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
Linsmith, G.; Rombauts, S.; Montanari, S.; Deng, C.H.; Celton, J.M.; Guérif, P.; Liu, C.; Lohaus, R.; Zurn, J.D.; Cestaro, A.; Bassil, N.V.; Bakker, L.V.; Schijlen, E.; Gardiner, S.E.; Lespinasse, Y.; Durel, C.E.; Velasco, R.; Neale, D.B.; 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, 8 (12): giz138. doi: 10.1093/gigascience/giz138 handle: http://hdl.handle.net/10449/58678
Pseudo-chromosome–length genome assembly of a double haploid “Bartlett” pear (Pyrus communis L.)
Linsmith, G.;Cestaro, A.;Troggio, M.
;Bianco, L.
Ultimo
2019-01-01
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 bretschneideriFile | Dimensione | Formato | |
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