MOESM3 of Emergence and loss of spliceosomal twin introns

Additional file 3: Table S3. Sequences used for the BioDA phylogeny (Fig. 6)

Strains used in the present work.

<p>Strains used in the present work.</p

Impact of <i>vel1</i> deletion or overexpression on growth and cellulase formation by <i>T. reesei</i> on lactose.

<p>Cellulase formation by <i>T. reesei</i> QM 9414, a Δ<i>vel1</i> mutant and a <i>vel1OE</i> strain during growth on lactose. Only one strain is shown, but other strains with the same genotype gave consistent data. Data shown are means of at least two independent experiments and three measurements. Blue line and empty blue circles: lactose concentration; dark red dotted line and empty triangles: cellulase activity; bright red dashed line and full red triangles, extracellular protein concentration; black dashed line and black squares, fungal biomass concentration.</p

The impact of VEL1 on the utilization of different carbon sources by <i>T. reesei</i>.

<p>Effect of <i>vel1</i> on the growth of <i>T. reesei</i> on various carbon sources either in light or in darkness Photos were taken 5 days (120 h) after inoculation of the plates. Additional 2 days of cultivation did not alter the phenotypes shown.</p

VEL1 is required for <i>T. reesei</i> development.

<p>(A) Effect of <i>vel1</i> on asexual development of <i>T. reesei</i>. Formation of conidia in the presence of ambient light (empty bars) and darkness (full bars) by <i>T. reesei</i> QM 9414 (1), in two <i>vel1OE</i> (2,3) and three <i>Δvel1</i> strains (4–6). Data are means of at least three independent biological experiments, and only results with p<0.05 are shown. (B) Phenotype of the parent strain and two <i>Δvel1</i> strains (RKA14 and RKA17; see <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0112799#pone-0112799-t001" target="_blank">Table 1</a>) after 5 days of growth on PDA. (C) absence of fruiting body formation between <i>Δvel1</i> (top) and the compatible mating partner strain CBS 999.79 (bottom) in the presence of ambient light,L, and darkness, D. (D) control plate between QM 9414 (left) and CBS 999.79 (right) in the presence of ambient light. Note that fruiting in the wild-type does not occur in darkness <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0112799#pone.0112799-Seiboth3" target="_blank">[35]</a>, and thus no such plate is shown. (E) Fruiting body formation between <i>vel1OE</i> (bottom) and CBS 999.79 (top) under ambient light (L) or darkness (D). One of at least three replicate experiments is shown. The insert represents a magnification of the boxed part, highlighting the primordia.</p

Impact of <i>vel1</i> deletion or overexpression on transcript levels of two cellulase, one hemicellulase and a cellulase regulator gene in <i>T. reesei</i> during growth on lactose.

<p>mRNA levels of two cellulase genes (<i>cel7a, cel6a</i>), one xylanase gene (<i>xyn2</i>) and the cellulase regulator <i>xyr1</i> in <i>T. reesei</i> QM 9414 (full circles and solid line), a <i>Δvel1</i> strain (empty circles and dotted line) and a <i>vel1OE</i> strain (full traingles and dashed line) under the fermentation conditions on lactose as shown in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0112799#pone-0112799-g005" target="_blank">Figure 5</a>. mRNA levels are given in arbitrary units, which were calculated by normalizing the ratio of the respective gene transcript to that of the housekeeping gene <i>tef1</i>, and relating all ratios to that obtained for the given gene at 17.5 hrs in <i>T. reesei</i> QM9414. Only one mutant strain is shown, but other strains with the same genotype gave consistent data. Data shown are means of at least two independent experiments and three measurements.</p

Effect of carbon source and light on <i>vel1</i> transcript levels in <i>T. reesei</i>.

<p>Transcript levels of <i>vel1</i> during growth on glucose, glycerol and lactose in <i>T. reesei</i> QM 9414 in the presence of ambient light (white bars) and darkness (full bars). Transcript levels are given in arbitrary units, which were calculated by normalizing the <i>vel1/tef1</i> ratio to that on glucose (12 h, ambient light). Data are means of at least 3 biological replicas. The asterisk indicates the time point where the cultures started to sporulate (this time point was the same in light and darkness).</p

The impact of VEL1 on morphology of <i>T. reesei</i> in submerged culture.

<p>Morphology of growing hyphae of <i>T. reesei</i> QM9414 (A–E) and the Δ<i>vel1</i> (F–L) strains during submerged growth on Mandels-Andreotti medium with glycerol (1%, w/v) as a carbon source at 12 (A–B and F–G), 48 (C and H–I) and 72 (D–E and J–K) hours following inoculation.</p

Impact of <i>vel1</i> deletion or overexpression on transcript levels of two cellulase, one hemicellulase and a cellulase regulator gene in <i>T. reesei</i> upon induction by sophorose.

<p>Transcript levels of two cellulase genes (<i>cel7a, cel6a</i>), one xylanase gene (<i>xyn2</i>) and the cellulase regulator <i>xyr1</i> in <i>T. reesei</i> QM 9414 (full symbols), a <i>vel1</i> strain (empty symbols) and a <i>vel1OE</i> strain (grey symbols) upon induction of mycelia, pregrown on glycerol for 20 hrs, by sophorose for 4 hrs. Transcript levels are given in arbitrary units, as specified in legend to <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0112799#pone-0112799-g006" target="_blank">figure 6</a>. The asterisks indicate cases were the relative mRNA level was below the limit of detection. Only one mutant strain is shown, but other strains with the same genotype gave consistent data. Data shown are means of at least two independent experiments and three measurements.</p