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.
