Objective The mitochondrial genome of a strain of Alternaria solani, the primary pathogen of early blight disease in potatoes, was assembled and characterized.

Methods DNA was extracted and sequenced from A. solani TA-0410 to study the mitogenome structure to compare with other similar strains for a clustering analysis.

Results The mitochondrial genome was 58,494bp with a GC content of 28.80% with 35.40% of A nucleotides, 35.80% of T, 13.90% of G, and 14.90% of C. It contained 24 protein-coding and 25 tRNA genes. The SSR analysis identified 224 short repeat sequences ranging from 2bp to 8bp in length. The 6 most frequently occurring short repeats were AT with 146 occurrences, followed by AAT with 26, AG with 25, AC with, AAG with 4, and ACT with 4 occurrences. In 29,387–29,419bp of the genome, 4 copies of 8bp repeat sequence of AATTATAT were found. A phylogenetic analysis based on 28 complete mitochondrial genomes indicated that A. solani was most closely related to the congeneric species, A. tenuissima and A. alternata, and relatively with 7 fungi from genera such as Stemphylium lycopersici, Curvularia clavate, Exserohilum rostratum, Exserohilum turcicum, Bipolaris cookie, Bipolaris oryzae and Bipolaris sorokiniana. The TA-0410 mitochondrial genome exhibited a significant codon usage bias that was primarily driven by natural selection and mutational pressure, as 47.62% of the codons had a RSCU greater than 1 with 90.63% ending in A or U, while 50.79% had the value less than 1 with 93.75% ending in C or G.

Conclusion The mitogenome of A. solani displayed an extensive collinearity with those of several other Alternaria species. Phylogenetically, they were evolutionarily close despite the significant bias on genetic codon usage due primarily to natural selection and domestication.