Comparative Analysis of the Mitochondrial Genome Sequences of Diaporthe longicolla (syn. Phomopsis longicolla) Isolates Causing Phomopsis Seed Decay in Soybean

<i>Diaporthe longicolla</i> (syn. <i>Phomopsis longicolla</i>) is an important seed-borne fungal pathogen and the primary cause of Phomopsis seed decay (PSD) in soybean. PSD is one of the most devastating seed diseases, reducing soybean seed quality and yield worldwide. As part of a genome sequencing project on the fungal <i>Diaporthe-Phomopsis</i> complex, draft genomes of eight <i>D. longicolla</i> isolates were sequenced and assembled. Sequences of mitochondrial genomes were extracted and analyzed. The circular mitochondrial genomes ranged from 52,534 bp to 58,280 bp long, with a mean GC content of 34%. A total of 14 core protein-coding genes, 23 tRNA, and 2 rRNA genes were identified. Introns were detected in the genes of <i>atp6</i>, <i>cob</i>, <i>cox1</i>, <i>cox2</i>, <i>cox3</i>, <i>nad1</i>, <i>nad2</i>, <i>nad5</i>, and <i>rnl</i>. Three isolates (PL7, PL10, and PL185E) had more introns than other isolates. Approximately 6.4% of the mitochondrial genomes consist of repetitive elements. Moreover, 48 single-nucleotide polymorphisms (SNPs) and were identified. The mitochondrial genome sequences of <i>D. longicolla</i> will be useful to further study the molecular basis of seed-borne pathogens causing seed diseases, investigate genetic variation among isolates, and develop improved control strategies for Phomopsis seed decay of soybean.