Comparative transcriptomics among peach, almond and their interspecific F1 hybrid reveal key common and...

Peach (Prunus persica) and almond (P. dulcis) are closely related species within the Prunus genus that exhibit strikingly different fruit characteristics, particularly in mesocarp expansion and ripening behaviour. To investigate the biological processes driving these differences, we performed a comprehensive transcriptomic analysis of fruit development in the peach cultivar 'Earlygold', the almond cultivar 'Texas', and their interspecific F1 hybrid. Fruit samples were collected at three developmental stages that are key in the different ripening behaviour of peach and almond: initial phase of rapid growth (T1), cell expansion and lignification (T2), and ripening (T3).

Global transcriptome profiling revealed almost identical expression patterns irrespective of the reference genome used for the RNA-seq analysis. We found 4,241, 3,862 and 2,922 DEGs between T1 and T2 in 'Earlygold', 'Texas' and F1 hybrid respectively, with most specific changes (55%, 76.6% and 51.3%) occurring during the first half of fruit development. Between T2 and T3, peach-type fruits continued active transcriptional regulation (2,665 DEGs in 'Earlygold', 2,199 in F1 hybrid), whereas almond showed limited late-stage changes (1,032 DEGs), reflecting its non-ripening phenotype. Enrichment analysis showed conserved cell division and photosynthesis-related genes enriched at T1 at both species. Peach displayed unique enrichment in pathways related to auxin signaling, DNA replication, and cyanogenic compound metabolism whereas almond for abscisic acid- and ethylene-related stress pathways. Allele-specific expression (ASE) analysis in the F1 hybrid revealed 79, 99 and 119 peach-biased ASE genes, and 27, 51 and 77 almond-biased ASE genes at T1, T2 and T3, respectively.

These findings reveal that peach and almond share conserved early developmental programs but diverge markedly from mid-development. Our data highlight auxin signaling, DNA replication, and ethylene-mediated ripening as central processes driving these developmental differences. The limited number of ASE genes and their parental bias patterns further illuminate cis-regulatory divergence between both species. This study provides new insights into the genetic regulation of fruit development in Prunus species and demonstrates a robust pipeline for cross-species transcriptomic analysis.