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

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Title: A full-body transcriptome and proteome resource for the European common carp.
Author(s): Kolder, IC
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
Item Type: Journal Article
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.
Publication Date: 2-Sep-2016
Date of Acceptance: 24-Aug-2016
URI: http://hdl.handle.net/10044/1/40085
DOI: http://dx.doi.org/10.1186/s12864-016-3038-y
ISSN: 1471-2164
Publisher: BioMed Central
Journal / Book Title: BMC Genomics
Volume: 17
Copyright Statement: This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.
Keywords: Cyprinus carpio
Genome
Proteomics
RNA-Seq
Transcriptomics tissue-specific expression
Cyprinus carpio
Genome
Proteomics
RNA-Seq
Transcriptomics tissue-specific expression
Bioinformatics
06 Biological Sciences
11 Medical And Health Sciences
08 Information And Computing Sciences
Publication Status: Published
Article Number: 701
Appears in Collections:Clinical Sciences
Molecular Sciences
Faculty of Medicine



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