Physical maps of mouse, medaka, sugar beet …. and ... · Pooled 35mer oligo probes on...
Transcript of Physical maps of mouse, medaka, sugar beet …. and ... · Pooled 35mer oligo probes on...
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Heinz HimmelbauerMax-Planck-Institute of
Molecular GeneticsBerlin, Germany
Physical maps of mouse, medaka, sugar beet …. and Physcomitrella
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Construction of a physical YAC/BAC map
of the mouse genome
IRS-PCR principle and application
Probe A Probe B
Strain X
Strain Y
IRS-products fromYAC pool DNA
IRS-products fromRH line DNA
IRS-products fromgenetic cross DNA
YAC clones Position onRH map
Position ongenetic map
YAC pool filter hybridisation
Scoring tool for data entry
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Advanced mouse YAC map including BAC frameworkdata access at www.molgen.mpg.de/~rodent
- Browse the map- Identify map intervals and clones- Obtain clones and markers- Query database- Download data
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Phylogenetic position of the medaka
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Probe poolplate1/A5-H5
Probe poolplate1/B1-B6
Pooled 35mer oligo probes on 36,864-clone medaka BAC array
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Total number of medaka BAC map segments (mapped, ambiguous, unmapped)1st generation map (January 2004)
464 4299
758
88
1878
0
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M A Un
ProbesMap segments
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Sugar beet (Beta vulgaris) BAC mapProject launched Sept 1st, 2004
Goal:
Phase-1 map:
* 10,000 probes (ESTs, BAC ends, genetically mapped markers) as 35-mer oligos* mapped onto 37,000 BACs (120 kb avg. insert size / 5 x coverage)* 1000 contigs, 800 kb avg. length
Phase-2 map* Further 2000 probes from contig ends* additional Bac resources (avg. insert size 160 kb)* final product: 500 contigs, 1.6 Mb avg. length
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Proposal for a Physcomitrella BAC map
Assumption: BAC library (36,000 clones avg. insert size 120 kb, 8.4 x coverage) available
Phase-1 map:
* 6000 BAC end probes (3000 BAC clones) as 35-mer oligos* 1000 ESTs* ~ 700 contigs, ~700 kb avg. length* ~ ~1500 genetically mapped markers are needed
Phase-2 map* Further 1400 probes from contig ends* final product: ~350 contigs, ~1.4 Mb avg. length