The Mitochondrial Genome of Pyrenophora tritici-repentis

An assembled mitochondrial genome of the dothideomycete wheat pathogen Pyrenophora tritici-repentis was blast-searched against a set of 258 conspecific EST sequences, 227 fungal 16S and 23S mitochondrial rRNA sequences extracted from GenBank, the LAHEDES database of homing endonucleases, and the nr protein database in GenBank.  The genome was also searched for tRNA sequences with tRNAscan-SE.  A perl script collated the results of these searches.  The searches hit 103520 of the 157006 total nucleotides in the genome, and 164 features (exons, rRNA, tRNA, and homing endonuclease sequences) were distinguished.  Three of the 38 tRNA genes contained an intron, accounting for 41 tRNA features.  Ten of the tRNA features clustered between nucleotide positions 48840 and 52858, with eight more between 59854 and 62515, and seven more accompanying the 23S rRNA locus between nucleotides 72606 and 78001.  The 16S rRNA locus is between nucleotides 55521 and 58144, and spans an intron.  Many of the remaining features were multiply annotated, since the nr database includes a number of homing endonucleases, and homing endonucleases appeared among the ESTs.  The 59 homing endonuclease features comprised 39178 nucleotides, or 25% of the genome.  Homing endonuclease features were distributed over introns and intergenic regions, which is perhaps consistent with very long initial transcripts that contain multiple genes in the style of a bacterial operon.  Other nr hits were not supported by EST hits, and it is not yet known how many of these are pseudogenes with premature stop codons, versus authentic genes that are weakly expressed.  Transcription of this circular genome is bidirectional, going forward from bases 0 to ca. 30500 and ca. 84500 to the end of the linearized sequence, and in reverse between bases ca. 84500 and ca. 30500.