Chromosome-level Thlaspi arvense genome provides new tools for translational research and for a newly domesticated cash cover crop of the cooler climates

Thlaspi arvense (Field Pennycress) is being domesticated as a winter annual oilseed crop capable of improving ecosystems and intensifying agricultural productivity without new land displacement. It is a selfing diploid with a short life cycle and is amenable to genetic manipulations, making it an accessible genetic field-based model species. The availability of a high quality reference genome is vital for untangling the genetic control of pennycress development and to understand its evolutionary history within the Brassicaceae. Here, we present a chromosome-level genome assembly of var. MN106-Ref with improved annotations and highlight transcript variation for two of the accessions (MN108 and Spring32-10) that are highly amenable to genetic transformation. In addition, we classified small RNAs, pseudogenes, and transposable elements, and highlighted tissue specific expression and methylation patterns. Resequencing of forty wild accessions identified genetic variation and putative QTL regions for flowering time and a leaf color phenotype. Altogether, these data will serve as a tool for pennycress improvement in general and for translational research across Brassicaceae.