A conifer genomics resource of 200,000 spruce (Picea spp.) ESTs and 6,464 high-quality, sequence-finished full-length cDNAs for Sitka spruce (Picea sitchensis).
A conifer genomics resource of 200,000 spruce (Picea spp.) ESTs and 6,464 high-quality, sequence-finished full-length cDNAs for Sitka spruce (Picea sitchensis).
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DOI：
10.1186/1471-2164-9-484
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发表时间：
2008-10-14
期刊：
影响因子：
4.4
通讯作者：
Bohlmann J
中科院分区：
文献类型：
--
作者：
Ralph SG;Chun HJ;Kolosova N;Cooper D;Oddy C;Ritland CE;Kirkpatrick R;Moore R;Barber S;Holt RA;Jones SJ;Marra MA;Douglas CJ;Ritland K;Bohlmann J
松科（Pinaceae）的成员，特别是云杉（Picea spp.）和松树（Pinus spp.），在世界上的温带和寒带森林中占主导地位。这些针叶林对全球生态系统稳定和生物多样性至关重要。它们还提供了世界上大部分的木材和纤维供应，并作为其他工业生物材料的可再生资源。与被子植物相比，针叶树或其他裸子植物的功能和比较基因组学研究受到缺乏相关参考基因组序列的限制。完整的全长cDNA序列和大量的表达序列标签（EST）对于基因发现、功能基因组学和未来的针叶树基因组注释工作至关重要。作为针叶树基因组学计划的一部分，以表征对昆虫的防御和对当地环境的适应，并发现用于生产生物材料的基因，我们开发了20个标准的，归一化的或全长富集的cDNA文库，来自锡特卡云杉（P. sitchensis），白色云杉（P. glauca），和室内云杉（P. glauca-engelmannii complex）。我们对这些文库中的206，875个3 '或5'端EST进行了测序和分析，并开发了来自锡特卡云杉的6，464个高质量序列完成的FLcDNA资源。147，146个3 '端EST的聚类和组装产生19，941个重叠群和26，804个单例，代表46，745个推定的独特转录本（PUTs）。6，464个FLcDNA全部从单一锡特卡云杉基因型获得，代表5，718个PUTs。本文对云杉EST和FLcDNA资源进行了详细的注释和质量评价。6，464个锡特卡云杉FLcDNA代表了任何植物物种的第三大序列验证FLcDNA资源，仅次于水稻（Oryza sativa）和拟南芥（Arabidopsis thaliana），也是裸子植物唯一的大量FLcDNA资源。我们的重点是捕获FLcDNA和EST的cDNA文库代表草食动物，伤口或激发子处理诱导云杉组织，沿着纳入标准化捕获罕见的转录本，导致功能基因组学和蛋白质组学研究的丰富资源。与5种植物基因组和非冗余GenBank蛋白质数据库的序列比较显示，相当数量的云杉转录本与已知的被子植物基因序列没有明显的相似性。比较和功能基因组学的序列和克隆资源的未来应用的机会进行了讨论。
Members of the pine family (Pinaceae), especially species of spruce (Picea spp.) and pine (Pinus spp.), dominate many of the world's temperate and boreal forests. These conifer forests are of critical importance for global ecosystem stability and biodiversity. They also provide the majority of the world's wood and fiber supply and serve as a renewable resource for other industrial biomaterials. In contrast to angiosperms, functional and comparative genomics research on conifers, or other gymnosperms, is limited by the lack of a relevant reference genome sequence. Sequence-finished full-length (FL)cDNAs and large collections of expressed sequence tags (ESTs) are essential for gene discovery, functional genomics, and for future efforts of conifer genome annotation. As part of a conifer genomics program to characterize defense against insects and adaptation to local environments, and to discover genes for the production of biomaterials, we developed 20 standard, normalized or full-length enriched cDNA libraries from Sitka spruce (P. sitchensis), white spruce (P. glauca), and interior spruce (P. glauca-engelmannii complex). We sequenced and analyzed 206,875 3'- or 5'-end ESTs from these libraries, and developed a resource of 6,464 high-quality sequence-finished FLcDNAs from Sitka spruce. Clustering and assembly of 147,146 3'-end ESTs resulted in 19,941 contigs and 26,804 singletons, representing 46,745 putative unique transcripts (PUTs). The 6,464 FLcDNAs were all obtained from a single Sitka spruce genotype and represent 5,718 PUTs. This paper provides detailed annotation and quality assessment of a large EST and FLcDNA resource for spruce. The 6,464 Sitka spruce FLcDNAs represent the third largest sequence-verified FLcDNA resource for any plant species, behind only rice (Oryza sativa) and Arabidopsis (Arabidopsis thaliana), and the only substantial FLcDNA resource for a gymnosperm. Our emphasis on capturing FLcDNAs and ESTs from cDNA libraries representing herbivore-, wound- or elicitor-treated induced spruce tissues, along with incorporating normalization to capture rare transcripts, resulted in a rich resource for functional genomics and proteomics studies. Sequence comparisons against five plant genomes and the non-redundant GenBank protein database revealed that a substantial number of spruce transcripts have no obvious similarity to known angiosperm gene sequences. Opportunities for future applications of the sequence and clone resources for comparative and functional genomics are discussed.
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影响因子：
6.9
作者：
Friedmann, Michael;Ralph, Steven G.;Douglas, Carl J.
通讯作者：
Douglas, Carl J.
影响因子：
4.4
作者：
Brenner ED;Katari MS;Stevenson DW;Rudd SA;Douglas AW;Moss WN;Twigg RW;Runko SJ;Stellari GM;McCombie WR;Coruzzi GM
通讯作者：
Coruzzi GM
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：
7
作者：
Carninci, P;Shibata, Y;Hayashizaki, Y
通讯作者：
Hayashizaki, Y
影响因子：
12.3
作者：
Brenner ED;Stevenson DW;McCombie RW;Katari MS;Rudd SA;Mayer KF;Palenchar PM;Runko SJ;Twigg RW;Dai G;Martienssen RA;Benfey PN;Coruzzi GM
通讯作者：
Coruzzi GM