A full-body transcriptome and proteome resource for the European common carp.
A full-body transcriptome and proteome resource for the European common carp.
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DOI：
10.1186/s12864-016-3038-y
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发表时间：
2016-09-02
期刊：
影响因子：
4.4
通讯作者：
Spaink HP
中科院分区：
文献类型：
--
作者：
Kolder IC;van der Plas-Duivesteijn SJ;Tan G;Wiegertjes GF;Forlenza M;Guler AT;Travin DY;Nakao M;Moritomo T;Irnazarow I;den Dunnen JT;Anvar SY;Jansen HJ;Dirks RP;Palmblad M;Lenhard B;Henkel CV;Spaink HP
普通鲤鱼（Cyprinus carpio）是最古老、最驯化和最养殖的食用鱼类之一。除了其经济重要性，鲤鱼也非常适合与动物模型斑马鱼（Danio rerio）结合进行比较生理和疾病研究。它们在遗传上密切相关，但为基础研究提供了互补的优势，鲤鱼的大体重为高级转录组和蛋白质组研究提供了获得足够细胞材料的可能性。在这里，我们使用了19种不同的组织，从F1杂交株的普通鲤鱼进行转录组分析，使用RNA-Seq。对于一部分组织，我们也进行了深入的蛋白质组学研究。作为参考，我们使用低覆盖率的Pacific Biosciences测序更新了欧洲普通鲤鱼基因组组装，以允许高质量的基因注释。这些注释的基因列表与斑马鱼同源物相关联，从而能够与已发表的数据集进行直接比较。使用聚类，我们已经确定了一组基因，这些基因是各种类型组织的潜在选择性标记。此外，我们提供了一个脚本的示意性解剖查看器可视化器官特异性表达数据。识别的转录组和蛋白质组数据鲤鱼组织代表了一个有用的资源，进一步翻译研究的组织特异性标记，为这个经济上重要的鱼类，可以导致新的标记器官发育。与斑马鱼表达模式的相似性证实了鲤鱼作为研究鲤科鱼类组织特异性表达的资源的价值。鲤鱼注释基因组的获得将为进一步的应用和基础研究提供基础。本文的在线版本（doi：10.1186/s12864-016-3038-y）包含补充材料，可供授权用户使用。
The common carp (Cyprinus carpio) is the oldest, most domesticated and one of the most cultured fish species for food consumption. Besides its economic importance, the common carp is also highly suitable for comparative physiological and disease studies in combination with the animal model zebrafish (Danio rerio). They are genetically closely related but offer complementary benefits for fundamental research, with the large body mass of common carp presenting possibilities for obtaining sufficient cell material for advanced transcriptome and proteome studies. Here we have used 19 different tissues from an F1 hybrid strain of the common carp to perform transcriptome analyses using RNA-Seq. For a subset of the tissues we also have performed deep proteomic studies. As a reference, we updated the European common carp genome assembly using low coverage Pacific Biosciences sequencing to permit high-quality gene annotation. These annotated gene lists were linked to zebrafish homologs, enabling direct comparisons with published datasets. Using clustering, we have identified sets of genes that are potential selective markers for various types of tissues. In addition, we provide a script for a schematic anatomical viewer for visualizing organ-specific expression data. The identified transcriptome and proteome data for carp tissues represent a useful resource for further translational studies of tissue-specific markers for this economically important fish species that can lead to new markers for organ development. The similarity to zebrafish expression patterns confirms the value of common carp as a resource for studying tissue-specific expression in cyprinid fish. The availability of the annotated gene set of common carp will enable further research with both applied and fundamental purposes. The online version of this article (doi:10.1186/s12864-016-3038-y) contains supplementary material, which is available to authorized users.
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DOI：
10.1093/bioinformatics/btu638
发表时间：
2015-01-15
期刊：
Bioinformatics (Oxford, England)
影响因子：
--
作者：
Anders S;Pyl PT;Huber W
通讯作者：
Huber W
影响因子：
1.7
作者：
Jurka, J;Kapitonov, VV;Walichiewicz, J
通讯作者：
Walichiewicz, J
DOI：
10.1093/bioinformatics/btr490
发表时间：
2011-11-15
期刊：
Bioinformatics (Oxford, England)
影响因子：
--
作者：
Howe EA;Sinha R;Schlauch D;Quackenbush J
通讯作者：
Quackenbush J
影响因子：
7
作者：
Kielbasa, Szymon M.;Wan, Raymond;Frith, Martin C.
通讯作者：
Frith, Martin C.
影响因子：
4
作者：
Dooley, K;Zon, LI
通讯作者：
Zon, LI