Staff Publications

Staff Publications

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    'Staff publications' is the digital repository of Wageningen University & Research

    'Staff publications' contains references to publications authored by Wageningen University staff from 1976 onward.

    Publications authored by the staff of the Research Institutes are available from 1995 onwards.

    Full text documents are added when available. The database is updated daily and currently holds about 240,000 items, of which 72,000 in open access.

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Record number 508101
Title A full-body transcriptome and proteome resource for the European common carp
Author(s) Kolder, I.C.R.M.; Plas-Duivesteijn, S.J. van der; Tan, G.; Wiegertjes, G.F.; Forlenza, M.; Guler, A.T.; Travin, D.Y.; Nakao, M.; Moritomo, T.; Irnazarow, I.; Dunnen, J.T. den; Anvar, S.Y.; Jansen, H.J.; Dirks, R.P.; Palmblad, M.; Lenhard, B.; Henkel, C.V.; Spaink, H.P.
Source BMC Genomics 17 (2016)1. - ISSN 1471-2164
DOI http://dx.doi.org/10.1186/s12864-016-3038-y
Department(s) Cell Biology and Immunology
WIAS
Chair Nutrition Metabolism and Genomics
Publication type Refereed Article in a scientific journal
Publication year 2016
Keyword(s) Cyprinus carpio - Genome - Proteomics - RNA-Seq - Transcriptomics tissue-specific expression
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.

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