Structural divergence and molecular adaptation of Rhodiola juparensis organelle genomes

Rhodiola juparensis, a cushion plant, plays a critical role in sustaining the fragile ecological environment of the Qinghai‑Tibet Plateau. Understanding its adaptive evolution is essential, yet the organelle genomic architecture and evolutionary dynamics of this species remain poorly characterized.

We sequenced and assembled the chloroplast (plastome) and mitochondrial (mitogenome) genomes of R. juparensis. Comprehensive comparative analyses were performed on organellar genome structure, RNA editing events, and positively selected genes. Divergence time estimation and genome‑wide positive selection scans were conducted using phylogenetic and bioinformatic approaches.

The plastome exhibited a more conserved structure but a faster nucleotide substitution rate, whereas the mitogenome showed greater structural complexity but a slower substitution rate. Divergence time estimation suggested that rapid differentiation of Crassulaceae species occurred around 7.15 Mya, likely linked to decreasing atmospheric CO₂ levels and the dramatic uplift of the Qinghai‑Tibet Plateau during the Late Miocene. Positive selection analysis identified three candidate genes (matR, ccmFc, and ATP8) under positive selection. Additionally, numerous pentatricopeptide repeat (PPR) proteins were detected in the nuclear genome.

The contrasting evolutionary patterns between the two organellar genomes highlight distinct selective constraints and mutation rates. The identified positively selected genes may contribute to mitochondrial function and stress adaptation. The abundance of nuclear‑encoded PPR proteins suggests a potential repair mechanism via RNA editing that could mitigate UV‑induced DNA damage, offering an adaptive advantage in the high‑altitude environment. Collectively, these findings provide valuable insights into the adaptive evolution of R. juparensis and the evolutionary history of Crassulaceae on the Qinghai‑Tibet Plateau.