An Anchored Framework BAC Map of Mouse Chromosome 11 Assembled Using Multiplex Oligonucleotide Hybridization

Cai, Wei-Wen; Reneker, Jeffrey; Chow, Chi-Wan; Vaishnav, Milan; Bradley, Allan

doi:10.1006/geno.1998.5620

Cited by 75 publications

(51 citation statements)

References 45 publications

(39 reference statements)

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“…A total of 10 genome equivalents of G. raimondii BACs has been fingerprinted using standard procedures (Marra et al, 1997). All genetically mapped probes have been incorporated into the fingerprint assembly using the overlapping oligonucleotides hybridization method (Cai et al, 1998). The assembly will be publicly available via a WebFPC site and incorporated into the existing BACMan resource at the Plant Genome Mapping Laboratory (www.plantgenome.uga.edu).…”

Section: What Resources Are Available?mentioning

confidence: 99%

Toward Sequencing Cotton (Gossypium) Genomes: Figure 1.

et al. 2007

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Despite rapidly decreasing costs and innovative technologies, sequencing of angiosperm genomes is not yet undertaken lightly. Generating larger amounts of sequence data more quickly does not address the difficulties of sequencing and assembling complex genomes de novo. The cotton (Gossypium spp.) genomes represent a challenging case. To this end, a coalition of cotton genome scientists has developed a strategy for sequencing the cotton genomes, which will vastly expand opportunities for cotton research and improvement worldwide.

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Section: What Resources Are Available?mentioning

confidence: 99%

Toward Sequencing Cotton (Gossypium) Genomes: Figure 1.

et al. 2007

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“…The fingerprints are used in selecting subsequent BACs for BAC-by-BAC sequencing. To anchor BACs to the linkage map "Tomato-EXPEN 2000" and construct a tomato physical map , DNA fragments from the fingerprinted BACs were hybridized to 1536 overlapping oligonucleotide (called "overgo") probes (Cai et al 1998) generated from markers mapped on the current high density linkage map. The overgo probes that matched to one or more BACs are referred to as "anchor points".…”

Section: Linkage Maps With Dna Markersmentioning

confidence: 99%

Genomic Databases for Tomato

Yano

Aoki

Shibata

2007

Plant Biotechnology

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“…In large genomes, however, hundreds of thousands of BESs are needed. DNA hybridization and PCRbased anchoring (6,7,20,21) is laborious and often produces equivocal results. Contig anchoring with highly multiplexed Illumina GoldenGate SNP assays overcomes some of these limitations (22), but its relatively high cost limits the number of markers that can be used.…”

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confidence: 99%

A 4-gigabase physical map unlocks the structure and evolution of the complex genome of Aegilops tauschii, the wheat D-genome progenitor

Luo

You

et al. 2013

Proc. Natl. Acad. Sci. U.S.A.

198

259

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The current limitations in genome sequencing technology require the construction of physical maps for high-quality draft sequences of large plant genomes, such as that of Aegilops tauschii, the wheat D-genome progenitor. To construct a physical map of the Ae. tauschii genome, we fingerprinted 461,706 bacterial artificial chromosome clones, assembled contigs, designed a 10K Ae. tauschii Infinium SNP array, constructed a 7,185-marker genetic map, and anchored on the map contigs totaling 4.03 Gb. Using whole genome shotgun reads, we extended the SNP marker sequences and found 17,093 genes and gene fragments. We showed that collinearity of the Ae. tauschii genes with Brachypodium distachyon, rice, and sorghum decreased with phylogenetic distance and that structural genome evolution rates have been high across all investigated lineages in subfamily Pooideae, including that of Brachypodieae. We obtained additional information about the evolution of the seven Triticeae chromosomes from 12 ancestral chromosomes and uncovered a pattern of centromere inactivation accompanying nested chromosome insertions in grasses. We showed that the density of noncollinear genes along the Ae. tauschii chromosomes positively correlates with recombination rates, suggested a cause, and showed that new genes, exemplified by disease resistance genes, are preferentially located in high-recombination chromosome regions. (2), and 90% of its genome was estimated to be repetitive DNA (3). The Ae. tauschii genome and the D genome of hexaploid wheat are closely related due to the recent origin of hexaploid wheat (4). Ae. tauschii is therefore an important resource for wheat breeding, and its genome is an invaluable reference for wheat genomics, as illustrated by the utility of its sequences in the analysis of the wheat gene space (5). The utility of Ae. tauschii for wheat genetics and genomics would be further enhanced by a high-quality draft sequence of its genome. With current technology, the only approach to produce a high-quality de novo draft sequence for a genome of this size and complexity is the orderedclone sequencing approach, which requires a physical map.Physical map construction necessitates fingerprinting multiple genome equivalents of bacterial artificial chromosome (BAC) clones, assembling them into contigs, and anchoring the contigs on a genetic map (6-8). Great strides have been made in BAC fingerprinting techniques (7, 9-12) and software for fingerprint editing and contig assembly (13-16). It is now possible with these technological advances to fingerprint and assemble contigs from hundreds of thousands of BAC clones (7,8,(17)(18)(19). In contrast, contig anchoring remains a weakness in physical mapping of large plant genomes because of their low gene density, extensive gene duplication, and abundance of repetitive DNA. BAC end sequences (BESs) are an effective means of contig anchoring in small genomes (11). In large genomes, however, hundreds of thousands of BESs are needed. DNA hybridization and PCRbased anchoring (6,7,20,21)...

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An Anchored Framework BAC Map of Mouse Chromosome 11 Assembled Using Multiplex Oligonucleotide Hybridization

Cited by 75 publications

References 45 publications

Toward Sequencing Cotton (Gossypium) Genomes: Figure 1.

Toward Sequencing Cotton (Gossypium) Genomes: Figure 1.

Genomic Databases for Tomato

A 4-gigabase physical map unlocks the structure and evolution of the complex genome of Aegilops tauschii, the wheat D-genome progenitor

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