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Vollheyde K, Dudley QM, Yang T, Oz MT, Mancinotti D, Fedi MO, Heavens D, Linsmith G, Chhetry M, Smedley MA, Harwood WA, Swarbreck D, Geu‐Flores F, Patron NJ. An improved Nicotiana benthamiana bioproduction chassis provides novel insights into nicotine biosynthesis. New Phytol 2023; 240:302-317. [PMID: 37488711 PMCID: PMC10952274 DOI: 10.1111/nph.19141] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Accepted: 06/28/2023] [Indexed: 07/26/2023]
Abstract
The model plant Nicotiana benthamiana is an increasingly attractive organism for the production of high-value, biologically active molecules. However, N. benthamiana accumulates high levels of pyridine alkaloids, in particular nicotine, which complicates the downstream purification processes. Here, we report a new assembly of the N. benthamiana genome as well as the generation of low-nicotine lines by CRISPR/Cas9-based inactivation of berberine bridge enzyme-like proteins (BBLs). Triple as well as quintuple mutants accumulated three to four times less nicotine than the respective control lines. The availability of lines without functional BBLs allowed us to probe their catalytic role in nicotine biosynthesis, which has remained obscure. Notably, chiral analysis revealed that the enantiomeric purity of nicotine was fully lost in the quintuple mutants. In addition, precursor feeding experiments showed that these mutants cannot facilitate the specific loss of C6 hydrogen that characterizes natural nicotine biosynthesis. Our work delivers an improved N. benthamiana chassis for bioproduction and uncovers the crucial role of BBLs in the stereoselectivity of nicotine biosynthesis.
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Affiliation(s)
- Katharina Vollheyde
- Department of Plant and Environmental SciencesUniversity of Copenhagen1871 FrederiksbergCopenhagenDenmark
| | | | - Ting Yang
- Department of Plant and Environmental SciencesUniversity of Copenhagen1871 FrederiksbergCopenhagenDenmark
| | - Mehmet T. Oz
- Earlham Institute, Norwich Research ParkNorwichNorfolkNR4 7UZUK
| | - Davide Mancinotti
- Department of Plant and Environmental SciencesUniversity of Copenhagen1871 FrederiksbergCopenhagenDenmark
| | | | - Darren Heavens
- Earlham Institute, Norwich Research ParkNorwichNorfolkNR4 7UZUK
| | - Gareth Linsmith
- Earlham Institute, Norwich Research ParkNorwichNorfolkNR4 7UZUK
| | - Monika Chhetry
- John Innes Centre, Norwich Research ParkNorwichNorfolkNR4 7UHUK
| | - Mark A. Smedley
- John Innes Centre, Norwich Research ParkNorwichNorfolkNR4 7UHUK
| | | | - David Swarbreck
- Earlham Institute, Norwich Research ParkNorwichNorfolkNR4 7UZUK
| | - Fernando Geu‐Flores
- Department of Plant and Environmental SciencesUniversity of Copenhagen1871 FrederiksbergCopenhagenDenmark
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Linsmith G, Rombauts S, Montanari S, Deng CH, Celton JM, Guérif P, Liu C, Lohaus R, Zurn JD, Cestaro A, Bassil NV, Bakker LV, Schijlen E, Gardiner SE, Lespinasse Y, Durel CE, Velasco R, Neale DB, Chagné D, Van de Peer Y, Troggio M, Bianco L. Pseudo-chromosome-length genome assembly of a double haploid "Bartlett" pear (Pyrus communis L.). Gigascience 2019; 8:giz138. [PMID: 31816089 PMCID: PMC6901071 DOI: 10.1093/gigascience/giz138] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2019] [Revised: 10/18/2019] [Accepted: 10/30/2019] [Indexed: 11/14/2022] Open
Abstract
BACKGROUND We report an improved assembly and scaffolding of the European pear (Pyrus communis L.) genome (referred to as BartlettDHv2.0), obtained using a combination of Pacific Biosciences RSII long-read sequencing, Bionano optical mapping, chromatin interaction capture (Hi-C), and genetic mapping. The sample selected for sequencing is a double haploid derived from the same "Bartlett" reference pear that was previously sequenced. Sequencing of di-haploid plants makes assembly more tractable in highly heterozygous species such as P. communis. FINDINGS A total of 496.9 Mb corresponding to 97% of the estimated genome size were assembled into 494 scaffolds. Hi-C data and a high-density genetic map allowed us to anchor and orient 87% of the sequence on the 17 pear chromosomes. Approximately 50% (247 Mb) of the genome consists of repetitive sequences. Gene annotation confirmed the presence of 37,445 protein-coding genes, which is 13% fewer than previously predicted. CONCLUSIONS We showed that the use of a doubled-haploid plant is an effective solution to the problems presented by high levels of heterozygosity and duplication for the generation of high-quality genome assemblies. We present a high-quality chromosome-scale assembly of the European pear Pyrus communis and demostrate its high degree of synteny with the genomes of Malus x Domestica and Pyrus x bretschneideri.
