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 A 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

15 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

Bibliographical note

Funding Information:
This material is based upon work that is supported by the Minnesota Department of Agriculture (J.A., K.F., R.C.) and by the National Institute of Food and Agriculture, U.S. Department of Agriculture, under award numbers 2018‐67009‐27374 (J.A., R.C., K.F.), and 2019‐67009‐29004 (M.D.M, J.S.) and the Agriculture and Food Research Initiative Competitive Grant No. 2019‐69012‐29851 (M.D.M, R.C., J.S.). This research was supported by the U.S. Department of Energy, Office of Science, Office of Biological and Environmental Research, Genomics Science Program grant no. DE‐SC0021286 (M.D.M, R.C.). This work was further funded by the Austrian Academy of Sciences (C.B., I.R.A., K.J., D.R.C.); the Max Planck Society (D.W., A.C.G., P.C.B., C.L.); the European Union’s Horizon 2020 research and innovation programme by the European Research Council (ERC), Grant Agreement No. 716823 ‘FEAR‐SAP’ (I.R.A., C.B.), by the Marie Sklodowska‐Curie ETN ‘EpiDiverse’, Grant Agreement No. 764965 (D.R.C., C.B.) and by Marie Sklodowska‐Curie, Grant Agreement MSCA‐IF No 797460 (P.C.B.); and the German Federal Ministry of Education and Research BMBF, Grant No. 031A538A, de.NBI‐RBC (A.N., P.F.S.).

Funding Information:
This material is based upon work that is supported by the Minnesota Department of Agriculture (J.A., K.F., R.C.) and by the National Institute of Food and Agriculture, U.S. Department of Agriculture, under award numbers 2018-67009-27374 (J.A., R.C., K.F.), and 2019-67009-29004 (M.D.M, J.S.) and the Agriculture and Food Research Initiative Competitive Grant No. 2019-69012-29851 (M.D.M, R.C., J.S.). This research was supported by the U.S. Department of Energy, Office of Science, Office of Biological and Environmental Research, Genomics Science Program grant no. DE-SC0021286 (M.D.M, R.C.). This work was further funded by the Austrian Academy of Sciences (C.B., I.R.A., K.J., D.R.C.); the Max Planck Society (D.W., A.C.G., P.C.B., C.L.); the European Union’s Horizon 2020 research and innovation programme by the European Research Council (ERC), Grant Agreement No. 716823 ‘FEAR-SAP’ (I.R.A., C.B.), by the Marie Sklodowska-Curie ETN ‘EpiDiverse’, Grant Agreement No. 764965 (D.R.C., C.B.) and by Marie Sklodowska-Curie, Grant Agreement MSCA-IF No 797460 (P.C.B.); and the German Federal Ministry of Education and Research BMBF, Grant No. 031A538A, de.NBI-RBC (A.N., P.F.S.). We thank Win Phippen, Thomas Gatter, Prabin Bajgain, Korbinian Schneeberger, Raúl Wijfjes, MPI DB Genome Center, Vienna Biocenter Core Facilities (VBCF), University of Minnesota Genomics Center (UMGC), Minnesota Supercomputing Institute (MSI), and all EpiDiverse network members and beneficiaries. We acknowledge the hard work of many who contributed to this study including Brett Heim, Krishan Rai, Nicole Folstad, Matthew A. Ott, Shweta Jain and many others.

Publisher Copyright:
© 2022 The Authors. Plant Biotechnology Journal published by Society for Experimental Biology and The Association of Applied Biologists and John Wiley & Sons Ltd.

Keywords

  • comparative genomics
  • genetic mapping
  • genome annotations
  • genome assembly
  • pennycress
  • Ecosystem
  • Molecular Sequence Annotation
  • Thlaspi/genetics
  • Translational Research, Biomedical
  • Chromosomes
  • Genome, Plant/genetics

PubMed: MeSH publication types

  • Journal Article
  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, Non-P.H.S.

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