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 development

Chagné, D.; Crowhurs, R.N.; Pindo, M.; Thrimawithana, A.; Deng, C.; Ireland, H.; Fiers, M.; Dzierzon, H.; Cestaro, A.; Fontana, P.; Bianco, L.; Lu, A.; Storey, R.; Knäbel, M.; Saeed, M.; Montanari, S.; Kyeong Kim, Y.; Nicolini, D.; Larger, S.; Stefani, E.; Allan, A.C.; Bowen, J.; Harvey, I.; Johnston, J.; Malnoy, M.A.; Troggio, M.; Perchepied, L.; Sawyer, G.; Wiedow, C.; Won, K.; Viola, R.; Hellens, R.P.; Brewer, L.; Bus, V.G.M.; Schaffer, R.J.; Gardiner, S.E.; Velasco, R. (2014). The draft genome sequence of European pear (Pyrus communis L. ‘Bartlett’). PLOS ONE, 9 (4): e92644. doi: 10.1371/journal.pone.0092644 handle: http://hdl.handle.net/10449/24656

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

Pindo, Massimo;Cestaro, Alessandro;Fontana, Paolo;Bianco, Luca;Montanari, Sara;Nicolini, Daniela;Larger, Simone;Stefani, Erika;Malnoy, Mickael Arnaud;Troggio, Michela;Viola, Roberto;Velasco, Riccardo
2014-01-01

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/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 development
Pyrus communis
Genome
Settore AGR/07 - GENETICA AGRARIA
2014
Chagné, D.; Crowhurs, R.N.; Pindo, M.; Thrimawithana, A.; Deng, C.; Ireland, H.; Fiers, M.; Dzierzon, H.; Cestaro, A.; Fontana, P.; Bianco, L.; Lu, A.; Storey, R.; Knäbel, M.; Saeed, M.; Montanari, S.; Kyeong Kim, Y.; Nicolini, D.; Larger, S.; Stefani, E.; Allan, A.C.; Bowen, J.; Harvey, I.; Johnston, J.; Malnoy, M.A.; Troggio, M.; Perchepied, L.; Sawyer, G.; Wiedow, C.; Won, K.; Viola, R.; Hellens, R.P.; Brewer, L.; Bus, V.G.M.; Schaffer, R.J.; Gardiner, S.E.; Velasco, R. (2014). The draft genome sequence of European pear (Pyrus communis L. ‘Bartlett’). PLOS ONE, 9 (4): e92644. doi: 10.1371/journal.pone.0092644 handle: http://hdl.handle.net/10449/24656
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