Comparative Genomic and Transcriptomic Analysis of lincRNA Evolution in Plants and Mammals Using Evolinc

Long intergenic non-coding RNAs (lincRNAs) are an abundant and functionally diverse class within eukaryotic transcriptomes. Reported lincRNA repertoires in mammals vary, but are commonly in the thousands to tens of thousands of transcripts, accounting for ~90% of the genome. In addition to understanding function, there is particular interest in understanding how lincRNAs evolve. However, aside from mammals, and in particular humans and mice, lincRNA populations have been sparsely sampled. Here we examine the evolution of lincRNAs within three plant families, Brassicaceae, Fabaceae, and Poaceae, as well as class Mammalia. Within the three plant families, we first use an application we developed, Evolinc, to identify lincRNAs in six species for which there are no current lincRNA datasets. We then use these lincRNAs in conjunction with Evolinc to perform large-scale comparative genomic and transcriptomic analyses to uncover rates of lincRNA evolution within each family. We identify sets of lincRNAs that are transcriptionally conserved within each family, including some that display a conserved transcriptional response to stress, providing insight into function for these molecules. We also use Evolinc to examine the evolutionary history of the human telomerase RNA (TERC) across 28 mammalian genomes. Here we demonstrate that the locus encoding for this essential lincRNA is conserved across mammalia with the striking exception of mouse and rat. We uncover putative origins of the TERC locus in mammals, unexpected duplication events, as well as the loss and subsequent acquisition of a novel TERC locus in the lineage leading to mice.