title: A bacterial artificial chromosome based physical map of the Ustilago maydis genome.
abstract: Ustilago maydis, a basidiomycete, is a model organism among phytopathogenic fungi. A physical map of U. maydis strain 521 was developed from bacterial artificial chromosome (BAC) clones. BAC fingerprints used polyacrylamide gel electrophoresis to separate restriction fragments. Fragments were labeled at the HindIII site and co-digested with HaeIII to reduce fragments to 50-750 bp. Contiguous overlapping sets of clones (contigs) were assembled at nine stringencies (from P < or = 1 x 10(-6) to 1 x 10(-24)). Each assembly nucleated contigs with different percentages of bands overlapping between clones (from 20% to 97%). The number of clones per contig decreased linearly from 41 to 12 from P < or = 1 x 10(-7) to 1 x 10 (-12). The number of separate contigs increased from 56 to 150 over the same range. A hybridization-based physical map of the same BAC clones was compared with the fingerprint contigs built at P < or = 1 x 10(-7). The two methods provided consistent physical maps that were largely validated by genome sequence. The combined hybridization and fingerprint physical map provided a minimum tile path composed of 258 BAC clones (18-20 Mbp) distributed among 28 merged contigs. The genome of U. maydis was estimated to be 20.5 Mbp by pulsed-field gel electrophoresis and 24 Mbp by BAC fingerprints. There were 23 separate chromosomes inferred by both pulsed-field gel electrophoresis and fingerprint contigs. Only 11 of the tile path BAC clones contained recognizable centromere, telomere, and subtelomere repeats (high-copy DNA), suggesting that repeats caused some false merges. There were 247 tile path BAC clones that encompassed about 17.5 Mbp of low-copy DNA sequence. BAC clones are available for repeat and unique gene cluster analysis including tDNA-mediated transformation. Program FingerPrint Contigs maps aligned with each chromosome can be viewed at http://www.siu.edu/~meksem/ustilago_maydis/.
authors.affiliation: Plants and Microbes Genomic and Genetics Laboratory, Department of Plant Soil and Agricultural Systems, Southern Illinois University at Carbondale, IL 62901-4415, USA. meksemk@siu.edu
authors.forename: Khalid
authors.initials: K
authors.lastname: Meksem
authors.forename: Jeffry
authors.initials: J
authors.lastname: Shultz
authors.forename: Faiza
authors.initials: F
authors.lastname: Tebbji
authors.forename: Aziz
authors.initials: A
authors.lastname: Jamai
authors.forename: Jürgen
authors.initials: J
authors.lastname: Henrich
authors.forename: Harald
authors.initials: H
authors.lastname: Kranz
authors.forename: Monika
authors.initials: M
authors.lastname: Arenz
authors.forename: Thomas
authors.initials: T
authors.lastname: Schlueter
authors.forename: Hirofumi
authors.initials: H
authors.lastname: Ishihara
authors.forename: Lavu N
authors.initials: LN
authors.lastname: Jyothi
authors.forename: Hong-Bin
authors.initials: HB
authors.lastname: Zhang
authors.forename: David A
authors.initials: DA
authors.lastname: Lightfoot
mesh_terms: D022202:Chromosomes, Artificial, Bacterial / Q000235:genetics*; D015825:Chromosomes, Fungal / Q000235:genetics*; D020451:Contig Mapping; D016681:Genome, Fungal; D015698:Genomic Library; D014588:Ustilago / Q000235:genetics*