Utilizing iPlant to Unearth Long Non-Coding RNAs and Characterize Their Evolution in the Plant Family Brassicaceae

Many long non-coding RNAs (lncRNAs) have been identified in various organisms, yet little is known about their function.  lncRNAs are typically expressed at low levels, polyadenylated, and spliced, must have a minimum length of 200 nts, and cannot have an open reading frame greater than 100 amino acids. As the biological significance of lncRNAs becomes more apparent, scientists are now revisiting RNA-seq data in an attempt to identify potentially functional lncRNAs.

Here we address issues in identification of biologically relevant lncRNAs by using comparative genomics and transcriptomics to recover and curate lncRNAs in the plant family Brassicaceae. We employed resources available in iPlant to assemble transcriptomes de novo from RNA-seq data for four different species in the plant family Brassicaceae, and then filtered these to generate a set of putative lncRNAs. We used CoGe to determine which lncRNAs were conserved in the genomes of 9 species within Brassicaceae, and two species sister to the lineage, working under the assumption that conservation implies function. Using BLAST and synteny, we identified a conservative subset of ~100 lncRNAs that are conserved in the genomes in all examined Brassicaceae species. Lastly, we determined by RT-PCR that 12 of these highly conserved lncRNA families were expressed in Aethionema arabicum, a member of the earliest diverging lineage of Brassicaceae. In sum, we leveraged iPlant and CoGe to develop a general pipeline for identification of broadly conserved and potentially functional lncRNAs.