difference in early 2022). When applied in non-model organisms, scSeq will allow for a deeper understanding of the relationship between genotype and phenotype and the basis for biological variation
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