Optical mapping as a routine tool for bacterial genome sequence finishing.
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.
Latreille
Phil
P
Monsanto Company, 800 North Lindbergh Boulevard St. Louis, MO 63167, USA. jplatre@monsanto.com
Norton
Stacie
S
Goldman
Barry S
BS
Henkhaus
John
J
Miller
Nancy
N
Barbazuk
Brad
B
Bode
Helge B
HB
Darby
Creg
C
Du
Zijin
Z
Forst
Steve
S
Gaudriault
Sophie
S
Goodner
Brad
B
Goodrich-Blair
Heidi
H
Slater
Steven
S
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*
D004251:DNA Transposable Elements; D004269:DNA, Bacterial; D012335:RNA, Ribosomal