title: A first generation physical map of the medaka genome in BACs essential for positional cloning and clone-by-clone based genomic sequencing.
abstract: In order to realize the full potential of the medaka as a model system for developmental biology and genetics, characterized genomic resources need to be established, culminating in the sequence of the medaka genome. To facilitate the map-based cloning of genes underlying induced mutations and to provide templates for clone-based genomic sequencing, we have created a first-generation physical map of the medaka genome in bacterial artificial chromosome (BAC) clones. In particular, we exploited the synteny to the closely related genome of the pufferfish, Takifugu rubripes, by marker content mapping. As a first step, we clustered 103,144 public medaka EST sequences to obtain a set of 21,121 non-redundant sequence entities. Avoiding oversampling of gene-dense regions, 11,254 of EST clusters were successfully matched against the draft sequence of the fugu genome, and 2363 genes were selected for the BAC map project. We designed 35mer oligonucleotide probes from the selected genes and hybridized them against 64,500 BAC clones of strains Cab and Hd-rR, representing 14-fold coverage of the medaka genome. Our data set is further supplemented with 437 results generated from PCR-amplified inserts of medaka cDNA clones and BAC end-fragment markers. Our current, edited, first generation medaka BAC map consists of 902 map segments that cover about 74% of the medaka genome. The map contains 2721 markers. Of these, 2534 are from expressed sequences, equivalent to a non-redundant set of 2328 loci. The 934 markers (724 different) are anchored to the medaka genetic map. Thus, genetic map assignments provide immediate access to underlying clones and contigs, simplifying molecular access to candidate gene regions and their characterization.
authors.affiliation: Department of Vertebrate Genomics, Max-Planck-Institute of Molecular Genetics, Ihnestrasse 73, 14195 Berlin, Dahlem, Germany.
authors.forename: Maryam Zadeh
authors.initials: MZ
authors.lastname: Khorasani
authors.forename: Steffen
authors.initials: S
authors.lastname: Hennig
authors.forename: Gabriele
authors.initials: G
authors.lastname: Imre
authors.forename: Shuichi
authors.initials: S
authors.lastname: Asakawa
authors.forename: Stefanie
authors.initials: S
authors.lastname: Palczewski
authors.forename: Anja
authors.initials: A
authors.lastname: Berger
authors.forename: Hiroshi
authors.initials: H
authors.lastname: Hori
authors.forename: Kiyoshi
authors.initials: K
authors.lastname: Naruse
authors.forename: Hiroshi
authors.initials: H
authors.lastname: Mitani
authors.forename: Akihiro
authors.initials: A
authors.lastname: Shima
authors.forename: Hans
authors.initials: H
authors.lastname: Lehrach
authors.forename: Jochen
authors.initials: J
authors.lastname: Wittbrodt
authors.forename: Hisato
authors.initials: H
authors.lastname: Kondoh
authors.forename: Nobuyoshi
authors.initials: N
authors.lastname: Shimizu
authors.forename: Heinz
authors.initials: H
authors.lastname: Himmelbauer
mesh_terms: D000818:Animals; D022202:Chromosomes, Artificial, Bacterial; D019295:Computational Biology; D015342:DNA Probes; D005819:Genetic Markers; D016678:Genome; D009990:Oryzias / Q000196:embryology / Q000235:genetics*; D020161:Physical Chromosome Mapping
chemical_list: D015342:DNA Probes; D005819:Genetic Markers