Figure 1. Detailed schematic diagram of the informatics pipeline for the identification of citrus lncRNAs.

Paired-end strand-specific RNA-Seq was performed for MT and WT. Clean reads were mapped and assembled according to the known citrus genome using TopHat and Cufflinks⁴⁹. Transcripts were filtered with the six criteria for identification of putative lncRNAs: (i) not citrus coding genes; (2) length >200 nucleotides and ORF < 100 amino acids; (iii) not encoding known protein domains; (iv) little coding potential; (v) not housekeeping ncRNAs; and (vi) not miRNA precursors. A total of 6,584 transcripts were obtained. CPC: coding potential calculator; PLEK: predictors of long non-coding RNAs and messenger RNAs based on an improved k-mer scheme; CNCI: coding non-coding index.