Characteristics of maize lncRNAs. (A) Distribution of lncRNAs along each chromosome. The abundance of HC-lncRNAs, pre-lncRNAs and FGS genes in physical bins of 10 Mb for each chromosome (generated using Circos). (B) Proportion of HC-lncRNAs and pre-lncRNAs that are located within 5 kb (upstream or downstream) or further than 5 kb from the nearest FGS gene. The proportion of FGS genes located within close proximity to other FGS genes is used as a control. (C) Lengths of HC-lncRNAs, pre-lncRNAs and FGS transcripts. (D) Numbers of exons in HC-lncRNAs, pre-lncRNAs and FGS. (E) Percentage of maize HC-lncRNAs and FGS transcripts that are conserved in the Arabidopsis, rice and sorghum genomes compared with the sequence conservation of intergenic or intronic fragments among species. Sequences were repetitive-sequence masked and aligned to the genomes of Arabidopsis, rice and sorghum with the significant cutoff E value <1.0E-10.