Transcriptome sequencing in an ecologically important tree species: assembly, annotation, and marker discovery.
Transcriptome sequencing in an ecologically important tree species: assembly, annotation, and marker discovery.
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DOI：
10.1186/1471-2164-11-180
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发表时间：
2010-03-16
期刊：
影响因子：
4.4
通讯作者：
Buerkle CA
中科院分区：
文献类型：
--
作者：
Parchman TL;Geist KS;Grahnen JA;Benkman CW;Buerkle CA
大规模并行测序现在是产生代表表达基因的大量序列集合的有效途径。这种方法为描述非模式生物的功能遗传变异提供了一个有价值的起点，特别是在全基因组测序工作目前成本和时间都令人望而却步的情况下。松树(Pinus spp.)阻碍了基因组资源的发展，尽管该集团具有生态和经济上的重要性。虽然大多数基因组研究都集中在单一物种(火炬松)上，但其他松树的基因组水平资源还没有得到充分的开发，无法促进生态基因组研究。小叶松是北美西部山地森林生态系统的重要基础树种，在其分布范围内表现出显著的适应性变异。在这里，我们描述了对螺旋藻表达基因的测序研究，包括它们的组装和注释，以及它们在支持群体和关联遗传学研究的分子标记开发方面的潜力。我们从454GS XLR70钛焦磷酸测序仪上获得了586,732个测序读数(平均长度：306个碱基对)。基于参考和从头组装的组合产生了63,657个重叠群，239,793个读数仍然是单一的。基于与已知蛋白质的序列相似性，这些序列代表了大约17,000个独特的基因，其中许多被重叠群序列很好地覆盖。这个序列收集还包括数量惊人的反转录转座子序列，这表明它们在我们采样的组织中具有高度的转录活性。我们在我们组装和注释的序列中定位并表征了数千个简单序列重复和单核苷酸多态作为潜在的分子标记。针对大量的SSR基因座设计了高质量的聚合酶链式反应引物，并在初步筛选中成功扩增出大量的SSR基因座。这个序列集合代表了青松的主要基因组资源，大量的遗传标记的特征应该有助于未来在该松树和其他松树中的研究。我们的结果说明了下一代测序作为非模式物种的标记开发和种群基因组学的基础的实用性。
Massively parallel sequencing of cDNA is now an efficient route for generating enormous sequence collections that represent expressed genes. This approach provides a valuable starting point for characterizing functional genetic variation in non-model organisms, especially where whole genome sequencing efforts are currently cost and time prohibitive. The large and complex genomes of pines (Pinus spp.) have hindered the development of genomic resources, despite the ecological and economical importance of the group. While most genomic studies have focused on a single species (P. taeda), genomic level resources for other pines are insufficiently developed to facilitate ecological genomic research. Lodgepole pine (P. contorta) is an ecologically important foundation species of montane forest ecosystems and exhibits substantial adaptive variation across its range in western North America. Here we describe a sequencing study of expressed genes from P. contorta, including their assembly and annotation, and their potential for molecular marker development to support population and association genetic studies. We obtained 586,732 sequencing reads from a 454 GS XLR70 Titanium pyrosequencer (mean length: 306 base pairs). A combination of reference-based and de novo assemblies yielded 63,657 contigs, with 239,793 reads remaining as singletons. Based on sequence similarity with known proteins, these sequences represent approximately 17,000 unique genes, many of which are well covered by contig sequences. This sequence collection also included a surprisingly large number of retrotransposon sequences, suggesting that they are highly transcriptionally active in the tissues we sampled. We located and characterized thousands of simple sequence repeats and single nucleotide polymorphisms as potential molecular markers in our assembled and annotated sequences. High quality PCR primers were designed for a substantial number of the SSR loci, and a large number of these were amplified successfully in initial screening. This sequence collection represents a major genomic resource for P. contorta, and the large number of genetic markers characterized should contribute to future research in this and other pines. Our results illustrate the utility of next generation sequencing as a basis for marker development and population genomics in non-model species.
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影响因子：
7.7
作者：
Castoe TA;Poole AW;Gu W;Jason de Koning AP;Daza JM;Smith EN;Pollock DD
通讯作者：
Pollock DD
DOI：
10.1073/pnas.0401513101
发表时间：
2004-07-06
影响因子：
11.1
作者：
Ganley, RJ;Brunsfeld, SJ;Newcombe, G
通讯作者：
Newcombe, G
通过454转录组测序发现SNP。
影响因子：
7.2
作者：
Barbazuk, W Brad;Emrich, Scott J;Chen, Hsin D;Li, Li;Schnable, Patrick S
通讯作者：
Schnable, Patrick S
影响因子：
30.8
作者：
Faulkner, Geoffrey J.;Kimura, Yasumasa;Carninci, Piero
通讯作者：
Carninci, Piero
影响因子：
3.3
作者：
Benkman, CW;Holimon, WC;Smith, JW
通讯作者：
Smith, JW