Table 1.
Summary statistics of RNA-Seq and ChIP-Seq reads (Illumina/HiSeq2500) collected from three biological replicates of rust-inoculated and mock-inoculated common bean.
Fig 1.
Identification of (A) H3K9me2 and (B) H4K12ac regions in mock-inoculated and inoculated common bean.
The number of peaks at 0, 12 and 84 hai were compared against their respective backgrounds, 0MI, 12MI and 84MI. The peaks were also compared between 12Ivs0I, 84Ivs0I and 84Ivs12I against two histone modifications.
Table 2.
Summary of peaks annotated, features extracted, and number of peaks identified per feature in common bean.
Fig 2.
Peak signals visualized on common bean chromosomes by using Genome Viewer.
Comparative visualization of a representative region on chromosome 11 in rust-inoculated common bean at 12 hai with mock-inoculated sample as background for H3K9me2 and H4K12ac modifications using Integrative Genomics Viewer (IGV).
Table 3.
Difference in marking of disease-resistance genes by H3K9me2 modification at various time points after inoculation.
Table 4.
Difference in marking of disease-resistance genes by H4K12ac modification at various time points after inoculation.
Fig 3.
Total number of significantly enriched genes identified between different time points (0, 12 and 84 hai) in rust-inoculated common bean from RNA-Seq analysis.
The number of uniquely and commonly enriched significant genes and their respective time points were depicted as a Venn diagram. For instance, the uniquely enriched significant genes and their respective time points include: 541 (12Ivs0I), 530 (84Ivs0I) and 739 (84Ivs12I).
Table 5.
Summary of differentially expressed stress-related genes at 12Ivs0I, 84Ivs0I and 84Ivs12I from RNA-Seq analysis.
Table 6.
Summary of defense-related genes from RNA-Seq analysis.
Fig 4.
Functional classification of significantly enriched genes in mock- and rust-inoculated (0, 12 and 84 hai) leaves of common bean.
The GO enriched genes are functionally classified based on EuKaryotic Orthologous Groups (KOGs). KOG categories are presented on X-axis and number of genes in the corresponding classes are shown on Y-axis.
Table 7.
Representative transcription factors (TFs) expressed in bean-rust interaction.
Fig 5.
Putative KEGG pathway (ID: 04626) identified in plant-pathogen (common bean-Uromyces appendiculatus) interaction.
The boxes highlighted in red are enzymes (10) identified in this study.
Fig 6.
Differentially expressed genes identified in bean-bean rust interaction pathway (ID: 04626) at 0, 12 and 84 hai.
The differential expression (Log2FC>2) of six selected genes (cyclic nucleotide-gated channel 14, callose synthase 5, PEP1 receptor 1, leucine-rich receptor-like protein kinase family protein, NB-ARC domain-containing disease resistance protein, and heat shock protein 90.1) at different time points is shown in the Figure.
Table 8.
Differentially marked H3K9me2 and H4K12ac modifications and transcription in common bean-rust interaction.
Table 9.
Genes and their functions associated with histone modifications and transcription in common bean-rust interaction.
Fig 7.
Validation of the relative expression levels of seven selected genes from ChIP-Seq analysis by quantitative Real-Time RT-PCR (qPCR).
Expression pattern of selected common bean genes in mock-inoculated and rust-inoculated leaf samples at different time points. The x-axis shows different time point and y-axis shows relative fold change value (Log2FC). Different alphabets in this Figure indicate statistically significant (p-value<0.05) difference in relative expression of each gene between different time points (0, 12, 84 hai) for both inoculated and mock-inoculated leaf samples. The qPCR results from two technical replicates were subjected to ANOVA by using Minitab17 software.
Fig 8.
Validation of the relative expression levels of seven selected genes from RNA-Seq analysis by quantitative Real-Time RT-PCR (qPCR).
Expression pattern of selected common bean genes in mock-inoculated and rust-inoculated leaf samples at different time points. The x-axis shows different time point and y-axis shows relative fold change value (Log2FC). Different alphabets in this Figure indicate statistically significant (p-value<0.05) difference in relative expression of each gene between different time points (0, 12, 84 hai) for both inoculated and mock-inoculated leaf samples. The qPCR results from two technical replicates were subjected to ANOVA by using Minitab17 software.