Scientists assemble the complete mitochondrial genome of Camellia pitardii

The mitochondrial genome of Camellia pitardii, an economically valuable tree prized for its ornamental flowers and seed oil, has been assembled and characterized in full for the first time. The work, published in BMC Genomics, used PacBio HiFi long-read sequencing to reconstruct an organellar genome of 895,290 base pairs with a GC content of 45.68 percent. The genome carries 38 protein-coding genes, three rRNA genes and 30 tRNA genes, giving researchers a complete molecular inventory of the mitochondria of this Camellia species.

The assembly revealed an unusually dynamic structure. The team detected 260 simple sequence repeats, 33 tandem repeats and 620 dispersed repeat pairs scattered across the genome. Three large repeat regions were predicted to mediate homologous recombination, a process that could generate eight alternative genomic conformations. This repeat-driven plasticity points to prominent structural complexity and suggests that the mitochondrial genome of C. pitardii is far from a static molecule, but instead exists as a shifting population of rearranged forms.

Codon usage analysis added another layer of detail. The researchers found a strong bias toward codons ending in A or U, with 92.86 percent of preferred codons, defined as those with a relative synonymous codon usage value above 1, terminating in these two bases. Such AT-ending bias shapes how synonymous codons are deployed across the mitochondrial protein-coding genes and reflects the nucleotide composition pressures acting on this genome.

RNA editing emerged as a major post-transcriptional feature. A total of 667 C-to-U RNA editing sites were predicted across the mitochondrial protein-coding genes, spanning 14 amino acid substitution types. The conversions were dominated by serine-to-leucine changes, and nearly half of the predicted editing events were expected to transform hydrophilic residues into hydrophobic amino acids, potentially altering the chemical properties of the encoded mitochondrial proteins.

To test these predictions, the team turned to transcriptome data. This verification identified 354 high-efficiency transcriptome-supported RNA editing sites, of which 349, or 98.6 percent, were canonical C-to-U conversions with a median editing efficiency of 0.961. The verified sites preferentially occurred at the second codon position and showed high consistency with the PmtREP prediction results, indicating conserved post-transcriptional modification patterns in the mitochondria of C. pitardii.

Phylogenetic analysis based on the new genome exposed a striking discrepancy. The mitochondrial tree and the chloroplast tree showed topological incongruence among Camellia lineages, meaning the two organellar genomes tell different stories about how these plants are related. The authors interpret this as evidence of reticulate and complex evolutionary histories within Camellia organellar genomes, a finding that complicates simple tree-based views of the genus.

The study closes a gap in plant genomics. Although Camellia includes species of major horticultural and economic importance, the mitochondrial genome of C. pitardii had remained poorly characterized, limiting a comprehensive understanding of organellar genomic structural dynamics and phylogenetic evolution within the genus. The new assembly provides a reference point for comparing mitochondrial genome organization across Camellia species.

Beyond the genome sequence itself, the integrated analyses of codon usage, RNA editing patterns and organellar phylogeny offer a template for studying how plant mitochondrial genomes evolve and how their transcripts are modified. The genomic resource is expected to support future phylogenetic resolution, germplasm conservation and genetic improvement of Camellia species, linking basic organellar biology to practical breeding goals.

The article is published as open access research in BMC Genomics, with the accepted version shared early under a citable permanent DOI ahead of the final Version of Record.

Subject of Research: Assembly and characterization of the mitochondrial genome of Camellia pitardii

Article Title: Assembly and characterization of the mitochondrial genome of Camellia pitardii

Article References: Chen, J., Chen, R., Li, H., & Huang, L. (2026). Assembly and characterization of the mitochondrial genome of Camellia pitardii. BMC Genomics. https://doi.org/10.1186/s12864-026-13508-x

Image Credits: AI Generated

DOI: 10.1186/s12864-026-13508-x

Keywords: Camellia pitardii, mitochondrial genome, PacBio HiFi, RNA editing, homologous recombination, codon usage, phylogenetics, organelle evolution, BMC Genomics, seed oil, repeat sequences, chloroplast