期刊
GIGASCIENCE
卷 8, 期 12, 页码 -出版社
OXFORD UNIV PRESS
DOI: 10.1093/gigascience/giz138
关键词
Pyrus communis L; chromosome-scale assembly; Hi-C; Pac-Bio sequencing
资金
- California Pear Advisory Board
- Pear Pest Management Research Fund
- Provincia Autonoma di Trento
- European Union Seventh Framework Programme (FP7/2007-2013) under European Research Council Advanced Grant [322739-DOUBLEUP]
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.
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