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.

中文翻译：

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双单倍体“ Bartlett”梨（Pyrus communis L.）的伪染色体长度基因组组装。

背景我们报告了欧洲梨（Pyrus communis L.）基因组（称为BartlettDHv2.0）的改进装配和脚手架，该基因组是使用Pacific Biosciences RSII长阅读测序，Bionano光学作图，染色质相互作用捕获（Hi -C）和基因作图。选择用于测序的样品是源自先前测序的相同“ Bartlett”参考梨的双单倍体。双单倍体植物的测序使组装在诸如P. communis的高度杂合的物种中更容易处理。结果将总计496.9 Mb（相当于估计的基因组大小的97％）组装到494个支架中。Hi-C数据和高密度遗传图谱使我们可以将87％的序列锚定和定向在17个梨染色体上。基因组中约50％（247 Mb）由重复序列组成。基因注释证实了37,445个蛋白质编码基因的存在，比以前的预测少了13％。结论我们表明，使用双倍单倍体植物是解决高水平杂合性和重复产生高质量基因组装配问题的有效解决方案。我们提出了欧洲梨梨Pyrus communis的高质量染色体规模的大会，并展示了其与海棠x Domestica和梨Pyrus x bretschneideri的基因组的高度共性。结论我们表明，使用双倍单倍体植物是解决高水平杂合性和重复产生高质量基因组装配问题的有效解决方案。我们提出了欧洲梨梨Pyrus communis的高质量染色体规模的大会，并展示了其与海棠x Domestica和梨Pyrus x bretschneideri的基因组的高度共性。结论我们表明，使用双倍单倍体植物是解决高水平杂合性和重复产生高质量基因组装配问题的有效解决方案。我们提出了欧洲梨梨Pyrus communis的高质量染色体规模的大会，并展示了其与海棠x Domestica和梨Pyrus x bretschneideri的基因组的高度共性。