Transposon dynamics in the emerging oilseed crop Thlaspi arvense

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 explore how the intraspecific diversity of TE polymorphisms is shaping the broad geographic success and adaptation capacity of the emerging oil crop Thlaspi arvense. We achieve this by classifying the TE inventory of this species based on a high-quality genome assembly, age estimation of retrotransposon TE families, and a comprehensive assessment of their mobilization potential. Our survey of TE insertion polymorphisms (TIPs) captures 280 accessions from 12 regions across the Northern hemisphere. We quantified over 90,000 TIPs, with their distribution paralleling genetic differentiation as measured by single nucleotide polymorphisms (SNPs). The number and types of mobile TE families varies substantially across populations, but there are also shared patterns common to all accessions. We found that Athila elements are the main drivers of TE diversity in T. arvense populations, while a single Alesia family might be particularly important for molding transcriptome divergence. We further observed that the number of retrotransposon TIPs is associated with variation at genes of the DNA methylation machinery, while DNA transposons are associated with variation at a Heat Shock Protein (HSP19). 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.