Pseudo-chromosome-length genome assembly of a double haploid "Bartlett" pear (Pyrus communis L.).

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. 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. 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 CH ，Celton JM ，Guérif P ，Liu C ，Lohaus R ，Zurn JD ，Cestaro A ，Bassil NV ，Bakker LV ，Schijlen E ，Gardiner SE ，Lespinasse Y ，Durel CE ，Velasco R ，Neale DB ，Chagné D ，Van de Peer Y ，Troggio M ，Bianco L ... -  《GigaScience》

The draft genome sequence of European pear (Pyrus communis L. 'Bartlett').

Chagné D ，Crowhurst RN ，Pindo M ，Thrimawithana A ，Deng C ，Ireland H ，Fiers M ，Dzierzon H ，Cestaro A ，Fontana P ，Bianco L ，Lu A ，Storey R ，Knäbel M ，Saeed M ，Montanari S ，Kim YK ，Nicolini D ，Larger S ，Stefani E ，Allan AC ，Bowen J ，Harvey I ，Johnston J ，Malnoy M ，Troggio M ，Perchepied L ，Sawyer G ，Wiedow C ，Won K ，Viola R ，Hellens RP ，Brewer L ，Bus VG ，Schaffer RJ ，Gardiner SE ，Velasco R ... -  《PLoS One》

Integrated high-density consensus genetic map of Pyrus and anchoring of the 'Bartlett' v1.0 (Pyrus communis) genome.

Genetic maps are essential tools for pear genetics and genomics research. In this study, we first constructed an integrated simple sequence repeat (SSR) and single nucleotide polymorphism (SNP)-based consensus genetic map for pear based on common SSR markers between nine published maps. A total of 5,085 markers, including 1,232 SSRs and 3,853 SNPs, were localized on a consensus map spanning 3,266.0 cM in total, with an average marker interval of 0.64 cM, which represents the highest density consensus map of pear to date. Using three sets of high-density SNP-based genetic maps with European pear genetic backgrounds, we anchored a total of 291.5 Mb of the 'Bartlett' v1.0 (Pyrus communis L.) genome scaffolds into 17 pseudo-chromosomes. This accounted for 50.5% of the genome assembly, which was a great improvement on the 29.7% achieved originally. Intra-genome and inter-genome synteny analyses of the new 'Bartlett' v1.1 genome assembly with the Asian pear 'Dangshansuli' (Pyrus bretschneideri Rehd.) and apple (Malus × domestica Borkh.) genomes uncovered four new segmental duplication regions. The integrated high-density SSR and SNP-based consensus genetic map provided new insights into the genetic structure patterns of pear and assisted in the genome assembly of 'Bartlett' through further exploration of different pear genetic maps.

Li L ，Deng CH ，Knäbel M ，Chagné D ，Kumar S ，Sun J ，Zhang S ，Wu J ... -  《-》

Chromosome level high-density integrated genetic maps improve the Pyrus bretschneideri 'DangshanSuli' v1.0 genome.

Chromosomal level reference genomes provide a crucial foundation for genomics research such as genome-wide association studies (GWAS) and whole genome selection. The chromosomal-level sequences of both the European (Pyrus communis) and Chinese (P. bretschneideri) pear genomes have not been published in public databases so far. To anchor the scaffolds of P. bretschneideri 'DangshanSuli' (DS) v1.0 genome into pseudo-chromosomes, two genetic maps (MH and YM maps) were constructed using half sibling populations of Chinese pear crosses, 'Mantianhong' (MTH) × 'Hongxiangsu' (HXS) and 'Yuluxiang' (YLX) × MTH, from 345 and 162 seedlings, respectively, which were prepared for SNP discovery using genotyping-by-sequencing (GBS) technology. The MH and YM maps, each with 17 linkage groups (LGs), were constructed from 2606 and 2489 SNP markers and spanned 1847 and 1668 cM, respectively, with average marker intervals of 0.7. The two maps were further merged with a previously published genetic map (BD) based on the cross 'Bayuehong' (BYH) × 'Dangshansuli' (DS) to build a new integrated MH-YM-BD map. By using 7757 markers located on the integrated MH-YM-BD map, 898 scaffolds (400.57 Mb) of the DS v1.0 assembly were successfully anchored into 17 pseudo-chromosomes, accounting for 78.8% of the assembled genome size. About 88.31% of them (793 scaffolds) were directionally anchored with two or more markers on the pseudo-chromosomes. Furthermore, the errors in each pseudo-chromosome (especially 1, 5, 7 and 11) were manually corrected and pseudo-chromosomes 1, 5 and 7 were extended by adding 19, 12 and 14 scaffolds respectively in the newly constructed DS v1.1 genome. Synteny analyses revealed that the DS v1.1 genome had high collinearity with the apple genome, and the homologous fragments between pseudo-chromosomes were similar to those found in previous studies. Moreover, the red-skin trait of Asian pear was mapped to an identical locus as identified previously. The accuracy of DS v1.1 genome was improved by using larger mapping populations and merged genetic map. With more than 400 MB anchored to 17 pseudo-chromosomes, the new DS v1.1 genome provides a critical tool that is essential for studies of pear genetics, genomics and molecular breeding.

Xue H ，Wang S ，Yao JL ，Deng CH ，Wang L ，Su Y ，Zhang H ，Zhou H ，Sun M ，Li X ，Yang J ... -  《BMC GENOMICS》

High-resolution genetic linkage map of European pear (Pyrus communis) and QTL fine-mapping of vegetative budbreak time.

Gabay G ，Dahan Y ，Izhaki Y ，Faigenboim A ，Ben-Ari G ，Elkind Y ，Flaishman MA ... -  《BMC PLANT BIOLOGY》