Identification of miRNA clusters and bidirectionally transcribed miRNAs

ublished miRNAs and precursor-miRNAs (pre-miRNAs) were downloaded from miRbase (, MirGeneDB (, and PmiREN (, which contained the miRNA annotations in 152 animals and plants, 45 animals and 179 plants (last accessed Oct 2021), respectively (Kozomara et al., 2019; Fromm et al., 2020; Guo et al., 2020). The genomic location of pre-miRNAs was compared against each other and calculate the relative distance. miRNAs with a relative distance below 10,000 bp with the same transcriptional orientations were grouped into a miRNA cluster. On the other side, pre-miRNAs that transcribed from opposite strands with > 10 bp sequence overlaps were determined as the candidate of bidirectionally transcribed miRNAs.