Informatics pipeline for the identification of maize lncRNAs. (A) Schematic diagram of the informatics pipeline. (B) The proportion of WGS transcripts with/without EST support. (C) Venn diagram showing the numbers of transcripts detected by the WGS, RNA-seq assemblies or by both assemblies. (D) The number of HC-lncRNAs and pre-lncRNAs derived from RNA-seq and WGS, respectively. (E) The proportion of transcripts from the WGS and RNA-seq with sequence similarity to maize repetitive elements. DB, DataBase; EST, expressed sequence tag; HC-lncRNAs, high confidence lncRNAs; ORF, open reading frame; WGS, working gene set.