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dc.contributor.author | Linsmith, Gareth | |
dc.contributor.author | Rombauts, Stephane | |
dc.contributor.author | Montanari, Sara | |
dc.contributor.author | Deng, Cecilia H. | |
dc.contributor.author | Celton, Jean-Marc | |
dc.contributor.author | Guerif, Philippe | |
dc.contributor.author | Liu, Chang | |
dc.contributor.author | Zurn, Jason D. | |
dc.contributor.author | Cestaro, Alessandro | |
dc.contributor.author | Bassil, Nahla V. | |
dc.contributor.author | Bakker, Linda V. | |
dc.contributor.author | Schijlen, Elio | |
dc.contributor.author | Gardiner, Susan E. | |
dc.contributor.author | Lespinasse, Yves | |
dc.contributor.author | Durel, Charles-Eric | |
dc.contributor.author | Velasco, Riccardo | |
dc.contributor.author | Neale, David B. | |
dc.contributor.author | Chagne, David | |
dc.contributor.author | Van de Peer, Yves | |
dc.contributor.author | Troggio, Michela | |
dc.contributor.author | Bianco, Luca | |
dc.date.accessioned | 2020-04-20T13:29:00Z | |
dc.date.available | 2020-04-20T13:29:00Z | |
dc.date.issued | 2019-12 | |
dc.description.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. | en_ZA |
dc.description.department | Biochemistry | en_ZA |
dc.description.department | Genetics | en_ZA |
dc.description.department | Microbiology and Plant Pathology | en_ZA |
dc.description.librarian | am2020 | en_ZA |
dc.description.sponsorship | The California Pear Advisory Board, the Pear Pest Management Research Fund and he California Pear Advisory Board and the Provincia Autonoma di Trent. Y.V.d.P. acknowledges support from the European Union Seventh Framework Programme (FP7/2007-2013) under European Research Council Advanced Grant Agreement 322739–DOUBLEUP. | en_ZA |
dc.description.uri | https://academic.oup.com/gigascience | en_ZA |
dc.identifier.citation | Linsmith, G., Rombauts, S., Montanari, S. et al. 2019, 'Pseudo-chromosome–length genome assembly of a double haploid “Bartlett” pear (Pyrus communis L.)', GigaScience, vol. 8, no. 12, pp. 1-17. | en_ZA |
dc.identifier.issn | 2047-217X (online) | |
dc.identifier.other | 10.1093/gigascience/giz138 | |
dc.identifier.uri | http://hdl.handle.net/2263/74313 | |
dc.language.iso | en | en_ZA |
dc.publisher | Oxford University Press | en_ZA |
dc.rights | © The Author(s) 2019. Published by Oxford University Press. This is an Open Access article distributed under the terms of the Creative Commons Attribution License. | en_ZA |
dc.subject | Pyrus communis L. | en_ZA |
dc.subject | Chromosome-scale assembly | en_ZA |
dc.subject | Hi-C | en_ZA |
dc.subject | Pac-Bio sequencing | en_ZA |
dc.title | Pseudo-chromosome–length genome assembly of a double haploid “Bartlett” pear (Pyrus communis L.) | en_ZA |
dc.type | Article | en_ZA |