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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

bioRxiv 2021
Nunn A. et al

Adam NunnIsaac Rodríguez-ArévaloZenith TandukarKatherine FrelsAdrián Contreras-GarridoPablo Carbonell-BejeranoPanpan ZhangDaniela Ramos-CruzKatharina JandrasitsChrista LanzAnthony BrusaMarie MirouzeKevin DornBrice JarvisJohn SedbrookDonald L. WyseChristian OttoDavid LangenbergerPeter F. StadlerDetlef WeigelM. David MarksJames A. AndersonClaude BeckerRatan Chopra

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 small RNAs, pseudogenes, and transposable elements, and highlight tissue specific expression and methylation patterns. Resequencing of forty wild accessions provides insights into genome-wide genetic variation as well as QTL regions for flowering time and a seedling color phenotype. Altogether, these data will serve as a tool for pennycress improvement in general and for translational research across the Brassicaceae.

Competing Interest Statement

The authors declare potential competing interests as intellectual property applications have been submitted on some of the genes discussed in this study.

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