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

KM Hoedjes*, S Grath, N Posnien, MG Ritchie, C Schlötterer, JK Abbott, I Almudi, M Coronado-Zamora, ED Mitchell, T Flatt, C Fricke, A Glaser-Schmitt, J González, L Holman, M Kankare, B Lenhart, DJ Orengo, RR Snook, VM Yilmaz, L Yusuf

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review


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.
Original languageEnglish
Number of pages11
JournalMolecular Ecology
VolumeEarly View
Early online date10 Jun 2024
Publication statusE-pub ahead of print - 10 Jun 2024


  • Bulk RNAseq
  • Cellular heterogeneity
  • Deconvolution
  • Gene expression
  • Single-cell RNAseq
  • Transcriptomics


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