Resequencing of CB4857, RC301, CB4856 and AB2 strains of C. elegans
A genomic bias for genotype-environment interactions in C. elegans
Strains CB4857, RC301, CB4856 and AB2 were obtained from the Caenorhabditis Genetics Center, and maintained at 20*C using standard culture methods (Brenner 1974). Genomic DNA was extracted by proteinase K digestion followed by two rounds of phenol-chloroform extraction, with an intermediate step of RNase A digestion in TE. Genomic DNA libraries were built using Illumina’s standard paired-end protocol and 100x2 bp were sequenced on the Illumina HiSeq 2000 following the manufacturer’s recommendations. The numbers of reads mapped to the N2 genome (Wormbase release 220) were: 119,071,331 (CB4857), 109,807,250 (RC301), 58,309,757 (CB4856) and 113,429,439 (AB2) with a coverage of 116X, 107X, 58X and 111X, respectively. SNP calling was performed using samtools utilities with the N2 genome as reference. SNPs with a variant quality score of at least 30 were selected. Overall 100,919 (CB4857), 85,776 (RC301), 184,912 (CB4856) and 98,415 (AB2) SNPs relative to N2 strain were detected.
We used Illumina resequencing of the CB4857, RC301, CB4856 and AB2 strains of C. elegans for the genome-wide discovery of single-nucleotide polymorphisms (SNP) relative to N2 (Bristol) strain.