The mitochondrial genome contribution to the phylogeny and identification of Metarhizium species and strains
The genus Metarhizium is composed of entomopathogenic fungal biological control agents (BCAs) used for invertebrate pest control. The phylogenetic relationships of species within this genus are still under scrutiny as several cryptic species can be found based on nuclear molecular markers. Mitochondrial (mt) molecular markers have been used successfully to characterize other fungal species and strains, due to their higher rate of mutations compared to the nuclear genome. In this work, the mt genome of Metarhizium brunneum ARSEF 4556 was fully sequenced and a comparative genome analysis was conducted with seven other available mt genomes belonging to five Metarhizium species, of which only two had been annotated previously. Specifically, the mt genomes of M. anisopliae, M. brunneum, M. robertsii, M. guizhouense and M. majus were studied. The mt genomes were highly conserved, with the exception of M. majus, which contained several introns and intronic or free standing genes that encode GIY-YIG and LAGLIDADG endonucleases. Therefore, Metarhizium appears to demonstrate greater conserved stability than other fungal mt genomes. Furthermore, this analysis located diverse mt regions ideal for species/ strain discrimination. Seven such regions were identified in both intergenic domains and gene fragments. The sequencing of these regions revealed several SNPs among 38 strains tested, 11 of which were uncharacterized. Single gene phylogenies presented variable results which may be used further for intra-species discrimination. Phylogenetic trees based on the concatenation of mt domains and the nuclear ITS1-5.8S-ITS2 region showed discrimination of the species studied and allowed the identification of uncharacterized strains. These were placed mostly within species M. anisopliae and M. brunneum. Five strains clustered together in a clade related to M. brunneum, suggesting that they comprise a cryptic sp