title: A full-body transcriptome and proteome resource for the European common carp.
abstract: 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.
authors: Institute of Biology Leiden, Leiden University, Sylvius Laboratory, Sylviusweg 72, 2300, RA, Leiden, The Netherlands.|Leiden Institute of Advanced Computer Science, Leiden University, Niels Bohrweg 1, 2333, CA, Leiden, The Netherlands.
authors: I C R M
authors: IC
authors: Kolder
authors: Center for Proteomics and Metabolomics, Leiden University Medical Center, 2300, RC, Leiden, The Netherlands.
authors: S J
authors: SJ
authors: van der Plas-Duivesteijn
authors: Computational Regulatory Genomics, MRC Clinical Sciences Centre, Faculty of Medicine, Imperial College London, Hammersmith Hospital Campus, Du Cane Road, London, W12 0NN, UK.
authors: G
authors: G
authors: Tan
authors: Cell Biology and Immunology group, Department of Animal Sciences, Wageningen University, P.O. Box 338, 6700, AH, Wageningen, The Netherlands.
authors: G F
authors: GF
authors: Wiegertjes
authors: Cell Biology and Immunology group, Department of Animal Sciences, Wageningen University, P.O. Box 338, 6700, AH, Wageningen, The Netherlands.
authors: M
authors: M
authors: Forlenza
authors: Center for Proteomics and Metabolomics, Leiden University Medical Center, 2300, RC, Leiden, The Netherlands.
authors: A T
authors: AT
authors: Guler
authors: Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, 119991, GSP-1, Moscow, Russia.
authors: D Y
authors: DY
authors: Travin
authors: Laboratory of Marine Biochemistry, Department of Bioscience and Biotechnology, Kyushu University, Fukuoka, 812-8581, Japan.
authors: M
authors: M
authors: Nakao
authors: Laboratory of Comparative Immunology, Department of Veterinary Medicine, Nihon University, Kameino 1866, Fujisawa, Kanagawa, 252-0880, Japan.
authors: T
authors: T
authors: Moritomo
authors: Polish Academy of Sciences, Ichthyobiology and Aquaculture Unit, Gołysz Zaborze, Kalinowa 2, 43-520, Chybie, Poland.
authors: I
authors: I
authors: Irnazarow
authors: Leiden Genome Technology Center, Human and Clinical Genetics, Leiden University Medical Center, Leiden, The Netherlands.
authors: J T
authors: JT
authors: den Dunnen
authors: Leiden Genome Technology Center, Human and Clinical Genetics, Leiden University Medical Center, Leiden, The Netherlands.
authors: S Y
authors: SY
authors: Anvar
authors: ZF-screens B.V., J.H, Oortweg 19, 2333, CH, Leiden, The Netherlands.
authors: H J
authors: HJ
authors: Jansen
authors: ZF-screens B.V., J.H, Oortweg 19, 2333, CH, Leiden, The Netherlands.
authors: R P
authors: RP
authors: Dirks
authors: Center for Proteomics and Metabolomics, Leiden University Medical Center, 2300, RC, Leiden, The Netherlands.
authors: M
authors: M
authors: Palmblad
authors: Computational Regulatory Genomics, MRC Clinical Sciences Centre, Faculty of Medicine, Imperial College London, Hammersmith Hospital Campus, Du Cane Road, London, W12 0NN, UK.
authors: B
authors: B
authors: Lenhard
authors: Institute of Biology Leiden, Leiden University, Sylvius Laboratory, Sylviusweg 72, 2300, RA, Leiden, The Netherlands.
authors: C V
authors: CV
authors: Henkel
authors: Institute of Biology Leiden, Leiden University, Sylvius Laboratory, Sylviusweg 72, 2300, RA, Leiden, The Netherlands. h.p.spaink@biology.leidenuniv.nl.
authors: H P
authors: HP
authors: Spaink
mesh_terms: D000818:Animals; D002347:Carps / Q000235:genetics* / Q000378:metabolism*; D019295:Computational Biology / Q000379:methods; D005060:Europe; D020869:Gene Expression Profiling; D016678:Genome; D023281:Genomics / Q000379:methods; D059014:High-Throughput Nucleotide Sequencing; D058977:Molecular Sequence Annotation; D009928:Organ Specificity; D020543:Proteome; D040901:Proteomics; D059467:Transcriptome
chemical_list: D020543:Proteome
keywords: Cyprinus carpio; Genome; Proteomics; RNA-Seq; Transcriptomics tissue-specific expression