Background: Long non-coding RNAs (LncRNAs) have been identified as gene regulatory elements that influence the transcription of their neighbouring protein-coding genes. The discovery of LncRNAs in animals has stimulated genome-wide scans for these elements across plant genomes. Recently, 6480 LincRNAs were putatively identified in Arabidopsis thaliana (Brassicaceae), however there is limited information on their conservation. Results: Using a phylogenomics approach, we assessed the positional and sequence conservation of these LncRNAs by analyzing the genomes of the basal Brassicaceae species Aethionema arabicum and Tarenaya hassleriana of the sister-family Cleomaceae. Furthermore, we generated transcriptomes for another three Aethionema species and one other Cleomaceae species to validate their transcriptional activity. We show that a subset of LncRNAs are highly diverged at the nucleotide level, but conserved by position (syntenic). Positionally conserved LncRNAs that are expressed neighbour important developmental and physiological genes. Interestingly, >65% of the positionally conserved LncRNAs are located within 2.5Mb of telomeres in Arabidopsis thaliana chromosomes. Conclusion: These results highlight the importance of analysing not only sequence conservation, but also positional conservation of non-coding genetic elements in plants including LncRNAs.
Mohammadin, S., Edger, P. P., Pires, J. C., & Schranz, M. E. (2015). Positionally-conserved but sequence-diverged: Identification of long non-coding RNAs in the Brassicaceae and Cleomaceae. BMC Plant Biology, 15(1). https://doi.org/10.1186/s12870-015-0603-5