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

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.

Mozo T ，Dewar K ，Dunn P ，Ecker JR ，Fischer S ，Kloska S ，Lehrach H ，Marra M ，Martienssen R ，Meier-Ewert S ，Altmann T ... -  《NATURE GENETICS》

zA map for sequence analysis of the Arabidopsis thaliana genome.

Arabidopsis thaliana has emerged as a model system for studies of plant genetics and development, and its genome has been targeted for sequencing by an international consortium (the Arabidopsis Genome Initiative; http://genome-www. stanford.edu/Arabidopsis/agi.html). To support the genome-sequencing effort, we fingerprinted more than 20,000 BACs (ref. 2) from two high-quality publicly available libraries, generating an estimated 17-fold redundant coverage of the genome, and used the fingerprints to nucleate assembly of the data by computer. Subsequent manual revision of the assemblies resulted in the incorporation of 19,661 fingerprinted BACs into 169 ordered sets of overlapping clones ('contigs'), each containing at least 3 clones. These contigs are ideal for parallel selection of BACs for large-scale sequencing and have supported the generation of more than 5.8 Mb of finished genome sequence submitted to GenBank; analysis of the sequence has confirmed the integrity of contigs constructed using this fingerprint data. Placement of contigs onto chromosomes can now be performed, and is being pursued by groups involved in both sequencing and positional cloning studies. To our knowledge, these data provide the first example of whole-genome random BAC fingerprint analysis of a eucaryote, and have provided a model essential to efforts aimed at generating similar databases of fingerprint contigs to support sequencing of other complex genomes, including that of human.

Marra M ，Kucaba T ，Sekhon M ，Hillier L ，Martienssen R ，Chinwalla A ，Crockett J ，Fedele J ，Grover H ，Gund C ，McCombie WR ，McDonald K ，McPherson J ，Mudd N ，Parnell L ，Schein J ，Seim R ，Shelby P ，Waterston R ，Wilson R ... -  《NATURE GENETICS》

Analysis of 1.9 Mb of contiguous sequence from chromosome 4 of Arabidopsis thaliana.

The plant Arabidopsis thaliana (Arabidopsis) has become an important model species for the study of many aspects of plant biology. The relatively small size of the nuclear genome and the availability of extensive physical maps of the five chromosomes provide a feasible basis for initiating sequencing of the five chromosomes. The YAC (yeast artificial chromosome)-based physical map of chromosome 4 was used to construct a sequence-ready map of cosmid and BAC (bacterial artificial chromosome) clones covering a 1.9-megabase (Mb) contiguous region, and the sequence of this region is reported here. Analysis of the sequence revealed an average gene density of one gene every 4.8 kilobases (kb), and 54% of the predicted genes had significant similarity to known genes. Other interesting features were found, such as the sequence of a disease-resistance gene locus, the distribution of retroelements, the frequent occurrence of clustered gene families, and the sequence of several classes of genes not previously encountered in plants.

Bevan M ，Bancroft I ，Bent E ，Love K ，Goodman H ，Dean C ，Bergkamp R ，Dirkse W ，Van Staveren M ，Stiekema W ，Drost L ，Ridley P ，Hudson SA ，Patel K ，Murphy G ，Piffanelli P ，Wedler H ，Wedler E ，Wambutt R ，Weitzenegger T ，Pohl TM ，Terryn N ，Gielen J ，Villarroel R ，De Clerck R ，Van Montagu M ，Lecharny A ，Auborg S ，Gy I ，Kreis M ，Lao N ，Kavanagh T ，Hempel S ，Kotter P ，Entian KD ，Rieger M ，Schaeffer M ，Funk B ，Mueller-Auer S ，Silvey M ，James R ，Montfort A ，Pons A ，Puigdomenech P ，Douka A ，Voukelatou E ，Milioni D ，Hatzopoulos P ，Piravandi E ，Obermaier B ，Hilbert H ，Düsterhöft A ，Moores T ，Jones JD ，Eneva T ，Palme K ，Benes V ，Rechman S ，Ansorge W ，Cooke R ，Berger C ，Delseny M ，Voet M ，Volckaert G ，Mewes HW ，Klosterman S ，Schueller C ，Chalwatzis N ... -  《NATURE》

A BAC-based physical map of the apple genome.

Genome-wide physical mapping is an essential step toward investigating the genetic basis of complex traits as well as pursuing genomics research of virtually all plant and animal species. We have constructed a physical map of the apple genome from a total of 74,281 BAC clones representing approximately 10.5x haploid genome equivalents. The physical map consists of 2702 contigs, and it is estimated to span approximately 927 Mb in physical length. The reliability of contig assembly was evaluated by several methods, including assembling contigs using variable stringencies, assembling contigs using fingerprints from individual libraries, checking consensus maps of contigs, and using DNA markers. Altogether, the results demonstrated that the contigs were properly assembled. The apple genome-wide BAC-based physical map represents the first draft genome sequence not only for any member of the large Rosaceae family, but also for all tree species. This map will play a critical role in advanced genomics research for apple and other tree species, including marker development in targeted chromosome regions, fine-mapping and isolation of genes/QTL, conducting comparative genomics analyses of plant chromosomes, and large-scale genomics sequencing.

Han Y ，Gasic K ，Marron B ，Beever JE ，Korban SS ... -  《GENOMICS》

A physical map of the highly heterozygous Populus genome: integration with the genome sequence and genetic map and analysis of haplotype variation.

As part of a larger project to sequence the Populus genome and generate genomic resources for this emerging model tree, we constructed a physical map of the Populus genome, representing one of the few such maps of an undomesticated, highly heterozygous plant species. The physical map, consisting of 2802 contigs, was constructed from fingerprinted bacterial artificial chromosome (BAC) clones. The map represents approximately 9.4-fold coverage of the Populus genome, which has been estimated from the genome sequence assembly to be 485 +/- 10 Mb in size. BAC ends were sequenced to assist long-range assembly of whole-genome shotgun sequence scaffolds and to anchor the physical map to the genome sequence. Simple sequence repeat-based markers were derived from the end sequences and used to initiate integration of the BAC and genetic maps. A total of 2411 physical map contigs, representing 97% of all clones assigned to contigs, were aligned to the sequence assembly (JGI Populus trichocarpa, version 1.0). These alignments represent a total coverage of 384 Mb (79%) of the entire poplar sequence assembly and 295 Mb (96%) of linkage group sequence assemblies. A striking result of the physical map contig alignments to the sequence assembly was the co-localization of multiple contigs across numerous regions of the 19 linkage groups. Targeted sequencing of BAC clones and genetic analysis in a small number of representative regions showed that these co-aligning contigs represent distinct haplotypes in the heterozygous individual sequenced, and revealed the nature of these haplotype sequence differences.

Kelleher CT ，Chiu R ，Shin H ，Bosdet IE ，Krzywinski MI ，Fjell CD ，Wilkin J ，Yin T ，DiFazio SP ，Ali J ，Asano JK ，Chan S ，Cloutier A ，Girn N ，Leach S ，Lee D ，Mathewson CA ，Olson T ，O'connor K ，Prabhu AL ，Smailus DE ，Stott JM ，Tsai M ，Wye NH ，Yang GS ，Zhuang J ，Holt RA ，Putnam NH ，Vrebalov J ，Giovannoni JJ ，Grimwood J ，Schmutz J ，Rokhsar D ，Jones SJ ，Marra MA ，Tuskan GA ，Bohlmann J ，Ellis BE ，Ritland K ，Douglas CJ ，Schein JE ... -  《PLANT JOURNAL》