Comprehensive Assembly and Comparative Analysis of Chloroplast Genome and Mitogenome of Prunus salicina var. cordata

<b>Background:</b><i>Prunus</i> plants are widely distributed across Asia and Europe, yet their intricate phylogenetic relationships pose significant challenges for systematic studies and interspecies identification. <b>Objectives</b>: To clarify the mitochondrial and chloroplast genomes of <i>Prunus salicina</i> var. <i>cordata</i>, and to reveal its evolutionary relationship and historical gene flow with domesticated cherries. <b>Methods</b>: In this study, we assembled, annotated, and analyzed the first mitochondrial and chloroplast genomes of <i>P. salicina</i> var. <i>cordata</i>, a species within the <i>Prunus</i> genus. <b>Results</b>: The mitochondrial genome was found to be 484,858 base pairs in length, exhibiting a typical circular conformation. Phylogenetic analysis revealed a close evolutionary relationship between <i>P. domestica</i> and <i>P. salicina</i>, suggesting historical gene flow between these two species last genomes; mitochondrial genomes; phylogeny analysis. <b>Conclusions</b>: To provide a genomic basis for resolving the phylogenetic controversies within the Li-associated plants, elucidating their evolutionary mechanisms, and formulating breeding strategies.