title: 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.
authors.affiliation: School of Plant Sciences, University of Arizona, Tucson, Arizona 85721 andrewnelson@email.arizona.edu.
authors.forename: Andrew D L
authors.identifier: 0000-0001-9896-1739
authors.initials: AD
authors.lastname: Nelson
authors.affiliation: School of Plant Sciences, University of Arizona, Tucson, Arizona 85721.
authors.forename: Evan S
authors.initials: ES
authors.lastname: Forsythe
authors.affiliation: Department of Forest Ecosystems and Society, Oregon State University, Corvalis, Oregon 97331.
authors.forename: Upendra K
authors.initials: UK
authors.lastname: Devisetty
authors.affiliation: Department of Statistics, University of Washington, Seattle, Washington 98195.
authors.forename: David S
authors.initials: DS
authors.lastname: Clausen
authors.affiliation: Genetics Graduate Interdisciplinary Group, University of Arizona, Tucson, Arizona 85721.
authors.forename: Asher K
authors.initials: AK
authors.lastname: Haug-Batzell
authors.affiliation: School of Plant Sciences, University of Arizona, Tucson, Arizona 85721.
authors.forename: Ari M R
authors.initials: AM
authors.lastname: Meldrum
authors.affiliation: School of Plant Sciences, University of Arizona, Tucson, Arizona 85721.
authors.forename: Michael R
authors.initials: MR
authors.lastname: Frank
authors.affiliation: School of Plant Sciences, University of Arizona, Tucson, Arizona 85721 Genetics Graduate Interdisciplinary Group, University of Arizona, Tucson, Arizona 85721.
authors.forename: Eric
authors.initials: E
authors.lastname: Lyons
authors.affiliation: School of Plant Sciences, University of Arizona, Tucson, Arizona 85721 andrewnelson@email.arizona.edu.
authors.forename: Mark A
authors.identifier: 0000-0002-3392-1389
authors.initials: MA
authors.lastname: Beilstein
mesh_terms: D017360:Arabidopsis / Q000235:genetics; D019607:Brassicaceae / Q000235:genetics; D017124:Conserved Sequence / Q000235:genetics; D019143:Evolution, Molecular; D020869:Gene Expression Profiling; D018506:Gene Expression Regulation, Plant; D018745:Genome, Plant; D023281:Genomics; D010802:Phylogeny; D062085:RNA, Long Noncoding / Q000096:biosynthesis / Q000235:genetics*
chemical_list: D062085:RNA, Long Noncoding
keywords: Brassicaceae; comparative genomics; evolution; lincRNA; transcriptomics