Figure 3
From: An atypical class of non-coding small RNAs is produced in rice leaves upon bacterial infection
A summary of xisRNAs features in the analyzed sRNA-seq datasets. In the complex heatmap layout, the top 60 xisRNA loci with the highest maximum treatment mean expression across datasets are described row-wise. The first component, on the left, reports on expression (reads per million) in the various inoculation treatments of the different datasets. In the type of treatment legend, the “Xoo_Af” and “Xoo_As” labels stand for African Xoo and Asian Xoo strains, respectively. The DE patterns component shows whether xisRNA loci were detected as DE in various comparisons. The “nDE” dot plot depicts the number of comparisons where the xisRNA locus was deferentially expressed. Cells in gray indicate that the xisRNA locus was not considered in the dataset because the loci was not detected by ShortStack or because reads in this dataset did not pass our xisRNA loci features criteria. The subsequent plots on the right depicts the size distribution of reads (“Read_Length_Rel_Freq”), the fraction of antisense reads (“AS_Fraction”), the proportion of antisense reads with distinct 5′-end first nucleotide (“AS_Reads_N1_Rel_Freq”) and the specific nucleotide mismatch ratios for relative positions − 22 to − 1 of antisense reads using xisRNA loci mapping reads from the “BAI3” and “Diversity” datasets. The MSU7 identifier of the gene overlapping with a xisRNA duplex locus is indicated together with the kinase subfamily into which the encoded protein is classified (“Kin_Fam.” column) as well as the RLCK protein name, when relevant and available. Finally, the “In_Exon” column indicates whether the xisRNA duplex loci is fully included in an exon of an annotated mRNA of the gene. All numerical values reported in the graphic were computed using reads mapping to the xisRNA duplex loci. Note that the antisense polarity is defined relative to the orientation of the underlying cis-gene. To compute values that incorporate a notion of polarity for xisRNA loci that do not overlap with an annotated gene, reads mapping to the top strand were arbitrarily considered to be in the sense orientation.
