Strawberry atlas: <i>Fragaria vesca</i> gene expression atlas for strawberry genomics

The resulting expression atlas captures a certain level of expression for ∼99% of 36,173 annotated genes that include TS genes. It also reveals robust clustering by tissue, underscoring the biological coherence of the integrated dataset. Expression profiling identified tissue-enriched genes in photosynthesis, flavonoid biosynthesis, and fruit ripening, and a core set of 719 stably expressed HK genes. SVs were significantly underrepresented in coding exons, and genes overlapping SVs had reduced expression. One example, <i>FvesChr6G00002800</i> (<i>FvH4_6g02210</i>), exhibited exonization of a TE-derived region in H4, supported by multiple datasets. The expression of GA20-oxidase family members revealed functional partitioning: <i>GA20ox3</i> was seed-specific, <i>GA20ox2</i> was active in early fruit, and <i>GA20ox1</i> showed broad, low-level expression across tissues, consistent with a subfunctionalization model. To support knowledge integration, we provide a v4-to-v6 gene ID conversion tool. All data, including SV and TE annotations, are available <i>via</i> a public web portal: https://strawberryatlas.org/easy_gdb, enabling rapid cross-tissue expression analysis.