Genome-wide variations in a natural isolate of the nematode Caenorhabditis elegans

BMC Genomics

Nansheng Chen²  Ke Wang²  Jeffrey SC Chu¹  Rong She²  Ting Zhang¹  Zhaozhao Qin¹  Jun Wang¹  Christian Frech¹  Maja Tarailo-Graovac¹  Ismael A Vergara¹ 

[1] Department of Molecular Biology and Biochemistry, Simon Fraser University, 8888 University Drive, Burnaby, British Columbia V5A 1S6, Canada;School of Computing Science, Simon Fraser University, 8888 University Drive, Burnaby, British Columbia V5A 1S6, Canada

关键词: Compound variation;    Large insertion;    Loss-of-function;    Genomic variation;    Next-generation DNA sequencing;    Natural isolate strain;    C. elegans;   

Others  :  1217563
DOI  :  10.1186/1471-2164-15-255

 received in 2013-06-29, accepted in 2014-03-03,  发布年份 2014

【 摘 要 】

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.

【 授权许可】

   
2014 Vergara et al.; licensee BioMed Central Ltd.

【 图 表 】

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