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Affiliation(s)
- Gareth Linsmith
- Center for Plant Systems Biology, VIB, Technologiepark 71, 9052, Gent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, 9052 Gent, Belgium
- Fondazione Edmund Mach, via E. Mach 1, 38010, San Michele all'Adige (TN), Italy
| | - Stephane Rombauts
- Center for Plant Systems Biology, VIB, Technologiepark 71, 9052, Gent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, 9052 Gent, Belgium
| | - Sara Montanari
- University of California Davis, Department of Plant Sciences, One Shields Ave, Davis, CA 95616, USA
| | - Cecilia H Deng
- The New Zealand Institute for Plant & Food Research Limited (PFR), Mt Albert Research Centre,120 Mt Albert Road, Sandringham, Auckland, 1025, New Zealand
| | - Jean-Marc Celton
- IRHS, INRA, Agrocampus-Ouest, Université d'Angers, SFR 4207 Quasav, 42 rue Georges Morel, F-49071 Beaucouzé, France
| | - Philippe Guérif
- IRHS, INRA, Agrocampus-Ouest, Université d'Angers, SFR 4207 Quasav, 42 rue Georges Morel, F-49071 Beaucouzé, France
| | - Chang Liu
- ZMBP, Allgemeine Genetik, Universität Tübingen, Auf der Morgenstelle 32, D-72076 Tübingen, Germany
| | - Rolf Lohaus
- Center for Plant Systems Biology, VIB, Technologiepark 71, 9052, Gent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, 9052 Gent, Belgium
| | - Jason D Zurn
- USDA-ARS National Clonal Germplasm Repository, 33447 Peoria Road, Corvallis, OR 97333, USA
| | - Alessandro Cestaro
- Fondazione Edmund Mach, via E. Mach 1, 38010, San Michele all'Adige (TN), Italy
| | - Nahla V Bassil
- USDA-ARS National Clonal Germplasm Repository, 33447 Peoria Road, Corvallis, OR 97333, USA
| | - Linda V Bakker
- Wageningen UR – Bioscience P.O. Box 16, 6700AA, Wageningen, The Netherlands
| | - Elio Schijlen
- Wageningen UR – Bioscience P.O. Box 16, 6700AA, Wageningen, The Netherlands
| | - Susan E Gardiner
- The New Zealand Institute for Plant & Food Research Limited (PFR), Palmerston North Research Centre, Palmerston North, New Zealand
| | - Yves Lespinasse
- IRHS, INRA, Agrocampus-Ouest, Université d'Angers, SFR 4207 Quasav, 42 rue Georges Morel, F-49071 Beaucouzé, France
| | - Charles-Eric Durel
- IRHS, INRA, Agrocampus-Ouest, Université d'Angers, SFR 4207 Quasav, 42 rue Georges Morel, F-49071 Beaucouzé, France
| | - Riccardo Velasco
- CREA Research Centre for Viticulture and Enology, Via XXVIII Aprile 26, 31015 Conegliano (TV), Italy
| | - David B Neale
- University of California Davis, Department of Plant Sciences, One Shields Ave, Davis, CA 95616, USA
| | - David Chagné
- The New Zealand Institute for Plant & Food Research Limited (PFR), Palmerston North Research Centre, Palmerston North, New Zealand
| | - Yves Van de Peer
- Center for Plant Systems Biology, VIB, Technologiepark 71, 9052, Gent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, 9052 Gent, Belgium
- Center for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Roper street, Pretoria 0028, South Africa
| | - Michela Troggio
- Fondazione Edmund Mach, via E. Mach 1, 38010, San Michele all'Adige (TN), Italy
| | - Luca Bianco
- Fondazione Edmund Mach, via E. Mach 1, 38010, San Michele all'Adige (TN), Italy
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Bianco L, Cestaro A, Linsmith G, Muranty H, Denancé C, Théron A, Poncet C, Micheletti D, Kerschbamer E, Di Pierro EA, Larger S, Pindo M, Van de Weg E, Davassi A, Laurens F, Velasco R, Durel CE, Troggio M. Development and validation of the Axiom(®) Apple480K SNP genotyping array. Plant J 2016; 86:62-74. [PMID: 26919684 DOI: 10.1111/tpj.13145] [Citation(s) in RCA: 60] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2015] [Revised: 02/03/2016] [Accepted: 02/05/2016] [Indexed: 05/18/2023]
Abstract
Cultivated apple (Malus × domestica Borkh.) is one of the most important fruit crops in temperate regions, and has great economic and cultural value. The apple genome is highly heterozygous and has undergone a recent duplication which, combined with a rapid linkage disequilibrium decay, makes it difficult to perform genome-wide association (GWA) studies. Single nucleotide polymorphism arrays offer highly multiplexed assays at a relatively low cost per data point and can be a valid tool for the identification of the markers associated with traits of interest. Here, we describe the development and validation of a 487K SNP Affymetrix Axiom(®) genotyping array for apple and discuss its potential applications. The array has been built from the high-depth resequencing of 63 different cultivars covering most of the genetic diversity in cultivated apple. The SNPs were chosen by applying a focal points approach to enrich genic regions, but also to reach a uniform coverage of non-genic regions. A total of 1324 apple accessions, including the 92 progenies of two mapping populations, have been genotyped with the Axiom(®) Apple480K to assess the effectiveness of the array. A large majority of SNPs (359 994 or 74%) fell in the stringent class of poly high resolution polymorphisms. We also devised a filtering procedure to identify a subset of 275K very robust markers that can be safely used for germplasm surveys in apple. The Axiom(®) Apple480K has now been commercially released both for public and proprietary use and will likely be a reference tool for GWA studies in apple.
