title: Genome physical mapping from large-insert clones by fingerprint analysis with capillary electrophoresis: a robust physical map of Penicillium chrysogenum.
abstract: Physical mapping with large-insert clones is becoming an active area of genomics research, and capillary electrophoresis (CE) promises to revolutionize the physical mapping technology. Here, we demonstrate the utility of the CE technology for genome physical mapping with large-insert clones by constructing a robust, binary bacterial artificial chromosome (BIBAC)-based physical map of Penicillium chrysogenum. We fingerprinted 23.1x coverage BIBAC clones with five restriction enzymes and the SNaPshot kit containing four fluorescent-ddNTPs using the CE technology, and explored various strategies to construct quality physical maps. It was shown that the fingerprints labeled with one or two colors, resulting in 40-70 bands per clone, were assembled into much better quality maps than those labeled with three or four colors. The selection of fingerprinting enzymes was crucial to quality map construction. From the dataset labeled with ddTTP-dROX, we assembled a physical map for P.chrysogenum, with 2-3 contigs per chromosome and anchored the map to its chromosomes. This map represents the first physical map constructed using the CE technology, thus providing not only a platform for genomic studies of the penicillin-producing species, but also strategies for efficient use of the CE technology for genome physical mapping of plants, animals and microbes.
authors.affiliation: Department of Soil and Crop Sciences, Texas A&M University College Station, TX 77843, USA.
authors.forename: Zhanyou
authors.initials: Z
authors.lastname: Xu
authors.forename: Marco A
authors.initials: MA
authors.lastname: van den Berg
authors.forename: Chantel
authors.initials: C
authors.lastname: Scheuring
authors.forename: Lina
authors.initials: L
authors.lastname: Covaleda
authors.forename: Hong
authors.initials: H
authors.lastname: Lu
authors.forename: Felipe A
authors.initials: FA
authors.lastname: Santos
authors.forename: Taesik
authors.initials: T
authors.lastname: Uhm
authors.forename: Mi-Kyung
authors.initials: MK
authors.lastname: Lee
authors.forename: Chengcang
authors.initials: C
authors.lastname: Wu
authors.forename: Steve
authors.initials: S
authors.lastname: Liu
authors.forename: Hong-Bin
authors.initials: HB
authors.lastname: Zhang
mesh_terms: D022202:Chromosomes, Artificial, Bacterial; D003001:Cloning, Molecular; D020451:Contig Mapping; D019075:Electrophoresis, Capillary; D016681:Genome, Fungal; D015698:Genomic Library; D010408:Penicillium chrysogenum / Q000235:genetics*; D020161:Physical Chromosome Mapping / Q000379:methods*; D017422:Sequence Analysis, DNA