Figure 3

Tandemly distributed small RNAs (sRNAs) identified on the highly structured microRNA (miRNA) precursor candidates in Dendrobium officinale.

(A) The transcript comp124801_c0_seq1 assembled by RNA-seq reads could form an internal hairpin structure with a long-stem region (partially delineated by a pink box). In addition to generating miRNAs (dof-miR340, dof-miR341, dof-miR1002 and dof-miR1004) and miRNA*s (dof-miR1002* and dof-miR1004*), the long-stem region potentially encodes three pairs of tandemly distributed sRNAs (124801_sRNA1 and 124801_sRNA6, 124801_sRNA2 and 124801_sRNA5 and 124801_sRNA3 and 124801_sRNA4). Each pair possesses 2-nt 3’ overhangs. Five degradome signatures (124801_degr1 to 124801_degr5) were detected at the ends of certain tandemly distributed sRNAs. And, 124801_degr3 also appeared at the 5’ ends of dof-miR-340 and dof-miR-341 and 124801_degr4 and 124801_degr5 are present at the 3’ ends of dof-miR-1004. The accumulation levels (normalized in RPM, reads per million; please refer to Materials and Methods for RPM calculation) of the degradome signatures, the miRNAs, the miRNA*s and the tandemly distributed sRNAs are shown in the diagrams on the right of the panel. Their accumulation levels in the stems of Dendrobium officinale were highlighted in pink background color. (B) The transcript comp168357_c1_seq6 assembled by RNA-seq reads could form an internal hairpin structure with a long-stem region (partially included in a pink box). Within this region, three pairs of sRNAs (including 168357_sRNA2 and 168357_sRNA6, 168357_sRNA3 and 168357_sRNA5 and the dof-miR-1023/dof-miR-1023* duplex) along with two unpaired sRNAs (168357_sRNA1 and 168357_sRNA4) were identified to be distributed tandemly. Each pair possesses 2-nt 3’ overhangs. Eleven degradome signatures (168357_degr1 to 168357_degr11) were detected at the ends of certain tandemly distributed sRNAs. The accumulation levels (in RPM) of the degradome signatures, the miRNAs, the miRNA*s and the tandemly distributed sRNAs are shown in the diagrams on the right of the panel. The secondary structures of the two transcripts were predicted by using RNAfold (http://rna.tbi.univie.ac.at/cgi-bin/RNAfold.cgi)²².