Identification of miRNA clusters and bidirectionally transcribed miRNAs
ublished miRNAs and precursor-miRNAs (pre-miRNAs) were downloaded from miRbase (https://www.mirbase.org/), MirGeneDB (https://mirgenedb.org/), and PmiREN (https://www.pmiren.com/), 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.