title: Whole-genome shotgun optical mapping of Rhodobacter sphaeroides strain 2.4.1 and its use for whole-genome shotgun sequence assembly.
abstract: Rhodobacter sphaeroides 2.4.1 is a facultative photoheterotrophic bacterium with tremendous metabolic diversity, which has significantly contributed to our understanding of the molecular genetics of photosynthesis, photoheterotrophy, nitrogen fixation, hydrogen metabolism, carbon dioxide fixation, taxis, and tetrapyrrole biosynthesis. To further understand this remarkable bacterium, and to accelerate an ongoing sequencing project, two whole-genome restriction maps (EcoRI and HindIII) of R. sphaeroides strain 2.4.1 were constructed using shotgun optical mapping. The approach directly mapped genomic DNA by the random mapping of single molecules. The two maps were used to facilitate sequence assembly by providing an optical scaffold for high-resolution alignment and verification of sequence contigs. Our results show that such maps facilitated the closure of sequence gaps by the early detection of nascent sequence contigs during the course of the whole-genome shotgun sequencing process.
authors.affiliation: Laboratory for Molecular and Computational Genomics, University of Wisconsin-Madison, UW Biotechnology Center, Madison, Wisconsin 53706, USA.
authors.forename: Shiguo
authors.initials: S
authors.lastname: Zhou
authors.forename: Erika
authors.initials: E
authors.lastname: Kvikstad
authors.forename: Andrew
authors.initials: A
authors.lastname: Kile
authors.forename: Jessica
authors.initials: J
authors.lastname: Severin
authors.forename: Dan
authors.initials: D
authors.lastname: Forrest
authors.forename: Rod
authors.initials: R
authors.lastname: Runnheim
authors.forename: Chris
authors.initials: C
authors.lastname: Churas
authors.forename: Jason W
authors.initials: JW
authors.lastname: Hickman
authors.forename: Chris
authors.initials: C
authors.lastname: Mackenzie
authors.forename: Madhusudan
authors.initials: M
authors.lastname: Choudhary
authors.forename: Timothy
authors.initials: T
authors.lastname: Donohue
authors.forename: Samuel
authors.initials: S
authors.lastname: Kaplan
authors.forename: David C
authors.initials: DC
authors.lastname: Schwartz
mesh_terms: D002876:Chromosomes, Bacterial / Q000235:genetics; D020451:Contig Mapping / Q000379:methods; D005819:Genetic Markers / Q000235:genetics; D016680:Genome, Bacterial; D008856:Microscopy, Fluorescence; D055095:Optics and Photonics; D015183:Restriction Mapping / Q000379:methods*; D012242:Rhodobacter sphaeroides / Q000235:genetics*; D016415:Sequence Alignment / Q000379:methods; D017422:Sequence Analysis, DNA / Q000379:methods*; D013045:Species Specificity
chemical_list: D005819:Genetic Markers