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

(2019) GIGASCIENCE. 8(12).
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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.
Keywords
Pyrus communis L, chromosome-scale assembly, Hi-C, Pac-Bio sequencing, ALIGNMENT, SEQUENCE, ANNOTATION, GENE, ALGORITHMS, RESOURCE, PLANTS, MODEL

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MLA
Linsmith, Gareth, et al. “Pseudo-Chromosome-Length Genome Assembly of a Double Haploid ‘Bartlett’ Pear (Pyrus Communis L.).” GIGASCIENCE, vol. 8, no. 12, 2019, doi:10.1093/gigascience/giz138.
APA
Linsmith, G., Rombauts, S., Montanari, S., Deng, C. H., Celton, J.-M., Guérif, P., … Bianco, L. (2019). Pseudo-chromosome-length genome assembly of a double haploid “Bartlett” pear (Pyrus communis L.). GIGASCIENCE, 8(12). https://doi.org/10.1093/gigascience/giz138
Chicago author-date
Linsmith, Gareth, Stephane Rombauts, Sara Montanari, Cecilia H Deng, Jean-Marc Celton, Philippe Guérif, Chang Liu, et al. 2019. “Pseudo-Chromosome-Length Genome Assembly of a Double Haploid ‘Bartlett’ Pear (Pyrus Communis L.).” GIGASCIENCE 8 (12). https://doi.org/10.1093/gigascience/giz138.
Chicago author-date (all authors)
Linsmith, Gareth, 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 B Neale, David Chagné, Yves Van de Peer, Michela Troggio, and Luca Bianco. 2019. “Pseudo-Chromosome-Length Genome Assembly of a Double Haploid ‘Bartlett’ Pear (Pyrus Communis L.).” GIGASCIENCE 8 (12). doi:10.1093/gigascience/giz138.
Vancouver
1.
Linsmith G, Rombauts S, Montanari S, Deng CH, Celton J-M, Guérif P, et al. Pseudo-chromosome-length genome assembly of a double haploid “Bartlett” pear (Pyrus communis L.). GIGASCIENCE. 2019;8(12).
IEEE
[1]
G. Linsmith et al., “Pseudo-chromosome-length genome assembly of a double haploid ‘Bartlett’ pear (Pyrus communis L.),” GIGASCIENCE, vol. 8, no. 12, 2019.
@article{8638380,
  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.}},
  articleno    = {{giz138}},
  author       = {{Linsmith, Gareth and Rombauts, Stephane and Montanari, Sara and Deng, Cecilia H and Celton, Jean-Marc and Guérif, Philippe and Liu, Chang and Lohaus, Rolf and Zurn, Jason D and Cestaro, Alessandro and Bassil, Nahla V and Bakker, Linda V and Schijlen, Elio and Gardiner, Susan E and Lespinasse, Yves and Durel, Charles-Eric and Velasco, Riccardo and Neale, David B and Chagné, David and Van de Peer, Yves and Troggio, Michela and Bianco, Luca}},
  issn         = {{2047-217X}},
  journal      = {{GIGASCIENCE}},
  keywords     = {{Pyrus communis L,chromosome-scale assembly,Hi-C,Pac-Bio sequencing,ALIGNMENT,SEQUENCE,ANNOTATION,GENE,ALGORITHMS,RESOURCE,PLANTS,MODEL}},
  language     = {{eng}},
  number       = {{12}},
  pages        = {{17}},
  title        = {{Pseudo-chromosome-length genome assembly of a double haploid 'Bartlett' pear (Pyrus communis L.)}},
  url          = {{http://dx.doi.org/10.1093/gigascience/giz138}},
  volume       = {{8}},
  year         = {{2019}},
}

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