Comparative organellar genomics of four Jasminum accessions reveals adaptive divergence and phylogenomic conflicts in Oleaceae

The genus Jasminum L. (Oleaceae), comprising ecologically and economically pivotal species, exhibits unresolved evolutionary dynamics in organellar genomes despite its global significance. A comparative analysis of chloroplast and mitochondrial genomes across four Jasminum accessions was presented, integrating high-throughput sequencing, structural annotation, and phylogenomic approaches. Chloroplast genomes displayed structural conservation (162,801–163,739 bp) with a quadripartite architecture, whereas mitochondrial genomes exhibited lineage-specific plasticity (480,663–508,932 bp), driven by repeat expansions (> 200 bp) and extensive RNA editing (326 C→U sites). Positive selection (Ka/Ks > 1) was detected in chloroplast genes linked to energy metabolism ( atpA , rps2 ) and stress adaptation ( ycf1 ), contrasting with stronger purifying selection in mitochondrial respiratory genes. Codon usage diverged markedly: chloroplasts favored A/T-ending codons (TTA-Leu, RSCU 1.84–1.92), while mitochondria exhibited CCT-Pro enrichment (RSCU 1.43–1.47). Phylogenomic conflicts between nuclear ITS and organellar data highlighted hybridization and incomplete lineage sorting, supported by horizontal gene transfer events involving tRNA and rRNA loci. Structural variations in chloroplast IR boundaries and mitochondrial repeat architectures underscored lineage-specific adaptations. Divergence time estimates revealed rapid radiation during the Miocene (15.07–12.93 Ma), coinciding with global cooling events. These findings elucidate how structural conservation, adaptive codon bias, and organellar genome plasticity shape the evolutionary trajectory of Jasminum , providing genomic resources for molecular marker development and clarifying taxonomic uncertainties in Oleaceae. • Comparative organellar genomics in Jasminum reveals evolutionary divergence: chloroplasts drive selection in energy metabolism, while mitochondria enhance stress resilience. • Key chloroplast genes ( atpA , rps2 , ycf1 ) under positive selection enhance photosynthesis and fragrance, vital for jasmine tea and perfume. • Mitochondrial repeat expansions (>500 bp) and RNA editing (326 C→U sites) reveal novel respiratory adaptations under climatic stress. • Hypervariable ycf1 and rps2-rpoC2 loci assist in identifying premium J. sambac , reducing essential oil loss by up to 40 % during extraction. • Phylogenomic discord resolved via organellar genome integration, enabling precise breeding of high-yield and climate-resilient jasmine.