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PLoS One. 2014 Apr 3;9(4):e92644. doi: 10.1371/journal.pone.0092644. eCollection 2014.

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

Author information

1
Palmerston North Research Centre, The New Zealand Institute for Plant & Food Research Limited (Plant & Food Research), Palmerston North, New Zealand.
2
Mount Albert Research Centre, Plant & Food Research, Auckland, New Zealand.
3
Istituto Agrario San Michele all'Adige (IASMA) Research and Innovation Centre, Foundation Edmund Mach (FEM), San Michele all' Adige, Trento, Italy.
4
Lincoln Research Centre, Plant & Food Research, Lincoln, New Zealand.
5
Palmerston North Research Centre, The New Zealand Institute for Plant & Food Research Limited (Plant & Food Research), Palmerston North, New Zealand; School of Biological Sciences, University of Auckland, Auckland, New Zealand.
6
Palmerston North Research Centre, The New Zealand Institute for Plant & Food Research Limited (Plant & Food Research), Palmerston North, New Zealand; Institute of Food, Nutrition and Human Health, Massey University, Palmerston North, New Zealand.
7
Palmerston North Research Centre, The New Zealand Institute for Plant & Food Research Limited (Plant & Food Research), Palmerston North, New Zealand; Istituto Agrario San Michele all'Adige (IASMA) Research and Innovation Centre, Foundation Edmund Mach (FEM), San Michele all' Adige, Trento, Italy; Institut de Recherche en Horticulture et Semences (IRHS), Institut National en Recherche Agronomique (INRA), Angers, France.
8
National Institute of Horticultural and Herbal Science (NIHHS), Rural Development Administration (RDA), Naju, Republic of Korea.
9
Mount Albert Research Centre, Plant & Food Research, Auckland, New Zealand; School of Biological Sciences, University of Auckland, Auckland, New Zealand.
10
Institut de Recherche en Horticulture et Semences (IRHS), Institut National en Recherche Agronomique (INRA), Angers, France.
11
Motueka Research Centre, Plant & Food Research, Motueka, New Zealand.
12
Hawke's Bay Research Centre, Plant & Food Research, Havelock North, New Zealand.

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.

PMID:
24699266
PMCID:
PMC3974708
DOI:
10.1371/journal.pone.0092644
[Indexed for MEDLINE]
Free PMC Article

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