Phenotypic diversification by enhanced genome restructuring after induction of multiple DNA double-strand breaks

Nature Communications
Nobuhiko MuramotoKunihiro Ohta

Abstract

DNA double-strand break (DSB)-mediated genome rearrangements are assumed to provide diverse raw genetic materials enabling accelerated adaptive evolution; however, it remains unclear about the consequences of massive simultaneous DSB formation in cells and their resulting phenotypic impact. Here, we establish an artificial genome-restructuring technology by conditionally introducing multiple genomic DSBs in vivo using a temperature-dependent endonuclease TaqI. Application in yeast and Arabidopsis thaliana generates strains with phenotypes, including improved ethanol production from xylose at higher temperature and increased plant biomass, that are stably inherited to offspring after multiple passages. High-throughput genome resequencing revealed that these strains harbor diverse rearrangements, including copy number variations, translocations in retrotransposons, and direct end-joinings at TaqI-cleavage sites. Furthermore, large-scale rearrangements occur frequently in diploid yeasts (28.1%) and tetraploid plants (46.3%), whereas haploid yeasts and diploid plants undergo minimal rearrangement. This genome-restructuring system (TAQing system) will enable rapid genome breeding and aid genome-evolution studies.

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Citations

Aug 30, 2019·PLoS Genetics·Aubin FleissGilles Fischer
Jun 25, 2020·The Plant Journal : for Cell and Molecular Biology·Hidenori TanakaKunihiro Ohta
Mar 21, 2020·Proceedings of the National Academy of Sciences of the United States of America·Vikas YadavJoseph Heitman
Dec 4, 2020·Nature Communications·Alessandro L V CoradiniIan M Ehrenreich
Mar 7, 2021·International Journal of Molecular Sciences·Janusz Blasiak
Oct 16, 2021·Chemical Society Reviews·Sijie ZhouYing-Jin Yuan

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Datasets Mentioned

BETA
AJ249909
DRA005252
DRA005268
GSE90027
GSE90025
GSE90026

Methods Mentioned

BETA
electrophoresis
Hi-C
chromosomal aberrations
chromosomal aberration
PCR
Feature Extraction
Illumina sequencing
transgenic
flow cytometry

Software Mentioned

TAQing
SAM
Adobe Photoshop CS
Basic Variant Detection
Genome Analysis ToolKit ( GATK )
GATK
SMRT Analysis
smrtpipe
Matlab
py

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