Characterization and Phylogenetic Analysis of the Complete Mitogenomes of Valsa mali and Valsa pyri

Apple Valsa canker, caused by Valsa mali and Valsa pyri, is a devastating disease of apple trees and poses a severe threat to the sustainable development of apple production. Although the two species’ whole genomes have been sequenced, their mitochondrial genomes are still uncharacterized. In this study, the complete mitochondrial genomes of V. mali and V. pyri were assembled, annotated, and compared by bioinformatic methods. The results indicate that the mitogenomes are both circular DNA molecules with sizes of 213,406 bp and 128,022 bp, respectively. The AT skew values of the two Valsa species’ mitogenomes were positive, while the GC skew values were negative. Comparative mitogenome analysis revealed that the length and base composition of protein-coding genes (PCGs), rRNA genes, and tRNA genes differed between the two Valsa species. It was found that the expansion of V. mali was primarily attributable to the intronic regions. There are large numbers of interspersed repetitive sequences (IRS) in both Valsa mitogenomes; however, the proportion of IRS in V. mali (43.56%) was much higher than that in V. pyri (2.41%). The alignment of large fragments between the mitochondrial and nuclear genomes of both V. mali (1.73 kb) and V. pyri (5.17 kb) indicates that gene transfer between mitochondrial and nuclear genomes occurred during evolution. The ka/ks ratios for 15 core PCGs were below one, suggesting that these genes were subjected to purifying selection pressure. Comparative mitogenomics revealed that the two fungi had significant mitogenomic collinearity and large-scale gene rearrangements. The results of phylogenetic analysis based on Bayesian inference (BI) and maximum likelihood (ML) using a combined mitochondrial gene set confirmed that V. mali and V. pyri were fully independent taxa with a high bootstrap value of 100 (ML) and a high posterior probability of 1.0 (BI). This is the first report on the mitogenomes within the genus Valsa. These results will pave the way to understanding the evolution and differentiation of mitogenomes in the genus Valsa.