ArticleBMC genomics2021
Large scale genomic rearrangements in selected Arabidopsis thaliana T-DNA lines are caused by T-DNA insertion mutagenesis.
Article in BMC genomics, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 46 papers.
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Who cites it
46 citing papers in PubMed.
- T-DNA Analyzer: A Long-Read Sequencing Pipeline for Characterizing T-DNA Insertion Sites in Transgenic Crops.International journal of molecular sciences · 2026Article
- Advances in Tissue Culture-Free Genetic Engineering and Genome Editing of Peanut.Molecular biotechnology · 2026Review
- Multiple redundant mechanisms account for the majority of gene silencing downstream of DNA methylation.bioRxiv : the preprint server for biology · 2026Article
- Cookbook for plant genome sequences.BMC genomics · 2026Review
- New alleles of Arabidopsis BIK1 reinforce its predominant role in pattern-triggered immunity and caution interpretations of other reported functions.Nature plants · 2026Article
- Connecting Epigenetic and Genetic Diversity of LTR Retrotransposons in Sunflower (Plants (Basel, Switzerland) · 2026Article
- Binary vector origin predictably determinesbioRxiv : the preprint server for biology · 2025Article
- Overexpression of VtF3'5'H and RhNHX Genes Alters Flower Color and Plant Morphology in Transgenic Rose 'Red Farm'.Plants (Basel, Switzerland) · 2025Article
- Field selection of elite events of East African highland bananas expressing elevated levels of pro-vitamin A.Plant biotechnology journal · 2025Article
- Isolation and characterization of a spore development mutant in Pyropia yezoensis (Rhodophyta) induced via insertional mutagenesis.Journal of phycology · 2025Article
- T-DNAreader: fast and precise identification of T-DNA insertion sites in plant genomes using RNA sequencing data.Genome biology · 2025Article
- DNA Methylation and Alternative Splicing Safeguard Genome and Transcriptome After a Retrotransposition Burst inInternational journal of molecular sciences · 2025Article
- Large-Scale Rice Mutant Establishment and High-Throughput Mutant Manipulation Help Advance Rice Functional Genomics.Plants (Basel, Switzerland) · 2025Review
- Mapping-based genome size estimation.BMC genomics · 2025Article
- Review
- Beyond a few bases: methods for large DNA insertion and gene targeting in plants.The Plant journal : for cell and molecular biology · 2025Review
- Comparative Analysis of Active LTR Retrotransposons in Sunflower (International journal of molecular sciences · 2024Article
- Localization data of the T-DNA insertion site in Arabidopsis line SALK_146824C.Data in brief · 2024Article
- Generation and characterisation of an Arabidopsis thaliana f3h/fls1/ans triple mutant that accumulates eriodictyol derivatives.BMC plant biology · 2024Article
- Structural variation and DNA methylation shape the centromere-proximal meiotic crossover landscape in Arabidopsis.Genome biology · 2024Article
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3 authors.
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Abstract
backgroundExperimental 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.
resultsWe 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.
conclusionsLong 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.
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