A Primer for Single-Cell Sequencing in Non-Model Organisms

Alfieri, James M.; Wang, Guosong; Jonika, Michelle M.; Gill, C. A.; Blackmon, Heath; Athrey, Giridhar

doi:10.3390/genes13020380

Cited by 19 publications

(18 citation statements)

References 70 publications

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“…Recent advances in single-cell RNA sequencing (scRNA-seq) have had significant effects on the study of complex tissues, leading to the discovery of novel cell types, cell states, and biomarkers [Stuart and Satija, 2019;Luecken and Theis, 2019;Alfieri et al, 2022;Zeng, 2022]. The scRNA-seq technology has opened up a plethora of opportunities to perform novel studies using new and classic model animals, including chickens (Gallus gallus) [Yamagata, 2022] and other birds [Chen et al, 2021;Colquitt et al, 2021].…”

Section: The Current State Of the Chicken Cell Atlasmentioning

confidence: 99%

Fourth Report on Chicken Genes and Chromosomes 2022

Smith¹,

Alfieri²,

Anthony³

et al. 2022

Cytogenet Genome Res

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Section: The Current State Of the Chicken Cell Atlasmentioning

confidence: 99%

Fourth Report on Chicken Genes and Chromosomes 2022

Smith¹,

Alfieri²,

Anthony³

et al. 2022

Cytogenet Genome Res

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“…Single-cell transcriptomics, such as that employed here, offers a promising way to correct for any potential false inferences of differential gene expression and patterns of sequence divergence that are associated with standard bulk-level sequencing of heterogeneous tissue samples. However, although scRNA-sequencing approaches are increasingly employed for disentangling the role of regulatory changes in the evolution of intra- and inter-specific phenotypic variation (Fuess and Bolnick, 2021; Murat et al 2021), the associated costs are still substantially higher compared to standard bulk RNA-sequencing and many technical challenges remain for non-model organisms (Alfieri et al 2022). Cell isolation protocols are non-trivial as cell physiology may differ across tissues and species, and often require organism-specific technical knowledge to avoid cell death or bias in expression profiles (Reichard and Asosingh, 2019; Wang et al 2021).…”

Section: Discussionmentioning

confidence: 99%

Sex-biased gene expression at single-cell resolution: Cause and consequence of sexual dimorphism

Darolti

Mank

2022

Preprint

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Gene expression differences between males and females are thought to be key for the evolution of sexual dimorphism, and sex-biased genes are often used to study the molecular footprint of sex-specific selection. However, gene expression is often measured from complex aggregations of diverse cell types, making it difficult to distinguish between sex differences in expression that are due to regulatory rewiring within similar cell types and those that are simply a consequence of developmental differences in cell type abundance. To determine the role of regulatory versus developmental differences underlying sex-biased gene expression, we use single-cell transcriptomic data from multiple somatic and reproductive tissues of male and female guppies, a species which exhibits extensive phenotypic sexual dimorphism. Our analysis of gene expression at single-cell resolution demonstrates that non-isometric scaling between the cell populations within each tissue and heterogeneity in cell type abundance between the sexes can influence inferred patterns of sex-biased gene expression by increasing both the false-positive and false-negative rates. Moreover, we show that at the bulk level, the subset of sex-biased genes that are the product of sex differences in cell type abundance can significantly confound patterns of coding-sequence evolution. Taken together, our results offer a unique insight into the evolution of sex-biased gene expression and highlight the power of single-cell RNA-sequencing in disentangling between genes that are a cause as opposed to a consequence of sexual dimorphism.

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“…In the first step, the sequence data are usually mapped against an annotated reference genome to determine read counts for genes (Section 5.2). While analysis frameworks exist that do not require this a reference genome, 156,157 they have not been widely benchmarked 155 . There are many considerations surrounding genome annotation that impact on data generation and interpretation.…”

Section: Bioinformatic and Analysis Considerationsmentioning

confidence: 99%

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

Daniels

Taylor

Robledo

et al. 2023

Reviews in Aquaculture

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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.

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A Primer for Single-Cell Sequencing in Non-Model Organisms

Cited by 19 publications

References 70 publications

Fourth Report on Chicken Genes and Chromosomes 2022

Fourth Report on Chicken Genes and Chromosomes 2022

Sex-biased gene expression at single-cell resolution: Cause and consequence of sexual dimorphism

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

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