Extrachromosomal circular DNA (eccDNA) exists outside chromosomes in many eukaryotes. A 2025 PLOS Biology study used CIDER-Seq and long-read sequencing to build a full-length eccDNA atlas in Arabidopsis.
Centromeric and pericentromeric regions were eccDNA hotspots
Full-length circles were enriched around centromeric regions, with many originating from Helitron and LTR transposable elements. Long reads are particularly useful because short-read methods struggle to reconstruct complete TE-derived circles.
Epigenetic mutants changed the eccDNA landscape
Mutants affecting DNA methylation and TE regulation—including dcl3, rdr6, ros1 and ddm1—showed altered eccDNA populations. LTR/Gypsy activation was notable in ros1, while actively dividing callus and shoot-apical-meristem tissues showed enrichment of LTR/Copia-derived eccDNA.
The atlas does not label most circles as junk or useful
The earlier article described most eccDNA as genomic waste with rare functional treasures. Functional eccDNA is known in other biological contexts, but this Arabidopsis study primarily mapped origins and regulation rather than assigning a biological function to each circle.
Future work must determine which circles are expressed, inherited, reintegrated or adaptive under stress.
For related context, see How Are Japanese Soybeans Genomically Different? A 462-Accession Pangenome—and Two Author Corrections.
For related context, see The 4.83-Gb Ophrys sphegodes Genome Links Sexual Deception to Odor-Gene Duplications and an LTR Burst.
For related context, see How Much “Breeding” Happened in This AI Breeding Study? Reading a Synthetic-Data bioRxiv Proof of Concept.
Reference
- Zaidi SS-e-A et al. A comprehensive atlas of full-length Arabidopsis eccDNA populations identifies their genomic origins and epigenetic regulation. PLOS Biology. 2025;23:e3003275. https://doi.org/10.1371/journal.pbio.3003275
Comments