Whole-genome sequencing and variant discovery in C. elegans (original) (raw)

References

  1. C. elegans Sequencing Consortium. Genome sequence of the nematode C. elegans: a platform for investigating biology. Science 282, 2012–2018 (1998).
  2. Waterston, R. et al. The genome of the nematode Caenorhabditis elegans. Cold Spring Harb. Symp. Quant. Biol. 58, 367–376 (1993).
    Article CAS Google Scholar
  3. Lander, E.S. et al. Initial sequencing and analysis of the human genome. Nature 409, 860–921 (2001).
    Article CAS Google Scholar
  4. International Human Genome Sequencing Consortium. Finishing the euchromatic sequence of the human genome. Nature 431, 931–945 (2004).
  5. Harris, T.W. et al. WormBase: a multi-species resource for nematode biology and genomics. Nucleic Acids Res. 32, D411–D417 (2004).
    Article CAS Google Scholar
  6. Stein, L.D. et al. The genome sequence of Caenorhabditis briggsae: a platform for comparative genomics. PLoS Biol. 1, e45 (2003).
    Article Google Scholar
  7. Hodgkin, J. & Doniach, T. Natural variation and copulatory plug formation in Caenorhabditis elegans. Genetics 146, 149–164 (1997).
    CAS PubMed PubMed Central Google Scholar
  8. Marth, G.T. et al. A general approach to single-nucleotide polymorphism discovery. Nat. Genet. 23, 452–456 (1999).
    Article CAS Google Scholar
  9. Bieri, T. et al. WormBase: new content and better access. Nucleic Acids Res. 35, D506–D510 (2007).
    Article CAS Google Scholar
  10. Tuzun, E. et al. Fine-scale structural variation of the human genome. Nat. Genet. 37, 727–732 (2005).
    Article CAS Google Scholar
  11. Denver, D.R., Morris, K. & Thomas, W.K. Phylogenetics in Caenorhabditis elegans: an analysis of divergence and outcrossing. Mol. Biol. Evol. 20, 393–400 (2003).
    Article CAS Google Scholar
  12. Smit, A.F. The origin of interspersed repeats in the human genome. Curr. Opin. Genet. Dev. 6, 743–748 (1996).
    Article CAS Google Scholar
  13. Bhangale, T.R., Stephens, M. & Nickerson, D.A. Automating resequencing-based detection of insertion-deletion polymorphisms. Nat. Genet. 38, 1457–1462 (2006).
    Article CAS Google Scholar
  14. Stephens, M., Sloan, J.S., Robertson, P.D., Scheet, P. & Nickerson, D.A. Automating sequence-based detection and genotyping of SNPs from diploid samples. Nat. Genet. 38, 375–381 (2006).
    Article CAS Google Scholar
  15. Nickerson, D.A., Kolker, N., Taylor, S.L. & Rieder, M.J. Sequence-based detection of single nucleotide polymorphisms. Methods Mol. Biol. 175, 29–35 (2001).
    CAS PubMed Google Scholar
  16. Koch, R., van Luenen, H.G., van der Horst, M., Thijssen, K.L. & Plasterk, R.H. Single nucleotide polymorphisms in wild isolates of Caenorhabditis elegans. Genome Res. 10, 1690–1696 (2000).
    Article CAS Google Scholar
  17. Gordon, D., Abajian, C. & Green, P. Consed: a graphical tool for sequence finishing. Genome Res. 8, 195–202 (1998).
    Article CAS Google Scholar

Download references

Acknowledgements

We acknowledge National Human Genome Research Institute funding (HG003079-04 to R.K.W. and HG003698 to G.T.M.). We thank K. Hall and D. Bentley of Illumina, Inc. for generously producing the paired-end read data described in the manuscript, M. Wendl for careful reading of the manuscript and T. Bieri for submitting the CB4858 variants to Wormbase.

Author information

Author notes

  1. LaDeana W Hillier and Gabor T Marth: These authors contributed equally to this work.

Authors and Affiliations

  1. Department of Genetics and Genome Sequencing Center, Washington University School of Medicine, 4444 Forest Park Blvd., St. Louis, 63108, Missouri, USA
    LaDeana W Hillier, David Dooling, Ginger Fewell, Paul Fox, Jarret I Glasscock, Matthew Hickenbotham, Vincent J Magrini, Ryan J Richt, Sacha N Sander, Todd Wylie, Tim Schedl, Richard K Wilson & Elaine R Mardis
  2. Department of Biology, Boston College, 140 Commonwealth Ave., Chestnut Hill, 02467, Massachusetts, USA
    Gabor T Marth, Aaron R Quinlan, Derek Barnett, Weichun Huang, Donald A Stewart, Michael Stromberg & Eric F Tsung

Authors

  1. LaDeana W Hillier
    You can also search for this author inPubMed Google Scholar
  2. Gabor T Marth
    You can also search for this author inPubMed Google Scholar
  3. Aaron R Quinlan
    You can also search for this author inPubMed Google Scholar
  4. David Dooling
    You can also search for this author inPubMed Google Scholar
  5. Ginger Fewell
    You can also search for this author inPubMed Google Scholar
  6. Derek Barnett
    You can also search for this author inPubMed Google Scholar
  7. Paul Fox
    You can also search for this author inPubMed Google Scholar
  8. Jarret I Glasscock
    You can also search for this author inPubMed Google Scholar
  9. Matthew Hickenbotham
    You can also search for this author inPubMed Google Scholar
  10. Weichun Huang
    You can also search for this author inPubMed Google Scholar
  11. Vincent J Magrini
    You can also search for this author inPubMed Google Scholar
  12. Ryan J Richt
    You can also search for this author inPubMed Google Scholar
  13. Sacha N Sander
    You can also search for this author inPubMed Google Scholar
  14. Donald A Stewart
    You can also search for this author inPubMed Google Scholar
  15. Michael Stromberg
    You can also search for this author inPubMed Google Scholar
  16. Eric F Tsung
    You can also search for this author inPubMed Google Scholar
  17. Todd Wylie
    You can also search for this author inPubMed Google Scholar
  18. Tim Schedl
    You can also search for this author inPubMed Google Scholar
  19. Richard K Wilson
    You can also search for this author inPubMed Google Scholar
  20. Elaine R Mardis
    You can also search for this author inPubMed Google Scholar

Contributions

L.W.H., N2 Bristol read, coverage, variant and gap analyses; G.T.M., CB4858 SNP discovery and N2 Bristol error profile analysis; A.R.Q., CB4858 SNP discovery and validation analysis; D.D., Solexa analysis pipeline; G.F., validation assay design and analysis, D.B., Solexa base quality value analysis, P.F., preparation of N2 Bristol and CB4858 DNA, J.I.G., N2 Bristol read analysis; M.H., Solexa libraries and sequencing, W.H., microrepeat analysis, V.J.M., Solexa libraries and sequencing, R.J.R., N2 Bristol analysis; S.N.S., validation assays; D.A.S., microrepeat masking of C. elegans; M.S., Mosaik adaptation; E.F.T., microrepeat finding; T.W., N2 Bristol analysis, T.S., C. elegans strain selection; R.K.W., project origination; E.R.M., project coordination and manuscript preparation.

Corresponding author

Correspondence toElaine R Mardis.

Supplementary information

Rights and permissions

About this article

Cite this article

Hillier, L., Marth, G., Quinlan, A. et al. Whole-genome sequencing and variant discovery in C. elegans.Nat Methods 5, 183–188 (2008). https://doi.org/10.1038/nmeth.1179

Download citation