EuroPineDB: a high-coverage web database for maritime pine transcriptome.
EuroPineDB: a high-coverage web database for maritime pine transcriptome.
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DOI：
10.1186/1471-2164-12-366
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发表时间：
2011-07-15
期刊：
影响因子：
4.4
通讯作者：
Claros MG
中科院分区：
文献类型：
--
作者：
Fernández-Pozo N;Canales J;Guerrero-Fernández D;Villalobos DP;Díaz-Moreno SM;Bautista R;Flores-Monterroso A;Guevara MÁ;Perdiguero P;Collada C;Cervera MT;Soto A;Ordás R;Cantón FR;Avila C;Cánovas FM;Claros MG
海岸松是一种重要的经济和生态树种，正逐渐成为木本裸子植物模式。其庞大的基因组规模使得全基因组测序方法难以应用。因此，必须对基因组的表达部分进行表征，并且必须将结果和注释存储在专用数据库中。EuroPineDB是可用于单一松树物种Pinus pinaster（海洋松）的最大序列集合，因为它包括从非标准化cDNA文库获得的951 641个原始序列读取，以及成年（木质部，韧皮部，根，茎，针叶，球果，球根）和胚胎（发芽胚，芽，愈伤组织）海洋松组织的高通量测序。使用开源工具，对序列进行最佳预处理、组装和广泛注释（GO、EC和KEGG术语、描述、SNP、SSR、ORF和InterPro代码）。结果表明，一个10.5× Pinaster的基因组被55322个UniGenes所覆盖和组装。共有32919个（59.5%）松树UniGenes被至少一个描述所注释，揭示了至少18466个不同的基因。完整的数据库，它被设计成可伸缩的，可维护的，可扩展的，可以在http://www.scbi.uma.es/pindb/上免费获得。它可以通过基因文库、松树物种、注释、UniGenes和微阵列（即，这些序列分布在双色微阵列中;这是提供这一信息的唯一针叶树数据库），并将定期更新。可以使用专用的可视化工具查看小组件，该工具将它们与SNP连接起来。可以下载屏幕上显示的任何序列或注释集。提供了用于序列和基因注释的检索机制。EuroPineDB及其集成信息可用于揭示新知识，提供易于使用的信息集合，以直接支持实验工作（包括微阵列杂交），并提供有关海洋松转录组的更深入知识。
Pinus pinaster is an economically and ecologically important species that is becoming a woody gymnosperm model. Its enormous genome size makes whole-genome sequencing approaches are hard to apply. Therefore, the expressed portion of the genome has to be characterised and the results and annotations have to be stored in dedicated databases. EuroPineDB is the largest sequence collection available for a single pine species, Pinus pinaster (maritime pine), since it comprises 951 641 raw sequence reads obtained from non-normalised cDNA libraries and high-throughput sequencing from adult (xylem, phloem, roots, stem, needles, cones, strobili) and embryonic (germinated embryos, buds, callus) maritime pine tissues. Using open-source tools, sequences were optimally pre-processed, assembled, and extensively annotated (GO, EC and KEGG terms, descriptions, SNPs, SSRs, ORFs and InterPro codes). As a result, a 10.5× P. pinaster genome was covered and assembled in 55 322 UniGenes. A total of 32 919 (59.5%) of P. pinaster UniGenes were annotated with at least one description, revealing at least 18 466 different genes. The complete database, which is designed to be scalable, maintainable, and expandable, is freely available at: http://www.scbi.uma.es/pindb/. It can be retrieved by gene libraries, pine species, annotations, UniGenes and microarrays (i.e., the sequences are distributed in two-colour microarrays; this is the only conifer database that provides this information) and will be periodically updated. Small assemblies can be viewed using a dedicated visualisation tool that connects them with SNPs. Any sequence or annotation set shown on-screen can be downloaded. Retrieval mechanisms for sequences and gene annotations are provided. The EuroPineDB with its integrated information can be used to reveal new knowledge, offers an easy-to-use collection of information to directly support experimental work (including microarray hybridisation), and provides deeper knowledge on the maritime pine transcriptome.
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影响因子：
3
作者：
Falgueras J;Lara AJ;Fernández-Pozo N;Cantón FR;Pérez-Trabado G;Claros MG
通讯作者：
Claros MG
影响因子：
14.9
作者：
Christoffels, A;van Gelder, A;Hide, W
通讯作者：
Hide, W
影响因子：
3.5
作者：
Canales, Javier;Flores-Monterrosso, Arantxa;Canovas, Francisco M.
通讯作者：
Canovas, Francisco M.
影响因子：
3.4
作者：
Gion, JM;Lalanne, C;Plomion, C
通讯作者：
Plomion, C
影响因子：
7.4
作者：
Brinker, M;van Zyl, L;von Arnold, S
通讯作者：
von Arnold, S