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Abstract Detail


Genomics / Proteomics

Moore, Michael J. [1], Dhingra, Amit [2], Soltis, Pamela S. [1], Farmerie, William G. [3], Folta, Kevin M. [2], Soltis, Douglas E. [4].

Rapid and accurate pyrosequencing of six angiosperm plastid genomes.

THE past five years have witnessed a dramatic increase in the number of completely sequenced plastid genomes, fuelled largely by advances in conventional Sanger sequencing technology. Here we report a further significant reduction in time and cost for plastid genome sequencing through the successful use of a newly available pyrosequencing platform, the 454 Life Sciences Corporationís Genome Sequencer 20 (GS 20) System, to sequence the whole plastid genomes of six species of angiosperms, representing several of the basal lineages of eudicots: Nandina domestica (Berberidaceae), Nelumbo nucifera (Nelumbonaceae), Platanus occidentalis (Platanaceae), Meliosma cuneifolia (Sabiaceae), Gunnera manicata (Gunneraceae), and Liquidambar styraciflua (Altingiaceae). More than 99.8% of each plastid genome was obtained during GS 20 sequence runs, to an average depth of coverage of ~20◊. To assess the accuracy of the GS 20 sequence, over 45 kilobases of sequence was generated for Nandina and Platanus using conventional methods. Overall error rates of 0.074% and 0.139% were observed in GS 20 sequence for Nandina and Platanus, respectively. More than 98% of all errors were associated with homopolymer runs, with ~80% of all errors associated with homopolymer runs of 5 or more nucleotides. Error rates were much higher in the single-copy regions of both plastid genomes than in the inverted repeat regions, and were generally higher in noncoding regions than in coding regions. The high accuracy of GS 20 plastid genome sequence is particularly important because it was obtained for approximately half the cost and time of traditional shotgun-based genome sequencing techniques. The GS 20 System should be broadly applicable to most plastid genome sequencing projects, and therefore promises to expand the scale of plant genetic and phylogenetic research dramatically.


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1 - University of Florida, Department of Botany, Florida Museum of Natural History, P.O. Box 117800, Gainesville, Florida, 32611-7800, USA
2 - University of Florida, Horticultural Sciences Department, P.O. Box 110690, Gainesville, Florida, 32611, USA
3 - University of Florida, ICBR Genome Sequencing Service Laboratory, P.O. Box 100156, Gainesville, Florida, 32611, USA
4 - University of Florida, Department of Botany, 220 Bartram Hall, P.O. Box 118526, Gainesville, Florida, 32611-8526, USA

Keywords:
plastid genomes
pyrosequencing
basal eudicots
Genome Sequencer 20
Nandina domestica
Nelumbo nucifera
Platanus occidentalis
Meliosma cuneifolia
Gunnera manicata
Liquidambar styraciflua
angiosperms
cpDNA.

Presentation Type: Oral Paper:Papers for Topics
Session: 61-1
Location: 268/Holt
Date: Tuesday, August 1st, 2006
Time: 3:15 PM
Abstract ID:163


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