physical maps of mouse, medaka, sugar beet …. and ... · pooled 35mer oligo probes on...
TRANSCRIPT
Heinz HimmelbauerMax-Planck-Institute of
Molecular GeneticsBerlin, Germany
Physical maps of mouse, medaka, sugar beet …. and Physcomitrella
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
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
Phylogenetic position of the medaka
Probe poolplate1/A5-H5
Probe poolplate1/B1-B6
Pooled 35mer oligo probes on 36,864-clone medaka BAC array
Total number of medaka BAC map segments (mapped, ambiguous, unmapped)1st generation map (January 2004)
464 4299
758
88
1878
0
200
400
600
800
1000
1200
1400
1600
1800
2000
M A Un
ProbesMap segments
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
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