Whole-genome sequencing and variant discovery in c. Elegans

ABSTRACT Massively parallel sequencing instruments enable rapid and inexpensive DNA sequence data production. Because these instruments are new, their data require characterization with

respect to accuracy and utility. To address this, we sequenced a _Caernohabditis elegans_ N2 Bristol strain isolate using the Solexa Sequence Analyzer, and compared the reads to the

reference genome to characterize the data and to evaluate coverage and representation. Massively parallel sequencing facilitates strain-to-reference comparison for genome-wide sequence

variant discovery. Owing to the short-read-length sequences produced, we developed a revised approach to determine the regions of the genome to which short reads could be uniquely mapped. We

then aligned Solexa reads from _C. elegans_ strain CB4858 to the reference, and screened for single-nucleotide polymorphisms (SNPs) and small indels. This study demonstrates the utility of

massively parallel short read sequencing for whole genome resequencing and for accurate discovery of genome-wide polymorphisms. Access through your institution Buy or subscribe This is a

preview of subscription content, access via your institution ACCESS OPTIONS Access through your institution Subscribe to this journal Receive 12 print issues and online access $259.00 per

year only $21.58 per issue Learn more Buy this article * Purchase on SpringerLink * Instant access to full article PDF Buy now Prices may be subject to local taxes which are calculated

during checkout ADDITIONAL ACCESS OPTIONS: * Log in * Learn about institutional subscriptions * Read our FAQs * Contact customer support SIMILAR CONTENT BEING VIEWED BY OTHERS DECIPHERING

COMPLEX GENOME REARRANGEMENTS IN _C. ELEGANS_ USING SHORT-READ WHOLE GENOME SEQUENCING Article Open access 14 September 2021 HIGHLY ACCURATE LONG-READ HIFI SEQUENCING DATA FOR FIVE COMPLEX

GENOMES Article Open access 17 November 2020 EFFICIENT COLLECTION OF A LARGE NUMBER OF MUTATIONS BY MUTAGENESIS OF DNA DAMAGE RESPONSE DEFECTIVE ANIMALS Article Open access 07 April 2021

REFERENCES * _C. elegans_ Sequencing Consortium. Genome sequence of the nematode _C. elegans_: a platform for investigating biology. _Science_ 282, 2012–2018 (1998). * 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  * Lander, E.S. et al. Initial sequencing and

analysis of the human genome. _Nature_ 409, 860–921 (2001). Article  CAS  Google Scholar  * International Human Genome Sequencing Consortium. Finishing the euchromatic sequence of the human

genome. _Nature_ 431, 931–945 (2004). * 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  * Stein, L.D. et al. The genome sequence of Caenorhabditis briggsae: a platform for comparative genomics. _PLoS Biol._ 1, e45 (2003). Article  Google Scholar  * Hodgkin, J.

& Doniach, T. Natural variation and copulatory plug formation in _Caenorhabditis elegans_. _Genetics_ 146, 149–164 (1997). CAS  PubMed  PubMed Central  Google Scholar  * Marth, G.T. et

al. A general approach to single-nucleotide polymorphism discovery. _Nat. Genet._ 23, 452–456 (1999). Article  CAS  Google Scholar  * Bieri, T. et al. WormBase: new content and better

access. _Nucleic Acids Res._ 35, D506–D510 (2007). Article  CAS  Google Scholar  * Tuzun, E. et al. Fine-scale structural variation of the human genome. _Nat. Genet._ 37, 727–732 (2005).

Article  CAS  Google Scholar  * 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  * Smit, A.F. The origin of interspersed repeats in the human genome. _Curr. Opin. Genet. Dev._ 6, 743–748 (1996). Article  CAS  Google Scholar 

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

AUTHORS AND AFFILIATIONS * 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 * 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 * LaDeana W Hillier View author publications You can also search for this author inPubMed Google Scholar * Gabor T Marth View author

publications You can also search for this author inPubMed Google Scholar * Aaron R Quinlan View author publications You can also search for this author inPubMed Google Scholar * David

Dooling View author publications You can also search for this author inPubMed Google Scholar * Ginger Fewell View author publications You can also search for this author inPubMed Google

Scholar * Derek Barnett View author publications You can also search for this author inPubMed Google Scholar * Paul Fox View author publications You can also search for this author inPubMed 

Google Scholar * Jarret I Glasscock View author publications You can also search for this author inPubMed Google Scholar * Matthew Hickenbotham View author publications You can also search

for this author inPubMed Google Scholar * Weichun Huang View author publications You can also search for this author inPubMed Google Scholar * Vincent J Magrini View author publications You

can also search for this author inPubMed Google Scholar * Ryan J Richt View author publications You can also search for this author inPubMed Google Scholar * Sacha N Sander View author

publications You can also search for this author inPubMed Google Scholar * Donald A Stewart View author publications You can also search for this author inPubMed Google Scholar * Michael

Stromberg View author publications You can also search for this author inPubMed Google Scholar * Eric F Tsung View author publications You can also search for this author inPubMed Google

Scholar * Todd Wylie View author publications You can also search for this author inPubMed Google Scholar * Tim Schedl View author publications You can also search for this author inPubMed 

Google Scholar * Richard K Wilson View author publications You can also search for this author inPubMed Google Scholar * Elaine R Mardis View author publications 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 to Elaine R Mardis. SUPPLEMENTARY INFORMATION SUPPLEMENTARY TEXT AND

FIGURES Supplementary Figures 1–4, Supplementary Data, Supplementary Methods, Supplementary Table 1 (PDF 1178 kb) RIGHTS AND PERMISSIONS Reprints 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 * Received: 19 September 2007 * Accepted: 21 December 2007 * Published: 20 January 2008 * Issue Date: February 2008 * DOI: https://doi.org/10.1038/nmeth.1179 SHARE THIS

ARTICLE Anyone you share the following link with will be able to read this content: Get shareable link Sorry, a shareable link is not currently available for this article. Copy to clipboard

Provided by the Springer Nature SharedIt content-sharing initiative