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

被引：107

作者：

DiGuistini, Scott ^{[2
]}

Liao, Nancy Y. ^{[1
]}

Platt, Darren ^{[3
]}

Robertson, Gordon ^{[1
]}

Seidel, Michael ^{[1
]}

Chan, Simon K. ^{[1
]}

Docking, T. Roderick ^{[1
]}

Birol, Inanc ^{[1
]}

Holt, Robert A. ^{[1
]}

Hirst, Martin ^{[1
]}

Mardis, Elaine ^{[4
]}

Marra, Marco A. ^{[1
]}

Hamelin, Richard C. ^{[5
]}

Bohlmann, Joerg ^{[6
]}

Breuil, Colette ^{[2
]}

Jones, Steven J. M. ^{[1
]}

机构：

[1] BC Canc Agcy Genome Sci Ctr, Vancouver, BC V5Z 4E6, Canada

[2] Univ British Columbia, Dept Wood Sci, Vancouver, BC V6T 1Z4, Canada

[3] Amyris Biotechnol Inc, Emeryville, CA 94608 USA

[4] Washington Univ, Sch Med, St Louis, MO 63108 USA

[5] Natl Res Canada, Ste Foy, PQ G1V 4C7, Canada

[6] Univ British Columbia, Michael Smith Labs, Vancouver, BC V6T 1Z3, Canada

来源：

GENOME BIOLOGY | 2009年 / 10卷 / 09期

基金：

加拿大自然科学与工程研究理事会;

关键词：

DNA; QUALITY; TOOL;

D O I：

10.1186/gb-2009-10-9-r94

中图分类号：

Q81 [生物工程学（生物技术）]; Q93 [微生物学];

学科分类号：

071005 ; 0836 ; 090102 ; 100705 ;

摘要：

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.

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