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. Stadler; Detlef Weigel; M. David Marks; James A. Anderson; Claude Becker; Ratan Chopra

doi:10.1111/pbi.13775

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 journal › Article › peer-review

26 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 language	English (US)
Pages (from-to)	944-963
Number of pages	20
Journal	Plant Biotechnology Journal
Volume	20
Issue number	5
DOIs	https://doi.org/10.1111/pbi.13775
State	Published - 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.

UN SDGs

This output contributes to the following UN Sustainable Development Goals (SDGs)

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10.1111/pbi.13775

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Nunn, A., Rodríguez-Arévalo, I., Tandukar, Z., Frels, K. A., Contreras-Garrido, A., Carbonell-Bejerano, P., Zhang, P., Ramos Cruz, D., Jandrasits, K., Lanz, C., Brusa, A., Mirouze, M., Dorn, K., Galbraith, D. W., Jarvis, B. A., Sedbrook, J. C., Wyse, D. L., Otto, C., Langenberger, D., ... Chopra, R. (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. https://doi.org/10.1111/pbi.13775

Nunn, A, Rodríguez-Arévalo, I, Tandukar, Z, Frels, KA, 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, R 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, vol. 20, no. 5, pp. 944-963. https://doi.org/10.1111/pbi.13775

@article{8aabb00c09f24ce893c1c0dbd1381295,

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

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.",

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

author = "Adam Nunn and Isaac Rodr{\'i}guez-Ar{\'e}valo and Zenith Tandukar and Frels, {Katherine A} and Adri{\'a}n Contreras-Garrido and Pablo Carbonell-Bejerano and Panpan Zhang and {Ramos Cruz}, Daniela and Katharina Jandrasits and Christa Lanz and Anthony Brusa and Marie Mirouze and Kevin Dorn and Galbraith, {David W.} and Jarvis, {Brice A.} and Sedbrook, {John C.} and Wyse, {Donald L.} and Christian Otto and David Langenberger and Stadler, {Peter F.} and Detlef Weigel and Marks, {M. David} and Anderson, {James A.} and Claude Becker and Ratan Chopra",

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{\textquoteright}s Horizon 2020 research and innovation programme by the European Research Council (ERC), Grant Agreement No. 716823 {\textquoteleft}FEAR‐SAP{\textquoteright} (I.R.A., C.B.), by the Marie Sklodowska‐Curie ETN {\textquoteleft}EpiDiverse{\textquoteright}, 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{\textquoteright}s Horizon 2020 research and innovation programme by the European Research Council (ERC), Grant Agreement No. 716823 {\textquoteleft}FEAR-SAP{\textquoteright} (I.R.A., C.B.), by the Marie Sklodowska-Curie ETN {\textquoteleft}EpiDiverse{\textquoteright}, 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, Ra{\'u}l 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: {\textcopyright} 2022 The Authors. Plant Biotechnology Journal published by Society for Experimental Biology and The Association of Applied Biologists and John Wiley & Sons Ltd.",

year = "2022",

month = may,

doi = "10.1111/pbi.13775",

language = "English (US)",

volume = "20",

pages = "944--963",

journal = "Plant Biotechnology Journal",

issn = "1467-7644",

publisher = "Wiley-Blackwell Publishing Ltd",

number = "5",

}

TY - JOUR

T1 - Chromosome-level Thlaspi arvense genome provides new tools for translational research and for a newly domesticated cash cover crop of the cooler climates

AU - Nunn, Adam

AU - Rodríguez-Arévalo, Isaac

AU - Tandukar, Zenith

AU - Frels, Katherine A

AU - Contreras-Garrido, Adrián

AU - Carbonell-Bejerano, Pablo

AU - Zhang, Panpan

AU - Ramos Cruz, Daniela

AU - Jandrasits, Katharina

AU - Lanz, Christa

AU - Brusa, Anthony

AU - Mirouze, Marie

AU - Dorn, Kevin

AU - Galbraith, David W.

AU - Jarvis, Brice A.

AU - Sedbrook, John C.

AU - Wyse, Donald L.

AU - Otto, Christian

AU - Langenberger, David

AU - Stadler, Peter F.

AU - Weigel, Detlef

AU - Marks, M. David

AU - Anderson, James A.

AU - Becker, Claude

AU - Chopra, Ratan

N1 - 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.

PY - 2022/5

Y1 - 2022/5

N2 - 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.

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 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.

KW - comparative genomics

KW - genetic mapping

KW - genome annotations

KW - genome assembly

KW - pennycress

KW - Ecosystem

KW - Molecular Sequence Annotation

KW - Thlaspi/genetics

KW - Translational Research, Biomedical

KW - Chromosomes

KW - Genome, Plant/genetics

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DO - 10.1111/pbi.13775

M3 - Article

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AN - SCOPUS:85124478515

SN - 1467-7644

VL - 20

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JO - Plant Biotechnology Journal

JF - Plant Biotechnology Journal

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ER -

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

Abstract

Bibliographical note

Keywords

PubMed: MeSH publication types

UN SDGs

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