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

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 appro...

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Bibliographic Details
Authors: Hoedjes, Katja M, Grath, Sonja, Posnien, Nico, Ritchie, Michael G, Schlötterer, Christian, Abbott, Jessica K, Almudi, Isabel, Coronado-Zamora, Marta, Durmaz Mitchell, Esra, Flatt, Thomas, Fricke, Claudia, Glaser-Schmitt, Amanda, González Pérez, Josefa, Holman, Luke, Kankare, Maaria, Lenhart, Benedict, Orengo, Dorcas J, Snook, Rhonda R, Yılmaz, Vera M, Yusuf, Leeban
Format: article
Status:Published version
Publication Date:2025
Country:España
Institution:Consejo Superior de Investigaciones Científicas (CSIC)
Repository:DIGITAL.CSIC. Repositorio Institucional del CSIC
OAI Identifier:oai:dnet:digitalcsic_::e43dfc0ccb2372078f694dedfc3786ee
Online Access:http://hdl.handle.net/10261/426382
https://api.elsevier.com/content/abstract/scopus_id/85195635847
Access Level:Open access
Keyword:Bulk RNAseq
Cellular heterogeneity
Deconvolution
Gene expression
Single‐cell RNAseq
Transcriptomics
Description
Summary: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.

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