Author:
Latreille Phil,Norton Stacie,Goldman Barry S,Henkhaus John,Miller Nancy,Barbazuk Brad,Bode Helge B,Darby Creg,Du Zijin,Forst Steve,Gaudriault Sophie,Goodner Brad,Goodrich-Blair Heidi,Slater Steven
Abstract
Abstract
Background
In sequencing the genomes of two Xenorhabdus species, we encountered a large number of sequence repeats and assembly anomalies that stalled finishing efforts. This included a stretch of about 12 Kb that is over 99.9% identical between the plasmid and chromosome of X. nematophila.
Results
Whole genome restriction maps of the sequenced strains were produced through optical mapping technology. These maps allowed rapid resolution of sequence assembly problems, permitted closing of the genome, and allowed correction of a large inversion in a genome assembly that we had considered finished.
Conclusion
Our experience suggests that routine use of optical mapping in bacterial genome sequence finishing is warranted. When combined with data produced through 454 sequencing, an optical map can rapidly and inexpensively generate an ordered and oriented set of contigs to produce a nearly complete genome sequence assembly.
Publisher
Springer Science and Business Media LLC
Cited by
90 articles.
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