Identiļ¬cation of B. rapa miRNAs responsive to cold
stress
To identify known miRNAs in our sequence libraries, we aligned the
sequenced reads with mature miRNAs in miRBase and the B. rapareference genome, allowing no more than two mismatches. In total, 77
mature miRNAs related to 184 conserved miRNA precursors were found in
our libraries. Among them, 52 miRNAs were conserved with those inArabidopsis , while 16 miRNAs were Brassica -specific miRNAs
(Table S2). To further identify novel miRNA candidates, the flanking
sequences of unknown small RNAs in genome were extracted for RNA
structure prediction. Based on the plant miRNA criteria (Axtell et al.,
2018), we identified 11 highly credible novel miRNAs (Table S3). Among
them, novel-miR1 and novel-miR11 were identified with more than 100
reads.
Among the 77 known miRNAs, 16 miRNAs were differentially expressed
between the cold treatment and the control (>1.5-fold)
(Table 1). Among these mature miRNAs, bra-miR157a~c,
bra-miR161, bra-miR393f, bra-miR396b, bra-miR319c, bra-miR156k,
bra-miR1140, bra-miR158a, and bra-miR156a~f were
down-regulated; and bra-miR168d, bra-miR403,
bra-miR390a~b, bra-miR398b~c,
bra-miR408, and bra-miR1885 were up-regulated under cold treatment.
Among them, the Brassica- specific bra-miR1885 was induced more
than four-fold by cold stress. Among the novel miRNAs, only novel-miR11
was cold-responsive. Taken together, the small RNA profiling provided
cues to cold-responsive miRNAs in B. rapa .