Triticeae resources in Ensembl Plants.
Triticeae resources in Ensembl Plants.
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DOI：
10.1093/pcp/pcu183
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发表时间：
2015-01
影响因子：
4.9
通讯作者：
Kersey P
中科院分区：
文献类型：
--
作者：
Bolser DM;Kerhornou A;Walts B;Kersey P
DNA测序的最新发展使许多作物物种的大而复杂的基因组首次得以确定，即使是那些以前由于其多倍体性质而难以确定的基因组。事实上，在过去的两年中，几种商业上重要的谷物，特别是大麦和面包小麦的基因组序列以及相关野生物种的基因组序列已经可用。虽然仍然不完整，但与其他更完整组装的物种相比，基因区域的覆盖率可能很高。Ensembl Plants（plants.ensembl.org）是一个整合的资源，组织，分析和可视化重要作物和模式植物的基因组信息。可用的数据包括参考基因组序列、变异位点、基因模型和功能注释。对于变异基因座，显示了个体和群体基因型、连锁信息和表型信息（如果可用）。对DNA和蛋白质序列比对进行比较分析。由此产生的基因组比对和基因树，代表了基因家族的隐含进化历史，可用于可视化和分析。在面包小麦案例的推动下，最近开发了对分析管道和网络界面的特定扩展，以支持多倍体基因组。Ensembl Plants中的数据可通过基因组浏览器访问，该浏览器包含针对不同数据类型的各种专业界面，并通过各种其他方法进行编程访问和数据挖掘。这些接口与Ensembl接口为非植物物种基因组提供的接口一致，包括植物病原体、害虫和传粉者的基因组，从而促进了对其环境中植物的研究。
Recent developments in DNA sequencing have enabled the large and complex genomes of many crop species to be determined for the first time, even those previously intractable due to their polyploid nature. Indeed, over the course of the last 2 years, the genome sequences of several commercially important cereals, notably barley and bread wheat, have become available, as well as those of related wild species. While still incomplete, comparison with other, more completely assembled species suggests that coverage of genic regions is likely to be high. Ensembl Plants (http://plants.ensembl.org) is an integrative resource organizing, analyzing and visualizing genome-scale information for important crop and model plants. Available data include reference genome sequence, variant loci, gene models and functional annotation. For variant loci, individual and population genotypes, linkage information and, where available, phenotypic information are shown. Comparative analyses are performed on DNA and protein sequence alignments. The resulting genome alignments and gene trees, representing the implied evolutionary history of the gene family, are made available for visualization and analysis. Driven by the case of bread wheat, specific extensions to the analysis pipelines and web interface have recently been developed to support polyploid genomes. Data in Ensembl Plants is accessible through a genome browser incorporating various specialist interfaces for different data types, and through a variety of additional methods for programmatic access and data mining. These interfaces are consistent with those offered through the Ensembl interface for the genomes of non-plant species, including those of plant pathogens, pests and pollinators, facilitating the study of the plant in its environment.
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DOI：
10.1093/dnares/dss028
发表时间：
2012-12
期刊：
DNA research : an international journal for rapid publication of reports on genes and genomes
影响因子：
--
作者：
Iehisa JC;Shimizu A;Sato K;Nasuda S;Takumi S
通讯作者：
Takumi S
影响因子：
--
作者：
Griffiths-Jones, Sam
通讯作者：
Griffiths-Jones, Sam
影响因子：
4.9
作者：
Cooper L;Walls RL;Elser J;Gandolfo MA;Stevenson DW;Smith B;Preece J;Athreya B;Mungall CJ;Rensing S;Hiss M;Lang D;Reski R;Berardini TZ;Li D;Huala E;Schaeffer M;Menda N;Arnaud E;Shrestha R;Yamazaki Y;Jaiswal P
通讯作者：
Jaiswal P
影响因子：
3.7
作者：
Fox SE;Geniza M;Hanumappa M;Naithani S;Sullivan C;Preece J;Tiwari VK;Elser J;Leonard JM;Sage A;Gresham C;Kerhornou A;Bolser D;McCarthy F;Kersey P;Lazo GR;Jaiswal P
通讯作者：
Jaiswal P
影响因子：
4.2
作者：
Dolezel, J;Greilhuber, J;Obermayer, R
通讯作者：
Obermayer, R