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

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, Josefa; Holman, Luke; Kankare, Maaria; Lenhart, Benedict; Orengo, Dorcas J.; Snook, Rhonda R.; Yılmaz, Vera M.; Yusuf, Leeban

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.

Citation

Hoedjes, K. M., Grath, S., Posnien, N., Ritchie, M. G., Schlötterer, C., Abbott, J. K., Almudi, I., Coronado‐Zamora, M., Durmaz Mitchell, E., Flatt, T., Fricke, C., Glaser‐Schmitt, A., González, J., Holman, L., Kankare, M., Lenhart, B., Orengo, D. J., Snook, R. R., Yılmaz, V. M., & Yusuf, L. (online). From whole bodies to single cells: A guide to transcriptomic approaches for ecology and evolutionary biology. Molecular Ecology, https://doi.org/10.1111/mec.17382

• Journal Article Type: Article
• Acceptance Date: Apr 29, 2024
• Online Publication Date: Jun 10, 2024
• Deposit Date: Jun 19, 2024
• Publicly Available Date: Jun 19, 2024
• Journal: Molecular Ecology
• Print ISSN: 0962-1083
• Electronic ISSN: 1365-294X
• Publisher: Wiley
• Peer Reviewed: Peer Reviewed
• DOI: https://doi.org/10.1111/mec.17382
• Keywords: transcriptomics, single‐cell RNAseq, deconvolution, bulk RNAseq, gene expression, cellular heterogeneity