Abstract

Abstract Description of aims and systems used Olive ( Olea europea L.) is one of the most economically important tree crops worldwide, especially for the countries in the Mediterranean basin. Given the economic and nutritional importance of the crop for olive oil and drupe production, we generated transcriptional atlases for the Greek olive cultivars “Chondrolia Chalkidikis” and “Koroneiki” which have contrasting characteristics in terms of fruit development, oil production properties, and use. Our analysis involved 14 different organs, tissue types, and developmental stages, including young and mature leaves, young and mature shoots, open and closed flowers, young and mature fruits (epicarp plus mesocarp), young and mature endocarps, stalks, as well as roots. The developed gene expression atlases and the associated resources offer a comprehensive insight into comparative gene expression patterns across several organs and tissue types between significant olive tree cultivars. The comparative analyses presented in this work between the “Koroneiki” cultivar, which performs better in olive oil production, and the “Chondrolia Chalkidikis,” which grows larger fruits, will be essential for understanding the molecular mechanisms underlying olive oil production and fruit shape and size development. The developed resource is also expected to support functional genomics and molecular breeding efforts to enhance crop quality and productivity in olive trees. Outline of data resources generated The transcriptome data were generated using paired‐end Illumina Next‐Generation Sequencing technologies. The sequencing yielded approximately 13 million reads per sample for “Chondrolia Chalkidikis” and around 24 million reads per sample for “Koroneiki.” The transcriptomes were comparatively analyzed to reveal tissue‐specific and differentially expressed genes and co‐expression gene modules within and between cultivars. Summary of key results The comparative analysis unveiled tissue‐specific and differentially expressed genes within and between cultivars. Hierarchical gene clustering revealed intra‐ and inter‐cultivar expression patterns, particularly for the endocarp and fruit tissues relevant to olive oil production and fruit development. Additionally, genes associated with oil production and fruit size/shape development, including those in fatty acid metabolism and developmental regulation, were identified. Broader utility of the resource To facilitate accessibility, the GrOlivedb ( www.GrOlivedb.com ) database was developed, housing the comprehensive transcriptomic data for all of the analyzed organs and tissue types per cultivar. This resource will be a useful molecular tool for future breeding studies in olive oil production and fruit development and a valuable resource for crop improvement.