Additional file 15: of Maize RNA PolIV affects the expression of genes with nearby TE insertions and has a genome-wide repressive impact on transcription

Distribution plots Pol IV silenced loci along maize genome. The distribution plots of the differentially expressed genes along the ten maize chromosomes indicate the preferential co-localization of rpd1/rmr6 de-repressed genes (left plots). The chromosomes were divided in 100Kbp not-overlapping windows and for each window the percentage of genes (with respect to the total chromosome genes; blue bars) and of over-expressed genes (with respect to the window gene content) are reported. Yellow and red bars depict the window percentage of up-regulated genes shared in at least three or two independent comparisons, respectively. As control, the distribution of 880 genes randomly selected from the list of 40,457 expressed genes is reported as green bars (plots on the right). The two distributions resulted strongly statistically different (P = 1 × 10−16, by Wilcoxon test), with the random genes uniformly distributed along the genome (they resulted included in 876 genome 100 Kb windows versus the 737 including the up-regulated genes). (PDF 1141 kb

Additional file 13: of Maize RNA PolIV affects the expression of genes with nearby TE insertions and has a genome-wide repressive impact on transcription

TE superfamilies identified amongst genes differentially expressed in rpd1/rmr6 mutant. The number and relative percentage of up- and down-regulated genes classified as TEs (loci with at least one transcript previously classified as HC-TE or pr-TE, see Methods) categorized in superfamilies. The relative abundance of each TEs superfamily within the 114,382 annotated genes is also reported. (DOCX 18 kb

Additional file 3: of Maize RNA PolIV affects the expression of genes with nearby TE insertions and has a genome-wide repressive impact on transcription

Analysis of the genome transcribed fraction at level of individual growth conditions. The tables summarize the increase in the fraction of genome transcribed (at least two mapped reads) observed in rpd1/rmr6 mutant compared to B73, independently calculated for each individual sample. The proportion of the genome transcribed was calculated considering either multi-mapped reads (MAPQ ≥ 1) or uniquely mapped reads (MAPQ = 50) after down-sampling at level of individual RNA-Seq library. Mean and standard deviation for the fraction of genome covered by at least two reads are reported too. (XLSX 13 kb

Additional file 15: of Maize RNA PolIV affects the expression of genes with nearby TE insertions and has a genome-wide repressive impact on transcription

Distribution plots Pol IV silenced loci along maize genome. The distribution plots of the differentially expressed genes along the ten maize chromosomes indicate the preferential co-localization of rpd1/rmr6 de-repressed genes (left plots). The chromosomes were divided in 100Kbp not-overlapping windows and for each window the percentage of genes (with respect to the total chromosome genes; blue bars) and of over-expressed genes (with respect to the window gene content) are reported. Yellow and red bars depict the window percentage of up-regulated genes shared in at least three or two independent comparisons, respectively. As control, the distribution of 880 genes randomly selected from the list of 40,457 expressed genes is reported as green bars (plots on the right). The two distributions resulted strongly statistically different (P = 1 × 10−16, by Wilcoxon test), with the random genes uniformly distributed along the genome (they resulted included in 876 genome 100 Kb windows versus the 737 including the up-regulated genes). (PDF 1141 kb

Additional file 23: of Maize RNA PolIV affects the expression of genes with nearby TE insertions and has a genome-wide repressive impact on transcription

Distribution plots of siRNA loci occupancy. The plots of siRNA loci coverage in flanking regions of subgenome genes, further split between homeologs and single copy genes of each subgenome, confirm that genes of the recessive subgenome 2 are preferentially siRNA-enriched in the upstream region, without differences between retained homeologs and single copy genes. (TIFF 395 kb

Additional file 7: of Maize RNA PolIV affects the expression of genes with nearby TE insertions and has a genome-wide repressive impact on transcription

Schematic representation of how genes were classified with respect to TEs. The “intersectBed” tool [98] was used to identify maize genes with transposon located within 1 Kb upstream of the transcription start site (A; −1 Kb TSS), in the gene body (B), or 1 Kb downstream of the transcription termination site (C; +1 Kb TTS). The same locus could be included in two or three classes when TEs resulted inserted in different gene locations. TEs inserted spanning the TSS in the −500/+500 bp range are indicated in grey in A and B. (TIFF 71 kb

Additional file 21: of Maize RNA PolIV affects the expression of genes with nearby TE insertions and has a genome-wide repressive impact on transcription

Summary of methylation levels at differentially expressed genes flanking regions obtained by permutation analysis. Methylation levels in each context (CG, CHG and CHH) were computed independently for the flanking regions (2 Kb for CG and CHG, 1 Kb for CHH; see Methods) of differentially expressed genes and compared to the average of genes in the genome using regioneR permutation approach [100]. Genes were divided into bins accordingly to fold change expression variation in rpd1/rmr6 mutant compared to wild-type (Additional file 19). For each bin the average methylation value is associated to the p-value obtained by permutation analysis, value that summarizes the statistical significance divergence between bin average methylation level and the average of annotated genes in the genome. Red and blue values indicate statistically higher and lower methylation levels, respectively, compared to the whole gene set. (DOCX 19 kb

Additional file 4: of Genome and transcriptome analysis of the Mesoamerican common bean and the role of gene duplications in establishing tissue and temporal specialization of genes

Supplementary datasets S8–S11. (XLS 395 kb

Additional file 5: of Genome and transcriptome analysis of the Mesoamerican common bean and the role of gene duplications in establishing tissue and temporal specialization of genes

Supplementary datasets S12–S24. (XLS 2190 kb

Additional file 3: of Genome and transcriptome analysis of the Mesoamerican common bean and the role of gene duplications in establishing tissue and temporal specialization of genes

Supplementary datasets S5–S7. (XLS 20553 kb