Whole-genome shotgun optical mapping of Rhodospirillum rubrum
- Univ. Wisc.-Madison
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.
- Research Organization:
- Board of the Regents of the University of Wisconsin System
- Sponsoring Organization:
- USDOE
- DOE Contract Number:
- FC02-01ER63175
- OSTI ID:
- 1088021
- Report Number(s):
- DOE/ER63175- Final Report
- Journal Information:
- Appl. Environ. Microbiol., Vol. 71, Issue 0
- Country of Publication:
- United States
- Language:
- English
Similar Records
Whole-genome shotgun optical mapping of Rhodobacter sphaeroides strain 2.4. 1 and its use for whole-genome shotgun sequence assembly
Complete genome sequence of Rhodospirillum rubrum type strain (S1T)