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; Peer, Yves Van de; Troggio, Michela; Bianco, Luca


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.