title: Optical mapping as a routine tool for bacterial genome sequence finishing.
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.
  
  
  CONCLUSIONS
  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.
authors.affiliation: Monsanto Company, 800 North Lindbergh Boulevard St. Louis, MO 63167, USA. jplatre@monsanto.com
authors.forename: Phil
authors.initials: P
authors.lastname: Latreille
authors.forename: Stacie
authors.initials: S
authors.lastname: Norton
authors.forename: Barry S
authors.initials: BS
authors.lastname: Goldman
authors.forename: John
authors.initials: J
authors.lastname: Henkhaus
authors.forename: Nancy
authors.initials: N
authors.lastname: Miller
authors.forename: Brad
authors.initials: B
authors.lastname: Barbazuk
authors.forename: Helge B
authors.initials: HB
authors.lastname: Bode
authors.forename: Creg
authors.initials: C
authors.lastname: Darby
authors.forename: Zijin
authors.initials: Z
authors.lastname: Du
authors.forename: Steve
authors.initials: S
authors.lastname: Forst
authors.forename: Sophie
authors.initials: S
authors.lastname: Gaudriault
authors.forename: Brad
authors.initials: B
authors.lastname: Goodner
authors.forename: Heidi
authors.initials: H
authors.lastname: Goodrich-Blair
authors.forename: Steven
authors.initials: S
authors.lastname: Slater
mesh_terms: D002876:Chromosomes, Bacterial; D003198:Computer Simulation; D020451:Contig Mapping; D004251:DNA Transposable Elements; D004269:DNA, Bacterial / Q000235:genetics; D016680:Genome, Bacterial; D007091:Image Processing, Computer-Assisted; D010957:Plasmids; D012335:RNA, Ribosomal; D015183:Restriction Mapping; D017422:Sequence Analysis, DNA / Q000379:methods*; D020593:Xenorhabdus / Q000235:genetics*
chemical_list: D004251:DNA Transposable Elements; D004269:DNA, Bacterial; D012335:RNA, Ribosomal