Decoding the complete mitochondrial genome of Hydrangea chinensis maxim.: insights into genomic recombination, gene...

The mitochondrial genome (mitogenome) of plants exhibits remarkable structural complexity and evolutionary plasticity, yet remains poorly characterized in many ornamental species. Hydrangea chinensis Maxim. (H. chinensis), an indigenous plant distributed across China, serves as a vital genetic resource owing to its morphological diversity, ecological adaptability, and utility in hybrid breeding programs. Despite its importance for enhancing hydrangea varieties, no genomic resources have been published for this species to date. To bridge this knowledge gap, we sequenced and assembled the complete mitogenome of H. chinensis, providing novel insights into its structure, evolution, and functional dynamics.

The mitochondrial genome of H. chinensis was successfully assembled using a hybrid sequencing approach integrating long-read and short-read technologies. The mitogenome spans 722,918 base pairs with a GC content of 45.33%, encoding 38 protein-coding genes along with 21 tRNA genes and 3 rRNA genes. Comprehensive analyses revealed extensive structural features including 335 repeat pairs, 211 simple sequence repeats (SSRs), and significant recombination events that contribute to its multi-branched architecture comprising both circular and linear contigs. We identified 613 C-to-U RNA editing sites affecting key mitochondrial genes such as nad4, suggesting functional roles in post-transcriptional regulation. Furthermore, the genome harbors 23 plastid-derived DNA fragments (MTPTs) spanning 11,059 bp-evidence of chloroplast-to-mitochondrial gene transfer with potential evolutionary implications. Phylogenetic analysis based on conserved mitochondrial protein-coding genes positioned H. chinensis within the Cornales order under Hydrangeaceae while revealing extensive collinearity variations among closely related species.

This study represents the inaugural comprehensive investigation of the mitogenome of H. chinensis, unveiling its intricate architecture shaped by repetitive sequences, dynamic recombination events, RNA editing processes, and inter-organelle gene transfers. These findings enhance our understanding of mitochondrial genome evolution and offer essential genetic resources to support future breeding strategies for hydrangea improvement.