Transposon dynamics in the emerging oilseed crop Thlaspi arvense.

Autor: Contreras-Garrido A; Department of Molecular Biology, Max Planck Institute for Biology Tübingen, Tübingen, Germany., Galanti D; Plant Evolutionary Ecology, University of Tübingen, Tübingen, Germany., Movilli A; Department of Molecular Biology, Max Planck Institute for Biology Tübingen, Tübingen, Germany., Becker C; LMU Biocenter, Faculty of Biology, Ludwig Maximilians University Munich, Martinsried, Germany., Bossdorf O; Plant Evolutionary Ecology, University of Tübingen, Tübingen, Germany., Drost HG; Computational Biology Group, Max Planck Institute for Biology Tübingen,Tübingen, Germany., Weigel D; Department of Molecular Biology, Max Planck Institute for Biology Tübingen, Tübingen, Germany.
Jazyk: angličtina
Zdroj: PLoS genetics [PLoS Genet] 2024 Jan 31; Vol. 20 (1), pp. e1011141. Date of Electronic Publication: 2024 Jan 31 (Print Publication: 2024).
DOI: 10.1371/journal.pgen.1011141
Abstrakt: Genome evolution is partly driven by the mobility of transposable elements (TEs) which often leads to deleterious effects, but their activity can also facilitate genetic novelty and catalyze local adaptation. We explored how the intraspecific diversity of TE polymorphisms might contribute to the broad geographic success and adaptive capacity of the emerging oil crop Thlaspi arvense (field pennycress). We classified the TE inventory based on a high-quality genome assembly, estimated the age of retrotransposon TE families and comprehensively assessed their mobilization potential. A survey of 280 accessions from 12 regions across the Northern hemisphere allowed us to quantify over 90,000 TE insertion polymorphisms (TIPs). Their distribution mirrored the genetic differentiation as measured by single nucleotide polymorphisms (SNPs). The number and types of mobile TE families vary substantially across populations, but there are also shared patterns common to all accessions. Ty3/Athila elements are the main drivers of TE diversity in T. arvense populations, while a single Ty1/Alesia lineage might be particularly important for transcriptome divergence. The number of retrotransposon TIPs is associated with variation at genes related to epigenetic regulation, including an apparent knockout mutation in BROMODOMAIN AND ATPase DOMAIN-CONTAINING PROTEIN 1 (BRAT1), while DNA transposons are associated with variation at the HSP19 heat shock protein gene. We propose that the high rate of mobilization activity can be harnessed for targeted gene expression diversification, which may ultimately present a toolbox for the potential use of transposition in breeding and domestication of T. arvense.
Competing Interests: I have read the journal’s policy and the authors of this manuscript have the following competing interests: D.W. holds equity in Computomics, which advises breeders. D.W. advises KWS SE, a plant breeder and seed producer. All the other authors have declared that no competing interests exist.

(Copyright: © 2024 Contreras-Garrido et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.)
Databáze: MEDLINE
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