Large scale genomic rearrangements in selected Arabidopsis thaliana T-DNA lines are caused by T-DNA insertion mutagenesis
Pucker B, Kleinbölting N, Weisshaar B (2021)
BMC Genomics 22: 599.
Zeitschriftenaufsatz
| Veröffentlicht | Englisch
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Einrichtung
Abstract / Bemerkung
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.
Stichworte
long read sequencing;
genome assembly;
structural variants;
translocations;
chromosome fusions;
reverse genetics;
chromosomal rearrangements;
GABI-Kat
Erscheinungsjahr
2021
Zeitschriftentitel
BMC Genomics
Band
22
Art.-Nr.
599
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Pucker B, Kleinbölting N, Weisshaar B. Large scale genomic rearrangements in selected Arabidopsis thaliana T-DNA lines are caused by T-DNA insertion mutagenesis. BMC Genomics. 2021;22: 599.
Pucker, B., Kleinbölting, N., & Weisshaar, B. (2021). Large scale genomic rearrangements in selected Arabidopsis thaliana T-DNA lines are caused by T-DNA insertion mutagenesis. BMC Genomics, 22, 599. https://doi.org/10.1186/s12864-021-07877-8
Pucker, Boas, Kleinbölting, Nils, and Weisshaar, Bernd. 2021. “Large scale genomic rearrangements in selected Arabidopsis thaliana T-DNA lines are caused by T-DNA insertion mutagenesis”. BMC Genomics 22: 599.
Pucker, B., Kleinbölting, N., and Weisshaar, B. (2021). Large scale genomic rearrangements in selected Arabidopsis thaliana T-DNA lines are caused by T-DNA insertion mutagenesis. BMC Genomics 22:599.
Pucker, B., Kleinbölting, N., & Weisshaar, B., 2021. Large scale genomic rearrangements in selected Arabidopsis thaliana T-DNA lines are caused by T-DNA insertion mutagenesis. BMC Genomics, 22: 599.
B. Pucker, N. Kleinbölting, and B. Weisshaar, “Large scale genomic rearrangements in selected Arabidopsis thaliana T-DNA lines are caused by T-DNA insertion mutagenesis”, BMC Genomics, vol. 22, 2021, : 599.
Pucker, B., Kleinbölting, N., Weisshaar, B.: Large scale genomic rearrangements in selected Arabidopsis thaliana T-DNA lines are caused by T-DNA insertion mutagenesis. BMC Genomics. 22, : 599 (2021).
Pucker, Boas, Kleinbölting, Nils, and Weisshaar, Bernd. “Large scale genomic rearrangements in selected Arabidopsis thaliana T-DNA lines are caused by T-DNA insertion mutagenesis”. BMC Genomics 22 (2021): 599.
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Wird zitiert von
Arabidopsis thaliana methylation pattern analysis based on ONT sequence reads
Schilbert H, Kleinbölting N, Weisshaar B, Pucker B (2021)
Bielefeld University.
Schilbert H, Kleinbölting N, Weisshaar B, Pucker B (2021)
Bielefeld University.
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PMID: 34362298
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Preprint: 10.1101/2021.03.03.433755
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