Annotation of non-coding RNAs (ncRNAs)
Transfer RNAs (tRNAs) were identified by tRNAscan-SE (Lowe & Eddy,
1997) with eukaryotic parameters. miRNA and snRNA genes were predicted
using INFERNAL (Nawrocki & Eddy, 2013) by searching against the Rfam
database (Griffiths-Jones et al ., 2003). rRNA genes were
predicted by aligning reads to Arabidopsis template rRNA
sequences using BLASTN with an e value of 1e-5.