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 431348
Title Comparison of the exomes of common carp (Cyprinus carpio) and zebrafish (Danio rerio)
Author(s) Henkel, C.V.; Dirks, R.P.; Jansen, H.J.; Forlenza, M.; Wiegertjes, G.F.; Howe, K.; Thillart, G.E. van den; Spaink, H.P.
Source Zebrafish 9 (2012)2. - ISSN 1545-8547 - p. 59 - 67.
DOI https://doi.org/10.1089/zeb.2012.0773
Department(s) Cell Biology and Immunology
WIAS
Publication type Refereed Article in a scientific journal
Publication year 2012
Keyword(s) transcriptome analysis - genetic-variability - antibody-production - nitrosative stress - dna-sequences - genome - fish - macrophages - lines - microsatellite
Abstract Research on common carp, Cyprinus carpio, is beneficial for zebrafish research because of resources available owing to its large body size, such as the availability of sufficient organ material for transcriptomics, proteomics, and metabolomics. Here we describe 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 1.4–1.5¿Gb. 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 in the carp evolutionary history, which—due to a higher degree of compactness—did not result in a genome larger than that of zebrafish.
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