From whole bodies to single cells: A guide to transcriptomic approaches for ecology and evolutionary biology

Abstract

RNA sequencing (RNAseq) methodology has experienced a burst of technological developments in the last decade, which has opened up opportunities for studying the mechanisms of adaptation to environmental factors at both the organismal and cellular level. Selecting the most suitable experimental approach for specific research questions and model systems can, however, be a challenge and researchers in ecology and evolution are commonly faced with the choice of whether to study gene expression variation in whole bodies, specific tissues, and/or single cells. A wide range of sometimes polarised opinions exists over which approach is best. Here, we highlight the advantages and disadvantages of each of these approaches to provide a guide to help researchers make informed decisions and maximise the power of their study. Using illustrative examples of various ecological and evolutionary research questions, we guide the readers through the different RNAseq approaches and help them identify the most suitable design for their own projects.

Keywords: bulk RNAseq; cellular heterogeneity; deconvolution; gene expression; single‐cell RNAseq; transcriptomics.

FIGURE 1

Advantages and disadvantages of RNAseq approaches, and opportunities for deconvolution. Each RNAseq approach, using either whole bodies, body parts or specific tissues (i.e. bulk RNAseq), or single cells (i.e. single‐cell RNAseq), has unique advantages and disadvantages that make them more or less suitable to address particular questions in the fields of ecology and evolution. Integrating different approaches can provide additional advantages, by harnessing the strengths of each approach. Here, we highlight deconvolution, by combining bulk and single‐cell RNAseq data, as a promising opportunity that has recently opened up for ecological and evolutionary research.