The draft genome sequence of European pear (Pyrus communis L. 'Bartlett').
The draft genome sequence of European pear (Pyrus communis L. 'Bartlett').
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DOI：
10.1371/journal.pone.0092644
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发表时间：
2014
期刊：
影响因子：
3.7
通讯作者：
Velasco R
中科院分区：
文献类型：
--
作者：
Chagné D;Crowhurst RN;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;Kim YK;Nicolini D;Larger S;Stefani E;Allan AC;Bowen J;Harvey I;Johnston J;Malnoy M;Troggio M;Perchepied L;Sawyer G;Wiedow C;Won K;Viola R;Hellens RP;Brewer L;Bus VG;Schaffer RJ;Gardiner SE;Velasco R
我们提出了一个欧洲梨(梨)‘Bartlett’基因组的组装草案。我们的组件是使用第二代测序技术(Roche 454)开发的，使用Newbler(2.7版)从单端、2kb和7kb插入配对末端读取。它包含142,083个超过499个碱基的支架(最大支架长度为1.2Mb)，总共覆盖577.3 Mb，代表了预期的600Mb梨基因组的大部分。通过‘路易丝·邦德·泽西’和‘老家’的重新测序，总共检测到829,823个可能的单核苷酸多态(SNP)。总共有2,279个遗传定位的SNP标记锚定了171 Mb的组装基因组。从头算基因预测与基于同源搜索的预测相结合，共检测到43,419个可能的基因模型。在这些蛋白质中，有1219个蛋白质(556个簇)是欧洲梨所特有的，与其他12个已测序的植物基因组相比。对扩展蛋白基因家族的分析为基因预测的质量和控制欧洲梨和苹果果实软化的一类细胞壁相关基因之间的关系提供了一个例子。‘Bartlett’基因组组合v1.0(http://www.rosaceae.org/species/pyrus/pyrus_communis/genome_v1.0)是鉴定梨主要园艺性状遗传控制的宝贵工具，并将使标记辅助和基因组选择的广泛应用成为可能，从而提高梨品种发展的速度和效率。
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.
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影响因子：
3.7
作者：
Chagné D;Crowhurst RN;Troggio M;Davey MW;Gilmore B;Lawley C;Vanderzande S;Hellens RP;Kumar S;Cestaro A;Velasco R;Main D;Rees JD;Iezzoni A;Mockler T;Wilhelm L;Van de Weg E;Gardiner SE;Bassil N;Peace C
通讯作者：
Peace C
影响因子：
3.4
作者：
Illa E;Sargent DJ;Lopez Girona E;Bushakra J;Cestaro A;Crowhurst R;Pindo M;Cabrera A;van der Knaap E;Iezzoni A;Gardiner S;Velasco R;Arús P;Chagné D;Troggio M
通讯作者：
Troggio M
影响因子：
64.8
作者：
Jaillon, Olivier;Aury, Jean-Marc;Wincker, Patrick
通讯作者：
Wincker, Patrick
影响因子：
6.4
作者：
Hiwasa, K;Rose, JKC;Kubo, Y
通讯作者：
Kubo, Y
影响因子：
3.7
作者：
Kumar S;Chagné D;Bink MC;Volz RK;Whitworth C;Carlisle C
通讯作者：
Carlisle C