Research output: Contribution to journal › Article › peer-review
Whole-genome shotgun optical mapping of Rhodospirillum rubrum. / 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.
In: Applied and Environmental Microbiology, Vol. 71, No. 9, 09.2005, p. 5511-5522.Research output: Contribution to journal › Article › peer-review
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TY - JOUR
T1 - Whole-genome shotgun optical mapping of Rhodospirillum rubrum
AU - Reslewic, Susan
AU - Zhou, Shiguo
AU - Place, Mike
AU - Zhang, Yaoping
AU - Briska, Adam
AU - Goldstein, Steve
AU - Churas, Chris
AU - Runnheim, Rod
AU - Forrest, Dan
AU - Lim, Alex
AU - Lapidus, Alla
AU - Han, Cliff S.
AU - Roberts, Gary P.
AU - Schwartz, David C.
PY - 2005/9
Y1 - 2005/9
N2 - 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 A. 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.
AB - 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 A. 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.
UR - http://www.scopus.com/inward/record.url?scp=25144504991&partnerID=8YFLogxK
U2 - 10.1128/AEM.71.9.5511-5522.2005
DO - 10.1128/AEM.71.9.5511-5522.2005
M3 - Article
C2 - 16151144
AN - SCOPUS:25144504991
VL - 71
SP - 5511
EP - 5522
JO - Applied Microbiology
JF - Applied Microbiology
SN - 0099-2240
IS - 9
ER -
ID: 90038391