digitatum Pd01 was performed using a Roche GS-FLX sequencer with

digitatum Pd01 was performed using a Roche GS-FLX sequencer with a half plate run. A total of 519 480 reads were finally obtained and automatically assembled by newbler software (454 Life Science; Li HY et al., unpublished data). All the assembled contigs were aligned to the mitochondrial genome of P. chrysogenum by BLASTN (Altschul et al., 1997), and contigs showing high identity were screened out as fragments of Pd01 mitochondrial DNA. PCR amplification was performed to finish and verify the mitochondrial genome sequence. The nucleotide sequence of Pictilisib in vivo the P. digitatum Pd01 mitochondrial genome has been deposited in GenBank under accession number HQ622809. Coding regions of the mitochondrial genome

were predicted by glimmer3.0 and manually checked (Delcher et al., 1999). Introns and rRNA genes were mainly identified by blast pairwise comparison between mitochondrial genomes of P. digitatum, Penicillium marneffei and P. chrysogenum. tRNA genes were predicted by tRNAscan-SE using the genetic code of mould (Lowe & Eddy, 1997). Cumulative codon usage and amino acid usage were calculated by gcua software (McInerney, 1998). Maximum-parsimony analysis was carried out with the I-BET-762 datasheet concatenated sequences of 14 mitochondrion encoded proteins (cox1, atp9, nad3, cox2,

nad4L, nad5, nad2, cytb, nad1, nad4, atp8, atp6, nad6 and cox3) using mega 4 software (Tamura et al., 2007). Sequence data used in comparative analysis and phylogenetic tree construction were obtained from GenBank: Allomyces macrogynus (NC_001715), Cryptococcus neoformans var. grubii (NC_004336), Saccharomyces cerevisiae (NC_001224), P. marneffei (NC_005256) and P. chrysogenum (AM920464). The draft SPTLC1 assembled genome of P. digitatum Pd01 consists of about 11 000 contigs, and one of them was predicted as a mitochondrial DNA fragment based on its high similarity to that of P. chrysogenum (>95%). A total of 10 026 reads were clustered

into this contig with the average coverage being 134.6-fold, while the average coverage of the chromosome was 12.5-fold. Subsequent PCR amplification was carried out and the mitochondrial genome was completed by sequencing of the products. The mitochondrial genome of P. digitatum Pd01 is a circular molecule with a length of 28 978 bp and an average A + T content of 74.7%. Fifteen protein coding genes were identified, as well as 27 tRNA genes and the large and small subunits of ribosomal RNA (rnl and rns), accounting for approximately 80% of the whole mitochondrial genome in total. All fifteen mitochondrial protein coding genes were conserved between P. digitatum, P. marneffei and P. chrysogenum, while levels of amino acid pairwise sequence similarity varied between 73% and 100% (Table 1). The rps5 gene was the least homologous followed by nad6. Other genes showed more than 90% amino acid identity between the three species, and atp8 was the most conserved, showing 100% identity between the three Penicillium species.

Leave a Reply

Your email address will not be published. Required fields are marked *

*

You may use these HTML tags and attributes: <a href="" title=""> <abbr title=""> <acronym title=""> <b> <blockquote cite=""> <cite> <code> <del datetime=""> <em> <i> <q cite=""> <strike> <strong>