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.

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Record number 423443
Title “All” the sequence polymorphisms between Hawaii (CB4856) and Bristol (N2)
Author(s) Snoek, L.B.; Brenchley, R.; Hof, A. van 't; Bevers, R.P.J.; Bono, M. de; Hajnal, A.; Schmid, T.; Weber, K.; Francesconi, M.; Lehner, B.; Cossins, A.; Kammenga, J.E.
Source In: Abstracts of papers presented at the Evolution of Caenorhabditis and Other Nematodes, Cold Spring Harbor Laboratory, New York, USA, 3-6 April 2012. - - p. 47 - 47.
Event Evolution of Caenorhabditis and Other Nematodes, Cold Spring Harbor Laboratory, New York, USA, 2012-04-03/2012-04-06
Department(s) Laboratory of Nematology
PE&RC
Publication type Abstract in scientific journal or proceedings
Publication year 2012
Abstract “All” the sequence polymorphisms between Hawaii (CB4856) and Bristol (N2) Basten L Snoek¹, Rachel Brenchley², Arjen van 't Hof², Roel P Bevers¹, Mario de Bono³, Alex Hajnal4, Tobias Schmid4, Kate Weber³, Mirko Francesconi5, Ben Lehner5, Andy Cossins², Jan E Kammenga¹ 1Wageningen University, Nematology, Wageningen, 7608PB, Netherlands, ²University of Liverpool, Institute of Integrative Biology, Liverpool, L69 7ZB, United Kingdom, ³Medical Research Council, Molecular Biology, Cambridge, CB2 0QH, United Kingdom, 4 University of Zurich, Molecular Life Sciences, Zurich, CH-8057 , Switzerland, 5EMBL-Centre for Genomic Regulation, Systems Biology, Barcelona, 08003, Spain The decreasing costs and increasing throughput of next generation sequencing over the last 5 years has put sequencing of different genotypes of one species within reach , also for C. elegans. The availability of the full genome sequences of individual genotypes will identify “all” the genetic polymorphisms between them. These can be used in several ways: I) to clone new mutations, II) to calculate genetic distances, III) to find genomic sites of positive selection and IV) to find the genes (and polymorphisms) causal for natural phenotypic variation. Since most induced mutations are made in an N2 background a different stain is used to find the exact site of this mutation, often this is CB4856. Most studies on the sources of natural variation have been done on a population derived from a cross between CB4856 and N2. Even though CB4856 is so frequently used it yet has to be sequenced. Here, we present the full genome sequence of CB4856 in a format that enables easy access to the worm community. Three independent strains of CB4856 were sequenced in three different labs (Kammenga/Cossins, De Bono and Hajnal). The Kammenga/Cossins approach used the sequences of 102 recombinant inbred lines, including CB4856 and N2, which together contain the full N2 and CB4856 genome. This led to a mean coverage over 500x. The de Bono and Hajnal labs both sequenced the CB4856 with 10x coverage. These were independently aligned to the N2 reference sequence after which polymorphisms were extracted. We found almost 93,000 SNPs between N2 and CB4856. Of those almost 11,000 led to an amino acid change in almost 6,300 genes. The polymorphisms were not distributed equally over the genome. Differences in SNP frequency between, as well as within, chromosomes were found. Also loci with a high frequency of amino acid polymorphisms could be identified. Several groups of genes were enriched for SNPs and amino acid changes; these include the chemo receptors, c-type lectins and f-box proteins. Funded by: ERASysBio+ project GRAPPLE - Iterative modelling of gene regulatory interactions underlying stress, disease and ageing in C. elegans EU 7th Framework Programme under the Research Project PANACEA, contract nr 222936.
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