MiRNA and IPS1-like lncRNA identification, and target prediction
Precursor sequences of P-responsive miRNAs, i.e. pre-miR399s, pre-miR2111s and pre-miR827s, from several plant species were retrieved from miRBase, and used to identify expressed transcripts harboring miR399, miR2111 or miR827 sequence motifs. RNAfold (Lorenz et al., 2011) was used to predict minimum free energy RNA hairpin structures characteristic for miRNA precursors. psRNATarget (Dai et al., 2018) was used to predict target genes for mature miRNAs using default parameters.INDUCED BY PHOSPHATE STARVATION1 (IPS1) -like, long non-coding RNAs (lncRNAs) were identified by modifying the psRNATarget scoring scheme to reveal central mismatches in the matching sequence with miR399. The multiple sequence alignment, neighbor-joining tree, and the miR399 sequence logo were generated using Geneious software.