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

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/py​rus_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 developmen

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

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

Molecular Mapping of Major Genes and QTLs in Pear

Pear breeding programs are mainly focused on resistance to biotic stress and fruit quality traits. In the last two decades, major efforts have been undertaken toward identification of major genes and quantitative trait loci (QTLs) linked to both biotic resistance and fruit quality traits, along with their associated molecular markers in order to enable marker-assisted selection and breeding. This chapter will cover most relevant results reported so far pertaining to markers and QTLs linked to resistance to pathogens and pests (such as fire blight, scab, brown and black spot, pear psylla, pear sludge, and blister mite), fruit quality (fruit size, firmness, skin overcolor, russeting, fruit sweetness, and fruit acidity), and other traits (such as tree habit, chilling requirement, and harvest time). Furthermore, summaries of findings of studies conducted before and after the beginning of the genomics era will be provided. In addition, all progenies and selected parental lines capable of conferring traits of interest to their progenies are described herein. The aim is to provide breeders with tools to identify pear ideotypes in which several traits can be combined into a single individual. Furthermore, knowledge of genes and their related functions should serve as the basis for pursuing new plant breeding technologies, such as cisgenesis or DNA editing. These unprecedented advances in genomics and breeding strategies promise to enable dramatic improvements in breeding efficiencies, even for pears, that will also reduce time and costs incurred in today\u2019s traditional genetic improvement efforts

Basic statistics on the <i>Pyrus communis</i> ‘Bartlett’ genome sequence.

<p>Figures are given in bp.</p><p>*: the assumed genome size of pear is 600 Mb.</p

Comparison of <i>de novo</i> predicted repeated elements between the European pear, Chinese pear and apple genomes. na: not available from [18].

<p>Comparison of <i>de novo</i> predicted repeated elements between the European pear, Chinese pear and apple genomes. na: not available from <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0092644#pone.0092644-Wu1" target="_blank">[18]</a>.</p

Phylogenetic tree of six rosids, four malvids, and three asterids constructed with 83 euKaryote Orthologous Genes (KOGs).

<p>Bootstrap values are listed on each branch. Nodes represent speciation events and branch length represents the degree of evolutional changes over time. The unit for the scale bar at the bottom is nucleotide substitutions per site. The high bootstrap values strongly support that the species in Rosaceae cluster together to the exclusion of any other, and that the European pear and Chinese pear separation event happened after apple speciation.</p

Protein-protein comparison between European pear and 12 other species: Chinese pear, apple, grape, strawberry, papaya, sweet orange, clementine, kiwifruit, tomato, potato, poplar and <i>Arabidopsis</i>.

<p>The figure shows every possible combination of species included in this proteome ortholog analysis, using concentric circles. Each ring represents a single plant species and is depicted in a unique colour. For the 13 species shown, there are hence a total of 2¹³–1 combination cases, from 556 ortholog groups found in European pear only, 682 clades in Chinese pear only, to 5393 clusters present in all thirteen species. For each combination, the number of ortholog groups discovered is labelled outside the outermost ring and the number of proteins for a species inside a coloured, circular cell that represents the particular species. As the angular width of the cells for each case is drawn proportional to its number of groups, there is no labelling where the angular width is too small. A complete list of all combination cases with detected ortholog genes is provided in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0092644#pone.0092644.s005" target="_blank">Table S4</a>.</p