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.

Figure 1. Phylogenetic tree of six rosids, four malvids, and three asterids constructed with 83 euKaryote Orthologous Genes (KOGs).

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.

Figure 2. Protein-protein comparison between European pear and 12 other species: Chinese pear, apple, grape, strawberry, papaya, sweet orange, clementine, kiwifruit, tomato, potato, poplar and Arabidopsis.

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 Table S4.

Figure 3. Phylogenetic and gene expression analysis of the expansin-like genes from apple and European pear.

A) Phylogenetic tree of predicted expansin-like genes from apple and European pear. Predicted expansin-like protein models from apple (MDP prefix) and European pear (PCP prefix) were aligned, and a conserved region of alignment of 313 residues was used to construct the phylogenetic tree Geneious 6.1.6 (Biomatters Ltd, Auckland, NZ). The linkage group (LG) of each model is shown where possible; some models are not anchored (LG-NA) to the genome. Models that represent the best hit for published expansins are labelled additionally as such. DdEXP2 from Dictyostelium discoideum was used as an out-group. Bootstrap proportions for 100 trees were calculated and bootstrap values ≥50 are shown. Scale indicates 0.4 substitutions per site. EXPA, α-expansins; EXPB, β-expansins; EXLA, alpha-like expansins; EXLB, beta-like expansins . mRNA-seq expression levels in ‘Comice’ melting pear (CM), ‘Nijisseki’ (NJ) crisp pear and ‘Royal Gala’ (RG) crisp apple, undergoing fruit ripening in storage show that one clade is strongly associated with fruit ripening (coloured green). The inserted graph shows the expression analysis by qPCR of EXP2 in fruit at harvest and during storage, which corresponds to the mRNA-seq data. Yellow bars: RG, red bars CM, orange bars NJ). RPKM: Reads Per Kilobase per Million mapped reads. Single arrow shows the apple expansin (MdEXPA7) mapped to a quantitative trait locus for fruit texture. B) Alignment of the first 170 bp of apple and pear homologues, demonstrating genome duplication preceded speciation.