PLoS ONE (Jan 2014)

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

  • David Chagné,
  • Ross N Crowhurst,
  • Massimo Pindo,
  • Amali Thrimawithana,
  • Cecilia Deng,
  • Hilary Ireland,
  • Mark Fiers,
  • Helge Dzierzon,
  • Alessandro Cestaro,
  • Paolo Fontana,
  • Luca Bianco,
  • Ashley Lu,
  • Roy Storey,
  • Mareike Knäbel,
  • Munazza Saeed,
  • Sara Montanari,
  • Yoon Kyeong Kim,
  • Daniela Nicolini,
  • Simone Larger,
  • Erika Stefani,
  • Andrew C Allan,
  • Judith Bowen,
  • Isaac Harvey,
  • Jason Johnston,
  • Mickael Malnoy,
  • Michela Troggio,
  • Laure Perchepied,
  • Greg Sawyer,
  • Claudia Wiedow,
  • Kyungho Won,
  • Roberto Viola,
  • Roger P Hellens,
  • Lester Brewer,
  • Vincent G M Bus,
  • Robert J Schaffer,
  • Susan E Gardiner,
  • Riccardo Velasco

DOI
https://doi.org/10.1371/journal.pone.0092644
Journal volume & issue
Vol. 9, no. 4
p. e92644

Abstract

Read online

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.