Identification of known and novel miRNAs in B. rapa
We aligned the clean reads with known miRNAs in the miRBase (https://www.mirbase.org/), allowing two mismatches using TopHat (http://ccb.jhu.edu/software/tophat/index.shtml). The potential miRNAs were mapped to B. rapa reference genome (http://brassicadb.cn/#/) to extract the 600-bp flanking sequence. The flanking sequence of miRNAs were also aligned with known pre-miRNAs to confirm their identities of miRNA family. The flanking sequence of unknown small RNAs was also used to predict secondary structures using RNAfold software (http://rna.tbi.univie.ac.at/cgi-bin/RNAWebSuite/RNAfold.cgi). Novel miRNAs were identified according to the plant miRNA criteria (Axtell et al., 2018). The novel miRNA sequences were named using the following format: novel-miR-number.