RT Journal Article
SR Electronic
T1 Chromosome-level <em>Thlaspi arvense</em> genome provides new tools for translational research and for a newly domesticated cash cover crop of the cooler climates
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 2021.07.30.454478
DO 10.1101/2021.07.30.454478
A1 Adam Nunn
A1 Isaac Rodríguez-Arévalo
A1 Zenith Tandukar
A1 Katherine Frels
A1 Adrián Contreras-Garrido
A1 Pablo Carbonell-Bejerano
A1 Panpan Zhang
A1 Daniela Ramos-Cruz
A1 Katharina Jandrasits
A1 Christa Lanz
A1 Anthony Brusa
A1 Marie Mirouze
A1 Kevin Dorn
A1 Brice Jarvis
A1 John Sedbrook
A1 Donald L. Wyse
A1 Christian Otto
A1 David Langenberger
A1 Peter F. Stadler
A1 Detlef Weigel
A1 M. David Marks
A1 James A. Anderson
A1 Claude Becker
A1 Ratan Chopra
YR 2021
UL http://biorxiv.org/content/early/2021/08/01/2021.07.30.454478.abstract
AB 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 StatementThe authors declare potential competing interests as intellectual property applications have been submitted on some of the genes discussed in this study.