title: Deletion-bias in DNA double-strand break repair differentially contributes to plant genome shrinkage.
abstract: 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.
authors.affiliation: Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), D-06466, Gatersleben, Germany.
authors.forename: Giang T H
authors.initials: GTH
authors.lastname: Vu
authors.affiliation: Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), D-06466, Gatersleben, Germany.
authors.forename: Hieu X
authors.initials: HX
authors.lastname: Cao
authors.affiliation: Max Planck Institute for Plant Breeding Research, 50829, Köln, Germany.
authors.forename: Bernd
authors.identifier: http://orcid.org/0000-0002-2521-4000
authors.initials: B
authors.lastname: Reiss
authors.affiliation: Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), D-06466, Gatersleben, Germany.
authors.forename: Ingo
authors.initials: I
authors.lastname: Schubert
mesh_terms: D017360:Arabidopsis / Q000235:genetics*; D029687:Capsella / Q000235:genetics; D053903:DNA Breaks, Double-Stranded; D059766:DNA End-Joining Repair; D004260:DNA Repair / Q000502:physiology*; D059646:Genome Size; D018745:Genome, Plant; D001467:Hordeum / Q000235:genetics*; D009154:Mutation; D017384:Sequence Deletion
keywords: double-strand break (DSB) repair; genome shrinkage; genome size evolution; nonhomologous end joining (NHEJ); single strand annealing (SSA)