Abstract
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.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-016-3038-y) contains supplementary material, which is available to authorized users.
Highlights
The common carp (Cyprinus carpio) is the oldest, most domesticated and one of the most cultured fish species for food consumption
Carp genome Carp fish line R3 x R8 are the hybrid offspring of a cross between carp of Hungarian origin (R8 strain) and of Polish origin (R3 strain) [12], each of which are kept purebred by single brother-sister matings [13,14,15]
Using the same DNA sample employed for the initial assembly [8], we have prepared three paired-end libraries using the Cre-LoxP Inverse PCR (CLIP) approach [16] with target insert sizes of 5, 6.5, and 7.5 kbp
Summary
The common carp (Cyprinus carpio) is the oldest, most domesticated and one of the most cultured fish species for food consumption. The common carp is 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. Further comparative genomics and transcriptomics studies using Hungarian, North American and Chinese carp strains have provided insights into the species structure, and identified genes associated with skin color and scale phenotypes [9]. Further analyses of carp transcriptomes are not yet abundant, with an emphasis on embryonic samples and mixed tissues [8, 9]
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