The Lettuce Expression Browser: from lab to LEB

bioRxiv (Cold Spring Harbor Laboratory), vol. 126, pp. e70962

Abstract

Summary Lettuce ( Lactuca sativa L.) is an economically important leafy vegetable within the Asteraceae family, cultivated worldwide across diverse agricultural systems. Recent advances in genomic and transcriptomic resources have positioned lettuce as a promising model system for functional genomics in the Asteraceae. However, currently available gene expression datasets lack comprehensive tissue-specific resolution, primarily focus on a single cultivar and are not visualised in an interpretable manner, limiting their utility for broader genetic and physiological studies. To bridge this gap, we developed the Lettuce Expression Browser (LEB), a publicly available platform providing high-resolution gene expression maps across various organs, tissues and developmental stages in both cultivated and wild lettuce species. The LEB integrates transcriptomic data from finely dissected seedlings, shoot tissues at various developmental stages and seedlings subjected to abiotic stresses (salt and far-red), visualised using the ggPlantmap R package. This platform offers an intuitive interface for exploring gene expression patterns and serves as a valuable resource for those studying lettuce development, stress responses, and evolutionary genomics. The LEB is hosted on the LettuceKnow Web Portal ( https://lettuce.bioinformatics.nl ) and can be expanded to include additional datasets, enhancing its role as a key tool for lettuce research and crop improvement. Significance statement The Lettuce Expression Browser (LEB) provides the first high-resolution gene expression atlas for both cultivated and wild lettuce species. This open-access resource enables detailed exploration of gene activity across development stages and stress conditions, advancing functional genomics in the Asteraceae family.

Authors 18

1. Dirk‐Jan M. van Workum

   Wageningen University & Research

   Affiliation as printed

   Wageningen University and Research;

2. Esther S. van den Bergh

   Utrecht University

   Affiliation as printed

   Utrecht University;

3. Siddhant S. Shetty

   Wageningen University & Research

   Affiliation as printed

   Wageningen University and Research;

4. Jelmer van Lieshout Aachen

   Leiden University

   Affiliation as printed

   Leiden University;

5. Tao Feng

   Wageningen University & Research

   Affiliation as printed

   Wageningen University and Research;

6. Marrit C. Alderkamp

   Utrecht University

   Affiliation as printed

   Utrecht University;

7. Gema Flores Andaluz

   Wageningen University & Research

   Affiliation as printed

   Wageningen University and Research;

8. Flip F. M. Mulder

   University Medical Center Utrecht

   Affiliation as printed

   UMC Utrecht

9. Dmitry Lapin

   Utrecht University

   Affiliation as printed

   Utrecht University;

10. Mark G. M. Aarts

    Wageningen University & Research

    Affiliation as printed

    Wageningen University and Research;

11. Guido F. J. M. Van den Ackerveken

    Utrecht University

    Affiliation as printed

    Utrecht University;

12. Remko Offringa Aachen

    Leiden University

    Affiliation as printed

    Leiden University;

13. Ronald Pierik

    Wageningen University & Research

    Affiliation as printed

    Wageningen University and Research;

14. Marcel C. G. Proveniers

    Utrecht University

    Affiliation as printed

    Utrecht University;

15. M. Eric Schranz

    Wageningen University & Research

    Affiliation as printed

    Wageningen University and Research;

16. Sandra Smit

    Wageningen University & Research

    Affiliation as printed

    Wageningen University and Research;

17. Renze Heidstra

    Wageningen University & Research

    Affiliation as printed

    Wageningen University and Research;

18. Anneke Horstman corresponding

    Wageningen University & Research

    Affiliation as printed

    Wageningen University and Research;