Figure 4

Much of the small RNA transcriptome of Miscanthus × giganteus ( Mxg ) matches high copy number genomic repeats. (a) Number of Mxg repeats, or gene space sequence reads, matching a small RNA (sRNA), as determined by matching repeat sequences to sRNA signatures produced by sequencing sRNA from three Mxg tissues. Repeats are annotated by broad category where known. Unclassified repeats match a sequence in the database without an assigned category; unannotated repeats do not have a database match. Gene space reads are genome survey reads that match sorghum filtered coding sequences (Figure 1). (b) Percentages of small RNA produced by different repeat classes. Normalized abundance of small RNA signatures was calculated in transcript per quarter (TPQ) million reads. In addition to the data shown, telomeres and telomere-associated repeats together produced 0.09% of the total amount of sRNA (a percentage too small to effectively display in the chart).