The complete mitogenome of <i>Alternaria tenuissima</i> (Kunze) Wiltshire 1933 (Pleosporaceae), a fungus causing apple leaf blotch disease

<i>Alternaria tenuissima</i> (Kunze) Wiltshire 1933 is a plant pathogenic fungus mainly causing leaf blotch disease. Here, we de novo assembled mitochondrial genome of <i>A. tenuissima</i> isolate AT-1224. The total mitogenome size is 57,475 bp with 29.00% G + C content. The genome contained 12 coding genes and 15 hypothetical proteins, 34 transfer RNA (tRNA) genes and 2 ribosomal RNA (rRNA). There are 227 SSR repeats, range from 2 to 4 base pairs, most five repeats were AT (144), AAT (54), AG (33), AC (13) and AAG (5). The results also found 13 tandem repeats (&gt;100 bp), the largest repeat were forward 2 times located from 13,405 to 20,024 bp and 25,549 to 32,168 bp. Phylogenetic analysis based on 17 species complete mitogenomes indicated that <i>A. tenuissima</i> mitogenome was closest to 2 species, <i>A. solani</i> and <i>A. alternata,</i> sister clade to 6 species, representing <i>Curvularia clavate</i>, <i>Exserohilum rostratum</i>, <i>Exserohilum turcicum</i>, <i>Bipolaris cookie</i>, <i>Bipolaris oryzae</i> and <i>Bipolaris sorokiniana</i>. Further analysis among common fungus in local apple orchards using mitochondrial protein-coding genes revealed <i>A. tenuissima</i> were closing to 2 Alternaria fungi and a fungus representing <i>Phoma</i> sp. These results provide a basic reference for identification and evolution studies of <i>A. tenuissima</i> on apple trees.