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.' Supplemental Dataset 1.   Annotation and values of differentially expressed genes in the comparison WT-Injury vs WT-Control.  The table is a list of genes of the WT strain responsive to injury in comparison with the control condition (FDR |1|). Supplemental Dataset 2.  Annotation and values of differentially expressed genes in the comparison Δdcr2-Injury vs Δdcr2-Control.  The table is a list of genes of the Δdcr2 strain responsive to injury in comparison with the control condition (FDR |1|). Supplemental Dataset 3. Annotation and values of differentially expressed genes in the comparison Δrdr3-Injury vs Δrdr3-Control.  The table is a list of genes of the Δdcr2 strain responsive to injury in comparison with the control condition (FDR |1|). Supplemental Dataset 4. Annotation of genes of the comparison of the transcriptional response to injury only in the WT strain.  The table is a list of genes responsive to injury exclusively in the WT strain with annotation and log2 Fold-change value.  Supplemental Dataset 5. Annotation and values of differentially expressed genes in the comparison Δdcr2+Δrdr3/2 vs WT both in response to wound and in the control condition.  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 Supplemental Dataset 6. Annotation and values of differentially expressed genes in the comparison Δdcr2 vs WT, both in response to injury and in the control condition.  The table is a list of differential genes between the Δdcr2 mutant and the WT strain, both growing in PDA medium and in response to injury (FDR Supplemental Dataset 7. Annotation and values of differentially expressed genes in the comparison Δrdr3 vs WT, both in response to injury and in the control condition.  The table is a list of differential genes between the Δdcr2 mutant and the WT strain, both growing in PDA medium and in response to injury (FDR Supplemental Dataset 8. The intersection between downregulated genes in the comparison Δdcr2-Injury vs WT-Injury and the genes contained in the Cell communication category. This table shows the profile of the cellular communication genes in the comparison Δdcr2-I vs WT-I, and their behavior in both the Δrdr3 and the milRNA2 mutant (FDR Supplemental Dataset 9. Differential expression analysis of sRNAs-clusters comparing Δdcr2 vs WT. 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. Supplemental Dataset 10. Differential expression analysis of ex-siRNAs in the comparison Δdcr2 vs WT, both in response to injury and in the control condition. 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 |1|). Supplemental Dataset 11. Annotation and values of differentially expressed genes in the comparison ΔmilRNA2 vs WT, both strains subject to injury.  The table is a list of differential genes between the ΔmilRNA2 mutant and the WT strain, both strains subject to injury (FDR Supplemental Dataset 12. Differential expression analysis of target genes in the genetic backgrounds dcr2 and milRNA2 mutants compared to the WT strain. The table shows the target genes of milRNA1, milRNA2 and milRNA2 and the values of fold-change in the contrasts Δdcr2-C vs WT-C, Δdcr2 vs WT-I and ΔmilRNA2-I vs WT-I. </p

The Genomes of Three Uneven Siblings: Footprints of the Lifestyles of Three Trichoderma Species.

The genus Trichoderma contains fungi with high relevance for humans, with applications in enzyme production for plant cell wall degradation and use in biocontrol. Here, we provide a broad, comprehensive overview of the genomic content of these species for "hot topic" research aspects, including CAZymes, transport, transcription factors, and development, along with a detailed analysis and annotation of less-studied topics, such as signal transduction, genome integrity, chromatin, photobiology, or lipid, sulfur, and nitrogen metabolism in T. reesei, T. atroviride, and T. virens, and we open up new perspectives to those topics discussed previously. In total, we covered more than 2,000 of the predicted 9,000 to 11,000 genes of each Trichoderma species discussed, which is >20% of the respective gene content. Additionally, we considered available transcriptome data for the annotated genes. Highlights of our analyses include overall carbohydrate cleavage preferences due to the different genomic contents and regulation of the respective genes. We found light regulation of many sulfur metabolic genes. Additionally, a new Golgi 1,2-mannosidase likely involved in N-linked glycosylation was detected, as were indications for the ability of Trichoderma spp. to generate hybrid galactose-containing N-linked glycans. The genomic inventory of effector proteins revealed numerous compounds unique to Trichoderma, and these warrant further investigation. We found interesting expansions in the Trichoderma genus in several signaling pathways, such as G-protein-coupled receptors, RAS GTPases, and casein kinases. A particularly interesting feature absolutely unique to T. atroviride is the duplication of the alternative sulfur amino acid synthesis pathway