This site is intended to offer genome data from many sources, including genome, transcriptome and proteome data from the European common carp (Cyprinus carpio) . The reason for offering these data here is that submission to general databases such as NCBI usually takes a long time and we want to make these data publicly available as fast as possible. In addition we do strive to submit the data offered on this site to general databases.

Cyprinus carpio

 

Other published genomes: Eelgenome

For more information about custom de novo genome assembly and transcriptome deep sequencing projects, please visit the ZF-genomics website.



Welcome to the carpgenome website

Introduction

The common carp, Cyprinus carpio, has been intensively studied for many purposes. Common carp is worldwide the most cultured fish species for food consumption (FAO, 2009). On one hand, it represents one of the most important species used in aquaculture, and therefore many studies have focused on physiological aspects such as nutrition and farming conditions, and on fish infectious diseases including bacterial, viral, and parasitic infections. On the other hand, its large body size has permitted fundamental research into organ structure and function and immune recognition that is not possible in small fish species such as zebrafish (Danio rerio) or medaka (Oryzias latipes). For instance, the common carp can yield sufficient numbers of blood cells for cell sorting of various subtypes of immune cells and subsequent transcriptome analyses. Since common carp and zebrafish both belong to the cyprinid family, we believe that the combined use of these animal models will yield results that are easily translated between these species and thereby will give the ‘‘best of both worlds’’ of a small genetically highly versatile model (zebrafish) and a fish model with a very large body size for which well-defined genetically highly inbred lines are available, as is the case with common carp. This combination can also be highly successful for future screens at the embryo level since the small clutch size of zebrafish (up to a few hundred eggs per female) can be complemented with the very large clutch size of common carp (up to several hundreds of thousands of eggs per female). For instance, small molecule screens against infectious disease in zebrafish that make use of robotics can be adapted for common carp. In this respect, the relatedness of these species also makes it likely that their response to pathogens or cancer cells would be very similar. An example has been recently shown for the response of carp larvae to Mycobacterium marinum infections leading to granuloma-like structures indistinguishable from those formed in zebrafish larvae.

Technology

Sequencing was performed at ZF-screens using an Illumina HISEQ2000 platform. ZF-screens constantly strives to upgrade its technology in collaboration with Leiden University. In their company branch ZF-genomics ZF-screens also offers commercial services at highly competitive prices with an emphasis on full assistance with a genome to publication workflow. Our emphasis is currently on highlighting the importance of bioinformatic assistance for which highly trained personal is available. For a overview of the package of services available see our ZF-genomics website.

Publications

  • Christiaan V. Henkel, Ron P. Dirks, Hans J. Jansen, Maria Forlenza, Geert Wiegertjes, Kerstin Howe, Guido E.E.J.M. van den Thillart, and Herman P. Spaink. Comparison of the Exomes of Common Carp (Cyprinus carpio) and Zebrafish (Danio rerio) ZEBRAFISH Volume 9, Number 2, 2012.
    Carp schemeThis manuscript was published in June 2012 and described the shot gun sequencing of a clonal double-haploid common carp line. The assembly consists of 511891 scaffolds with an N50 of 17 kb, predicting a total genome size of 1.4–1.5Gb. A detailed analysis of the ten largest scaffolds indicates that the carp genome has a considerably lower repeat coverage than zebrafish, whilst the average intron size is significantly smaller, making it comparable to the fugu genome. The quality of the scaffolding was confirmed by comparisons with RNA deep sequencing data sets and a manual analysis for synteny with the zebrafish, especially the Hox gene clusters. In the ten largest scaffolds analyzed, the synteny of genes is almost complete. Comparisons of predicted exons of common carp with those of the zebrafish revealed only few genes specific for either zebrafish or carp, most of these being of unknown function. This supports the hypothesis of an additional genome duplication event inthe carp evolutionary history, which—due to a higher degree of compactness—did not result in a genome larger than that of zebrafish.

Downloadable files

This data is distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source of the data are credited by referring to the listed publications above.

The raw reads of the above data files are planned to be submitted to the trace database of NCBI later this year.  These data can also be provided on a personal basis before this time. Please contact Dr. Ron Dirks for these data.

This website is maintained by ZF-screens and Leiden University, Institute of Biology.
For questions contact Dr. Ron Dirks (dirks@zfscreens.com).