First Complete Mitochondrial Genome of Chinese Dwarf Cherry Assembled with PacBio HiFi Reads

Researchers have assembled the first complete mitochondrial genome of Prunus humilis, the Chinese dwarf cherry, a perennial dwarf shrub endemic to China valued for its ecological, economic, and medicinal properties. Using PacBio HiFi long-read sequencing data, the team produced a circular assembly of 491,011 base pairs with a GC content of 45.5 percent, filling a gap in the genomic resources of a genus whose chloroplast and nuclear genomes had been studied but whose mitochondrial DNA remained poorly characterized. The mitogenome encodes 36 unique protein-coding genes, 18 tRNA genes, and three rRNA genes.

Comparative analysis across Prunus species revealed two notable features: P. humilis has lost the gene rps19, and it shows the highest level of gene duplication recorded in the comparison, with eight genes present in two copies each — atp4, atp6, atp8, atp9, ccmC, cox3, rps3, and sdh4. Phylogenetic analyses using maximum likelihood and Bayesian inference placed P. humilis as a sister lineage to a clade comprising P. davidiana and P. dulcis, supported by an ultrafast bootstrap value of 89 and a posterior probability of 1.0. Comparative genomics across Prunus mitogenomes revealed both conserved syntenic regions and structural variation, indicating that while large-scale gene order is partly maintained, rearrangements have occurred during the diversification of the group.

Sequence diversity was uneven among genes: nad1, cox2, and atp1 showed relatively high nucleotide diversity, whereas 14 protein-coding genes exhibited significant positive-selection signals. The authors conclude that this first complete mitogenome provides a valuable genomic resource for future molecular and evolutionary studies in Prunus, and that the observed mixture of structural conservation and variation, together with heterogeneous patterns of sequence diversity and selective pressure among mitochondrial genes, offers new insights into mitochondrial genome evolution and diversification within the genus.

Subject of Research: Complete mitochondrial genome assembly of Prunus humilis using PacBio HiFi sequencing

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

Article References: Wang, S., Sun, P., Zhang, L., & Li, Z. (2026). De novo assembly and characterization of the first complete mitochondrial genome of Prunus humilis based on PacBio HiFi sequencing. BMC Plant Biology. https://doi.org/10.1186/s12870-026-10234-0

Image Credits: AI Generated

DOI: 10.1186/s12870-026-10234-0

Keywords: Prunus humilis, mitochondrial genome, PacBio HiFi, Chinese dwarf cherry, genomics, gene duplication, RNA editing, phylogenetics, positive selection, BMC Plant Biology, novo, assembly