Repositorium
Deletion-bias in DNA double-strand break repair differentially contributes to plant genome shrinkage
220
Journal Article / 2017
Vu, Giang T. H.; Cao, Hieu X.; Reiss, Bernd; Schubert, Ingo
In order to prevent genome instability, cells need to be protected by a number of repair mechanisms, including DNA double-strand break (DSB) repair. The extent to which DSB repair, biased towards deletions or insertions, contributes to evolutionary diversification of genome size is still under debate. We analyzed mutation spectra in Arabidopsis thaliana and in barley (Hordeum vulgare) by PacBio sequencing of three DSB-targeted loci each, uncovering repair via gene conversion, single strand annealing (SSA) or nonhomologous end-joining (NHEJ). Furthermore, phylogenomic comparisons between A. thaliana and two related species were used to detect naturally occurring deletions during Arabidopsis evolution. Arabidopsis thaliana revealed significantly more and larger deletions after DSB repair than barley, and barley displayed more and larger insertions. Arabidopsis displayed a clear net loss of DNA after DSB repair, mainly via SSA and NHEJ. Barley revealed a very weak net loss of DNA, apparently due to less active break-end resection and easier copying of template sequences into breaks. Comparative phylogenomics revealed several footprints of SSA in the A. thaliana genome. Quantitative assessment of DNA gain and loss through DSB repair processes suggests deletion-biased DSB repair causing ongoing genome shrinking in A. thaliana, whereas genome size in barley remains nearly constant.
Techniques
ID | Corresponding Author Country |
Plant Species | GE Technique Sequence Identifier |
Trait Type of Alteration |
Progress in Research Key Topic |
---|---|---|---|---|---|
513 |
Vu, Giang T.H.; Schubert, Ingo Germany |
Arabidopsis thaliana |
Meganucleases DU.GUS |
No information SDN1 |
Basic research Basic research |
514 |
Vu, Giang T.H.; Schubert, Ingo Germany |
Arabidopsis thaliana |
Meganucleases GUS |
GUS expression SDN1 |
Basic research Basic research |
515 |
Vu, Giang T.H.; Schubert, Ingo Germany |
Arabidopsis thaliana |
Meganucleases IU.GUS |
No information SDN1 |
Basic research Basic research |
516 |
Vu, Giang T.H.; Schubert, Ingo Germany |
Hordeum vulgare |
Meganucleases DU.GUS |
No information SDN1 |
Basic research Basic research |
517 |
Vu, Giang T.H.; Schubert, Ingo Germany |
Hordeum vulgare |
Meganucleases GUS |
GUS expression SDN1 |
Basic research Basic research |
518 |
Vu, Giang T.H.; Schubert, Ingo Germany |
Hordeum vulgare |
Meganucleases IU.GUS |
No information SDN1 |
Basic research Basic research |