Assembly and characterization of the mitochondrial genome of Camellia pitardii

Abstract Camellia pitardii Coh.-St., an economically important tree species in the genus Camellia valued for both its seed oil and ornamental traits, currently lacks a systematically characterized mitochondrial genome. In this study, we assembled and annotated the complete mitogenome of C. pitardii using a hybrid approach that combined Illumina NovaSeq 6000 short reads and Oxford Nanopore long reads. Using bioinformatics tools, we systematically analyzed repetitive sequences, codon usage bias, and RNA editing sites. Furthermore, we constructed phylogenetic trees based on conserved protein-coding genes from both mitochondrial and chloroplast genomes to elucidate the phylogenetic position of these genes. The assembled C. pitardii mitogenome is 895,290 bp in length with a GC content of 45.68%. Annotation revealed a total of 38 protein-coding genes (PCGs), three rRNA genes, and 30 tRNA genes. We identified 260 simple sequence repeats (SSRs), 33 tandem repeats, and 620 pairs of dispersed repeats. Among these, three pairs of long repeats are predicted to mediate the formation of eight potential genomic substructures. The mitogenome exhibited a distinct codon usage bias, with 92.86% of the highly preferred codons (relative synonymous codon usage [RSCU] > 1) ending in A or U. Additionally, 667 RNA editing sites were predicted across the 38 PCGs, encompassing 14 types of amino acid substitutions; 46.48% of these editing events resulted in the conversion of hydrophilic residues to hydrophobic ones. Phylogenetic analyses revealed topological incongruence between the mitochondrial and chloroplast gene trees regarding the placement of several Camellia clades, suggesting a complex evolutionary history for the organelles of C. pitardii and its close relatives. In conclusion, this study characterizeed the fundamental features of the C. pitardii mitogenome, providing valuable baseline data for comparative organellar genomics, phylogenetic reconstruction, and the utilization of germplasm resources within the genus Camellia.