Generation and analysis of ESTs from the eastern oyster, Crassostrea virginica Gmelin and identification of microsatellite and SNP markers.
Generation and analysis of ESTs from the eastern oyster, Crassostrea virginica Gmelin and identification of microsatellite and SNP markers.
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DOI：
10.1186/1471-2164-8-157
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发表时间：
2007-06-08
期刊：
影响因子：
4.4
通讯作者：
Liu Z
中科院分区：
文献类型：
--
作者：
Quilang J;Wang S;Li P;Abernathy J;Peatman E;Wang Y;Wang L;Shi Y;Wallace R;Guo X;Liu Z
东部牡蛎Crassostrea virginica（Gmelin 1791）是北美许多地区养殖的一种重要经济物种。由于其滤食行为对水质的影响，它在生态上也很重要。C的人口。弗吉尼亚一直受到过度捕捞、栖息地退化和疾病的威胁。通过基因组研究，正在制定扭转其人口下降的战略。然而，大规模的表达序列标签（EST）资源一直缺乏该物种。从这个物种的EST资源的有效生成一直受到阻碍的转录本的高冗余。本研究的目的是构建一个标准化的cDNA文库，以有效的EST分析，产生数以千计的EST，并分析微卫星和潜在的单核苷酸多态性（SNP）的EST。一个标准化的和减去的C。从血细胞、外套膜、鳃、性腺和消化道、肌肉和整个幼牡蛎中分离的合并RNA构建了virginica cDNA文库。从该文库中共对6，528个克隆进行测序，产生5，542个高质量的EST序列。聚类分析表明存在635个重叠群和4，053个单例，共产生4，688个独特序列。大约46%（2，174）的独特EST与非冗余蛋白质数据库有显著匹配（E值≤ 1 e-05）;其中1，104个使用基因本体（GO）术语进行注释。从这些EST中共鉴定出35个微卫星，其中18个具有足够的侧翼序列用于引物设计。使用东部牡蛎的所有现有和新产生的EST资源，共确定了6，533个推定的SNP。构建了高质量的标准化cDNA文库。总共产生了5，542个EST，代表4，688个独特序列。确定了推定的微卫星和SNP标记。这些基因组资源为未来的微阵列开发、标记验证、遗传连锁和QTL分析提供了物质基础。
The eastern oyster, Crassostrea virginica (Gmelin 1791), is an economically important species cultured in many areas in North America. It is also ecologically important because of the impact of its filter feeding behaviour on water quality. Populations of C. virginica have been threatened by overfishing, habitat degradation, and diseases. Through genome research, strategies are being developed to reverse its population decline. However, large-scale expressed sequence tag (EST) resources have been lacking for this species. Efficient generation of EST resources from this species has been hindered by a high redundancy of transcripts. The objectives of this study were to construct a normalized cDNA library for efficient EST analysis, to generate thousands of ESTs, and to analyze the ESTs for microsatellites and potential single nucleotide polymorphisms (SNPs). A normalized and subtracted C. virginica cDNA library was constructed from pooled RNA isolated from hemocytes, mantle, gill, gonad and digestive tract, muscle, and a whole juvenile oyster. A total of 6,528 clones were sequenced from this library generating 5,542 high-quality EST sequences. Cluster analysis indicated the presence of 635 contigs and 4,053 singletons, generating a total of 4,688 unique sequences. About 46% (2,174) of the unique ESTs had significant hits (E-value ≤ 1e-05) to the non-redundant protein database; 1,104 of which were annotated using Gene Ontology (GO) terms. A total of 35 microsatellites were identified from the ESTs, with 18 having sufficient flanking sequences for primer design. A total of 6,533 putative SNPs were also identified using all existing and the newly generated EST resources of the eastern oysters. A high quality normalized cDNA library was constructed. A total of 5,542 ESTs were generated representing 4,688 unique sequences. Putative microsatellite and SNP markers were identified. These genome resources provide the material basis for future microarray development, marker validation, and genetic linkage and QTL analysis.
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影响因子：
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作者：
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通讯作者：
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影响因子：
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作者：
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DOI：
10.1046/j.1471-8286.2003.00406.x
发表时间：
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期刊：
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通讯作者：
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