A full-body transcriptome and proteome resource for the European common carp

BMC Genomics

Research Article

M. Forlenza¹  G. F. Wiegertjes¹  A. T. Guler²  M. Palmblad²  S. J. van der Plas-Duivesteijn²  B. Lenhard³  G. Tan³  D. Y. Travin⁴  C. V. Henkel⁵  H. P. Spaink⁵  I. C. R. M. Kolder⁶  T. Moritomo⁷  M. Nakao⁸  J. T. den Dunnen⁹  S. Y. Anvar⁹  I. Irnazarow^1,10  H. J. Jansen^1,11  R. P. Dirks^1,11 

[1] Cell Biology and Immunology group, Department of Animal Sciences, Wageningen University, P.O. Box 338, 6700, Wageningen, AH, The Netherlands;Center for Proteomics and Metabolomics, Leiden University Medical Center, 2300, Leiden, RC, The Netherlands;Computational Regulatory Genomics, MRC Clinical Sciences Centre, Faculty of Medicine, Imperial College London, Hammersmith Hospital Campus, Du Cane Road, W12 0NN, London, UK;Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, 119991, GSP-1, Moscow, Russia;Institute of Biology Leiden, Leiden University, Sylvius Laboratory, Sylviusweg 72, 2300, Leiden, RA, The Netherlands;Institute of Biology Leiden, Leiden University, Sylvius Laboratory, Sylviusweg 72, 2300, Leiden, RA, The Netherlands;Leiden Institute of Advanced Computer Science, Leiden University, Niels Bohrweg 1, 2333, Leiden, CA, The Netherlands;Laboratory of Comparative Immunology, Department of Veterinary Medicine, Nihon University, Kameino 1866, 252-0880, Fujisawa, Kanagawa, Japan;Laboratory of Marine Biochemistry, Department of Bioscience and Biotechnology, Kyushu University, 812-8581, Fukuoka, Japan;Leiden Genome Technology Center, Human and Clinical Genetics, Leiden University Medical Center, Leiden, The Netherlands;Polish Academy of Sciences, Ichthyobiology and Aquaculture Unit, Gołysz Zaborze, Kalinowa 2, 43-520, Chybie, Poland;ZF-screens B.V., J.H, Oortweg 19, 2333, Leiden, CH, The Netherlands;

关键词: Cyprinus carpio;    Genome;    Transcriptomics tissue-specific expression;    RNA-Seq;    Proteomics;   

DOI  :  10.1186/s12864-016-3038-y

 received in 2016-03-23, accepted in 2016-08-24,  发布年份 2016

来源: Springer

【 摘 要 】

BackgroundThe 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.ResultsHere 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.ConclusionsThe 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.

【 授权许可】

CC BY   
© The Author(s). 2016