Ultra-deep sequencing reveals dramatic alteration of organellar genomes in Physcomitrella patens due to biased asymmetric recombination

Masaki Odahara,Kensuke Nakamura,Yasuhiko Sekine,Taku Oshima

doi:10.1038/s42003-021-02141-x

Abstract

Destabilization of organelle genomes causes organelle dysfunction that appears as abnormal growth in plants and diseases in human. In plants, loss of the bacterial-type homologous recombination repair (HRR) factors RECA and RECG induces organelle genome instability. In this study, we show the landscape of organelle genome instability in Physcomitrella patens HRR knockout mutants by deep sequencing in combination with informatics approaches. Genome-wide maps of rearrangement positions in the organelle genomes, which exhibited prominent mutant-specific patterns, were highly biased in terms of direction and location and often associated with dramatic variation in read depth. The rearrangements were location-dependent and mostly derived from the asymmetric products of microhomology-mediated recombination. Our results provide an overall picture of organelle-specific gross genomic rearrangements in the HRR mutants, and suggest that chloroplasts and mitochondria share common mechanisms for replication-related rearrangements.

Highlights

Destabilization of organelle genomes causes organelle dysfunction that appears as abnormal growth in plants and diseases in human
Land plant cpDNA is mapped as a ~100–200 kb circular structure, with large single-copy (LSC) and small single-copy (SSC) regions separated by a pair of large inverted repeat (IR) regions
The number of reads mapped for cpDNA revealed little or moderate increase in RECA1 and RECG KO mutants as compared to the WT, whereas an apparent decrease was observed in RECA2 KO mutants (Fig. 1, Supplementary Fig. 1, and Supplementary Table 2)

Summary

Introduction

Destabilization of organelle genomes causes organelle dysfunction that appears as abnormal growth in plants and diseases in human. Loss of the bacterial-type homologous recombination repair (HRR) factors RECA and RECG induces organelle genome instability. 1234567890():,; Chloroplasts (cp) and mitochondria (mt) are organelles of endosymbiotic origin that conduct photosynthesis and respiration, respectively To perform their energy production functions, both of these organelles have their own genomic DNA and gene expression system. P. patens nuclear DNA encodes two homologs of the bacterial-type RecA recombinase involved in homologous recombination repair (HRR); the gene products of RECA1 and RECA2 are localized to mitochondria and chloroplasts, respectively[20,21]. Knockout of RECA2 results in a modest growth defect, chloroplast genome instability due to induced recombination between SDRs, and a moderate decrease in the overall level of cpDNA23.

Methods

Results

Conclusion