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.
Citation
Hoedjes , KM , Grath , S , Posnien , N , Ritchie , MG , Schlötterer , C , Abbott , JK , Almudi , I , Coronado-Zamora , M , Mitchell , ED , Flatt , T , Fricke , C , Glaser-Schmitt , A , González , J , Holman , L , Kankare , M , Lenhart , B , Orengo , DJ , Snook , RR , Yilmaz , VM & Yusuf , L 2024 , ' From whole bodies to single cells : a guide to transcriptomic approaches for ecology and evolutionary biology ' , Molecular Ecology , vol. Early View . https://doi.org/10.1111/mec.17382
Publication
Molecular Ecology
Status
Peer reviewed
ISSN
0962-1083Type
Journal article
Description
Funding: The authors were assisted by a Special Topics Network (STN) grant from the European Society for Evolutionary Biology (ESEB) to facilitate networking of the European Drosophila Population Genomics consortium (DrosEU; https://droseu.net/). SG and NP are supported by a Deutsche Forschungsgemeinschaft grant (GR 4495/4-1, PO 1648/7-1, PO 1648/4-1). MGR is supported by Natural Environment Research Council, UK (NE/V001566/1). CS is supported by the Austrian Science Funds (P32935, P33734, W1225). TF is supported by the Swiss National Science Foundation (310030_219283, FZEB-0-214654, 31003A-182262). JG is supported by grant PID2020-115874GB-I00 funded by MCIN/AEI/10.13039/501100011033 and from grant 2021 SGR 00417 funded by Departament de Recerca i Universitats, Generalitat de Catalunya. MK was supported by the grant 322980 from The Research Council of Finland.Collections
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