The compactin-producing strain P. solitum 20-01 was obtained from the laboratory collection of Centre ‘Bioengineering’ RAS. Culture conditions and harvesting of mycelia were as described before (Dzhavakhiya & Voinova, 2006).
Mycelia were freeze-dried and ground to fine powder. Total DNA was isolated using DNeasy Plant Mini Kit (Qaigen) according to the manufacturer’s instructions. Mitochondrial genome sequencing was performed using a total genomic DNA sample without prior isolation of the mitochondrial DNA. The genome was sequenced on a Roche Genome Sequencer Z-VAD-FMK purchase FLX using Titanium protocol for a shotgun genome library. The GS FLX run resulted in the generation of about 470 MB of sequences of an average read length of 379 bp. The GS FLX reads were assembled into contigs using the ‘GS de novo assembler’. Sequence coverage was 22×. A single 28 601-bp contig was identified as representing the mtDNA on the basis of extensive sequence similarity to known yeast mitochondrial genomes. MFannot tool (http://megasun.bch.umontreal.ca/cgi-bin/mfannot/mfannotInterface.pl) with default settings was used for mitochondrial genome annotation, which was manually adjusted by sequence alignment of deduced genes with their intronless orthologs from related species. Putative proteins encoded by gene
models with no similarity to characterized genes were analysed by blast homology search against NCBI protein database The codon frequency ABT-888 in vivo was determined with CodonW (Peden, 2005) for concatenated ORFs for all protein-coding genes in the P. solitum mitochondrial genome. Genome contigs, corresponding to P. chrysogenum, A. oryzae and A. terreus mitochondrial genomes, all contained ‘extra’ sequences that were actually duplications of a region of rnL gene and adjacent tRNA gene cluster. These ‘extra’ sequences were considered as assembly artefacts and were manually deleted in the course of annotation. The complete mtDNA sequence of P. solitum 20-01 mtDNA is available in GenBank PLEKHB2 (JN696111,
BioProject ID: PRJNA72889). Whole genome DNA comparison was performed using megablast (Altschul et al., 1997) against NCBI database and mVISTA genome visualization and comparison tool (Frazer et al., 2004). Genome visualization, search for conserved sequence motifs and DNA repeats were performed with Vector NTI (Lu & Moriyama, 2004) and Ugene (http://ugene.unipro.ru/). For phylogenetic analysis, 14 mitochondrial proteins, including subunits of the respiratory chain complexes (cox1-cox3, cob), ATPase subunits (atp6, atp8 and atp9), and seven NADH:quinone reductase subunits (nad1, nad2, nad3, nad4, nad4L, nad5 and nad6), were concatenated and aligned using the MUSCLE algorithm included in the mega5 package (Tamura et al., 2011). The sequence data for 25 filamentous fungi and yeast species with complete mitochondrial genomes were used as follows: Arthroderma obtusum (FJ385029), A. oryzae (AP007176), Aspergillus tubingensis (DQ217399), A. terreus (AAJN01000268.