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Journal articles
High-quality de novo assembly of the apple genome and methylome dynamics of early fruit development
Nicolas Daccord
1
Jean-Marc Celton
1
G. Linsmith
2
C. Becker
3, 4
Nathalie Choisne
5
E. Schijlen
6
H. van de Geest
6
L. Bianco
2
D. Micheletti
2
R. Velasco
2
E. A. Di Pierro
7
Jerome Gouzy
8
D. Jasper G. Rees
9
Philippe Guérif
1
Helene Muranty
1
Charles Eric Durel
1
Francois Laurens
1
Yves Lespinasse
1
Sylvain Gaillard
1
Sebastien Aubourg
1
Hadi Quesneville
5
D. Weigel
3
E. van de Weg
10
M. Troggio
2
Etienne Bucher
1
Nicolas Daccord 1
Author
Jean-Marc Celton 1
Author Employer institution : Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement
G. Linsmith 2
Author
C. Becker 3, 4
Author
D. Micheletti 2
Author
R. Velasco 2
Author
E. A. Di Pierro 7
Author
Jerome Gouzy 8
Author IdHAL : jerome-gouzy ORCID : https://orcid.org/0000-0001-5695-4557
D. Jasper G. Rees 9
Author
Philippe Guérif 1
Author Employer institution : Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement
Helene Muranty 1
Author Employer institution : Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement IdHAL : helene-muranty ORCID : https://orcid.org/0000-0003-3956-3807
Charles Eric Durel 1
Author Employer institution : Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement IdHAL : charles-eric-durel ORCID : https://orcid.org/0000-0003-3856-2837
Francois Laurens 1
Author Employer institution : Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement
Yves Lespinasse 1
Author
Sylvain Gaillard 1
Author IdHAL : syl-gaillard ResearcherId : http://www.researcherid.com/rid/F-8087-2011 ORCID : https://orcid.org/0000-0002-1802-169X
Sebastien Aubourg 1
Author Employer institution : Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement IdHAL : sebastien-aubourg ORCID : https://orcid.org/0000-0002-0695-4767
Hadi Quesneville 5
Author IdHAL : hadi-quesneville ORCID : https://orcid.org/0000-0003-3001-4908
D. Weigel 3
Author
E. van de Weg 10
Author
M. Troggio 2
Author
Etienne Bucher 1
Author Employer institution : Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement
1
IRHS - Institut de Recherche en Horticulture et Semences (Institut Agro Agrocampus Ouest, UMR1345 IRHS, F-49045 Angers, France - France)
- UA - Université d'Angers : UMR1345 (Université d'Angers - 40 Rue de Rennes, BP 73532 - 49035 Angers CEDEX 01 - France)
- INRAE - Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement : UMR1345 (France)
- INSTITUT AGRO Agrocampus Ouest (65 rue de Saint Brieuc CS 84215 35042 Rennes CEDEX - France)
3
Department of Molecular Biology (Interfacultary Institute for Cell Biology Tübingen - Germany)
- Eberhard Karls Universität Tübingen = Eberhard Karls University of Tuebingen ( Geschwister-Scholl-Platz 72074 Tübingen - Germany)
4
Institute of Molecular Plant Biology, Vienna Biocenter (VBC), (Austria)
- OeAW - Austrian Academy of Sciences (Doktor-Ignaz-Seipel-Platz 2, 1010 Wien - Austria)
5
URGI - Unité de Recherche Génomique Info (INRA, Centre de recherche de Versailles, bat.18 Route de Saint Cyr 78000 Versailles - France)
- INRA - Institut National de la Recherche Agronomique : UR1164 (France)
6
UR–Bioscience (Netherlands)
- WUR - Wageningen University and Research [Wageningen] (Droevendaalsesteeg 4, 6708 PB Wageningen - Netherlands)
7
Department of Biosciences (Preventive Nutrition, Novum, 141 57 Huddinge - Sweden)
- Karolinska Institutet [Stockholm] (Solnavägen 1, 171 77 Solna Stockholm - Sweden)
8
LIPM - Laboratoire des interactions plantes micro-organismes (Chemin de Borde-Rouge - BP 27 31326 CASTANET TOLOSAN CEDEX - France)
- INRA - Institut National de la Recherche Agronomique : UMR0441 (France)
- CNRS - Centre National de la Recherche Scientifique : UMR2594 (France)
9
Agricultural Research Council, Biotechnology Platform (South Africa)
10
UR–Plant Breeding (Netherlands)
- WUR - Wageningen University and Research [Wageningen] (Droevendaalsesteeg 4, 6708 PB Wageningen - Netherlands)
Abstract : Using the latest sequencing and optical mapping technologies, we have produced a high-quality de novo assembly of the apple (Malus domestica Borkh.) genome. Repeat sequences, which represented over half of the assembly, provided an unprecedented opportunity to investigate the uncharacterized regions of a tree genome; we identified a new hyper-repetitive retrotransposon sequence that was over-represented in heterochromatic regions and estimated that a major burst of different transposable elements (TEs) occurred 21 million years ago. Notably, the timing of this TE burst coincided with the uplift of the Tian Shan mountains, which is thought to be the center of the location where the apple originated, suggesting that TEs and associated processes may have contributed to the diversification of the apple ancestor and possibly to its divergence from pear. Finally, genome-wide DNA methylation data suggest that epigenetic marks may contribute to agronomically relevant aspects, such as apple fruit development.
Keywords :
genome
Mots-clés :
malus domestica borkh
développement du fruit
Document type :
Journal articles
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https://hal.archives-ouvertes.fr/hal-01602554
Contributor : Archive Ouverte Prodinra Connect in order to contact the contributor
Submitted on : Tuesday, May 26, 2020 - 6:04:32 PM
Last modification on : Friday, May 20, 2022 - 9:04:59 AM
Contributor : Archive Ouverte Prodinra Connect in order to contact the contributor
Submitted on : Tuesday, May 26, 2020 - 6:04:32 PM
Last modification on : Friday, May 20, 2022 - 9:04:59 AM
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Distributed under a Creative Commons Attribution 4.0 International License
Identifiers
- HAL Id : hal-01602554, version 1
- DOI : 10.1038/ng.3886
- PRODINRA : 400602
- WOS : 000404253300019
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INRAE | CNRS | IRHS | UNIV-ANGERS | INRA | UNIV-PARIS-SACLAY | UNAM
Citation
Nicolas Daccord, Jean-Marc Celton, G. Linsmith, C. Becker, Nathalie Choisne, et al.. High-quality de novo assembly of the apple genome and methylome dynamics of early fruit development. Nature Genetics, Nature Publishing Group, 2017, 49 (7), pp.1099-1108. ⟨10.1038/ng.3886⟩. ⟨hal-01602554⟩
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