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

The existing genome annotations for the strawberry cultivar 'Benihoppe' contain incomplete or inaccurate gene models, particularly lacking alternative isoforms and complete untranslated regions, which impedes precise transcriptomic analysis. Here FxaBHv1.0.a2 is presented, a substantially improved genome annotation generated by integrating 257 short-read, and 33 full-length PacBio/Nanopore RNA-seq libraries that encompass diverse tissues, developmental stages, and abiotic stress treatments. Benchmarking Universal Single-Copy Orthologs (BUSCO) completeness increased from 96.2% to 99.5%, fragmented models were eliminated, and 89% of genes now possess complete 5′ and 3′ untranslated regions. Comprehensive functional information was assigned to 90% of the 103,316 protein-coding loci, and 6,167 ncRNAs. Leveraging this high-quality annotation, a high-confidence transcriptional network controlling fruit development and ripening was reconstructed. Using an integrative approach that combined Mfuzz clustering, Weighted Gene Co-expression Network Analysis (WGCNA), and Gene Network Inference with Ensemble of Trees (GENIE3) causal network inference, key regulators were identified and prioritised. The present results pinpoint several high-confidence candidate master regulators, including the known factor MYB1 (a MYB10 homolog), the recently validated SENSITIVE TO PROTON RHIZOTOXICITY 1 (STOP1), and a novel hub, a BTB/POZ domain and ankyrin repeat-containing protein (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.