Transposon dynamics in the emerging oilseed crop < i > Thlaspi arvense < /i >

by Adri án Contreras-Garrido, Dario Galanti, Andrea Movilli, Claude Becker, Oliver Bossdorf, Hajk-Georg Drost, Detlef Weigel

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 cropThlaspi 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 inT.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 inBROMODOMAIN AND ATPase DOMAIN-CONTAINING PROTEIN 1 (BRAT1), whil...

Source: PLoS Genetics - January 31, 2024 Category: Genetics & Stem Cells Authors: Adri án Contreras-Garrido Source Type: research