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Thlaspi arvense (field pennycress) is being domesticated as a winter annual oilseed crop capable of improving ecosystems and intensifying agricultural productivity without increasing land use. It is a selfing diploid with a short life cycle and is amenable to genetic manipulations, making it an accessible field-based model species for genetics and epigenetics. The availability of a high-quality reference genome is vital for understanding pennycress physiology and for clarifying its evolutionary history within the Brassicaceae. Here, we present a chromosome-level genome assembly of var. MN106-Ref with improved gene annotation and use it to investigate gene structure differences between two accessions (MN108 and Spring32-10) that are highly amenable to genetic transformation. We describe non-coding RNAs, pseudogenes and transposable elements, and highlight tissue-specific expression and methylation patterns. Resequencing of forty wild accessions provided insights into genome-wide genetic variation, and QTL regions were identified for a seedling colour phenotype. Altogether, these data will serve as a tool for pennycress improvement in general and for translational research across the Brassicaceae., This material is based upon work that is supported by the Minnesota Department of Agriculture (J.A., K.F., R.C.) and by the National Institute of Food and Agriculture, U.S. Department of Agriculture, under award numbers 2018-67009-27374 (J.A., R.C., K.F.), and 2019-67009-29004 (M.D.M, J.S.) and the Agriculture and Food Research Initiative Competitive Grant No. 2019-69012-29851 (M.D.M, R.C., J.S.). This research was supported by the U.S. Department of Energy, Office of Science, Office of Biological and Environmental Research, Genomics Science Program grant no. DE-SC0021286 (M.D.M, R.C.). This work was further funded by the Austrian Academy of Sciences (C.B., I.R.A., K.J., D.R.C.); the Max Planck Society (D.W., A.C.G., P.C.B., C.L.); the European Union’s Horizon 2020 research and innovation programme by the European Research Council (ERC), Grant Agreement No. 716823 ‘FEAR-SAP’ (I.R.A., C.B.), by the Marie Sklodowska-Curie ETN ‘EpiDiverse’, Grant Agreement No. 764965 (D.R.C., C.B.) and by Marie Sklodowska-Curie, Grant Agreement MSCA-IF No 797460 (P.C.B.); and the German Federal Ministry of Education and Research BMBF, Grant No. 031A538A, de.NBI-RBC (A.N., P.F.S.).

Reproductive versatility of plants is an important part of their success. We investigated environmental factors that influence the reproductive strategies of three non-native plants and investigate the larger impact of these factors at the population level. Initial work consisted of two studies with Trifolium repens. A two month experiment was conducted under a factorial design, testing a combination of resource abundance and heterogeneity. Resource distribution had no effect on reproductive strategy. Resource abundance increased the amount of biomass allocated to horizontal stem development and foraging, but showed no effect on flowering at two months. A four month study showed that fertilizer does increase inflorescence development. The conflict between the two studies is evidence that reproductive strategy and flowering cues in Trifolium repens are strongly influenced by density depended effects. Two studies were performed with Ailanthus altissma, a high impact invasive tree species. A germination study was conducted on seeds from Ailanthus altissima based on human land use legacy, in the form of brownfield and non-brownfield sites. Brownfield sites showed a significant reduction in seed germination, this difference in germination was independent of initial seed mass. These two factors indicate that individuals from a brownfield site have a reduced fitness benefit for the same amount of resources invested in seeds. Population genetics of Ailanthus altissima were surveyed across six sites, using a set of eight microsatellite loci. Despite a strong propensity for clonal growth, the microsatellites revealed no evidence of clonal reproduction at the population level. Geneflow between sites was found to be independent of geographic distance, rather, geneflow was linked to the level of human traffic at a site. Evidence was also found that land management practices were effective at inhibiting geneflow into managed sites. Finally, an investigation was conducted into the possibility of ecotypes and reproductive isolation in Schismus arabicus in the Sonoran and Mojave deserts, based on the extreme heterogeneity of the nurse plant dominated landscape. Results from the ITS marker showed no evidence of ecotypes at either site. Number of SNPs between individuals were not correlated with distance, indicating that high internal geneflow prevents the level of isolation necessary for the formation of ecotypes. MCMC modeling also showed a small, but consistent, unidirectional geneflow from the Mojave to the Sonoran desert site. This was taken as evidence of anthropogenic geneflow. Ultimately, it is shown that reproductive strategy and population structure are strongly influenced by anthropogenic factors such as nutrient level, land-use legacy, management practices, and anthropogenic transport.