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.