2nd TOMATO FINISHING WORKSHOP chromosome 9. Wageningen, April 24-25, 2008. CURRENT STATUS OF CHROMOSOME 9. Originally, 142 MARKERS -Most of them in heterocromatin -Very few associated to BACs -Gap of 46cM. New BACs anchored to chr9: -Syngenta data -Filter hybridization
Wageningen, April 24-25, 2008
Originally, 142 MARKERS
-Most of them in heterocromatin
-Very few associated to BACs
-Gap of 46cM
New BACs anchored to chr9:
-IL mapping of BACs at ramdom
12 BACs en HTG 1
33 BACs en HTG 2
20 BACs en HTG 3
COMPLETE 65 BACs
IN PROGRESS9 BACs
2 BACs sequencing
7 BACs in finishing pipeline
12 FPC data
5 mapping IL (chr12)
4 extending BACs
VERIFYING 35 BACs
extraction, fragmentation & reparation
sequencing(Big-dye terminator, AB3730)
~15 kb overlap/BAC
Phred, Phrap, Consed
read pair info
11 BACs were sequenced with 454-Roche technology
Elegibility criteria: size, difficulty (repeats, poli-A/T tails…), HTG phase
Results (100kb BAC, 15-20x):
-No risk of loosing parts during library construction
-In general, gaps are small
-It resolves A-T poli-tails but only if the coverage is high.
-If repeats are present the number of contigs increases substantially
-Sequencing stops when AT is repeated several times
-If ex. AAATTTTTTTTAAAAA, bases at both sides are not clear unless coverage is high
Some tomato jokes:
There were three tomatoes: a mum, a dad and a son. The son lagged behind and fell splat on the floor. His dad yelled to him, “Ketchup, son”.
A faucet, lettuce and a tomato were in a race... what happened? The faucet was running, the lettuce was ahead, and the tomato was trying to ketchup!
What is a tomato with a cloak?
What is a potato with a cloak?
A potato with a super-tomato costume