Predicted milRNAs and the appearance of their reads within the three datasets.

<p>Predicted milRNAs and the appearance of their reads within the three datasets.</p

Characterization of Dicer-dependent small RNAs.

<p>(A) Strain-specific and overrepresented unique reads in ∆<i>ku70</i>FRT2 compared to ∆<i>dcl2</i>∆<i>dcl1</i> and <i>vice versa</i>. (B) Nucleotide preference and size distribution of Dicer-dependent small RNAs. (C) Pie graphs of the relative abundance of Dicer-dependent sRNAs and (D) Dicer-dependent sRNA-producing loci in accordance to their strand bias.</p

Accumulation of sRNAs along representative coding-sequences.

<p>(A) Normalized read count (TPTM: transcripts per ten million) of ∆<i>ku70</i>FRT2 (grey graph) and ∆<i>dcl2</i>∆<i>dcl1</i> (black graph) of two representative Dicer-dependent coding regions, the Copia13-like transposable element Pc17g00440 and the putative DNA-binding protein Pc12g14660. (B) Dicer-independent sRNA accumulation for the coding region of the putative cell-wall protein Pc20g06530 and for a histidine tRNA-gene cluster. To ensure a faultless representation of Dicer-independent reads the graphs for ∆<i>dcl2</i>∆<i>dcl1</i> were slightly moved to the right.</p

Statistical summary of small RNA sequencing data and distribution of small RNAs with perfect match to the genome sequence of <i>P</i>. <i>chrysogenum</i>.

<p>Statistical summary of small RNA sequencing data and distribution of small RNAs with perfect match to the genome sequence of <i>P</i>. <i>chrysogenum</i>.</p

Chromosomal distribution of small RNAs and sRNA-producing loci.

<p>Pie graphs for total reads (A) and unique reads (B) are showing the relative abundance of sRNAs located in tRNAs, rRNAs, intergenic, exonic and intronic regions in ∆<i>ku70</i>FRT2. Alignments of sRNA-producing loci of ∆<i>ku70</i>FRT2 (C) and ∆<i>dcl2</i>∆<i>dcl1</i> (D) show that the number of sRNAs that map to both DNA strands of one feature have strongly increased and that the fraction of sRNA loci that align to exonic regions in sense orientation has decreased substantially in ∆<i>dcl2</i>∆<i>dcl1</i> compared to ∆<i>ku70</i>FRT2.</p

Length distribution of <i>P</i>. <i>chrysogenum</i> small RNA population.

<p>Length distribution of mapping sRNA reads for the datasets of total (A) and unique (B) reads obtained from three different samples. Frequency of the 5'-nucleotide of the unique reads of ∆<i>ku70</i>FRT2 (C) and ∆<i>dcl2</i>∆<i>dcl1</i> (D) in dependency of their read length.</p

Characterization of small RNA producing loci.

<p>Characterization of small RNA producing loci.</p

Validation and expression analysis of (A) milR-1 and (B) milR-21.

<p>Total RNA from strain P2niaD18, the recipient ∆<i>ku70</i>FRT2 as well as Dicer single and double mutant strains were used for polyacrylamide gel electrophoresis and northern blot analysis. Mature milRNAs (milRs) and milRNA precursors (pre-milRs) were detected with revers complement ³²P-labled DNA probes. Below, loading controls of the total RNA, stained with ethidium bromide (EtBr), and the predicted secondary structures of milRNA precursors are given. On the secondary structures, milRNA sequences are highlighted in red and arrows indicate the expected Dicer cleavage sites.</p

Horizontal gene transfer of beta-lactam biosynthesis genes from prokaryotes to eukaryotes.

<p>The antibiotic biosynthesis genes are derived either from gram-positive (e.g. <i>Streptomyces</i> spp.) or gram-negative (e.g. <i>Lysobacter</i> spp.) bacteria. The first two steps of both penicillin and cephalosporin C biosynthesis are catalyzed by the gene products of <i>pcbAB</i> and <i>pcbC. P. chrysogenum</i> harbors one additional gene, <i>penDE</i> (not shown), to perform the last step of penicillin biosynthesis, whereas <i>Ac. chrysogenum</i> has obtained several additional genes for production of cephalosporin C. Genetic engineering approaches have been used to introduce these genes into <i>P. chrysogenum</i>. Chemical engineering approaches have enabled the precursors of both the <i>Ac. chrysogenum</i> and <i>P. chrysogenum</i> biosynthesis pathway to be used for the production of new cephalosporin derivatives.</p

Selected fungal products from different compound classes, their application, and producers.

<p>Selected fungal products from different compound classes, their application, and producers.</p