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Landscape of plastid DNA breaks in Arabidopsis during development and environmental stimulus

ABSTRACT: Exposure to external and internal environmental factors can lead to the genomic DNA modifications and even DNA breaks. While the landscapes of DNA break in eukaryotic nuclear genomes have been extensively studied, the frequencies and genomic loci of DNA breaks in endosymbiotic organelle remain poorly understood. Here, we employ DEtail-seq, a deep sequencing-based assay, to profile the DNA breaks in the Arabidopsis plastid genome. We find that plastid DNAs (ptDNA) in cotyledons and true leaves remains relatively stable during the juvenile stage but undergoes extensive breaks in older tissues. The break levels in seeds are significantly lower than those in leaves. Notably, rDNA regions experience more breaks, with a preference for the template strands. Additionally, we examine variations in ptDNA break patterns between the wild-type (Col-0) and mutants defective in DNA repair, replication, and transcription under varying environmental conditions, including light, temperature, and photoperiod. While wild-type plants maintain genome integrity under most tested conditions, the ptDNA damage repair and replication mutants why1/3/reca1, why1/3/polIb, and atrnh1c do not. Additionally, shortening the photoperiod alleviates ptDNA breaks in Col-0, with an even more pronounced effect in atrnh1c. This study provides a comprehensive and detailed view of ptDNA breaks, advancing our understanding of endosymbiotic organellar genome damage and repair mechanisms.

ORGANISM(S): Arabidopsis thaliana

PROVIDER: GSE308159 | GEO | 2026/08/05

REPOSITORIES: GEO

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Landscape of plastid DNA breaks in Arabidopsis during development and environmental stimulus [2]

Project description:Exposure to external and internal environmental factors can lead to the genomic DNA modifications and even DNA breaks. While the landscapes of DNA break in eukaryotic nuclear genomes have been extensively studied, the frequencies and genomic loci of DNA breaks in endosymbiotic organelle remain poorly understood. Here, we employ DEtail-seq, a deep sequencing-based assay, to profile the DNA breaks in the Arabidopsis plastid genome. We find that plastid DNAs (ptDNA) in cotyledons and true leaves remains relatively stable during the juvenile stage but undergoes extensive breaks in older tissues. The break levels in seeds are significantly lower than those in leaves. Notably, rDNA regions experience more breaks, with a preference for the template strands. Additionally, we examine variations in ptDNA break patterns between the wild-type (Col-0) and mutants defective in DNA repair, replication, and transcription under varying environmental conditions, including light, temperature, and photoperiod. While wild-type plants maintain genome integrity under most tested conditions, the ptDNA damage repair and replication mutants why1/3/reca1, why1/3/polIb, and atrnh1c do not. Additionally, shortening the photoperiod alleviates ptDNA breaks in Col-0, with an even more pronounced effect in atrnh1c. This study provides a comprehensive and detailed view of ptDNA breaks, advancing our understanding of endosymbiotic organellar genome damage and repair mechanisms.

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