AT-rich codons are much more abundant, reflecting the high AT content of the P. solitum mitochondrial genome. Codons for amino acids with nonpolar side chains (Phe, Leu and Ile) are very frequent, which is not surprising given the hydrophobic nature of encoded proteins of respiratory membrane complexes. Among

the 27 tRNA genes, there are several isoacceptor tRNAs for glycine, arginine, leucine, serine and isoleucine. The abundant ATA codons for isoleucine are probably read by one of the three predicted tRNA-M following the Daporinad molecular weight cytosine to lysidine modification of the CAU anticodon, like in fungal, protist and fission yeast mitochondrial genomes (Bullerwell et al., 2003; Grayburn et al., 2004). Phylogenetic relationships find more among Eurotiales based on multigene comparison of nuclear-encoded genes are well established (Spatafora et al., 2006). Our

phylogenetic analysis based on concatenated mitochondrial protein sequences confirmed the monophletic origin of Eurotiomycetidae and the current view of the taxonomic position of Aspergilli and Penicilli within Onygenales and related taxa (Geyser, 2006). Phylogenetic trees constructed using both ML and Bayesian approaches were essentially congruent (Fig. 2 and Fig. S4). Aspergillus and Penicillium species were divided into two well-resolved clades with high support. Interestingly, the determined phylogenetic position of the pathogenic dimorphic fungus P. marneffei suggests that this species is more distantly related to the studied members of Trichocomaceae. The higher degree of divergence of mitochondrial protein sequences ioxilan between P. marneffei and other members of Trichocomaceae correlates with the difference of gene order in P. marneffei mitochondrial genome relative to the mitochondrial genomes of A. nidulans and other Aspergillus and Penicillium mtDNAs described here. Altogether, these observations question the current taxonomic position of P. marneffei and suggest that this fungus may represent a separate genus within Trichocomaceae, as suggested earlier during nuclear genome comparisons (van den Berg et al., 2008). The extensive similarity of Aspergillus and Penicillium mitochondrial genomes

in terms of gene size, content and sequence homology (Table 1) was also reflected in the almost perfect conservation of mitochondrial gene order in compared species. The genus-specific syntenic regions cover whole genomes, include all main protein- and RNA-encoding genes and are only interrupted by insertions of several ORFs with unknown functionality. The very high degree of colinearity of Aspergillus and Penicillium genomes is also evident from the intergenera gene order comparison (Fig. S2). The main architectural features, such as the presence of two clusters of tRNA genes flanking the rnL gene and clusters of atp and nad genes characteristic of syntenic patterns and specific to Pezizomycotina mitochondrial genomes, are present (Ghikas et al., 2006).