Mitochondrial Genome Insights into Evolution and Gene Regulation in Phragmites australis

As a globally distributed perennial Gramineae, <i>Phragmites australis</i> can adapt to harsh ecological environments and has significant economic and environmental values. Here, we performed a complete assembly and annotation of the mitogenome of <i>P. australis</i> using genomic data from the PacBio and BGI platforms. The <i>P. australis</i> mitogenome is a multibranched structure of 501,134 bp, divided into two circular chromosomes of 325,493 bp and 175,641 bp, respectively. A sequence-simplified succinate dehydrogenase 4 gene was identified in this mitogenome, which is often translocated to the nuclear genome in the mitogenomes of gramineous species. We also identified tissue-specific mitochondrial differentially expressed genes using RNAseq data, providing new insights into understanding energy allocation and gene regulatory strategies in the long-term adaptive evolution of <i>P. australis</i> mitochondria. In addition, we studied the mitogenome features of <i>P. australis</i> in more detail, including repetitive sequences, gene Ka/Ks analyses, codon preferences, intracellular gene transfer, RNA editing, and multispecies phylogenetic analyses. Our results provide an essential molecular resource for understanding the genetic characterisation of the mitogenome of <i>P. australis</i> and provide a research basis for population genetics and species evolution in Arundiaceae.