Genome-wide SNP genotyping to infer the effects on gene functions in tomato.
Genome-wide SNP genotyping to infer the effects on gene functions in tomato.
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DOI：
10.1093/dnares/dst005
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发表时间：
2013-06
期刊：
影响因子：
--
通讯作者：
Tabata S
中科院分区：
文献类型：
--
作者：
Hirakawa H;Shirasawa K;Ohyama A;Fukuoka H;Aoki K;Rothan C;Sato S;Isobe S;Tabata S
使用Illumina的Infinium和GoldenGate分析平台收集了40个番茄品系（包括自交系，F1杂交种和野生近缘种）的7054个单核苷酸多态性（SNP）位点的基因型数据，后者在我们以前的研究中使用。基于基因型数据构建的聚类图与番茄及其近缘野生种的育种类型相吻合。根据SNPs在番茄基因组序列预测基因中的位置，将SNPs分为6类。通过对核苷酸和蛋白质数据库的同源性搜索以及结构域搜索来注释具有SNP的基因，并且将它们分类到由NCBI的真核生物直链组（KOG）定义的功能类别中。为了推断SNPs对基因功能的影响，通过同源建模构建了由具有引起错义突变的SNPs的基因编码的843个蛋白质的三维结构，并认为这些蛋白质中的200个在预测的功能位点中携带非同义氨基酸取代。本研究中获得的SNP信息可在Kazusa Tomato Genomics Database（）中获得。
The genotype data of 7054 single nucleotide polymorphism (SNP) loci in 40 tomato lines, including inbred lines, F1 hybrids, and wild relatives, were collected using Illumina's Infinium and GoldenGate assay platforms, the latter of which was utilized in our previous study. The dendrogram based on the genotype data corresponded well to the breeding types of tomato and wild relatives. The SNPs were classified into six categories according to their positions in the genes predicted on the tomato genome sequence. The genes with SNPs were annotated by homology searches against the nucleotide and protein databases, as well as by domain searches, and they were classified into the functional categories defined by the NCBI's eukaryotic orthologous groups (KOG). To infer the SNPs' effects on the gene functions, the three-dimensional structures of the 843 proteins that were encoded by the genes with SNPs causing missense mutations were constructed by homology modelling, and 200 of these proteins were considered to carry non-synonymous amino acid substitutions in the predicted functional sites. The SNP information obtained in this study is available at the Kazusa Tomato Genomics Database ().
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DOI：
10.1093/dnares/dsq024
发表时间：
2010-12
期刊：
DNA research : an international journal for rapid publication of reports on genes and genomes
影响因子：
--
作者：
Shirasawa K;Isobe S;Hirakawa H;Asamizu E;Fukuoka H;Just D;Rothan C;Sasamoto S;Fujishiro T;Kishida Y;Kohara M;Tsuruoka H;Wada T;Nakamura Y;Sato S;Tabata S
通讯作者：
Tabata S
番茄测序项目，这是国际茄科项目（SOL）的第一个基石。
影响因子：
--
作者：
Mueller, LA;Tanksley, SD;Giovannoni, JJ;van Eck, J;Stack, S;Choi, D;Kim, BD;Chen, MS;Cheng, ZK;Li, CY;Ling, HQ;Xue, YB;Seymour, G;Bishop, G;Bryan, G;Sharma, R;Khurana, J;Tyagi, A;Chattopadhyay, D;Singh, NK;Stiekema, W;Lindhout, P;Jesse, T;Lankhorst, RK;Bouzayen, M;Shibata, D;Tabata, S;Granell, A;Botella, MA;Giullano, G;Frusciante, L;Causse, M;Zamir, D
通讯作者：
Zamir, D
影响因子：
14.9
作者：
Lee, Phil Hyoun;Shatkay, Hagit
通讯作者：
Shatkay, Hagit
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：
5.8
作者：
Bradbury, Peter J.;Zhang, Zhiwu;Buckler, Edward S.
通讯作者：
Buckler, Edward S.