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

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In this study, the complete mitogenomes of three Diaporthe species ( Diaporthe eres ZM79-3, D. phaseolorum ZM33-4 and Diaporthe sp. ZM41-5) were sequenced, assembled and compared with the other three previously sequenced Diaporthe mitogenomes ( D. caulivora VNIIKR SE Dcaul3, D. longicolla MSPL 10-6 and D. sojae VNIIKR SE Dps12). The six Diaporthe mitogenomes were found to be circular DNA molecules, with lengths ranging from 53,646 bp to 108,865 bp. The mitogenomes of the six Diaporthe 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 nad1 gene had the least K2P genetic distance of the 15 core PCGs among the 13 Diaporthales 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 Diaporthe mitogenomes. Frequent intron loss/gain events were detected to have occurred in the cox1 gene during the evolution of the Diaporthales mitogenomes. Although the mitogenomes of 13 species from Diaporthales had undergone large-scale gene rearrangements, six mitogenomes of Diaporthe species had identical gene arrangements. Phylogenetic analysis based on combined mitochondrial gene datasets showed that the six Diaporthe species formed well-supported topologies. To our knowledge, this study is the first report on the mitogenomes of D. phaseolorum ZM33-4 and Diaporthe sp. ZM41-5, as well as the first comparison of mitogenomes among Diaporthe species. Our findings will further promote investigations of the genetics, evolution and phylogeny of the Diaporthe species.

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