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

I. C.R.M. Kolder, S. J. van der Plas-Duivesteijn, G. Tan, G. F. Wiegertjes, M. Forlenza, A. T. Guler, D. Y. Travin, M. Nakao, T. Moritomo, I. Irnazarow, J. T. den Dunnen, S. Y. Anvar, H. J. Jansen, R. P. Dirks, M. Palmblad, B. Lenhard, C. V. Henkel, H. P. Spaink

Research output: Contribution to journalArticle

16 Citations (Scopus)

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.

Original languageEnglish
Article number701
JournalBMC Genomics
Volume17
Issue number1
DOIs
Publication statusPublished - Sep 2 2016

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Carps
Proteome
Transcriptome
Zebrafish
Fishes
Genes
Molecular Sequence Annotation
Gene Expression Profiling
Research
Proteomics
Cluster Analysis
Animal Models
Economics
Genome
RNA
Food

All Science Journal Classification (ASJC) codes

  • Biotechnology
  • Genetics

Cite this

Kolder, I. C. R. M., van der Plas-Duivesteijn, S. J., Tan, G., Wiegertjes, G. F., Forlenza, M., Guler, A. T., ... Spaink, H. P. (2016). A full-body transcriptome and proteome resource for the European common carp. BMC Genomics, 17(1), [701]. https://doi.org/10.1186/s12864-016-3038-y

A full-body transcriptome and proteome resource for the European common carp. / Kolder, I. C.R.M.; van der Plas-Duivesteijn, S. J.; Tan, G.; Wiegertjes, G. F.; Forlenza, M.; Guler, A. T.; Travin, D. Y.; Nakao, M.; Moritomo, T.; Irnazarow, I.; den Dunnen, J. T.; Anvar, S. Y.; Jansen, H. J.; Dirks, R. P.; Palmblad, M.; Lenhard, B.; Henkel, C. V.; Spaink, H. P.

In: BMC Genomics, Vol. 17, No. 1, 701, 02.09.2016.

Research output: Contribution to journalArticle

Kolder, ICRM, van der Plas-Duivesteijn, SJ, Tan, G, Wiegertjes, GF, Forlenza, M, Guler, AT, Travin, DY, Nakao, M, Moritomo, T, Irnazarow, I, den Dunnen, JT, Anvar, SY, Jansen, HJ, Dirks, RP, Palmblad, M, Lenhard, B, Henkel, CV & Spaink, HP 2016, 'A full-body transcriptome and proteome resource for the European common carp', BMC Genomics, vol. 17, no. 1, 701. https://doi.org/10.1186/s12864-016-3038-y
Kolder ICRM, van der Plas-Duivesteijn SJ, Tan G, Wiegertjes GF, Forlenza M, Guler AT et al. A full-body transcriptome and proteome resource for the European common carp. BMC Genomics. 2016 Sep 2;17(1). 701. https://doi.org/10.1186/s12864-016-3038-y
Kolder, I. C.R.M. ; van der Plas-Duivesteijn, S. J. ; Tan, G. ; Wiegertjes, G. F. ; Forlenza, M. ; Guler, A. T. ; Travin, D. Y. ; Nakao, M. ; Moritomo, T. ; Irnazarow, I. ; den Dunnen, J. T. ; Anvar, S. Y. ; Jansen, H. J. ; Dirks, R. P. ; Palmblad, M. ; Lenhard, B. ; Henkel, C. V. ; Spaink, H. P. / A full-body transcriptome and proteome resource for the European common carp. In: BMC Genomics. 2016 ; Vol. 17, No. 1.
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AU - Irnazarow, I.

AU - den Dunnen, J. T.

AU - Anvar, S. Y.

AU - Jansen, H. J.

AU - Dirks, R. P.

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