Organellar genome evolution in Camellia tianeensis (Theaceae): comparative insights into RNA editing, codon usage, and DNA transfer between chloroplast and mitochondrion

TL;DR

This study explores the chloroplast and mitochondrial genomes of Camellia tianeensis, revealing insights into RNA editing, DNA transfer, and genome evolution in this economically important plant.

Contribution

The study provides the first complete organellar genomes for Camellia tianeensis and reveals extensive RNA editing and inter-organelle DNA transfer.

Findings

The mitochondrial genome of C. tianeensis has 404 RNA-editing sites, significantly more than the chloroplast genome.

Nine chloroplast-derived fragments totaling 42.9 kb were found in the mitochondrial genome, indicating active DNA transfer.

Both genomes show a strong bias toward A/U-ending codons, suggesting translational selection.

Abstract

Camellia tianeensis, a rare member of sect. Chrysantha Chang of the family Theaceae, is widely known for its ornamental and medicinal importance and is often referred to “Queen of the Tea Family”. Despite its biological and economic value, little is known about the structure and evolution of its organellar genomes. In this study, we assembled and compared the complete chloroplast and mitochondrial genomes of C. tianeensis using combined short- and long-read sequencing. The chloroplast genome was 156,865 bp in length and encoded 131 genes, whereas the mitochondrial genome measured 1,098,121 bp and contained 51 genes. Four protein-coding genes—rps12, rps14, rps16, and rps7—were shared by both organelles. The mitochondrial genome exhibited 404 RNA-editing sites, about 6.2 times more than the chloroplast genome (65 sites), primarily resulting in conversions from hydrophilic to hydrophobic amino acids. The mitochondrial genome contained more simple sequence repeats (SSRs) and dispersed repeats than the chloroplast genome, with complementary repeats absent in both. Codon-usage analysis revealed a strong bias toward A/U-ending codons in both genomes, with ten optimal codons shared, suggesting the action of translational selection. Phylogenetic analysis confirmed that C. tianeensis belongs to sect. Chrysantha and showed close affinity to C. nitidissima. Moreover, nine chloroplast-derived fragments totaling 42.9 kb were identified within the mitochondrial genome, indicating active inter-organelle DNA transfer. These results provide the first comprehensive organellar genomic resources for sect. Chrysantha and offer valuable insights into organelle evolution, RNA-editing diversity, and horizontal DNA exchange in higher plants.

The online version contains supplementary material available at 10.1186/s12864-026-12522-3.

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