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)
bioRxiv.

Preprint | Veröffentlicht | Englisch
 
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Abstract / Bemerkung
Background Experimental proof of gene function assignments in plants is heavily 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, suggesting that the number of T-DNA insertions per line was 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. Conclusion Long read sequencing was demonstrated to be a very 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
bioRxiv
Page URI
https://pub.uni-bielefeld.de/record/2952434

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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. bioRxiv. 2021.
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. bioRxiv. https://doi.org/10.1101/2021.03.03.433755
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. bioRxiv.
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. bioRxiv.
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”, bioRxiv, 2021.
Pucker, B., Kleinbölting, N., Weisshaar, B.: Large scale genomic rearrangements in selected Arabidopsis thaliana T-DNA lines are caused by T-DNA insertion mutagenesis. bioRxiv. (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”. bioRxiv (2021).
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Preprint: 10.1101/2021.03.03.433755

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