Identiļ¬cation of B. rapa miRNAs responsive to cold
stress
To identify known miRNAs in our sequence libraries, we aligned the small
RNA sequences 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
secondary structure prediction using RNAfold. Based on the plant miRNA
criteria (Axtell et al., 2018, see the detail in the method), 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 sample under 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, theBrassica- 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
potential candidates of cold-responsive miRNAs in B. rapa .