The Draft Genome Sequence of European Pear (Pyrus communis L. ‘Bartlett’)

Abstract

We present a draft assembly of the genome of European pear (Pyrus communis) ‘Bartlett’. Our assembly was developed employing second generation sequencing technology (Roche 454), from single-end, 2 kb, and 7 kb insert paired-end reads using Newbler (version 2.7). It contains 142,083 scaffolds greater than 499 bases (maximum scaffold length of 1.2 Mb) and covers a total of 577.3 Mb, representing most of the expected 600 Mb Pyrus genome. A total of 829,823 putative single nucleotide polymorphisms (SNPs) were detected using re-sequencing of ‘Louise Bonne de Jersey’ and ‘Old Home’. A total of 2,279 genetically mapped SNP markers anchor 171 Mb of the assembled genome. Ab initio gene prediction combined with prediction based on homology searching detected 43,419 putative gene models. Of these, 1219 proteins (556 clusters) are unique to European pear compared to 12 other sequenced plant genomes. Analysis of the expansin gene family provided an example of the quality of the gene prediction and an insight into the relationships among one class of cell wall related genes that control fruit softening in both European pear and apple (Malus×domestica). The ‘Bartlett’ genome assembly v1.0 (http://www.rosaceae.org/species/pyrus/pyrus_communis/genome_v1.0) is an invaluable tool for identifying the genetic control of key horticultural traits in pear and will enable the wide application of marker-assisted and genomic selection that will enhance the speed and efficiency of pear cultivar development.

De novo assembly, functional annotation, and marker development of Asian pear (Pyrus pyrifolia) fruit transcriptome through massively parallel sequencing

“…In addition, we identified reliable markers of 30,560 SNPs and 7443 SSRs. Along with various existing pear transcriptome databases (Wu et al, 2013;Chagne et al, 2014;Liang et al, 2015); these results can aid the investigation of pear fruit development. This work highlights the applicability of NGS for marker and gene discovery; we isolated thousands of genetic markers for parentage analysis, and identified several members of a specific gene family in P. pyrifolia.…”

“…Due to self-incompatibility and interspecies compatibility, pear is highly heterozygous (Wu et al, 2013). There is no public Asian pear genome platforms reported to date (Wu et al, 2013;Chagne et al, 2014).…”

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“…The transferability of these markers allowed the comparison of maps from apple and pear, and indicated a high level of synteny between the two genomes. The close evolutionary relationship between the two species was clearly demonstrated with the recent publication of the genomes of the Japanese (Wu et al 2013) and the European (Chagné et al 2014) pears. In fact, the high transferability of molecular markers between pear and apple allowed a combination of SNPs from both species to be arrayed in the same platform for the genotyping of the two crops interchangeably (Montanari et al 2013).…”

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“…Whole genome sequence is available for strawberry (Shulaev et al 2011), apple (Velasco et al 2010), peach (Verde et al 2013), pear (Wu et al 2013;Chagné et al 2014), and Prunus mume (Zhang et al 2012), with more to come. Genome sequence has allowed cross-species comparisons at the genome level and within gene families.…”