A complete BAC-based physical map of the Arabidopsis thaliana genome

Abstract

Arabidopsis thaliana is a small flowering plant that serves as the major model system in plant molecular genetics. The efforts of many scientists have produced genetic maps that provide extensive coverage of the genome (http://genome-www. stanford.edu/Arabidopsis/maps.html). Recently, detailed YAC, BAC, P1 and cosmid-based physical maps (that is, representations of genomic regions as sets of overlapping clones of corresponding libraries) have been established that extend over wide genomic areas ranging from several hundreds of kilobases to entire chromosomes. These maps provide an entry to gain deeper insight into the A. thaliana genome structure. A. thaliana has been chosen as the subject of the first large-scale project intended to determine the full genome sequence of a plant. This sequencing project, together with the increasing interest in map-based gene cloning, has highlighted the requirement for a complete and accurate physical map of this plant species. To supply the scientific community with a high-quality resource, we present here a complete physical map of A. thaliana using essentially the IGF BAC library. The map consists of 27 contigs that cover the entire genome, except for the presumptive centromeric regions, nucleolar organization regions (NOR) and telomeric areas. This is the first reported map of a complex organism based entirely on BAC clones and it represents the most homogeneous and complete physical map established to date for any plant genome. Furthermore, the analysis performed here serves as a model for an efficient physical mapping procedure using BAC clones that can be applied to other complex genomes.

The bacterial artificial chromosome (BAC) library of the narrow-leafed lupin (Lupinus angustifolius L.)

“…The new BAC library will be used to integrate genetic and physical mapping in lupin and to study the organization of plant genomes. Molecular cytogenetics can contribute to genome mapping through the assignment of genetic linkage groups to chromosomes [47,48]. Localization of BAC clones using fluorescence in situ hybridization (BAC-FISH) was shown to be an effective approach to physically map specific DNA sequences and develop chromosome-specific cytogenetic markers [49,50].…”

Comparative Physical Mapping Between Oryza sativa (AA Genome Type) and O. punctata (BB Genome Type)

“…FPC can assemble thousands of clone fingerprints into ''contigs,'' bundled together on the basis of their linear overlaps, evidenced by shared CBs. FPC maps have served crucial roles in genome research projects (Marra et al 1997;Mozo et al 1999 DNA was extracted from 36,864 BAC clones by a modified alkaline lysis method in a 96-well format. Briefly, BAC clones of O. punctata were inoculated into a deep 96-well plate (Marsh) containing 1.2 ml of 23 YT media plus 12.5 mg/ml chloramphenicol.…”

“…FPC can assemble thousands of clone fingerprints into ''contigs,'' bundled together on the basis of their linear overlaps, evidenced by shared CBs. FPC maps have served crucial roles in genome research projects (Marra et al 1997;Mozo et al 1999;International Human Genome Mapping Consortium 2001;Chen et al 2002) for map-based cloning, clone-byclone sequencing, or selecting a minimal tiling path of clones (Engler et al 2003).…”

Software for Automated Analysis of DNA Fingerprinting Gels

“…Maps constructed from fingerprinted large-insert bacterial clones (Marra et al 1997) have been constructed to support whole-genome and localized DNA sequencing activities, as well as gene cloning studies, in plants Mozo et al 1999;Tao et al 2001;Chen et al 2002), animals (McPherson et al 2001;Gregory et al 2002), the nematodes Caenorhabditis elegans (Coulson et al 1995;The C. elegans Genome Sequencing Consortium 1998) and Caenorhabditis briggsae (J. Schein and M. Marra, unpubl.…”