Complete organelle genomes of the threatened aquatic species <i>Scheuchzeria palustris</i> (Scheuchzeriaceae): Insights into adaptation and phylogenomic placement

<i>Scheuchzeria palustris</i>, the only species in the Scheuchzeriaceae family, plays a crucial role in methane production and transportation, influencing the global carbon cycle and maintaining ecosystem stability. However, it is now threatened by human activities and global warming. In this study, we generated new organelle genomes for <i>S. palustris</i>, with the plastome (pt) measuring 158,573 bp and the mitogenome (mt) measuring 420,724 bp. We predicted 296 RNA editing sites in mt protein-coding genes (PCGs) and 142 in pt-PCGs. Notably, abundant RNA editing sites in pt-PCGs likely originated from horizontal gene transfer between the plastome and mitogenome. Additionally, we identified positive selection signals in four mt-PCGs (<i>atp4</i>, <i>ccmB</i>, <i>nad3</i>, and <i>sdh4</i>) and one pt-PCG (<i>rps7</i>), which may contribute to the adaptation of <i>S. palustris</i> to low-temperature and high-altitude environments. Furthermore, we identified 35 mitochondrial plastid DNA (MTPT) segments totaling 58,479 bp, attributed to dispersed repeats near most MTPT. Phylogenetic trees reconstructed from mt- and pt-PCGs showed topologies consistent with the APG IV system. However, the conflicting position of <i>S. palustris</i> can be explained by significant differences in the substitution rates of its mt- and pt-PCGs (<i>p</i> < .001). In conclusion, our study provides vital genomic resources to support future conservation efforts and explores the adaptation mechanisms of <i>S. palustris</i>.