Assembly and characterization of the complete mitochondrial genome of Setaria viridis (L.) Beauv

Setaria viridis (L.) Beauv. is rapidly emerging as a model plant within the Panicoideae subfamily of Poaceae for studying C4 photosynthesis. The 'Fangshan' ecotype of S. viridis exhibits high adaptability to drought and nutrient-poor environments and holds historical significance in traditional Chinese medicine. Nevertheless, cytoplasmic genomic resources for this species, particularly its mitochondrial genome, remain entirely uncharacterized. To address this gap, we assembled the complete mitochondrial genome of the 'Fangshan' ecotype de novo using a hybrid approach combining Oxford Nanopore long reads and Illumina short reads. The mitochondrial genome adopts a predominantly single circular conformation with a total length of 437, 906 bp and a GC content of 43.96%, containing 33 unique protein-coding genes, 20 tRNA genes, and 3 rRNA genes. Furthermore, 111 Simple Sequence Repeats (SSRs), 33 tandem repeats, and 493 pairs of dispersed repeats were identified. Analysis revealed 31 plastid-derived DNA sequences integrated into the mitochondrial genome, constituting 3.19% of its total length. These sequences include one protein-coding gene and nine tRNA genes. Phylogenetic reconstruction demonstrated that the S. viridis clusters closely with S. italica, and Poaceae species form a distinct clade. Subsequently, in silico prediction identified 463 potential RNA editing sites (exclusively C-to-U conversions) across the 33 mitochondrial protein-coding genes. ccmC, ccmFN, and nad2 carried the highest numbers of predicted editing sites (36, 30, and 30, respectively). As core components of the mitochondrial electron transport chain, extensive editing in these genes may reflect strong functional constraints essential for energy metabolism during foxtail millet domestication. This study establishes a foundational genomic resource for investigating cytoplasmic genome evolution and the genetic basis of environmental adaptation in the genus Setaria.