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BMC Genomics. 2016 Sep 2;17:701. doi: 10.1186/s12864-016-3038-y.

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

Author information

1
Institute of Biology Leiden, Leiden University, Sylvius Laboratory, Sylviusweg 72, 2300, RA, Leiden, The Netherlands.
2
Leiden Institute of Advanced Computer Science, Leiden University, Niels Bohrweg 1, 2333, CA, Leiden, The Netherlands.
3
Center for Proteomics and Metabolomics, Leiden University Medical Center, 2300, RC, Leiden, The Netherlands.
4
Computational Regulatory Genomics, MRC Clinical Sciences Centre, Faculty of Medicine, Imperial College London, Hammersmith Hospital Campus, Du Cane Road, London, W12 0NN, UK.
5
Cell Biology and Immunology group, Department of Animal Sciences, Wageningen University, P.O. Box 338, 6700, AH, Wageningen, The Netherlands.
6
Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, 119991, GSP-1, Moscow, Russia.
7
Laboratory of Marine Biochemistry, Department of Bioscience and Biotechnology, Kyushu University, Fukuoka, 812-8581, Japan.
8
Laboratory of Comparative Immunology, Department of Veterinary Medicine, Nihon University, Kameino 1866, Fujisawa, Kanagawa, 252-0880, Japan.
9
Polish Academy of Sciences, Ichthyobiology and Aquaculture Unit, Gołysz Zaborze, Kalinowa 2, 43-520, Chybie, Poland.
10
Leiden Genome Technology Center, Human and Clinical Genetics, Leiden University Medical Center, Leiden, The Netherlands.
11
ZF-screens B.V., J.H, Oortweg 19, 2333, CH, Leiden, The Netherlands.
12
Institute of Biology Leiden, Leiden University, Sylvius Laboratory, Sylviusweg 72, 2300, RA, Leiden, The Netherlands. h.p.spaink@biology.leidenuniv.nl.

Abstract

BACKGROUND:

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.

RESULTS:

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.

CONCLUSIONS:

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.

KEYWORDS:

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

PMID:
27590662
PMCID:
PMC5009708
DOI:
10.1186/s12864-016-3038-y
[Indexed for MEDLINE]
Free PMC Article

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