The Draft Genome Sequence of European Pear (Pyrus communis L. 'Bartlett')

被引：202

作者：

Chagne, David ^{[1
]}

Crowhurst, Ross N. ^{[2
]}

Pindo, Massimo ^{[3
]}

Thrimawithana, Amali ^{[2
]}

Deng, Cecilia ^{[2
]}

Ireland, Hilary ^{[2
]}

Fiers, Mark ^{[4
]}

Dzierzon, Helge ^{[1
]}

Cestaro, Alessandro ^{[3
]}

Fontana, Paolo ^{[3
]}

Bianco, Luca ^{[3
]}

Lu, Ashley ^{[4
]}

Storey, Roy ^{[2
]}

Knaebel, Mareike ^{[1
,5
]}

Saeed, Munazza ^{[1
,6
]}

Montanari, Sara ^{[1
,3
,7
]}

Kim, Yoon Kyeong ^{[8
]}

Nicolini, Daniela ^{[3
]}

Larger, Simone ^{[3
]}

Stefani, Erika ^{[3
]}

Allan, Andrew C. ^{[2
,5
]}

Bowen, Judith ^{[2
]}

Harvey, Isaac ^{[2
]}

Johnston, Jason ^{[2
]}

Malnoy, Mickael ^{[3
]}

Troggio, Michela ^{[3
]}

Perchepied, Laure ^{[7
]}

Sawyer, Greg ^{[1
]}

Wiedow, Claudia ^{[1
]}

Won, Kyungho ^{[8
]}

Viola, Roberto ^{[3
]}

Hellens, Roger P. ^{[2
]}

Brewer, Lester ^{[9
]}

Bus, Vincent G. M. ^{[10
]}

Schaffer, Robert J. ^{[2
,5
]}

Gardiner, Susan E. ^{[1
]}

Velasco, Riccardo ^{[3
]}

机构：

[1] New Zealand Inst Plant & Food Res Ltd Plant & Foo, Palmerston North Res Ctr, Palmerston North, New Zealand

[2] DSIR, Mt Albert Res Ctr, Auckland, New Zealand

[3] FEM, Res & Innovat Ctr, IASMA, Trento, Italy

[4] Lincoln Res Ctr, Lincoln, NE, New Zealand

[5] Univ Auckland, Sch Biol Sci, Auckland 1, New Zealand

[6] Massey Univ, Inst Food Nutr & Human Hlth, Palmerston North, New Zealand

[7] INRA, IRHS, F-49000 Angers, France

[8] RDA, NIHHS, Naju, South Korea

[9] Motueka Res Ctr, Motueka, New Zealand

[10] Hawkes Bay Res Ctr, Havelock North, New Zealand

来源：

PLOS ONE | 2014年 / 9卷 / 04期

关键词：

WALL-MODIFYING ENZYMES; GENETIC-LINKAGE MAPS; EXPANSIN GENES; APPLE; EXPRESSION; CLASSIFICATION; IDENTIFICATION; ALIGNMENT; ETHYLENE; JAPANESE;

D O I：

10.1371/journal.pone.0092644

中图分类号：

O [数理科学和化学]; P [天文学、地球科学]; Q [生物科学]; N [自然科学总论];

学科分类号：

07 ; 0710 ; 09 ;

摘要：

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 (Malusxdomestica). 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.

引用

页数：12

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