Unraveling Mitochondrial Genome Evolution in <i>Puccinia striiformis</i> f. sp. <i>elymi</i>, the Elymus Stripe Rust Fungus

<i>Puccinia striiformis</i> f. sp. <i>elymi</i> (<i>Pse</i>) is a specialized forma specialis of stripe rust infecting <i>Elymus dahuricus</i>, yet its mitochondrial evolution remains poorly understood. In this study, we assembled the complete mitogenome of <i>Pse</i> using PacBio HiFi sequencing, yielding a circular mitogenome of 72,952 bp. This reveals a striking asymmetric evolutionary pattern with a 28.34% genomic contraction compared to the wheat stripe rust <i>P. striiformis</i> f. sp. <i>tritici</i> (<i>Pst</i>-CYR32). Our analysis demonstrates that this streamlining is strictly driven by a massive and systematic loss of mitochondrial introns. The <i>Pse</i> mitogenome exhibits negative GC-skew (-0.0184) consistent with strand-asymmetric mutational pressure, while maintaining a strictly conserved and syntenic complement of all 14 core protein-coding genes (PCGs), alongside 24 tRNAs and 2 rRNAs. Phylogenomic analysis positions <i>Pse</i> as sister to the <i>Pst</i> clade with strong support (100% bootstrap). A 748-bp SNP cluster within <i>nad4</i> (14.2% sequence divergence versus 3.1% genome-wide average) provides a candidate molecular marker for lineage differentiation, pending population-level validation. This study establishes a genomic foundation for investigating mitochondrial reductive evolution in host-specialized rust lineages, highlighting the dynamic role of introns in driving organellar genome size variation.