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
 
Download
Es wurden keine Dateien hochgeladen. Nur Publikationsnachweis!
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
Page URI
https://pub.uni-bielefeld.de/record/2952434

Zitieren

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, 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.
Alle Dateien verfügbar unter der/den folgenden Lizenz(en):
Creative Commons Namensnennung 4.0 International Public License (CC-BY 4.0):
Link(s) zu Volltext(en)
Access Level
OA Open Access
Material in PUB:
Wird zitiert von
Arabidopsis thaliana methylation pattern analysis based on ONT sequence reads
Schilbert H, Kleinbölting N, Weisshaar B, Pucker B (2021)
Bielefeld University.

Export

Markieren/ Markierung löschen
Markierte Publikationen

Open Data PUB

Web of Science

Dieser Datensatz im Web of Science®

Quellen

PMID: 34362298
PubMed | Europe PMC

Preprint: 10.1101/2021.03.03.433755

Suchen in

Google Scholar