Genome-wide variations in a natural isolate of the nematode Caenorhabditis elegans.
BACKGROUND
Increasing genetic and phenotypic differences found among natural isolates of C. elegans have encouraged researchers to explore the natural variation of this nematode species.


RESULTS
Here we report on the identification of genomic differences between the reference strain N2 and the Hawaiian strain CB4856, one of the most genetically distant strains from N2. To identify both small- and large-scale genomic variations (GVs), we have sequenced the CB4856 genome using both Roche 454 (~400 bps single reads) and Illumina GA DNA sequencing methods (101 bps paired-end reads). Compared to previously described variants (available in WormBase), our effort uncovered twice as many single nucleotide variants (SNVs) and increased the number of small InDels almost 20-fold. Moreover, we identified and validated large insertions, most of which range from 150 bps to 1.2 kb in length in the CB4856 strain. Identified GVs had a widespread impact on protein-coding sequences, including 585 single-copy genes that have associated severe phenotypes of reduced viability in RNAi and genetics studies. Sixty of these genes are homologs of human genes associated with diseases. Furthermore, our work confirms previously identified GVs associated with differences in behavioural and biological traits between the N2 and CB4856 strains.


CONCLUSIONS
The identified GVs provide a rich resource for future studies that aim to explain the genetic basis for other trait differences between the N2 and CB4856 strains.
Ismael A
IA
Vergara
Maja
M
Tarailo-Graovac
Christian
C
Frech
Jun
J
Wang
Zhaozhao
Z
Qin
Ting
T
Zhang
Rong
R
She
Jeffrey S C
JS
Chu
Ke
K
Wang
Department of Molecular Biology and Biochemistry, Simon Fraser University, 8888 University Drive, Burnaby, British Columbia V5A 1S6, Canada. chenn@sfu.ca.
Nansheng
N
Chen
D000818:Animals; D001482:Base Composition; D017173:Caenorhabditis elegans / Q000187:drug effects / Q000235:genetics*; D002874:Chromosome Mapping; D003062:Codon; D055028:Comparative Genomic Hybridization; D019295:Computational Biology; D004251:DNA Transposable Elements; D004351:Drug Resistance / Q000235:genetics; D056726:Genetic Association Studies; D014644:Genetic Variation; D049751:Genome, Helminth; D005838:Genotype; D059014:High-Throughput Nucleotide Sequencing; D054643:INDEL Mutation; D005810:Multigene Family; D016254:Mutagenesis, Insertional; D016366:Open Reading Frames; D010641:Phenotype; D020641:Polymorphism, Single Nucleotide; D017384:Sequence Deletion
D003062:Codon; D004251:DNA Transposable Elements