De novo assembly and characterization of the first complete mitochondrial genome of Prunus humilis based on PacBio HiFi sequencing

Abstract Background Prunus humilis (Chinese dwarf cherry) is a perennial dwarf shrub fruit tree endemic to China with considerable ecological, economic, and medicinal value. Although its chloroplast and nuclear genomes have been studied, its mitochondrial genome remains poorly characterized. Results Based on PacBio HiFi long-read sequencing data, we assembled the mitochondrial genome of P. humilis and obtained a circular assembly representation. The mitogenome was a circular molecule of 491,011 bp, comprising 36 unique protein-coding genes (PCGs), 18 tRNA genes, and three rRNA genes, with a GC content of 45.5%. Notably, comparative analysis across Prunus species revealed that P. humilis lost one gene ( rps19 ) and exhibited the highest level of gene duplication, with eight genes present in two copies ( atp4 , atp6 , atp8 , atp9 , ccmC , cox3 , rps3 , and sdh4 ). Codon usage analysis revealed a strong A/U bias at the third codon position, while RNA editing site prediction indicated that nad4 harbored the highest number of predicted RNA editing sites (43). Phylogenetic analyses based on ML and BI indicated that P. humilis formed a sister lineage to the P. davidiana + P. dulcis clade (UFBoot = 89, PP = 1.0). Comparative analyses revealed conserved syntenic regions and structural variation among Prunus mitogenomes. nad1 , cox2 , and atp1 showed relatively high nucleotide diversity, while 14 PCGs exhibited significant positive-selection signals. Conclusions This study presents the first complete mitochondrial genome of P. humilis , providing a valuable genomic resource for future molecular and evolutionary studies in Prunus . The results reveal substantial structural conservation and variation among Prunus mitogenomes, together with heterogeneous patterns of sequence diversity and selective pressure among mitochondrial genes, providing new insights into mitochondrial genome evolution and diversification within the genus.