Sequence and epigenetic landscapes of active and silenced nucleolus organizers in Arabidopsis

Arabidopsis thaliana has two ribosomal RNA gene loci, nucleolus organizer regions NOR2 and NOR4, whose complete sequences remain undefined. Ultra-long DNA sequences assembled using an unconventional approach yielded 5.5 and 3.9 Mbp sequences for NOR2 and NOR4 (in the reference strain, Col-0), revealing their distinct gene subtype compositions. RNA sequencing and identification of genes associated with flow-sorted nucleoli of wild-type or silencing-defective mutant plants shows that most of NOR4 is comprised of active genes whereas most, but not all, NOR2 genes are epigenetically silenced. Long intervals of low CG and CHG methylation overlap regions of gene activity and gene subtype homogenization. Collectively, the data reveal the genetic and epigenetic landscapes of the NORs and implicate transcription in rRNA gene concerted evolution. One Sentence SummaryNOR2 and NOR4 sequences fill genome gaps and enable megabase-scale analyses of rRNA gene regulation and concerted evolution.