Introns were detected in the cox1, cox2, nad5, rns and rnl genes. All of these are type I introns, except for the single type II intron in rns. All type I introns contained endonuclease-like gene sequences with the conserved LAGLIDADG motif, except for the first intron in the cox1 gene, which had the GIY-YIG motif. The endonuclease in cox1 intron-12 appears to be truncated and does not have the full LAGLIDADG domain. Of the genes found in the mitochondrial genome of T. cingulata, the structure of cox1 is the most complex. Of the 16 exons that

make up the cox1 gene, five are smaller than 20 nt long, with the smallest two being only 11 nt. All 15 introns have at least one ORF larger than 100 codons. ORFs encoding endonuclease-like sequences BIBF 1120 mouse were also seen in all other introns, except for intron-1 of cox2. The reading frames of the exons 1 and Avasimibe in vivo 2 of nad5 continue well beyond the predicted splice sites into the respective introns. These extended reading frames also encode endonuclease-like sequences within an ORF (Fig. 1). While the coding regions have been well conserved among the Agaricomycotina

and to a lesser extent with U. maydis, the introns show less similarities (Fig. 1). Trametes cingulata intronic ORFs show greater sequence similarity to P. ostreatus and M. perniciosa than to the more distantly related U. maydis. Schizophyllum commune and C. neoformans do not have introns in the same genes as T. cingulata. The DNA and RNA polymerases dpo and rpo, which have been reported in P. ostreatus and M. perniciosa, are not present in the T. cingulata mitochondrial genome nor were they annotated or obvious in the S. commune, C. neoformans or U. maydis mitochondrial genomes. The 25 identified tRNAs genes

represent all 20 amino acids and include three copies encoding tRNAMet and two each of tRNAArg, tRNASer and tRNALeu. Single genes encode the other 16 tRNAs. We analyzed codon usage for the 15 protein-encoding annotated genes (Supporting Information, Table S1) and found that all of these genes use TAA Amylase as the stop codon, except for nad5, which uses TAG. nad5 is also the only gene that uses GAG as a codon for glutamic acid and AGG for arginine, which is otherwise encoded exclusively by AGA. Other codons for arginine, CGG, CGT and CGC, are not used. The glycine codon GGC is also not used. At least one of these four otherwise unused codons is used one or more times in all five of the unidentified ORFs, lending additional support to the hypothesis that these ORFs are not expressed genes. The alternate codon for tryptophan TGA that differs from the standard codon table is not used either as a codon for tryptophan or to represent a stop codon in the 15 protein-encoding annotated genes. However, it is present twice in ORF111 and once in ORF158. Nad4L is the only gene that uses AAG to code for lysine and does it only at one position. Only 13% of the codons for tyrosine use TAC, with the rest using TAT.