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De novo genome sequence assembly of a filamentous fungus using Sanger, 454 and Illumina sequence data

Scott DiGuistini1, Nancy Y Liao2, Darren Platt3, Gordon Robertson2, Michael Seidel2, Simon K Chan2, T Roderick Docking2, Inanc Birol2, Robert A Holt2, Martin Hirst2, Elaine Mardis4, Marco A Marra2, Richard C Hamelin5, Jörg Bohlmann6, Colette Breuil1 and Steven JM Jones2*

  • * Corresponding author: Steven JM Jones sjones@bcgsc.ca

  • † Equal contributors

Author Affiliations

1 Department of Wood Science, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada

2 BC Cancer Agency Genome Sciences Centre, Vancouver, BC, V5Z 4E6, Canada

3 Amyris Biotechnologies, Inc., Hollis Street, Emeryville, CA 94608, USA

4 Washington University School of Medicine, Forest Park Ave, St Louis, MO 63108, USA

5 Natural Resources Canada, rue du PEPS, Ste-Foy, Quebec, G1V 4C7, Canada

6 Michael Smith Laboratories, University of British Columbia, Vancouver, BC, V6T 1Z3, Canada

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Genome Biology 2009, 10:R94  doi:10.1186/gb-2009-10-9-r94

Published: 11 September 2009

Abstract

Sequencing-by-synthesis technologies can reduce the cost of generating de novo genome assemblies. We report a method for assembling draft genome sequences of eukaryotic organisms that integrates sequence information from different sources, and demonstrate its effectiveness by assembling an approximately 32.5 Mb draft genome sequence for the forest pathogen Grosmannia clavigera, an ascomycete fungus. We also developed a method for assessing draft assemblies using Illumina paired end read data and demonstrate how we are using it to guide future sequence finishing. Our results demonstrate that eukaryotic genome sequences can be accurately assembled by combining Illumina, 454 and Sanger sequence data.