Whole-genome shotgun optical mapping of rhodospirillumrubrum

Journal Article · Thu Jul 01 04:00:00 EDT 2004 · Applied and Environmental Microbiology

OSTI ID:861355

Reslewic, Susan; Zhou, Shiguo; Place, Mike; Zhang, Yaoping; Briska, Adam; Goldstein, Steve; Churas, Chris; Runnheim, Rod; Forrest, Dan; Lim, Alex; Lapidus, Alla; Han, Cliff S; Roberts, Gary P; Schwartz, David C

Rhodospirillum rubrum is a phototrophic purple non-sulfur bacterium known for its unique and well-studied nitrogen fixation and carbon monoxide oxidation systems, and as a source of hydrogen and biodegradable plastics production. To better understand this organism and to facilitate assembly of its sequence, three whole-genome restriction maps (Xba I, Nhe I, and Hind III) of R. rubrum strain ATCC 11170 were created by optical mapping. Optical mapping is a system for creating whole-genome ordered restriction maps from randomly sheared genomic DNA molecules extracted directly from cells. During the sequence finishing process, all three optical maps confirmed a putative error in sequence assembly, while the Hind III map acted as a scaffold for high resolution alignment with sequence contigs spanning the whole genome. In addition to highlighting optical mapping's role in the assembly and validation of genome sequence, our work underscores the unique niche in resolution occupied by the optical mapping system. With a resolution ranging from 6.5 kb (previously published) to 45 kb (reported here), optical mapping advances a ''molecular cytogenetics'' approach to solving problems in genomic analysis.

• Research Organization: Ernest Orlando Lawrence Berkeley NationalLaboratory, Berkeley, CA (US)
• Sponsoring Organization: USDOE Director. Office of Science. Office of Biological andEnvironmental Research; National Institutes of Health Grants 2R01-HG000225-10 and 5 T32 GM08349 and GM65891
• DOE Contract Number: AC02-05CH11231
• OSTI ID: 861355
• Report Number(s): LBNL--56606; BnR: KP1103010
• Journal Information: Applied and Environmental Microbiology, Journal Name: Applied and Environmental Microbiology Journal Issue: 9 Vol. 71; ISSN AEMIDF; ISSN 0099-2240
• Country of Publication: United States
• Language: English

Related Subjects

08 HYDROGEN
60 APPLIED LIFE SCIENCES
ALIGNMENT
CARBON MONOXIDE
CONTIGS
DNA
HYDROGEN
NITROGEN FIXATION
OXIDATION
PLASTICS
PRODUCTION
RESOLUTION
RHODOSPIRILLUM
STRAINS
VALIDATION