The Complete Mitogenome of Alternaria brassicae Causing Black Spot Disease on Rapeseed-Mustard

Alternaria brassicae is a destructive fungal pathogen that causes black spot disease on rapeseed-mustard and other cruciferous crops, leading to significant yield losses worldwide. Despite its economic importance, the mitochondrial genome of A. brassicae has remained unreported. De novo assembly of publicly available PacBio HiFi reads using the HiMT toolkit generated a circular mitochondrial DNA molecule of 50,713 bp with an average sequencing coverage of 309.0×. The genome encodes 19 protein-coding genes, comprising 12 named mitochondrial genes (atp6, cox1, cox3, cob, nad1, nad2, nad3, nad4, nad4L, nad5, nad6, and rps3) and seven intronic open reading frames (lagli_0–lagli_5 and giy), two rRNA genes (rrnL, rrnS), and 37 tRNA genes, with an overall GC content of 29.3%. Intron-containing structures were predicted in the nad4, nad4L, nad5, cox3, cob, and cox1 genes; these predictions were not validated with transcript data. A total of 33 simple sequence repeat (SSR) loci were detected, predominantly A/T mononucleotide repeats, with a density of one SSR per 1.52 kb. Tandem repeats clustered mainly in two regions (33–40 kb and 45–50 kb), and interspersed repeat analysis revealed 45.83% inverted, 30.28% complementary, 12.22% direct, and 11.67% palindromic repeats. Maximum-likelihood phylogenetic analysis of 22 mitogenomes placed A. brassicae (CNSA: CNP0008733) as sister to A. burnsii with 65% bootstrap support; the deeper grouping with A. gossypina had 25% support. Compared with the published A. tenuissima mitogenome (57,475 bp, 34 tRNAs, and two rRNAs), the present assembly is 6762 bp shorter and contains three additional tRNAs. This first complete mitogenomic resource for A. brassicae provides a valuable foundation for future studies on population genetics, molecular diagnostics, and evolutionary dynamics, aiding the development of improved management strategies for black spot diseases in cruciferous crops.