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Pseudo-chromosome length genome assembly of a double haploid ‘Bartlett’ pear (Pyrus communis L.)

Gareth Linsmith, Stephane Rombauts, Sara Montanari, Cecilia H. Deng, Jean-Marc Celton, Philippe Guérif, Chang Liu, Rolf Lohaus, Jason D. Zurn, Alessandro Cestaro, Nahla V. Bassil, Linda V. Bakker, Elio Schijlen, Susan E. Gardiner, Yves Lespinasse, Charles-Eric Durel, Riccardo Velasco, David Neale, David Chagné, Yves Van de Peer, Michela Troggio, View ORCID ProfileLuca Bianco
doi: https://doi.org/10.1101/651778
Gareth Linsmith
1Center for Plant Systems Biology, VIB, Ghent, Belgium
2Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
3Fondazione Edmund Mach, San Michele all’Adige (TN), Italy
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Stephane Rombauts
1Center for Plant Systems Biology, VIB, Ghent, Belgium
2Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
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Sara Montanari
7University of California Davis, Department of Plant Sciences, Davis, CA USA
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Cecilia H. Deng
10The New Zealand Institute for Plant & Food Research Limited (PFR), Mt Albert Research Centre, Auckland, New Zealand
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Jean-Marc Celton
6IRHS, INRA, Agrocampus-Ouest, Université d’Angers, SFR 4207 Quasav, 42 rue Georges Morel, F-49071 Beaucouzé, France
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Philippe Guérif
6IRHS, INRA, Agrocampus-Ouest, Université d’Angers, SFR 4207 Quasav, 42 rue Georges Morel, F-49071 Beaucouzé, France
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Chang Liu
5ZMBP, Allgemeine Genetik, Universität Tübingen, Auf der Morgenstelle 32, D-72076 Tübingen, Germany
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Rolf Lohaus
1Center for Plant Systems Biology, VIB, Ghent, Belgium
2Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
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Jason D. Zurn
11USDA-ARS National Clonal Germplasm Repository, 33447 Peoria Road, Corvallis, OR 97333
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Alessandro Cestaro
3Fondazione Edmund Mach, San Michele all’Adige (TN), Italy
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Nahla V. Bassil
11USDA-ARS National Clonal Germplasm Repository, 33447 Peoria Road, Corvallis, OR 97333
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Linda V. Bakker
8Wageningen UR – Bioscience P.O. Box 16, 6700AA, Wageningen, The Netherlands
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Elio Schijlen
8Wageningen UR – Bioscience P.O. Box 16, 6700AA, Wageningen, The Netherlands
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Susan E. Gardiner
9The New Zealand Institute for Plant & Food Research Limited (PFR), Palmerston North Research Centre, Palmerston North, New Zealand
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Yves Lespinasse
6IRHS, INRA, Agrocampus-Ouest, Université d’Angers, SFR 4207 Quasav, 42 rue Georges Morel, F-49071 Beaucouzé, France
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Charles-Eric Durel
6IRHS, INRA, Agrocampus-Ouest, Université d’Angers, SFR 4207 Quasav, 42 rue Georges Morel, F-49071 Beaucouzé, France
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Riccardo Velasco
12CREA Research Centre for Viticulture and Enology, Via XXVIII Aprile 26, 31015 Conegliano (TV), Italy
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David Neale
7University of California Davis, Department of Plant Sciences, Davis, CA USA
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David Chagné
9The New Zealand Institute for Plant & Food Research Limited (PFR), Palmerston North Research Centre, Palmerston North, New Zealand
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Yves Van de Peer
1Center for Plant Systems Biology, VIB, Ghent, Belgium
2Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
4Center for Microbial Ecology and Genomics Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria 0028, South Africa
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  • For correspondence: luca.bianco@fmach.it
Michela Troggio
3Fondazione Edmund Mach, San Michele all’Adige (TN), Italy
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  • For correspondence: luca.bianco@fmach.it
Luca Bianco
3Fondazione Edmund Mach, San Michele all’Adige (TN), Italy
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  • ORCID record for Luca Bianco
  • For correspondence: luca.bianco@fmach.it
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Abstract

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 (PacBio), Bionano optical mapping, chromatin interaction capture (Hi-C), and genetic mapping. A total of 496.9 million bases (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 chromosomes of the pear genome. About 50% (247 Mb) of the genome consists of repetitive sequences. Comparison with previous assemblies of Pyrus communis and Pyrus x bretschneideri confirmed the presence of 37,445 protein-coding genes, which is 13% fewer than previously predicted.

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Posted May 27, 2019.
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Pseudo-chromosome length genome assembly of a double haploid ‘Bartlett’ pear (Pyrus communis L.)
Gareth Linsmith, Stephane Rombauts, Sara Montanari, Cecilia H. Deng, Jean-Marc Celton, Philippe Guérif, Chang Liu, Rolf Lohaus, Jason D. Zurn, Alessandro Cestaro, Nahla V. Bassil, Linda V. Bakker, Elio Schijlen, Susan E. Gardiner, Yves Lespinasse, Charles-Eric Durel, Riccardo Velasco, David Neale, David Chagné, Yves Van de Peer, Michela Troggio, Luca Bianco
bioRxiv 651778; doi: https://doi.org/10.1101/651778
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Pseudo-chromosome length genome assembly of a double haploid ‘Bartlett’ pear (Pyrus communis L.)
Gareth Linsmith, Stephane Rombauts, Sara Montanari, Cecilia H. Deng, Jean-Marc Celton, Philippe Guérif, Chang Liu, Rolf Lohaus, Jason D. Zurn, Alessandro Cestaro, Nahla V. Bassil, Linda V. Bakker, Elio Schijlen, Susan E. Gardiner, Yves Lespinasse, Charles-Eric Durel, Riccardo Velasco, David Neale, David Chagné, Yves Van de Peer, Michela Troggio, Luca Bianco
bioRxiv 651778; doi: https://doi.org/10.1101/651778

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