Sequence and Expression Evolution of Plant Long Intergenic Noncoding RNA

Long intergenic non-coding RNAs (lincRNAs) play diverse roles in many biological processes in plants. We characterized the evolution of lincRNAs in five plant species by analyzing homologs and syntenic loci in 55 plant genomes. Plant lincRNA loci in general show considerably less conservation than protein-coding genes and slightly less conservation compared to microRNAs. While most lincRNAs appear to be specific to a plant family, some have very ancient origins including a few with homologs in non-flowering plants. We detected highly conserved regions in lincRNAs that are under stronger selective constraints than surrounding regions of the lincRNA locus. We analyzed expression patterns of lincRNAs and found that evolutionarily ancient lincRNAs tend to have broader expression patterns than lineage-specific lincRNAs. We found that lincRNAs show rapid divergence of expression between closely related species compared with protein coding genes. This study provides insights into the rapid evolution in sequence and expression patterns of plant lincRNAs, as well as identifies highly conserved lincRNAs of ancient origins.