A. Deep-sequencing analysis of the Y-sat small RNAs in
N. benthamiana plants infected with
CMV-Y and Y-sat. Location and frequency of Y-sat-derived small RNAs
(21–24 nt) were mapped to the Y-sat sequence in either sense
(above the x-axis) or antisense (below the
x-axis) orientation. Data from 21-, 22-, 23-, and
24-nt small RNAs are color-coded in green (21 nt), red (22 nt), blue (23
nt) and yellow (24 nt). The table shows the small RNA reads and
percentage of each size of the small RNA. The graph surrounded by broken
lines shows an enlarged graph covering the number of small RNAs from
–20,000 to 40,000 for better visibility of the small RNAs
distribution. Double-headed arrows show the major hot spots where
abundant siRNAs are generated from the Y-sat. B. Histogram of location,
frequency and size distribution of small RNAs corresponding to the
satellite yellow region (SYR) in Y-sat. Numbers on
x-axis refer to location of SYR in the Y-sat sequence.
The number of reads for the siRNAs homologous to SYR is given below the
histogram. SYR is in bold face. C. Detection of siRNAs corresponding to
SYR in 16c:YsatIR and Y-sat-infected plans in Northern blots. As a
helper virus, CMV strain Y was used. LNA probes specific to SYR of Y-sat
were used for hybridization. Ribosomal RNAs were used as a loading
control. Left image was taken after 4 h exposure; right image is an
overnight exposure of the same membrane.