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

Abstract

Arabidopsis thaliana has two ribosomal RNA gene loci, nucleolus organizer regions NOR2 and NOR4, whose complete sequences remain unknown. Using ultra-long DNA sequencing technology, we generated 5.5 and 3.9 Mbp sequence assemblies for NOR2 and NOR4 (in the reference strain, Col-0), revealing their distinctive gene subtype compositions. RNA sequencing, and gene identification within flow-sorted nucleoli, in both wild-type and histone deacetylase 6 mutants, shows that most, but not all, NOR4 genes are active 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 illuminate the genetic and epigenetic landscapes of the NORs and implicate transcription in rRNA gene concerted evolution.

Measure of major contents in animal and plant genomes, using Gnodes, finds under-assemblies of model plant, Daphnia, fire ant and others

“…The model plant now has a complete genome assembly including its long repetitive telo- and centro-meres, with a size that is 20% above what many genome informatics publications consider the “complete” model plant genome. This despite the fact that since the first At genome assembly (Arabidopsis Genome Initiative, 2000) it has been known to be incomplete; a portion of the chromosomes were found to be too repetitive to assemble, and that portion has only now, 23 years later, been added (Fultz et al 2023, Naish et al 2021). At has a classic simple genome structure: mostly unique, euchromatic, gene-bearing arms of its five chromosomes, with repetitive centromeres midway, flanked by transposon-rich spans, and long repetitive telomeres on two chromosomes, containing nucleolus organizing regions.…”

“…at23_CaNOR6ref, is built using contigs of at22vcan2d, updated with published NOR assemblies of Fultz et al 2023, and scaffolded with ntLink and ONT DNA to chromosome level.…”

Atlas of telomeric repeat diversity inArabidopsis thaliana

“…The next two questions concern the two chromosome ends next to the 45S rDNA clusters. One challenge will be to accurately assign telomeric reads adjacent to rDNA to specific chromosome ends, which is hampered here by a lack of complete assemblies of rDNA arrays in diverse genomes (Fultz et al 2023). Another one is why there are significantly fewer variant repeats present in these two chromosome ends compared with the other eight non-rDNA chromosome ends.…”

“…In A. thaliana , two out of ten chromosome ends have large 45S rDNA repeat arrays adjacent to the telomeric repeats, causing most assemblies collapse and thus preventing correct mapping of telomeric sequences (Fultz et al 2023; Copenhaver and Pikaard 1996). Two alternative strategies were employed to extract telomeric sequences, depending on whether the sequence was adjacent to long 45S rDNA sequences.…”