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 Stadler; Detlef Weigel; M David Marks; James A Anderson; Claude Becker; Ratan Chopra; University of Minnesota, St. Paul, MN (United States)

doi:10.1111/pbi.13775

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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

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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

Adam Nunn, Isaac Rodríguez-Arévalo, Zenith Tandukar, Katherine Frels, Adrián Contreras-Garrido, Pablo Carbonell-Bejerano, Panpan Zhang, Daniela Ramos Cruz, Katharina Jandrasits, Christa Lanz, …

Plant biotechnology journal, Vol.20(5), pp.944-963

05/2022

DOI: https://doi.org/10.1111/pbi.13775

PMID: 34990041

Résumé

Chromosomes

Ecosystem

Genome, Plant - genetics

Molecular Sequence Annotation

Thlaspi - genetics

Translational Research, Biomedical

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.

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Titre: Chromosome-level Thlaspi arvense genome provides new tools for translational research and for a newly domesticated cash cover crop of the cooler climates
Créateurs - sans rôle: Adam Nunn - Department of Computer Science, Leipzig University, Leipzig, Germany
Isaac Rodríguez-Arévalo - Gregor Mendel Institute of Molecular Plant Biology GmbH, Austrian Academy of Sciences (ÖAW), Vienna BioCenter (VBC), Vienna, Austria
Zenith Tandukar - Department of Agronomy and Plant Genetics, University of Minnesota, Saint Paul, MN, USA
Katherine Frels - Department of Agronomy and Horticulture, University of Nebraska, Lincoln, NE, USA
Adrián Contreras-Garrido - Department of Molecular Biology, Max Planck Institute for Developmental Biology, Tübingen, Germany
Pablo Carbonell-Bejerano - Max Planck Institute for Developmental Biology
Panpan Zhang - Laboratory of Plant Genome and Development, University of Perpignan, Perpignan, France
Daniela Ramos Cruz - Gregor Mendel Institute of Molecular Plant Biology GmbH, Austrian Academy of Sciences (ÖAW), Vienna BioCenter (VBC), Vienna, Austria
Katharina Jandrasits - Gregor Mendel Institute of Molecular Plant Biology GmbH, Austrian Academy of Sciences (ÖAW), Vienna BioCenter (VBC), Vienna, Austria
Christa Lanz - Department of Molecular Biology, Max Planck Institute for Developmental Biology, Tübingen, Germany
Anthony Brusa - Department of Agronomy and Plant Genetics, University of Minnesota, Saint Paul, MN, USA
Marie Mirouze - Laboratory of Plant Genome and Development, University of Perpignan, Perpignan, France
Kevin Dorn - USDA-ARS, Soil Management and Sugarbeet Research, Fort Collins, CO, USA
David W Galbraith - BIO5 Institute, Arizona Cancer Center, Department of Biomedical Engineering, University of Arizona, School of Plant Sciences, Tucson, AZ, USA
Brice A Jarvis - School of Biological Sciences, Illinois State University, Normal, IL, USA
John C Sedbrook - School of Biological Sciences, Illinois State University, Normal, IL, USA
Donald L Wyse - Department of Agronomy and Plant Genetics, University of Minnesota, Saint Paul, MN, USA
Christian Otto - ecSeq Bioinformatics GmbH, Leipzig, Germany
David Langenberger - ecSeq Bioinformatics GmbH, Leipzig, Germany
Peter F Stadler - Max Planck Institute for Mathematics in the Sciences
Detlef Weigel - Max Planck Institute for Developmental Biology
M David Marks - Department of Plant and Microbial Biology, University of Minnesota, Saint Paul, MN, USA
James A Anderson - Department of Agronomy and Plant Genetics, University of Minnesota, Saint Paul, MN, USA
Claude Becker - Gregor Mendel Institute of Molecular Plant Biology GmbH, Austrian Academy of Sciences (ÖAW), Vienna BioCenter (VBC), Vienna, Austria
Ratan Chopra - Department of Plant and Microbial Biology, University of Minnesota, Saint Paul, MN, USA
University of Minnesota, St. Paul, MN (United States)
Détails de publication: Plant biotechnology journal, Vol.20(5), pp.944-963
Identifiants: 99136556109311
Unité académique: Diversité, Adaptation et Développement des plantes - DIADE
Langue: English
Type de ressource: Journal article