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Whole-Genome Shotgun Optical Mapping of Rhodospirillum rubrum

Laboratory for Molecular and Computational Genomics, University of Wisconsin—Madison, Madison, Wisconsin 53706,¹ Department of Chemistry, University of Wisconsin—Madison, Madison, Wisconsin 53706,² Department of Bacteriology, University of Wisconsin—Madison, Madison, Wisconsin 53706,³ OpGen, Inc., Madison, Wisconsin, 53719,⁴ Microbial Genomics, Department of Energy Joint Genome Institute, Walnut Creek, California 94598,⁵ Los Alamos National Laboratory Center for Human Genome Studies, Los Alamos, New Mexico 87545,⁶ Laboratory of Genetics, University of Wisconsin—Madison, Madison, Wisconsin 53706⁷

Received 9 January 2005/ Accepted 11 April 2005

Rhodospirillum rubrum is a phototrophic purple nonsulfur bacterium known for its unique and well-studied nitrogen fixation and carbon monoxide oxidation systems and as a source of hydrogen and biodegradable plastic production. To better understand this organism and to facilitate assembly of its sequence, three whole-genome restriction endonuclease maps (XbaI, NheI, and HindIII) of R. rubrum strain ATCC 11170 were created by optical mapping. Optical mapping is a system for creating whole-genome ordered restriction endonuclease maps from randomly sheared genomic DNA molecules extracted from cells. During the sequence finishing process, all three optical maps confirmed a putative error in sequence assembly, while the HindIII 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 confirmation of genome sequence, this 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.

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