The six whole mitochondrial genomes for the Diaporthe species: features, evolution and phylogeny

In this study, the complete mitogenomes of three <i>Diaporthe</i> species (<i>Diaportheeres</i> ZM79-3, <i>D.phaseolorum</i> ZM33-4 and <i>Diaporthe</i> sp. ZM41-5) were sequenced, assembled and compared with the other three previously sequenced <i>Diaporthe</i> mitogenomes (<i>D.caulivora</i> VNIIKR SE Dcaul3, <i>D.longicolla</i> MSPL 10-6 and <i>D.sojae</i> VNIIKR SE Dps12). The six <i>Diaporthe</i> mitogenomes were found to be circular DNA molecules, with lengths ranging from 53,646 bp to 108,865 bp. The mitogenomes of the six <i>Diaporthe</i> species mainly comprised the same set of 15 core protein-coding genes (PCGs), two rRNAs, and a certain number of tRNAs and unidentified open reading frames (ORFs). The PCG length, AT skew and GC skew showed large variability among the 15 PCGs in the six mitogenomes. The <i>nad1</i> gene had the least K2P genetic distance of the 15 core PCGs among the 13 <i>Diaporthales</i> species, indicating that this gene was highly conserved. The Ka/Ks values for all 15 core PCGs were < 1, suggesting that these genes were all subject to purifying selection. Comparative mitogenome analysis showed that introns contributed the most to the size variation of <i>Diaporthe</i> mitogenomes. Frequent intron loss/gain events were detected to have occurred in the <i>cox1</i> gene during the evolution of the <i>Diaporthales</i> mitogenomes. Although the mitogenomes of 13 species from <i>Diaporthales</i> had undergone large-scale gene rearrangements, six mitogenomes of <i>Diaporthe</i> species had identical gene arrangements. Phylogenetic analysis based on combined mitochondrial gene datasets showed that the six <i>Diaporthe</i> species formed well-supported topologies. To our knowledge, this study is the first report on the mitogenomes of <i>D.phaseolorum</i> ZM33-4 and <i>Diaporthe</i> sp. ZM41-5, as well as the first comparison of mitogenomes among <i>Diaporthe</i> species. Our findings will further promote investigations of the genetics, evolution and phylogeny of the <i>Diaporthe</i> species.