Update of the octoploid strawberry genome annotation and gene regulatory network analysis revealed key factors in strawberry fruit maturation

The existing genome annotations for strawberry cultivar 'Benihoppe' contain incomplete or inaccurate gene models, particularly lacking different isoforms and incomplete untranslated regions, which impedes precise transcriptomic analysis. Here, we report a substantially improved genome annotation for 'Benihoppe' (FxaBHv1.0.a2) generated by integrating an extensive collection of 257 short-read and 33 long-read (PacBio and Nanopore) RNA-seq datasets spanning diverse tissues, developmental stages, and stress conditions. The updated annotation demonstrates a remarkable increase in quality, with the BUSCO completeness score rising from 96.2% to 99.5% and fragmented BUSCOs being eliminated. Notably, the annotation of UTRs was significantly enhanced, with 89% of genes now featuring these crucial regulatory regions. Comprehensive functional information was assigned to 90% of the 103,316 predicted genes desides 6,167 ncRNA. Leveraging this high-fidelity resource, we conducted an in-depth analysis of the transcriptional regulatory network governing fruit development and ripening. Using an integrative approach that combined Mfuzz clustering, Weighted Gene Co-expression Network Analysis (WGCNA), and GENIE3 causal network inference, we identified and prioritized key regulators. Our results pinpoint several high-confidence candidate master regulators, including known factors like MYB1 (a MYB10 homolog) and novel hubs such as STOP1 and NBCL. These transcription factors are predicted to orchestrate the critical hormonal transition from auxin repression to abscisic acid (ABA)-driven maturation by targeting core components of their respective signaling pathways. This work not only provides a foundational genomic tool for the strawberry research community but also delivers novel insights into the regulatory architecture of fruit ripening, identifying high-priority targets for future functional validation and crop improvement.