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.
| Original language | English |
|---|---|
| Title of host publication | Abstracts of papers presented at the Evolution of Caenorhabditis and Other Nematodes, Cold Spring Harbor Laboratory, New York, USA, 3-6 April 2012 |
| Pages | 47-47 |
| Publication status | Published - 2012 |
| Event | Evolution of Caenorhabditis and Other Nematodes, Cold Spring Harbor Laboratory, New York, USA - Duration: 3 Apr 2012 → 6 Apr 2012 |
Conference/symposium
| Conference/symposium | Evolution of Caenorhabditis and Other Nematodes, Cold Spring Harbor Laboratory, New York, USA |
|---|---|
| Period | 3/04/12 → 6/04/12 |