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

Adam Nunn, Isaac Rodríguez-Arévalo, Zenith Tandukar, Katherine Frels, Adrián Contreras-Garrido, Pablo Carbonell-Bejerano, Panpan Zhang, Daniela Ramos Cruz, Katharina Jandrasits, Christa Lanz, Anthony Brusa, Marie Mirouze, Kevin Dorn, David W. Galbraith, Brice A. Jarvis, John C. Sedbrook, Donald L. Wyse, Christian Otto, David Langenberger, Peter F. StadlerDetlef Weigel, M. David Marks, James A. Anderson, Claude Becker, Ratan Chopra

Research output: Contribution to journalArticlepeer-review

1 Scopus citations

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.

Original languageEnglish (US)
Pages (from-to)944-963
Number of pages20
JournalPlant Biotechnology Journal
Volume20
Issue number5
DOIs
StatePublished - May 2022

Keywords

  • comparative genomics
  • genetic mapping
  • genome annotations
  • genome assembly
  • pennycress

ASJC Scopus subject areas

  • Biotechnology
  • Agronomy and Crop Science
  • Plant Science

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