The complete and annotated mitochondrial genome of Hemileia vastatrix Race I, causal agent of coffee leaf rust

<ns3:p> <ns3:italic>Hemileia vastatrix</ns3:italic> is the fungal pathogen responsible for coffee leaf rust (CLR), the most economically important disease of <ns3:italic>Coffea arabica</ns3:italic> worldwide. Recently, the nuclear genome of this fungus was completely deciphered. However, the mitochondrial genome of <ns3:italic>H. vastatrix</ns3:italic> has remained undercharacterized. Here, we present the complete, circularized mitochondrial genome of <ns3:italic>H. vastatrix</ns3:italic> Race I (isolate HvRI), assembled using a hybrid approach combining PacBio HiFi long reads and BGIseq short reads. The genome is 173,525 bp in length with a GC content of 33.1% and encodes 41 functional genes, including 15 protein-coding genes, 2 rRNAs, and 24 tRNAs. The assembly reveals significant structural complexity, driven by intron expansion in the <ns3:italic>cox1</ns3:italic> and <ns3:italic>cob</ns3:italic> genes. Notably, the <ns3:italic>atp8</ns3:italic> gene contains a group II intron, rare for this locus, whose internal open reading frame displays evidence of pseudogenization via internal stop codons.. We also characterized a putative replication initiation zone (~1.2 kb) defined by a poly-G homopolymer and conserved regulatory motifs. The mitogenome of the HvRI isolate does not contain <ns3:italic>cob</ns3:italic> mutations that lead to amino acid substitutions G143A and F129L associated with the quinone outside inhibitor (QoI) fungicide resistance. This high-quality mitogenome is an important resource for comparative mitogenomics, population diversity studies, and the molecular surveillance of QoI fungicide resistance. </ns3:p>