Complete mitochondrial and chloroplast genomes of Haematoxylum campechianum L. reveal insights into gene transfer and RNA editing events

Abstract

Logwood (Haematoxylum campechianum L.) is an economically valuable tree species with diverse medicinal properties. However, the organelle genomes of logwood have not yet been elucidated, thereby hindering phylogenetic studies and comparative analyses within the Caesalpinioideae subfamily as well as limiting genetic investigations of its bioactive metabolite biosynthesis pathways. In this study, the mitochondrial genome (mitogenome) and chloroplast genome of H. campechianum were assembled and annotated successfully. The results demonstrated that the logwood mitogenome spanned 672,957 bp, including 36 protein-coding genes (PCGs), 23 tRNAs, and 3 rRNAs. In comparison, the chloroplast genome of logwood was 157,156 bp long and contained 79 PCGs, 28 tRNA genes, and 4 rRNA genes. In addition, phylogenetic reconstruction revealed topological discordance between mitogenome- and chloroplast-based trees, attributable to mitochondrial mutation rate acceleration. Furthermore, 16 mitochondrial plastid DNA segments were identified, evidencing inter-organellar gene transfer, along with 286 predicted RNA editing sites showing the 87.23 % validation rate. Taken together, this study provided the valuable organelle genome resources for the Caesalpinioideae subfamily, elucidated the phylogenetic relationships, and supplied essential resources for probing the evolution of logwood.