Trichoderma atroviride hyphal regeneration and conidiation depend on cell -signaling processes regulated by a micro-RNA-like RNA

Supplementary Material data for 'Trichoderma atroviride hyphal regeneration and conidiation depend on cell -signaling processes regulated by a micro-RNA-like RNA.' <br> <br> <strong>Supplemental Dataset 1. </strong> <strong>Annotation and values of differentially expressed genes in the comparison WT-Injury vs WT-Control.</strong> The table is a list of genes of the WT strain responsive to injury in comparison with the control condition (FDR &lt; 0.05; fold-change &gt; |1|). <strong>Supplemental Dataset 2. Annotation and values of differentially expressed genes in the comparison Δ</strong><em><strong>dcr2</strong></em><strong>-Injury vs Δ</strong><em><strong>dcr2</strong></em><strong>-Control.</strong> The table is a list of genes of the Δ<em>dcr2</em> strain responsive to injury in comparison with the control condition (FDR &lt; 0,05; log2 fold-change &gt; |1|). <strong>Supplemental Dataset 3. Annotation and values of differentially expressed genes in the comparison Δ</strong><em><strong>rdr3</strong></em><strong>-Injury vs Δ</strong><em><strong>rdr3</strong></em><strong>-Control.</strong> The table is a list of genes of the Δ<em>dcr2</em> strain responsive to injury in comparison with the control condition (FDR &lt; 0,05; log2 fold-change &gt; |1|). <strong>Supplemental Dataset 4. Annotation of genes of the comparison of the transcriptional response to injury only in the WT strain.</strong> The table is a list of genes responsive to injury exclusively in the WT strain with annotation and log2 Fold-change value<strong>. </strong> <strong>Supplemental Dataset 5. Annotation and values of differentially expressed genes in the comparison Δ</strong><em><strong>dcr2</strong></em><strong>+Δ</strong><em><strong>rdr3</strong></em><strong>/2 vs WT both in response to wound and in the control condition.</strong> The table is a list of genes that have the same expression profile in both mutants with respect to the WT strain, both in the injury and during the vegetative growth in PDA (control condition) (FDR &lt; 0.05; without a fold-change filter). <strong>Supplemental Dataset 6. Annotation and values of differentially expressed genes in the comparison Δ</strong><em><strong>dcr2</strong></em><strong> vs WT, both in response to injury and in the control condition.</strong> The table is a list of differential genes between the Δ<em>dcr2</em> mutant and the WT strain, both growing in PDA medium and in response to injury (FDR &lt; 0,05; without fold-change filter). <strong>Supplemental Dataset 7. Annotation and values of differentially expressed genes in the comparison Δ</strong><em><strong>rdr3</strong></em><strong> vs WT, both in response to injury and in the control condition.</strong> The table is a list of differential genes between the Δ<em>dcr2</em> mutant and the WT strain, both growing in PDA medium and in response to injury (FDR &lt; 0,05; without fold-change filter). <strong>Supplemental Dataset 8. The intersection between downregulated genes in the comparison Δ</strong><em><strong>dcr2</strong></em><strong>-Injury vs WT-Injury and the genes contained in the Cell communication category. </strong>This table shows the profile of the cellular communication genes in the comparison Δ<em>dcr2</em>-I vs WT-I, and their behavior in both the Δ<em>rdr3</em> and the milRNA2 mutant (FDR &lt; 0,05; without fold-change filter). <strong>Supplemental Dataset 9. Differential expression analysis of sRNAs-clusters comparing Δ</strong><em><strong>dcr2 </strong></em><strong>vs WT.</strong> This table shows the values of fold-change of the sRNAs-clusters and their annotation by genomic region. Cells containing the data of the main milRNAs are highlighted in yellow. <strong>Supplemental Dataset 10. Differential expression analysis of ex-siRNAs in the comparison Δ</strong><em><strong>dcr2</strong></em><strong> vs WT, both in response to injury and in the control condition.</strong> This table shows the values of fold-change of the siRNAs and their annotation of the coding region from which they are derived, negative values imply decrease in sRNA (FDR &lt; 0.05; log2 fold-change &gt; |1|). <strong>Supplemental Dataset 11. Annotation and values of differentially expressed genes in the comparison ΔmilRNA2 vs WT, both strains subject to injury.</strong> The table is a list of differential genes between the ΔmilRNA<em>2</em> mutant and the WT strain, both strains subject to injury (FDR &lt; 0,05; without fold-change filter). <strong>Supplemental Dataset 12. Differential expression analysis of target genes in the genetic backgrounds </strong><em><strong>dcr2</strong></em><strong> and milRNA2 mutants compared to the WT strain. </strong>The table shows the target genes of milRNA1, milRNA2 and milRNA2 and the values of fold-change in the contrasts Δ<em>dcr2</em>-C vs WT-C, Δ<em>dcr2 </em>vs WT-I and ΔmilRNA2-I vs WT-I.

