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BMC Plant Biol. 2015 Sep 11;15:217. doi: 10.1186/s12870-015-0603-5.

Positionally-conserved but sequence-diverged: identification of long non-coding RNAs in the Brassicaceae and Cleomaceae.

Author information

1
Biosystematics, Plant Science Group, Wageningen University, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands. setarehi@gmail.nl.
2
Division of Biological Sciences, University of Missouri, Columbia, MO, 65211, USA. pedger@gmail.com.
3
Division of Biological Sciences, University of Missouri, Columbia, MO, 65211, USA. piresjc@missouri.edu.
4
Biosystematics, Plant Science Group, Wageningen University, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands. eric.schranz@wur.nl.

Abstract

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 2.5 Mb 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.

PMID:
26362138
PMCID:
PMC4566204
DOI:
10.1186/s12870-015-0603-5
[Indexed for MEDLINE]
Free PMC Article

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