The transition to ripening in non-climacteric species is governed by several signals, including hormones that enhance or counteract the abscisic acid (ABA)-promoting effect. The SQUAMOSA Promoter-binding protein-Like (SPL) transcription factors are involved in ripening through the modulation of anthocyanin biosynthesis. In sweet cherry fruits, several miR156-targeted PavSPLs are expressed before and during ripening. Recently, some PavSPLs were found in the transition from development to ripening in cultivars contrasting in maturity time. Additionally, several forms of miR156 were expressed in sweet cherry seeds of an early-season cultivar. In this work, we addressed the relevance of endocarp lignification and PavSPLs expression for the transition to ripening. First, we characterized early- and late-season sweet cherry cultivars, ‘Celeste’ and ‘Regina’, focusing on fruit and seed development, endocarp lignification, and PavSPL expression profile. Fruit growth dynamics revealed an earlier onset of color development and lignification in ‘Celeste’, while ‘Regina’ exhibited a prolonged lag phase and delayed embryo development. Transcript profiling at the light green stage showed a higher expression of PavSPL genes in fruits and identified cultivar-specific expressions, especially between ‘Regina’ and ‘Celeste’ seeds. Co-expression networks linked PavSPLs to genes involved in lignin and anthocyanin biosynthesis. We focused on PavSPL2 and PavSPL9, which were targeted by mtr-miR156a and gma-miR156f. Both PavSPLs and miRNAs were expressed in fruits and seeds at the yellow stage, an advanced point in the transition to ripening in sweet cherry. Exogenous application of auxin-related compounds in the mid-season cultivar ‘Lapins’ modulated endocarp lignification and pigmentation. Notably, p-IBA treatment, which enzymatically targets the lignin pathway, transiently increased anthocyanin accumulation and reduced lignin deposition, effects that correlated with the downregulation of PavSPL gene expression. These findings highlight the interplay between lignification, color evolution, and pigment biosynthesis during the transition from development to ripening in sweet cherry fruits, and suggest a role for PavSPL genes in this transition.

Next-generation sequencing (NGS) methods are transforming our capacity to detect pathogens and perform disease diagnosis. Although sequencing advances have enabled accessible and point-of-care NGS, data analysis pipelines have yet to provide robust tools for precise and certain diagnosis, particularly in cases of low sequencing coverage. Lack of standardized metrics and harmonized detection thresholds confound the problem further, impeding the adoption and implementation of these solutions in real-world applications. In this work, we tackle these issues and propose biologically-informed viral genome assembly coverage as a method to improve diagnostic certainty. We use the identification of viral replicases, an essential function of viral life cycles, to define genome coverage thresholds in which biological functions can be described. We validate the analysis pipeline, Viroscope, using field samples, synthetic and published datasets and demonstrate that it provides sensitive and specific viral detection. Furthermore, we developed Viroscope.io a web-service to provide on-demand NGS data viral diagnosis to facilitate adoption and implementation by phytosanitary agencies to enable precise viral diagnosis.

Perennial deciduous trees such as Prunus avium undergo seasonal transitions, culminating in bud dormancy establishment that involves coordinated physiological and metabolic adjustments. Dormancy monitoring in orchard systems still relies primarily on temperature-based models and forcing assays, which rarely incorporate physiological or biochemical indicators. Here, we tested whether seasonal metabolic dynamics associated with dormancy progression differ between sweet cherry genotypes and whether these physiological differences are reflected in canopy-scale vegetation indices derived from satellite observations. Field measurements were conducted in two genotypes with contrasting chilling behavior (‘Regina’ and ‘210’) during the transition from vegetative growth to dormancy. Leaf gas exchange and chlorophyll fluorescence were monitored across the season, polar metabolites in floral buds were profiled by gas chromatography-mass spectrometry, and satellite-derived vegetation indices were used to characterize canopy dynamics. Dormancy progression was associated with declines in CO₂ assimilation, transpiration, PSII photochemical efficiency, and electron transport rate, accompanied by increases in intercellular CO₂ concentration and non-regulated energy dissipation. Metabolomic analysis revealed that genotype explained a larger proportion of metabolite variation than dormancy stage (PERMANOVA R² = 0.483, p = 0.001), while principal component analysis accounted for 79.7% of total variance. Fructose showed the strongest genotype difference during paradormancy I, corresponding to an approximately 9.5-fold increase in ‘Regina’. Pathway enrichment analysis highlighted starch and sucrose metabolism and pyruvate metabolism as the most represented pathways during dormancy progression. Satellite-derived vegetation indices captured seasonal canopy decline and were significantly associated with several physiological variables. These results provide an integrated description of physiological and metabolic adjustments during dormancy establishment in sweet cherry and highlight the potential of combining metabolomics, plant physiology, and open-access satellite observations to monitor phenological transitions in orchard systems at scalable spatial and temporal resolutions.

The transition from development to ripening is governed by several hormones that interplay with abscisic acid (ABA) in non-climacterics, including auxin. In sweet cherry (Prunus avium), auxin has been shown to promote fruit coloration and ABA accumulation, in contrast to other non-climacteric models. Thus, this work aims to explore the role of auxin during the transition to ripening in sweet cherry by assessing the global gene expression response to an auxin homeostasis disturbance. For this, we used 5d, a fluorescently labeled compound with previously reported anti-auxin activity, which was applied to fruits at the light-green stage. This compound desynchronized fruit coloring and ripening, as fruit coloration and IAD were enhanced, while softening and soluble solid content increase were delayed. Enriched functional categories in the treatment were related to auxin export, signaling and response, flavonol biosynthesis, malate transport, inositol metabolism, and cell wall organization. A subset of genes downregulated by the anti-auxin 5d contributed to the enrichment of categories associated with ABA response. Anti-auxin 5d prevented ABA increase observed in control fruits, upregulated ABA receptor genes, and altered ABA-responsive gene expression, supporting auxin-ABA crosstalk. The treatment with the anti-auxin 5d also upregulated genes related to gibberellin (GA) biosynthesis, suggesting that auxin may influence ripening through modulation of GA production. Co-expression analyses revealed that auxin-related genes encoding SAUR72 and PIN-LIKES 3-like were anchors, having connections with ripening-related genes, including those involved in ABA response and degradation, cell wall softening and hormone methylation, further supporting a pro-ripening role for auxin in sweet cherry.