Genome-wide identification and evolutionary analysis of long non-coding RNAs in cereals

Abstract

We identified lncRNA candidates in four economically important cereals (Poaceae): 7,196 in Zea mays, 1,974 in Sorghum bicolor, 4,236 in Setaria italica and 2,542 in Oryza sativa, using computational methods; we then compared these RNAs across the species. Our approach involved screening a reference-guided transcriptome assembly of RNA-Seq data for RNAs that were at least 200 bases in length with at most 70 amino acids in open reading frames and with a lack of homology in the Uniprot database. A sequence composition analysis of the lncRNA candidates, in comparison to protein-coding transcripts, highlighted distinctive features, including a low GC content, a paucity of introns and a hexamer usage bias, consistent with what has been found for mammalian lncRNAs. RepeatMasker identified from 1% (rice) to 19% (maize) of the candidate lncRNAs as being transcribed from transposable elements, based on a dataset with 3,853 transposable elements. We compared the candidate lncRNAs with 25,141 miRNAs from miRBase, and found that less than 1% of them could be potential miRNA precursors. The cross-species comparisons, which included a sequence- and structure-based lncRNA homology search, synteny analysis, and lncRNA secondary structure prediction, uncovered some limited sequence similarity. In sub-regions, we predicted conserved secondary structures using covariation analysis. We used the comparative sequence and synteny analyses to predict the existence of lncRNAs in S. italica; experimental tests confirmed the presence of these RNAs. Our results are consistent with a model of very rapid evolution of lncRNAs.