2.6 Non-coding RNA identification
Transfer RNAs (tRNAs) were identified using the tRNAscan-SE program
(version 1.3.1, with default parameters for eukaryotes) (Chan & Lowe,
2019). RNAmmer (version 1.2,
parameters set to “-s euk -m tsu, ssu, lsu”) was used to identify 5S/
8S, 16S/ 18S and 23S/ 28S ribosomal RNAs (rRNAs) (Karin et al., 2007).
rRNAs, microRNAs (miRNAs) and small nuclear RNAs (snRNAs) were
identified based on the Rfam database (version 12.2) using BLASTN
(E-value ≤1×10−5)
(Kalvari et al., 2017).