A catalogue of putative unique transcripts from Douglas-fir (Pseudotsuga menziesii) based on 454 transcriptome sequencing of genetically diverse, drought stressed seedlings.
A catalogue of putative unique transcripts from Douglas-fir (Pseudotsuga menziesii) based on 454 transcriptome sequencing of genetically diverse, drought stressed seedlings.
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DOI：
10.1186/1471-2164-13-673
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发表时间：
2012-11-28
期刊：
影响因子：
4.4
通讯作者：
Schmid KJ
中科院分区：
文献类型：
--
作者：
Müller T;Ensminger I;Schmid KJ
花旗松（花旗松）延伸到广泛的对比环境条件，反映了大量的地方适应。因此，它是研究植物适应性和全球气候变化的影响的一个有趣的模式物种，例如温度升高和严重干旱时期对个别树木和整个森林景观的影响。然而，基因组数据和工具，研究自然种群的遗传变异，以了解适应的遗传和生理机制，目前缺少花旗松。这项研究代表了第一步，以454测序的12个cDNA文库的基础上表征花旗松转录组。文库构建从沿海和内陆种源的针叶和木材组织进行干旱胁迫实验。12个标准化cDNA文库的454次测序产生360万个读段，从中组装了一组170，859个推定的独特转录物（PUT）。通过BLAST搜索和基因本体映射的功能注释表明，功能类的组成与其他植物转录组非常相似，并表明大部分花旗松转录组被PUTs标记。基于进化保守性，我们确定了大约1,000个与干旱胁迫相关的候选基因。三种SNP检测工具共检测到187，653个单核苷酸多态性（SNP）。然而，所有三种方法仅鉴定出27，688个SNP，表明SNP检测取决于所使用的特定方法。27，688个SNPs中约60%的两个等位基因在沿海和内陆种源中同时分离，这表明这两个生态和表型不同的品种之间存在高比例的祖先共享多态性或高水平的基因流。建立了花旗松PUTs目录和大型SNP数据库。这两个将作为一个有用的资源，为进一步表征的基因组和转录组的花旗松和遗传变异的分析，使用基因分型或重测序方法。
Douglas-fir (Pseudotsuga menziesii) extends over a wide range of contrasting environmental conditions, reflecting substantial local adaptation. For this reason, it is an interesting model species to study plant adaptation and the effects of global climate change such as increased temperatures and significant periods of drought on individual trees and the forest landscape in general. However, genomic data and tools for studying genetic variation in natural populations to understand the genetic and physiological mechanisms of adaptation are currently missing for Douglas-fir. This study represents a first step towards characterizing the Douglas-fir transcriptome based on 454 sequencing of twelve cDNA libraries. The libraries were constructed from needle and wood tissue of coastal and interior provenances subjected to drought stress experiments. The 454 sequencing of twelve normalized cDNA libraries resulted in 3.6 million reads from which a set of 170,859 putative unique transcripts (PUTs) was assembled. Functional annotation by BLAST searches and Gene Ontology mapping showed that the composition of functional classes is very similar to other plant transcriptomes and demonstrated that a large fraction of the Douglas-fir transcriptome is tagged by the PUTs. Based on evolutionary conservation, we identified about 1,000 candidate genes related to drought stress. A total number of 187,653 single nucleotide polymorphisms (SNPs) were detected by three SNP detection tools. However, only 27,688 SNPs were identified by all three methods, indicating that SNP detection depends on the particular method used. The two alleles of about 60% of the 27,688 SNPs are segregating simultaneously in both coastal and interior provenances, which indicates a high proportion of ancestral shared polymorphisms or a high level of gene flow between these two ecologically and phenotypically different varieties. We established a catalogue of PUTs and large SNP database for Douglas-fir. Both will serve as a useful resource for the further characterization of the genome and transcriptome of Douglas-fir and for the analysis of genetic variation using genotyping or resequencing methods.
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影响因子：
9.4
作者：
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通讯作者：
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作者：
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