Whole-genome Shotgun Optical Mapping of Rhodospirillum Rubrum

Overview

Journal Appl Environ Microbiol

Specialties Environmental Health
Microbiology

Date 2005 Sep 10

PMID 16151144

Citations 41

Authors

Susan Reslewic

Shiguo Zhou

Mike Place

Yaoping Zhang

Adam Briska

Steve Goldstein

Chris Churas

Rod Runnheim

Dan Forrest

Alex Lim

Alla Lapidus

Cliff S Han

Gary P Roberts

David C Schwartz

Affiliations

Soon will be listed here.

Abstract

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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