Integrative analysis of organellar genomes and transcriptomes reveals key organelle-nuclear crosstalk modules in Paliurus hemsleyanus

Paliurus hemsleyanus Rehd. is recognized for its robustness, economic value, and ornamental appeal, and it is commonly employed as a rootstock for Ziziphus jujuba Mill.. Although this species holds ecological and economic importance, the organelle genome resources and the interplay networks between nuclear and organellar genes in this species are still scarce. This work presents the first high-quality assembly and systematic comparative analysis of the mitochondrial and chloroplast genomes of P. hemsleyanus . Organelle genomic features were comprehensively investigated, covering genomic organization, gene composition, codon preference, repeat elements, RNA editing modification, MTPT transfer events, collinearity relationships, phylogenetic relationships, and adaptive selection pressure (Ka/Ks ratios). In addition to structural genomic analysis, transcriptome datasets derived from roots, stems and leaves were further integrated to dissect the protein-protein interaction network between nuclear and organellar components in P. hemsleyanus . Some hub genes were finally screened out, which serve as vital regulators to modulate the molecular crosstalk between nuclear-derived and organelle-coding genes. This high-quality organellar genome clarifies the evolutionary trajectory of P. hemsleyanus and identifies core molecular targets for leaf development improvement in future breeding. It also establishes a novel framework for exploring organellar-nuclear co-evolution in Rhamnaceae, and offers fundamental genetic resources for evolutionary analysis, functional genomics, molecular breeding and germplasm conservation of Rhamnaceous species.