Polymorphisms

Polymorphisms (snip-SNPs and indels) in C. briggsae

Publication

Koboldt et al. (2010). A toolkit for rapid gene mapping in the nematode Caenorhabditis briggsae. BMC Genomics 11:236. (Read here)

Summary The C. briggsae genetic map consortium consisting of four laboratories (Raymond Miller, WashU St. Louis; Bhagwati Gupta, McMaster; Eric Haag, Maryland College Park; Helen Chamberlin, Ohio State Columbus; Scott Baird, Wright State Dayton) was funded by NIH to identify polymorphisms and to construct a genetic linkage map of the organism.

The latest release (Build 4) consists of 23,829 SNPs in HK104, 9,111 in VT847, 5,164 in HK105, and 322 in PB800. The AF16 was used as a reference strain in all cases. Of the HK104 SNPs, 23,130 are now positioned on the cb3 genome sequence assembly.

A total of 1,987 RFLP (restriction fragment length polymorphism) assays were designed from 1,362 SNPs since these can be easily detected by restriction enzyme digestion followed by agarose gel electrophoresis (snip-SNPs).

In addition to SNPs, we also identified a large number of insertion-deletion (indel) polymorphisms. These include 212 medium size indels (50-2000 bp) and 627 small indels (7-49 bp). We developed PCR length polymorphism (PLP) assays for 212 medium indels and 436 small indels.

These polymorphisms serve as useful resource for mutant mapping and promise to accelerate genetic and functional studies of C. briggsae genes.

Raw sequence reads

The four C. briggsae isolates – HK104, VT847, HK105, and PB800 – were sequenced by capillary electrophoresis at Washington University Genome Center (St. Louis). The raw sequence reads are available for download. The following links contain zipped directories (in Polyphred structure) along with other useful information such as quality scores.

HK104 (G_AA-HK104.tar.gz)
VT847 (G_AD-VT847.tar.gz)
HK105 (G_AB-HK105.tar.gz)
PB800 (G_AC-PB800.tar.gz)

Other resources

C. briggsae SNP Research Facility website for more details on polymorphisms and other related information (Washington University School Of Medicine, St. Louis)

Polymorphisms identified by other labs