Arabidopsis chloroplast genome breaks during development and environmental stimuli (ssDRIP-Seq)

ABSTRACT: Exposures from the external and internal environments lead to the modification of genomic DNA and even DNA breaks. The landscapes of DNA breaks in eukaryotic nuclear genomes have been extensively studied, while the frequencies and genomic loci of DNA breaks in endosymbiotic organelle are enigmatic. Here, we utilize DEtail-seq, a deep sequencing-based assay, to profile the DNA breaks in the Arabidopsis plastid genome. We find that the plastid DNAs (ptDNA) in cotyledons and true leaves are relatively stable during the juvenile stage but intensively broken in old age. The break level in seeds is much less than those in leaves. Overall, the rDNA regions suffer more breaks with a preference for template strands. Further, we determinate the variation of ptDNA break pattern in response to temperature and photoperiod stimulus. The wild-type plants are capable of maintaining genome integrity under most conditions we tested, while the ptDNA damage repair mutant atrnh1c is not. Moreover, reducing the photoperiod could relieve the ptDNA breaks in Col-0 and more obviously in atrnh1c. Our study provides a systematic and refined view of ptDNA breaks enabling a better understanding of endosymbiotic organellar genome damage and repair.

ORGANISM(S): Arabidopsis thaliana

PROVIDER: GSE242391 | GEO | 2026/08/05

REPOSITORIES: GEO