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

Nunn, A; Rodríguez-Arévalo, I; Tandukar, Z; Frels, K; Contreras-Garrido, A; Carbonell-Bejerano, P; Zhang, P; Ramos Cruz, D; Jandrasits, K; Lanz, C; Brusa, A; Mirouze, M; Dorn, K; Galbraith, DW; Jarvis, BA; Sedbrook, JC; Wyse, DL; Otto, C; Langenberger, D; Stadler, PF; Weigel, D; Marks, MD; Anderson, JA; Becker, C; Chopra, A

doi:10.1111/pbi.13775

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

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Lanz, C
Department Molecular Biology, Max Planck Institute for Developmental Biology, Max Planck Society;

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Weigel, D
Department Molecular Biology, Max Planck Institute for Developmental Biology, Max Planck Society;

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Citation

Nunn, A., Rodríguez-Arévalo, I., Tandukar, Z., Frels, K., Contreras-Garrido, A., Carbonell-Bejerano, P., et al. (2022). Chromosome-level Thlaspi arvense genome provides new tools for translational research and for a newly domesticated cash cover crop of the cooler climates. Plant Biotechnology Journal, 20(5), 944-963. doi:10.1111/pbi.13775.

Cite as: https://hdl.handle.net/21.11116/0000-000A-391B-9

Abstract

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.