2.9 Prediction of non-coding RNA
We annotated tRNA, rRNA, snRNA, and miRNAs across the assembled genome sequence. Non-coding RNA sequence was predicted using tRNAscan-SE 1.3.1(Lowe et al., 1997) (http://lowelab.ucsc.edu/tRNAscan-SE/) based on the RNA structure. The rRNA sequences in the Chinese walnut genome were predicted using BLASTN to search for conserved characteristics with related species such as J. regia . The miRNA and snRNA in the assembled Chinese walnut genome were identified using INFERNAL software (Nawrocki and Eddy, 2013) against the Rfam 13.0 database (Griffiths-Jones et al., 2005).