The Almond Expression Atlas: A comprehensive multi-tissue transcriptomic resource for almond gene expression
- 1Department of Plant Breeding, Fruit Breeding Group, CEBAS-CSIC, Espinardo, Murcia, Spain
Abstract
Background: Improving crop adaptation and enhancing agronomic and quality traits requires a deeper understanding of gene expression regulation, for which expression atlases are valuable tools. Almond (Prunus dulcis (Mill.) D.A. Webb) is one of the most economically important tree nut crops worldwide. However, an integrated transcriptomic resource for this species is still lacking. Available data remain fragmented across independent studies, limiting their comparability and reuse. Results: Here, we present the first almond gene expression atlas: a comprehensive multi-tissue transcriptomic resource integrating publicly available RNA sequencing data. A total of 142 high-quality untreated and control samples from 17 independent projects were curated through a metadata standardization process and analyzed using a unified bioinformatics pipeline. Standardized expression profiles were generated for 25,225 annotated genes in the Prunus dulcis Texas v2.0 reference genome. The atlas integrates two complementary expression approaches: a median TPM approach capturing quantitative expression levels and a rank-based strategy implemented using the Bgee expression calling method, designed to improve comparability across heterogeneous datasets. This design enables the identification of tissue-specific candidate genes and the exploration of expression patterns across tissues and developmental stages. Its applicability is demonstrated through two use cases, highlighting its ability to identify biologically meaningful gene sets associated with bud dormancy transitions and to prioritize candidate reference genes for RT-qPCR normalization in almond. Conclusions: The Almond Expression Atlas v1.0 is publicly available through FruitDBase (fruitdbase.csic.es), providing an interactive platform for gene expression exploration and visualization. This resource supports functional genomics studies and facilitates candidate gene discovery in almond, while ensuring data traceability and promoting data reusability.
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BibTeX
@misc{lopezfernandez2026almond,
title = {{The Almond Expression Atlas: A comprehensive multi-tissue transcriptomic resource for almond gene expression}},
author = {E. M. Lopez-Fernandez and M. Zwieniecki and A. Tixier and J. A. Botia and P. J. Martinez-Garcia},
howpublished = {bioRxiv},
year = {2026},
month = oct,
doi = {10.64898/2026.10.30.763019},
url = {https://www.biorxiv.org/content/10.64898/2026.10.30.763019v1},
note = {CC BY},
}
RIS
TY - UNPB
TI - The Almond Expression Atlas: A comprehensive multi-tissue transcriptomic resource for almond gene expression
AU - E. M. Lopez-Fernandez
AU - M. Zwieniecki
AU - A. Tixier
AU - J. A. Botia
AU - P. J. Martinez-Garcia
PY - 2026
DA - 2026/10/30
PB - bioRxiv
DO - 10.64898/2026.10.30.763019
UR - https://www.biorxiv.org/content/10.64898/2026.10.30.763019v1
AB - Background: Improving crop adaptation and enhancing agronomic and quality traits requires a deeper understanding of gene expression regulation, for which expression atlases are valuable tools. Almond (Prunus dulcis (Mill.) D.A. Webb) is one of the most economically important tree nut crops worldwide. However, an integrated transcriptomic resource for this species is still lacking. Available data remain fragmented across independent studies, limiting their comparability and reuse. Results: Here, we present the first almond gene expression atlas: a comprehensive multi-tissue transcriptomic resource integrating publicly available RNA sequencing data. A total of 142 high-quality untreated and control samples from 17 independent projects were curated through a metadata standardization process and analyzed using a unified bioinformatics pipeline. Standardized expression profiles were generated for 25,225 annotated genes in the Prunus dulcis Texas v2.0 reference genome. The atlas integrates two complementary expression approaches: a median TPM approach capturing quantitative expression levels and a rank-based strategy implemented using the Bgee expression calling method, designed to improve comparability across heterogeneous datasets. This design enables the identification of tissue-specific candidate genes and the exploration of expression patterns across tissues and developmental stages. Its applicability is demonstrated through two use cases, highlighting its ability to identify biologically meaningful gene sets associated with bud dormancy transitions and to prioritize candidate reference genes for RT-qPCR normalization in almond. Conclusions: The Almond Expression Atlas v1.0 is publicly available through FruitDBase (fruitdbase.csic.es), providing an interactive platform for gene expression exploration and visualization. This resource supports functional genomics studies and facilitates candidate gene discovery in almond, while ensuring data traceability and promoting data reusability.
ER -