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PMID: 17868451 Published · epublish English Journal Article Research Support, Non-U.S. Gov't Research Support, U.S. Gov't, Non-P.H.S.

Optical mapping as a routine tool for bacterial genome sequence finishing.

BMC genomics ·Vol. 8 ·2007-09-14 ·Pages 321

Latreille P, Norton S, Goldman BS, Henkhaus J, Miller N, Barbazuk B, Bode HB, Darby C, Du Z, Forst S, Gaudriault S, Goodner B, Goodrich-Blair H, Slater S

Abstract

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. 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. 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.

MeSH Terms
Chromosomes, Bacterial Computer Simulation Contig Mapping DNA Transposable Elements DNA, Bacterial/genetics Genome, Bacterial Image Processing, Computer-Assisted Plasmids RNA, Ribosomal Restriction Mapping Sequence Analysis, DNA/methods Xenorhabdus/genetics
Chemicals
DNA Transposable Elements DNA, Bacterial RNA, Ribosomal
Authors & Affiliations
14 authors, click to expand affiliations / ORCID
Latreille Phil
Monsanto Company, 800 North Lindbergh Boulevard St. Louis, MO 63167, USA. jplatre@monsanto.com
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
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Article Info
Journal
BMC genomics
Abbr.
BMC Genomics
ISSN
1471-2164
DOI
10.1186/1471-2164-8-321
Email
jplatre@monsanto.com
Published
2007-09-14
Epub
2007-00-14
Pages
321
Language
English
Region
England
NLM ID
100965258
PMCID
PMC2045679
Subset
IM
External Links
PubMed source DOI: 10.1186/1471-2164-8-321 PMC Full Text View journal details
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