Phylogenetic reconstruction and species delimitation in Stipeae with special reference to Stipa (Poaceae, Pooideae) using mitochondrial genomes

Compared to plastid genomes, plant mitochondrial genomes have been less frequently used for species discrimination and phylogenetic studies due to assembly challenges, lower substitution rates and rapid structural evolution. However, this study demonstrates that mitochondrial genome fragments can be valuable for both molecular species identification and phylogenetic analysis in grasses of the tribe Stipeae. To explore this potential, we first assembled the complete mitochondrial genome of Nassella tenuissima-the first fully described mitogenome in Stipeae-which served as a reference for selecting 29 aligned mitochondrial genome fragments totalling 139 680 bp. These fragments were then analysed across 49 representatives of the tribe, including 43 Stipa species and six other taxa. The mitochondrial fragments achieved a species discrimination efficiency of 75%, slightly exceeding the 71% efficiency observed for plastid super-barcodes. Additionally, comparative phylogenetic analyses using plastid and mitochondrial genomes underscored the utility of mitochondrial data in resolving phylogenetic relationships within Stipeae. Our findings provide a valuable resource for future research in transcriptomics, comparative genomics, phylogenomics and phylogeography of grasses.