Characterization of the Zoarces viviparus liver transcriptome using massively parallel pyrosequencing.
Characterization of the Zoarces viviparus liver transcriptome using massively parallel pyrosequencing.
复制标题
DOI：
10.1186/1471-2164-10-345
复制
发表时间：
2009-07-31
期刊：
影响因子：
4.4
通讯作者：
Larsson DG
中科院分区：
文献类型：
--
作者：
Kristiansson E;Asker N;Förlin L;Larsson DG
胎生硬骨鱼生活在北欧海岸，长期以来一直是海洋生态和环境监测的模式生物。然而，关于该物种基因组的稀缺信息限制了有效的分子水平分析的使用，例如基因表达微阵列。在这项研究中，我们首次全面描述了胎盘沼虾肝脏转录组的特征。从大规模平行焦磷酸测序产生的400,000个读数中，超过50,000个假定转录本被组装、注释和功能分类。据估计，这些数据覆盖了大约40%的转录组，并确定了大约一半刺鱼基因的同源基因。因此，序列数据被用于设计用于大规模基因表达分析的寡核苷酸微阵列。我们的结果表明，使用454生命科学/罗氏公司的基因组测序仪FLX一次运行就能产生足够的基因组信息，足以在高等脊椎动物中对大量基因进行充分的从头组装。生成的序列数据，包括经过验证的微阵列探针，可以公开获得，以促进对胎生斑节鱼全基因组的研究。
The teleost Zoarces viviparus (eelpout) lives along the coasts of Northern Europe and has long been an established model organism for marine ecology and environmental monitoring. The scarce information about this species genome has however restrained the use of efficient molecular-level assays, such as gene expression microarrays. In the present study we present the first comprehensive characterization of the Zoarces viviparus liver transcriptome. From 400,000 reads generated by massively parallel pyrosequencing, more than 50,000 pieces of putative transcripts were assembled, annotated and functionally classified. The data was estimated to cover roughly 40% of the total transcriptome and homologues for about half of the genes of Gasterosteus aculeatus (stickleback) were identified. The sequence data was consequently used to design an oligonucleotide microarray for large-scale gene expression analysis. Our results show that one run using a Genome Sequencer FLX from 454 Life Science/Roche generates enough genomic information for adequate de novo assembly of a large number of genes in a higher vertebrate. The generated sequence data, including the validated microarray probes, are publicly available to promote genome-wide research in Zoarces viviparus.
登录
查看更多内容
影响因子：
14.9
作者：
UniProt Consortium
通讯作者：
UniProt Consortium
影响因子：
1.7
作者：
Jurka, J;Kapitonov, VV;Walichiewicz, J
通讯作者：
Walichiewicz, J
影响因子：
12.3
作者：
Huse SM;Huber JA;Morrison HG;Sogin ML;Welch DM
通讯作者：
Welch DM
影响因子：
4.4
作者：
Gunnarsson L;Kristiansson E;Förlin L;Nerman O;Larsson DG
通讯作者：
Larsson DG
影响因子：
12.3
作者：
Gentleman RC;Carey VJ;Bates DM;Bolstad B;Dettling M;Dudoit S;Ellis B;Gautier L;Ge Y;Gentry J;Hornik K;Hothorn T;Huber W;Iacus S;Irizarry R;Leisch F;Li C;Maechler M;Rossini AJ;Sawitzki G;Smith C;Smyth G;Tierney L;Yang JY;Zhang J
通讯作者：
Zhang J