title: Positionally-conserved but sequence-diverged: identification of long non-coding RNAs in the Brassicaceae and Cleomaceae.
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.
  
  
  CONCLUSIONS
  These results highlight the importance of analysing not only sequence conservation, but also positional conservation of non-coding genetic elements in plants including LncRNAs.
authors.affiliation: Biosystematics, Plant Science Group, Wageningen University, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands. setarehi@gmail.nl.
authors.forename: Setareh
authors.initials: S
authors.lastname: Mohammadin
authors.affiliation: Division of Biological Sciences, University of Missouri, Columbia, MO, 65211, USA. pedger@gmail.com.
authors.forename: Patrick P
authors.initials: PP
authors.lastname: Edger
authors.affiliation: Division of Biological Sciences, University of Missouri, Columbia, MO, 65211, USA. piresjc@missouri.edu.
authors.forename: J Chris
authors.initials: JC
authors.lastname: Pires
authors.affiliation: Biosystematics, Plant Science Group, Wageningen University, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands. eric.schranz@wur.nl.
authors.forename: Michael Eric
authors.initials: ME
authors.lastname: Schranz
mesh_terms: D019607:Brassicaceae / Q000235:genetics / Q000378:metabolism; D017124:Conserved Sequence; D019143:Evolution, Molecular; D018745:Genome, Plant; D019684:Magnoliopsida / Q000235:genetics* / Q000378:metabolism; D010802:Phylogeny; D062085:RNA, Long Noncoding / Q000235:genetics* / Q000378:metabolism; D018749:RNA, Plant / Q000235:genetics* / Q000378:metabolism; D017422:Sequence Analysis, DNA
chemical_list: D062085:RNA, Long Noncoding; D018749:RNA, Plant