本材料为论文《深绿木霉（Trichoderma atroviride）菌丝再生与产孢依赖于类微小RNA（micro-RNA-like RNA）调控的细胞信号转导过程》的补充数据集。

<strong>补充数据集1.</strong> <strong>野生型（WT）损伤组与野生型（WT）对照组比较中的差异表达基因注释与数值</strong>。本表格列出了损伤响应的野生型菌株基因相较于对照条件的差异表达基因集合（错误发现率（FDR, False Discovery Rate）<0.05；倍数变化（fold-change）的绝对值大于1）。
<strong>补充数据集2.</strong> <strong>Δdcr2损伤组与Δdcr2对照组比较中的差异表达基因注释与数值</strong>。本表格列出了Δdcr2突变体菌株损伤响应相较于对照条件的差异表达基因列表（错误发现率（FDR, False Discovery Rate）<0.05；对数2倍数变化（log2 fold-change）的绝对值大于1）。
<strong>补充数据集3.</strong> <strong>Δrdr3损伤组与Δrdr3对照组比较中的差异表达基因注释与数值</strong>。本表格列出了Δdcr2突变体菌株损伤响应相较于对照条件的差异表达基因列表（错误发现率（FDR, False Discovery Rate）<0.05；对数2倍数变化（log2 fold-change）的绝对值大于1）。
<strong>补充数据集4.</strong> <strong>仅野生型菌株损伤转录响应比较中的基因注释</strong>。本表格列出了仅在野生型菌株中响应损伤的基因列表，包含基因注释与对数2倍数变化（log2 fold-change）数值。
<strong>补充数据集5.</strong> <strong>Δdcr2+Δrdr3/2突变体与野生型（WT）在损伤与对照条件下的比较中的差异表达基因注释与数值</strong>。本表格列出了相较于野生型菌株，Δdcr2与Δrdr3两个突变体在损伤处理及马铃薯葡萄糖琼脂（PDA, Potato Dextrose Agar）培养基营养生长（对照条件）中具有相同表达谱的基因集合（错误发现率（FDR, False Discovery Rate）<0.05；无倍数变化过滤条件）。
<strong>补充数据集6.</strong> <strong>Δdcr2与野生型（WT）在损伤与对照条件下的比较中的差异表达基因注释与数值</strong>。本表格列出了Δdcr2突变体与野生型菌株在马铃薯葡萄糖琼脂（PDA, Potato Dextrose Agar）培养基培养及损伤响应条件下的差异基因集合（错误发现率（FDR, False Discovery Rate）<0.05；无倍数变化过滤条件）。
<strong>补充数据集7.</strong> <strong>Δrdr3与野生型（WT）在损伤与对照条件下的比较中的差异表达基因注释与数值</strong>。本表格列出了Δdcr2突变体与野生型菌株在马铃薯葡萄糖琼脂（PDA, Potato Dextrose Agar）培养基培养及损伤响应条件下的差异基因集合（错误发现率（FDR, False Discovery Rate）<0.05；无倍数变化过滤条件）。
<strong>补充数据集8.</strong> <strong>Δdcr2损伤组与野生型损伤组比较中下调基因与细胞通信类别基因的交集</strong>。本表格展示了Δdcr2-Injury vs WT-Injury比较中的细胞通信基因表达谱，以及这些基因在Δrdr3与milRNA2突变体中的表达特征（错误发现率（FDR, False Discovery Rate）<0.05；无倍数变化过滤条件）。
<strong>补充数据集9.</strong> <strong>Δdcr2与野生型（WT）比较中的小RNA簇（sRNAs-clusters, small RNAs-clusters）差异表达分析</strong>。本表格展示了小RNA簇的倍数变化数值及其基因组区域注释，其中包含主要类微小RNA（milRNAs）的单元格以黄色高亮标注。
<strong>补充数据集10.</strong> <strong>Δdcr2与野生型（WT）在损伤与对照条件下比较中的外源小干扰RNA（ex-siRNAs, exogenous small interfering RNAs）差异表达分析</strong>。本表格展示了小干扰RNA（siRNAs, small interfering RNAs）的倍数变化数值及其来源编码区的注释，负值代表小RNA表达量下调（错误发现率（FDR, False Discovery Rate）<0.05；对数2倍数变化（log2 fold-change）的绝对值大于1）。
<strong>补充数据集11.</strong> <strong>ΔmilRNA2与野生型（WT）在损伤处理条件下的比较中的差异表达基因注释与数值</strong>。本表格列出了ΔmilRNA2突变体与野生型菌株在损伤处理条件下的差异基因集合（错误发现率（FDR, False Discovery Rate）<0.05；无倍数变化过滤条件）。
<strong>补充数据集12.</strong> <strong>dcr2与milRNA2突变体遗传背景下靶基因相较于野生型（WT）菌株的差异表达分析</strong>。本表格展示了milRNA1、milRNA2与milRNA2的靶基因，以及Δdcr2-C vs WT-C、Δdcr2-I vs WT-I与ΔmilRNA2-I vs WT-I比较中的倍数变化数值。