Mitochondrial and nuclear gene sequences to infer the phylogeny of Pezizomycotina (Ascomycota)
Pezizomycotina is the largest subphylum of Ascomycota. It includes filamentous species widespread in nature, where they live as saprotrophs, mutualists and/or parasites of animal, plants and fungi. We evaluated the phylogeny of such an important subphylum not only by analyzing the sequence of nuclear genes but also of the core mitochondrial ones, since this organelle may provide additional information. Hence, we compared the phylogenetic reconstitution provided by the concatenated nucleotide sequences of 12 core mitochondrial genes (atp6, cob, cox1-3, nad1-6 and nad4L) and the individual and concatenated nucleotide sequences of 5 widely used nuclear genes (β-tub, tef-1α, gpd, rpb1 and rpb2) of 28 Pezizomycotina species. Alignments were generated with ClustalW and automatically curated with Gblocks 0.91b. Best-fit model of evolution was selected with jModelTest 2.1.7 and data matrices were analyzed under maximum likelihood and bayesian criteria in PhyML 3.0 and MrBayes 3.2, respectively. We found that only rpb2 and the concatenated nuclear and mitochondrial datasets clustered species in accordance with the current systematic of this subphylum, although incongruences were observed in some internal nodes. Discrepancies between the remaining datasets are indicative of the complex evolutionary histories and confirmed that the genes for an accurate phylogenetic estimation should be chosen with special care.