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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. LU orcid ; Almudi, Isabel ; Coronado-Zamora, Marta ; Durmaz Mitchell, Esra and Flatt, Thomas , et al. (2024) In Molecular Ecology
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... (More)

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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organization
publishing date
type
Contribution to journal
publication status
in press
subject
keywords
bulk RNAseq, cellular heterogeneity, deconvolution, gene expression, single-cell RNAseq, transcriptomics
in
Molecular Ecology
publisher
Wiley-Blackwell
external identifiers
  • scopus:85195635847
  • pmid:38856653
ISSN
0962-1083
DOI
10.1111/mec.17382
language
English
LU publication?
yes
id
ff831e8a-ee2e-47a1-b811-d8bd5d554fc2
date added to LUP
2024-09-16 15:29:52
date last changed
2025-07-23 09:39:04
@article{ff831e8a-ee2e-47a1-b811-d8bd5d554fc2,
  abstract     = {{<p>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.</p>}},
  author       = {{Hoedjes, Katja M. and Grath, Sonja and Posnien, Nico and Ritchie, Michael G. and Schlötterer, Christian and Abbott, Jessica K. and Almudi, Isabel and Coronado-Zamora, Marta and Durmaz Mitchell, Esra and Flatt, Thomas and Fricke, Claudia and Glaser-Schmitt, Amanda and González, Josefa and Holman, Luke and Kankare, Maaria and Lenhart, Benedict and Orengo, Dorcas J. and Snook, Rhonda R. and Yılmaz, Vera M. and Yusuf, Leeban}},
  issn         = {{0962-1083}},
  keywords     = {{bulk RNAseq; cellular heterogeneity; deconvolution; gene expression; single-cell RNAseq; transcriptomics}},
  language     = {{eng}},
  publisher    = {{Wiley-Blackwell}},
  series       = {{Molecular Ecology}},
  title        = {{From whole bodies to single cells : A guide to transcriptomic approaches for ecology and evolutionary biology}},
  url          = {{http://dx.doi.org/10.1111/mec.17382}},
  doi          = {{10.1111/mec.17382}},
  year         = {{2024}},
}