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Long non-coding RNAs (lncRNAs) are under-studied and under-annotated in plants. In mammals, lncRNA loci are nearly as ubiquitous as protein-coding genes, and their expression has been shown to be highly variable between individuals of the same species. UsingA. thalianaas a model, we aimed to understand the true scope of lncRNA transcription across plants from different regions and study its natural variation. Using RNA-seq data spanning hundreds of natural lines and several developmental stages to create a more comprehensive annotation of lncRNAs, we found over 10,000 new loci — three times as many as in the current public annotation. While lncRNA transcription is ubiquitous in the genome, most loci appear to be actively silenced and their expression is extremely variable between natural lines. This high expression variability is largely caused by the high variability of repressive chromatin levels at lncRNA loci. This was particularly common for intergenic lncRNAs, where pieces of transposable elements (TEs) present in 50% of the loci are associated with increased silencing and variation, and such lincRNAs tend to be targeted by TE silencing machinery. We create the most comprehensiveA. thalianalncRNA annotation to date and improve our understanding of plant lncRNA genome biology, raising fundamental questions about what causes transcription and what causes silencing across the genome.Graphical abstract |