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Affiliation(s)
- Luca Bianco
- Research and Innovation Centre, Fondazione Edmund Mach, via Edmund Mach 1, 38010, San Michele all'Adige, Trento, Italy
| | - Alessandro Cestaro
- Research and Innovation Centre, Fondazione Edmund Mach, via Edmund Mach 1, 38010, San Michele all'Adige, Trento, Italy
| | - Gareth Linsmith
- Research and Innovation Centre, Fondazione Edmund Mach, via Edmund Mach 1, 38010, San Michele all'Adige, Trento, Italy
| | - Hélène Muranty
- Institut de Recherche en Horticulture et Semences - UMR1345, Institut National de la Recherche Agronomique (INRA), SFR 4207 QUASAV, 42 Rue Georges Morel, F-49071, Beaucouzé, France
| | - Caroline Denancé
- Institut de Recherche en Horticulture et Semences - UMR1345, Institut National de la Recherche Agronomique (INRA), SFR 4207 QUASAV, 42 Rue Georges Morel, F-49071, Beaucouzé, France
| | - Anthony Théron
- Plateforme Gentyane, INRA UMR1095 Genetics, Diversity and Ecophysiology of Cereals, 5 Chemin de Beaulieu, 63039, Clermont-Ferrand, France
| | - Charles Poncet
- Plateforme Gentyane, INRA UMR1095 Genetics, Diversity and Ecophysiology of Cereals, 5 Chemin de Beaulieu, 63039, Clermont-Ferrand, France
| | - Diego Micheletti
- Research and Innovation Centre, Fondazione Edmund Mach, via Edmund Mach 1, 38010, San Michele all'Adige, Trento, Italy
| | - Emanuela Kerschbamer
- Research and Innovation Centre, Fondazione Edmund Mach, via Edmund Mach 1, 38010, San Michele all'Adige, Trento, Italy
| | - Erica A Di Pierro
- Department of Biosciences, University of Milan, via Celoria 26, 20133, Milano, Italy
| | - Simone Larger
- Research and Innovation Centre, Fondazione Edmund Mach, via Edmund Mach 1, 38010, San Michele all'Adige, Trento, Italy
| | - Massimo Pindo
- Research and Innovation Centre, Fondazione Edmund Mach, via Edmund Mach 1, 38010, San Michele all'Adige, Trento, Italy
| | - Eric Van de Weg
- Wageningen UR Plant Breeding, Wageningen University and Research Centre, PO Box 16, 6700 AA, Wageningen, The Netherlands
| | - Alessandro Davassi
- Affymetrix UK Ltd, Mercury Park, Wycombe Lane, Wooburn Green, High Wycombe, HP10 0HH, UK
| | - François Laurens
- Institut de Recherche en Horticulture et Semences - UMR1345, Institut National de la Recherche Agronomique (INRA), SFR 4207 QUASAV, 42 Rue Georges Morel, F-49071, Beaucouzé, France
| | - Riccardo Velasco
- Research and Innovation Centre, Fondazione Edmund Mach, via Edmund Mach 1, 38010, San Michele all'Adige, Trento, Italy
| | - Charles-Eric Durel
- Institut de Recherche en Horticulture et Semences - UMR1345, Institut National de la Recherche Agronomique (INRA), SFR 4207 QUASAV, 42 Rue Georges Morel, F-49071, Beaucouzé, France
| | - Michela Troggio
- Research and Innovation Centre, Fondazione Edmund Mach, via Edmund Mach 1, 38010, San Michele all'Adige, Trento, Italy
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