Fig. 1

Flowchart diagram of the integrated pipeline PmiRDiscVali. The raw small RNA sequencing (sRNA-seq) and RNA sequencing (RNA-seq) data in FASTQ format was pre-treated and converted to FASTA format by FASTX-Toolkit. The sRNA-seq data was used to search for the conserved mature microRNA (miRNA) candidates according to the current plant miRNA registries in miRBase (release 21). Relying on the availability of the reference genome, distinct strategy (reference-based or de novo) was employed for transcriptome assembly by using the processed RNA-seq data. Then, the assembled transcripts and the sRNA-seq data were used for miRNA prediction by using miRDeep-P. The prediction results were parsed by an in-house Perl script, in order to graphically present the structures and the sRNA expression patterns of the miRNA precursors. If the degradome sequencing (degradome-seq) data was available, the pipeline would perform degradome signature mapping to seek for the processing evidence supporting the miRNA candidates