A Genomic Analysis of Factors Driving lincRNA Diversification: Lessons from Plants

Abstract

Transcriptomic analyses from across eukaryotes indicate that most of the genome is transcribed at some point in the developmental trajectory of an organism. One class of these transcripts is termed long intergenic noncoding RNAs (lincRNAs). Recently, attention has focused on understanding the evolutionary dynamics of lincRNAs, particularly their conservation within genomes. Here, we take a comparative genomic and phylogenetic approach to uncover factors influencing lincRNA emergence and persistence in the plant family Brassicaceae, to which Arabidopsis thaliana belongs. We searched 10 genomes across the family for evidence of > 5000 lincRNA loci from A. thaliana. From loci conserved in the genomes of multiple species, we built alignments and inferred phylogeny. We then used gene tree/species tree reconciliation to examine the duplication history and timing of emergence of these loci. Emergence of lincRNA loci appears to be linked to local duplication events, but, surprisingly, not whole genome duplication events (WGD), or transposable elements. Interestingly, WGD events are associated with the loss of loci for species having undergone relatively recent polyploidy. Lastly, we identify 1180 loci of the 6480 previously annotated A. thaliana lincRNAs (18%) with elevated levels of conservation. These conserved lincRNAs show higher expression, and are enriched for stress-responsiveness and cis-regulatory motifs known as conserved noncoding sequences (CNSs). These data highlight potential functional pathways and suggest that CNSs may regulate neighboring genes at both the genomic and transcriptomic level. In sum, we provide insight into processes that may influence lincRNA diversification by providing an evolutionary context for previously annotated lincRNAs.

Splicing conservation signals in plant long non-coding RNAs

“…Although the functional characterization of lncRNAs is confined to a small number of cases, plant lncRNAs are being reported at a rapidly increasing pace (Nelson et al, 2016). As in the case of animals, it is important therefore find evidence for the functionality of individual transcripts.…”

Long non-coding RNAs in wild wheat progenitors

“…tauschii. In fact, both processed and unprocessed (those that no longer have a recognizable parental gene) pseudogenes, when transcribed, can be functional through the production of lncRNAs (Milligan and Lipovich 2014 (Nelson et al 2016).…”

Evolinc: a comparative transcriptomics and genomics pipeline for quickly identifying sequence conserved lincRNAs for functional analysis

“…We suggest starting at an E-value cutoff of 1E-20 because we found that, across 10 Brassicaceae genomes, and independently between human, orangutan and mouse, this value was optimal for recovering reciprocal and syntenic sequence homologs (Nelson et al, 2016).…”

“…Evolinc-II is an automated and improved version of a workflow we previously used to determine the depth to which Liu-lincRNAs (Liu et al, 2012) were conserved in other species of the Brassicaceae (Nelson et al, 2016). The Evolinc-II workflow is outlined in Figure 2A.…”