Generation, annotation, analysis and database integration of 16,500 white spruce EST clusters.
Generation, annotation, analysis and database integration of 16,500 white spruce EST clusters.
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16,500 个白云杉 EST 簇的生成、注释、分析和数据库集成。
DOI：
10.1186/1471-2164-6-144
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发表时间：
2005-10-19
期刊：
影响因子：
4.4
通讯作者：
MacKay J
中科院分区：
文献类型：
--
作者：
Pavy N;Paule C;Parsons L;Crow JA;Morency MJ;Cooke J;Johnson JE;Noumen E;Guillet-Claude C;Butterfield Y;Barber S;Yang G;Liu J;Stott J;Kirkpatrick R;Siddiqui A;Holt R;Marra M;Seguin A;Retzel E;Bousquet J;MacKay J
目前，对针叶树进行大规模基因发现和注释的唯一可行方法是EST的测序和分析，因为针叶树非常大的基因组在不久的将来不太可能被测序。我们的目标是产生大量的EST和cDNA克隆，以支持白色云杉（云杉[Moench] Voss）的cDNA微阵列和基因发现的制造。我们从不同组织和各种处理中产生了16个cDNA文库，并对50，000个cDNA克隆进行了部分测序。将高质量的3'和5'读段组装成16，578个共有序列，其中45%代表全长插入物。将来源于相同cDNA克隆的5'和3'读段的共有序列连接以定义14，471个转录物。大部分（84%）的云杉序列与松树序列相匹配，但只有68%的云杉转录本在拟南芥或水稻中具有同源物。几乎所有与大叶杨基因组（唯一测序的树木基因组）匹配的序列也与水稻或拟南芥基因组匹配。我们使用了几种序列相似性搜索方法来分配假定的功能，包括对一般和专门数据库（转录因子，细胞壁相关蛋白）的blast搜索，基因本体论术语分配和隐马尔可夫模型搜索PFAM蛋白家族和结构域。总的来说，70%的云杉转录本与Uniref 100数据库中已知或未知功能的蛋白质相匹配（blastx e值<1 e-10）。我们确定了多基因家族，出现在云杉比拟南芥或水稻基因组。详细分析的抑制控制的肿瘤蛋白和S-腺苷甲硫氨酸合成酶家族证实了两倍的大小差异。将序列和注释组织在专用数据库SpruceDB中。开发了几种搜索工具来挖掘数据，无论是基于它们在cDNA文库中的出现或功能注释。这份报告说明了大规模的基因发现和注释的生物体，是非常遥远的相关的任何完全测序的基因组的具体方法。ArboreaSet序列和cDNA克隆代表了从植物比较基因组学到应用针叶树遗传学的研究的宝贵资源。
The sequencing and analysis of ESTs is for now the only practical approach for large-scale gene discovery and annotation in conifers because their very large genomes are unlikely to be sequenced in the near future. Our objective was to produce extensive collections of ESTs and cDNA clones to support manufacture of cDNA microarrays and gene discovery in white spruce (Picea glauca [Moench] Voss). We produced 16 cDNA libraries from different tissues and a variety of treatments, and partially sequenced 50,000 cDNA clones. High quality 3' and 5' reads were assembled into 16,578 consensus sequences, 45% of which represented full length inserts. Consensus sequences derived from 5' and 3' reads of the same cDNA clone were linked to define 14,471 transcripts. A large proportion (84%) of the spruce sequences matched a pine sequence, but only 68% of the spruce transcripts had homologs in Arabidopsis or rice. Nearly all the sequences that matched the Populus trichocarpa genome (the only sequenced tree genome) also matched rice or Arabidopsis genomes. We used several sequence similarity search approaches for assignment of putative functions, including blast searches against general and specialized databases (transcription factors, cell wall related proteins), Gene Ontology term assignation and Hidden Markov Model searches against PFAM protein families and domains. In total, 70% of the spruce transcripts displayed matches to proteins of known or unknown function in the Uniref100 database (blastx e-value < 1e-10). We identified multigenic families that appeared larger in spruce than in the Arabidopsis or rice genomes. Detailed analysis of translationally controlled tumour proteins and S-adenosylmethionine synthetase families confirmed a twofold size difference. Sequences and annotations were organized in a dedicated database, SpruceDB. Several search tools were developed to mine the data either based on their occurrence in the cDNA libraries or on functional annotations. This report illustrates specific approaches for large-scale gene discovery and annotation in an organism that is very distantly related to any of the fully sequenced genomes. The ArboreaSet sequences and cDNA clones represent a valuable resource for investigations ranging from plant comparative genomics to applied conifer genetics.
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影响因子：
5.1
作者：
Lindroth, AM;Saarikoski, P;von Arnold, S
通讯作者：
von Arnold, S
影响因子：
5.1
作者：
Dubos, C;Plomion, C
通讯作者：
Plomion, C
影响因子：
3.9
作者：
Egertsdotter, U;van Zyl, LM;Sederoff, R
通讯作者：
Sederoff, R
影响因子：
7
作者：
Ashburner, M;Ball, CA;Yoon, J
通讯作者：
Yoon, J
DOI：
10.1073/pnas.1132171100
发表时间：
2003-06-10
影响因子：
11.1
作者：
Kirst, M;Johnson, AF;Sederoff, R
通讯作者：
Sederoff, R