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 B. Neale, David Chagné, Yves Van de Peer & 2 others Michela Troggio, Luca Bianco

Research output: Contribution to journalArticleAcademicpeer-review

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.

Original languageEnglish
Article numbergiz138
JournalGigaScience
Volume8
Issue number12
DOIs
Publication statusPublished - Dec 2019

Fingerprint

Pyrus
Haploidy
Chromosomes
Genes
Genome
Synteny
Molecular Sequence Annotation
Genome Size
Chromosomes, Human, Pair 17
Nucleic Acid Repetitive Sequences
Malus
Anchors
Scaffolds
Chromatin
Proteins

Keywords

  • chromosome-scale assembly
  • Hi-C
  • Pac-Bio sequencing
  • Pyrus communis L

Cite this

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), [giz138]. https://doi.org/10.1093/gigascience/giz138
Linsmith, Gareth ; Rombauts, Stephane ; Montanari, Sara ; Deng, Cecilia H. ; Celton, Jean Marc ; Guérif, Philippe ; Liu, Chang ; Lohaus, Rolf ; Zurn, Jason D. ; Cestaro, Alessandro ; Bassil, Nahla V. ; Bakker, Linda V. ; Schijlen, Elio ; Gardiner, Susan E. ; Lespinasse, Yves ; Durel, Charles Eric ; Velasco, Riccardo ; Neale, David B. ; Chagné, David ; Van de Peer, Yves ; Troggio, Michela ; Bianco, Luca. / Pseudo-chromosome-length genome assembly of a double haploid "Bartlett" pear (Pyrus communis L.). In: GigaScience. 2019 ; Vol. 8, No. 12.
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title = "Pseudo-chromosome-length genome assembly of a double haploid {"}Bartlett{"} pear (Pyrus communis L.)",
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 = "chromosome-scale assembly, Hi-C, Pac-Bio sequencing, Pyrus communis L",
author = "Gareth Linsmith and Stephane Rombauts and Sara Montanari and Deng, {Cecilia H.} and Celton, {Jean Marc} and Philippe Gu{\'e}rif and Chang Liu and Rolf Lohaus and Zurn, {Jason D.} and Alessandro Cestaro and Bassil, {Nahla V.} and Bakker, {Linda V.} and Elio Schijlen and Gardiner, {Susan E.} and Yves Lespinasse and Durel, {Charles Eric} and Riccardo Velasco and Neale, {David B.} and David Chagn{\'e} and {Van de Peer}, Yves and Michela Troggio and Luca Bianco",
year = "2019",
month = "12",
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language = "English",
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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 2019, 'Pseudo-chromosome-length genome assembly of a double haploid "Bartlett" pear (Pyrus communis L.)', GigaScience, vol. 8, no. 12, giz138. https://doi.org/10.1093/gigascience/giz138

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

In: GigaScience, Vol. 8, No. 12, giz138, 12.2019.

Research output: Contribution to journalArticleAcademicpeer-review

TY - JOUR

T1 - Pseudo-chromosome-length genome assembly of a double haploid "Bartlett" pear (Pyrus communis L.)

AU - Linsmith, Gareth

AU - Rombauts, Stephane

AU - Montanari, Sara

AU - Deng, Cecilia H.

AU - Celton, Jean Marc

AU - Guérif, Philippe

AU - Liu, Chang

AU - Lohaus, Rolf

AU - Zurn, Jason D.

AU - Cestaro, Alessandro

AU - Bassil, Nahla V.

AU - Bakker, Linda V.

AU - Schijlen, Elio

AU - Gardiner, Susan E.

AU - Lespinasse, Yves

AU - Durel, Charles Eric

AU - Velasco, Riccardo

AU - Neale, David B.

AU - Chagné, David

AU - Van de Peer, Yves

AU - Troggio, Michela

AU - Bianco, Luca

PY - 2019/12

Y1 - 2019/12

N2 - 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.

AB - 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.

KW - chromosome-scale assembly

KW - Hi-C

KW - Pac-Bio sequencing

KW - Pyrus communis L

U2 - 10.1093/gigascience/giz138

DO - 10.1093/gigascience/giz138

M3 - Article

VL - 8

JO - GigaScience

JF - GigaScience

SN - 2047-217X

IS - 12

M1 - giz138

ER -

Linsmith G, Rombauts S, Montanari S, Deng CH, Celton JM, Guérif P et al. Pseudo-chromosome-length genome assembly of a double haploid "Bartlett" pear (Pyrus communis L.). GigaScience. 2019 Dec;8(12). giz138. https://doi.org/10.1093/gigascience/giz138