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Fig. 1 | BMC Genomics

Fig. 1

From: Spatiotemporal expression profile of novel and known small RNAs throughout rice plant development focussing on seed tissues

Fig. 1

sRNA-seq read mapping on the rice genome and novel sRNA loci. A Fraction of mapped reads aligning to ribosomal RNA (rRNA), transfer RNA (tRNA), small nuclear RNA (snRNA) or small nucleolar RNA (snoRNA) loci. B Size distribution of 18-40 nt mapped reads. In all cases, error bars indicate the standard deviation. Veg = vegetative phase; Gen = generative phase. Veg shoot indicates leaves and gen shoot indicates leaf blades. C Number of novel loci for each sRNA type. Classification is based on the results of ShortStack cluster calling [25]. D Frequency of occurrence of each nucleotide at the 5′ end of novel sRNA loci. E Association of the different types of novel sRNA loci with TE regions in the rice genome. Permutation tests with 1000 permutations were performed to estimate the null distribution of sRNA loci randomly overlapping with the regions of interest, using regioneR. z-scores were calculated as the deviation of the actual number of overlaps from the number of overlaps under the null distribution, relative to the standard deviation. Stars indicate significant enrichment/depletion * = p < 0.05; ** = p < 0.01; *** = p < 0.001. In all panels siRNAx = locus mainly producing reads of length x; OtherRNA = loci where less than 80% of the reads are of 20-24 nt length, therefore considered as not processed by DCL enzymes and thus not classified as siRNA or miRNA

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