TY  - GEN
AB  - Background: 
Experimental proof of gene function assignments in plants is based on mutant analyses. T-DNA
insertion lines provided an invaluable resource of mutants and enabled systematic reverse genetics-based
investigation of the functions of Arabidopsis thaliana genes during the last decades.
Results: 
We sequenced the genomes of 14 A. thaliana GABI-Kat T-DNA insertion lines, which eluded flanking
sequence tag-based attempts to characterize their insertion loci, with Oxford Nanopore Technologies (ONT) long
reads. Complex T-DNA insertions were resolved and 11 previously unknown T-DNA loci identified, resulting in about
2 T-DNA insertions per line and suggesting that this number was previously underestimated. T-DNA mutagenesis
caused fusions of chromosomes along with compensating translocations to keep the gene set complete
throughout meiosis. Also, an inverted duplication of 800 kbp was detected. About 10 % of GABI-Kat lines might be
affected by chromosomal rearrangements, some of which do not involve T-DNA. Local assembly of selected reads
was shown to be a computationally effective method to resolve the structure of T-DNA insertion loci. We
developed an automated workflow to support investigation of long read data from T-DNA insertion lines. All steps
from DNA extraction to assembly of T-DNA loci can be completed within days.
Conclusions: 
Long read sequencing was demonstrated to be an effective way to resolve complex T-DNA insertions
and chromosome fusions. Many T-DNA insertions comprise not just a single T-DNA, but complex arrays of multiple
T-DNAs. It is becoming obvious that T-DNA insertion alleles must be characterized by exact identification of both
T-DNA::genome junctions to generate clear genotype-to-phenotype relations.
DA  - 2021
DO  - 10.1186/s12864-021-07877-8
KW  - long read sequencing
KW  - genome assembly
KW  - structural variants
KW  - translocations
KW  - chromosome fusions
KW  - reverse genetics
KW  - chromosomal rearrangements
KW  - GABI-Kat
LA  - eng
PY  - 2021
TI  - Large scale genomic rearrangements in selected Arabidopsis thaliana T-DNA lines are caused by T-DNA insertion mutagenesis
UR  - https://nbn-resolving.org/urn:nbn:de:0070-pub-29524342
Y2  - 2024-11-22T07:42:40
ER  -