De Novo assembly and characterization of Aria alnifolia Chloroplast and mitochondrial genomes reveal homologous conformational changes mediated by repeat regions and gene transfer

Abstract

Background

Aria alnifolia is an ornamental landscape species widely distributed in East Asia. However, its mitochondrial genome remains largely unexplored. We used PacBio long reads and Illumina short reads to sequence and assemble the organelle genomes, aiming to understand the evolutionary relationship between the plastids and mitochondria of A. alnifolia. This study focused on the homologous conformational changes mediated by repeat regions and gene transfer between organelle genomes. We also conducted comparative genomic and phylogenetic analyses with other Rosaceae species to clarify the evolutionary placement of A. alnifolia within the family.

Results

The mitochondrial genome is 455,361 bp long with a GC content of 45.2%, while the chloroplast genome is 160,303 bp long with a GC content of 36.5%. The mitochondrial genome contains 59 genes, including 35 protein-coding genes, 4 rRNA genes, and 20 tRNA genes. The chloroplast genome comprises 128 genes, with 84 protein-coding genes, 8 rRNA genes, and 37 tRNA genes. The subcircular structure of the mitochondrial genome was inferred from two double-branch structures (DBSs) among 12 identified DBSs in A. alnifolia using a combination of long and short reads. In the mitochondrial genome, 128 simple sequence repeats were identified, compared to 69 in the chloroplast genome. Additionally, both organelles contained 239 dispersed repeats of at least 30 bp. We also confirmed gene transfer between the chloroplasts and mitochondria through shared repeats. Furthermore, we observed a region in the mitochondrial genome with high similarity to the chloroplast-encoded psaA gene, suggesting a possible inter-organellar gene transfer event. Phylogenetic analysis of the mitochondrial genomes revealed that A. alnifolia is closely related to Pyrus communis, albeit with low resolution.

Conclusion

This study provides one of the first comprehensive analyses of the organelle genomes (chloroplast and mitochondria) in the genus Aria. These results serve as a valuable reference for future taxonomic and molecular evolutionary studies of the Rosaceae family.