Organelle genome assembly and analysis of Euonymus chloranthoides, insights into an endemic and endangered species

Background Plant organellar genomes (chloroplasts and mitochondria) are valuable resources for understanding plant evolution, phylogenetics, and genetic diversity. Euonymus chloranthoides is a species within the family Celastraceae, yet its organellar genomes have remained uncharacterized. In this study, we assembled, annotated, and comprehensively analyzed the organellar genomes of this species. Results The chloroplast genome of E. chloranthoides is 157,967 bp in length, exhibits a typical quadripartite structure, encodes 125 genes, and is characterized by a low abundance and diversity of repeat sequences. In stark contrast, its mitochondrial genome is large and complex, with a size of 968,269 bp, assembled into six contigs forming an intricate structure. Comparative analyses further revealed that the chloroplast genome possesses a stronger and more widespread codon usage bias than the mitochondrial genome. Moreover, we predicted 508 C-to-U RNA editing sites in mitochondrial protein-coding genes, the majority of which result in non-synonymous changes. Eleven short mitochondrial plastid DNAs (MTPTs) were detected between the two organelles, four of which contain intact tRNA genes that were likely transferred from the chloroplast genome. We also identified 18 repeat pairs that may mediate homologous recombination in the mitochondrial genome. Among these, three long repeat pairs showed recombination frequencies close to 50%, while the recombination rates of the remaining short repeat pairs were less than or close to 1%. Conclusions This study presents the first complete characterization of both organellar genomes in E. chloranthoides , revealing their distinctly different evolutionary landscapes. The findings provide a valuable genomic resource and fundamental insights for comparative and evolutionary genomics of organelles within the family Celastraceae.