Figure 1

Xanthomonas-induced small RNAs (xisRNA) signatures and loci possess distinctive attributes. (A) Box plot representation (median, 1st and 3rd quartile and 1.5 × IQR) of the distribution of the length of the experimental sRNA loci, contrasted as a function of whether they correspond to a xisRNA or not. Note that 388 loci were excluded from the plot because their length is above 2000 bp. (B) Distribution of the fraction of reads mapping to the genomic top strand for experimental sRNA loci contrasted as a function of whether the loci correspond to xisRNA, MIRNA or other loci. (C) Distribution of sRNA reads length and mean expression at the 64 xisRNA loci. The hierarchical clustering of xisRNA loci is based on the profiles of reads proportions for individual length values. Mean expression values in each treatment (shades of pink) are represented on a log10 scale. (D) Distribution of mean normalized expression in reads per million (rpm) for pri-miRNA loci (n = 87) versus xisRNA loci (n = 64) in libraries derived from various leaf inoculation treatments. (E) Proportions of the type of rice annotation features overlapping with experimental sRNA loci, contrasted as a function of whether sRNA loci correspond to a xisRNA or not. Overlaps are included in the counts if spanning at least 20 bp. Experimental sRNA loci overlapping both a gene and an exon annotation range are classified as ‘Exon’. Those overlapping a gene annotation element only are classified as ‘Gene’. Others are classified as ‘Intergenic’. (F) Genome browser snapshot of the MSU7 LOC_Os03g15770 locus annotation overlapping with the xisRNA002 ShortStack segment and read coverage tracks (reads per million) for the various experimental treatments. Shorter exon boxes correspond to untranslated regions. Coverage of reads mapping to the top genomic strand is represented with positive values and a violet colored area whereas coverage of reads mapping to the opposite strand is represented with negative values and a golden colored area. The multiple sequence alignment below the genome browser graph corresponds to the three most abundant unique mapping signatures per strand of the ShortStack loci as well as the genomic sequence (LOC ID). In the sequence title, the two numbers indicate, respectively, the count of reads with this sequence in the “BAI3” treatment libraries and the length of the unique sequence. The “–” sign indicates that the original read sequences map to the complementary strand of the genomic locus. In this case, the displayed sequences are thus the reverse complement of the original read sequences. (G) Same as E but for the LOC_Os04g56160 locus region overlapping with xisRNA023. (H) Counts of nucleotides matching (Nmatches) or not matching (Nmismatches) the xisRNA002 loci genomic sequences along the read alignment region. Positions on the x-axis are expressed relative to the sRNA reads 3′-end (last nucleotide is − 1). Positive values are computed for reads mapping to the annotated sense strand of the LOC_Os03g15770 locus. Conversely, negative values correspond to reads mapping to the antisense strand of the annotated loci. (I) Distribution of genomic sequence mismatch ratios along relative positions within reads for xisRNA loci. Each data point represents the ratio of the number of mismatches over the total number of comparisons with the genomic sequence of the MSU annotated transcript for that position of all the reads mapping to a xisRNA locus in the sense orientation (violet) or antisense orientation (golden). Positions where a two-sided Wilcoxon signed rank test measuring differences in xisRNA mismatch ratios between read orientations were significant (BY adjusted p-value ≤ 0.05) are marked with a “*” sign. Here, three “*” indicate an adj. P-val. ≤ 0.001. The bar graph on the top reports on the total count of comparisons for each orientation.