title: 6-10× pyrosequencing is a practical approach for whole prokaryote genome studies.
abstract: Next generation 454 pyrosequencing technology for whole bacterial genome sequencing involves a deep sequencing strategy with at least 15-20× in depth proposed by official protocols but usually done with over 20× in practices. In this study, we carried out a comprehensive evaluation of quality of the de novo assemblies based on realistic pyrosequencing simulated data from 1480 prokaryote genomes and 7 runs of machine-generated data. Our results demonstrated that for most of the prokaryote genomes, 6-10× sequencing in qualified runs with 400 bp reads could produce high quality draft assembly (>98% genome coverage, <100 contigs with N50 size >100 kb, single base accuracy >99.99, indel error rate <0.01%, false gene loss/duplication rate <0.5%). Our study proves the power of low depth pyrosequencing strategy, which provides a cost-effective way for sequencing whole prokaryote genomes in a short time and enables further studies in microbial population diversity and comparative genomics.
authors.affiliation: School of Biological Sciences, Faculty of Science, The University of Hong Kong, China. lijun.sci@hku.hk
authors.forename: Jun
authors.initials: J
authors.lastname: Li
authors.forename: Jingwei
authors.initials: J
authors.lastname: Jiang
authors.forename: Frederick C
authors.initials: FC
authors.lastname: Leung
mesh_terms: D016678:Genome; D011387:Prokaryotic Cells; D017422:Sequence Analysis, DNA / Q000379:methods*