De novo sequencing of plant genomes using second-generation technologies

Imelfort, Michael and Edwards, David (2009) De novo sequencing of plant genomes using second-generation technologies. Briefings in Bioinformatics, 10 6: 609-618. doi:10.1093/bib/bbp039

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Author Imelfort, Michael
Edwards, David
Title De novo sequencing of plant genomes using second-generation technologies
Journal name Briefings in Bioinformatics   Check publisher's open access policy
ISSN 1477-4054
Publication date 2009-11-01
Year available 2009
Sub-type Article (original research)
DOI 10.1093/bib/bbp039
Volume 10
Issue 6
Start page 609
End page 618
Total pages 8
Editor Martin Bishop
Place of publication United Kingdom
Publisher Oxford University Press
Language eng
Subject C1
829999 Plant Production and Plant Primary Products not elsewhere classified
060102 Bioinformatics
Abstract The ability to sequence the DNA of an organism has become one of the most important tools in modern biological research. Until recently, the sequencing of even small model genomes required substantial funds and international collaboration. The development of ‘second-generation’ sequencing technology has increased the throughput and reduced the cost of sequence generation by several orders of magnitude. These new methods produce vast numbers of relatively short reads, usually at the expense of read accuracy. Since the first commercial second-generation sequencing system was produced by 454 Technologies and commercialised by Roche, several other companies including Illumina, Applied Biosystems, Helicos Biosciences and Pacific Biosciences have joined the competition. Because of the relatively high error rate and lack of assembly tools, short-read sequence technology has mainly been applied to the re-sequencing of genomes. However, some recent applications have focused on the de novo assembly of these data. De novo assembly remains the greatest challenge for DNA sequencing and there are specific problems for second generation sequencing which produces short reads with a high error rate. However, a number of different approaches for short-read assembly have been proposed and some have been implemented in working software. In this review, we compare the current approaches for second-generation genome sequencing, explore the future direction of this technology and the implications for plant genome research.
Keyword Genome sequencing
Second generation
Next generation
Roche 454
De novo assembly
Short DNA sequences
Arabidopsis Thaliana
Draft sequence
Maize genome
Short reads
Q-Index Code C1
Q-Index Status Confirmed Code
Institutional Status UQ

Document type: Journal Article
Sub-type: Article (original research)
Collections: 2010 Higher Education Research Data Collection
School of Agriculture and Food Sciences
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Citation counts: TR Web of Science Citation Count  Cited 68 times in Thomson Reuters Web of Science Article | Citations
Scopus Citation Count Cited 78 times in Scopus Article | Citations
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Created: Sun, 13 Dec 2009, 10:07:23 EST