Raw notes from the tomato session, Dundee, Sept 7, 2010, 20:30

1. Assembly (Sandra Smit)

Giovanni presented most of it during his talk - assembly basically done and now at version 2.3. Assembled 781MB of data, on 3200 scaffold, 95% of data is in 100 scaffolds which were mapped to the chromosomes (91 placed and oriented, containing 97% of the data). chromosomes between 55 and 95% done.

Longest scaffold is 42MB.

454 data shotgun and paired end, + Sanger sequence
base error correction using Solexa and SOLiD datasets
gaps filled in assembly
Sanger clone end sequences for long range scaffolding (a lot of data was linked by this)
Available full BAC sequences (phase 2+3) were integrated (99% of BACs integrated).
2 physical maps and 1 genetic maps used to create pseudomolecules

each country checked their chromosome

Q: what is the missing sequence
A: Probably repetitive sequences. Interscaffold gaps are more difficult to size etc.

Q: how many ESTs are in the sequence?
A: Previously, > 95%. Current

2. Annotation (Lukas)

ITAG annotation still ongoing, structural genes are finished, functional annotation still running.

3. Paper (Dani)

Potato is a bit further ahead. Potato should go whenever they are ready.
First responsibility to produce best product possible and doing nice analyses that tell an interesting story, which may take some time.

Comparative elements with potato will be part of the tomato paper.

Tomato paper will also contain the pimpinellifolium sequence (wild ancestor of cultivated tomato), done at CSHL (Zach Lippman) . Pimp/Lycopersicum inbred lines are available (same pimp was used in sequencing project). Problem: Lack of polymorphisms. Population has been grown already.

figure one will have representative chromosome, linearized pachytene chromosomes, fish data, annotations of repeats, ESTs, transposons, etc, on pseudomolecule, genetic map, recombination module map.

Rest of the figures should highlight biological elements. Comparing pimp to cultivated tomato, SNP distribution, genome organization etc. whole genome duplication (done by Andy Paterson).

Giovanni, Jim, Graham, Dani look at fruit specific genes.

Synaptonemal complexes in interspecific crosses already visible with pimp.

Q (Klaus): What is part of the tomato - potato comparison in the tomato paper?
A: It's going to be a more technical comparison of the assemblies... Mainly it's going to be comparisons with pimp, unless there are very compelling stories with potato.


What's next? (Rene)

How can we improve the chromsome down the line? EU-SOL is a little bit in a hurry, because funding ends in May next year.
There will be a Schiphol meeting at the beginning of October.

Comment (by Jane Rogers): Chromosome 4 is already doing some finishing.

Jim: We have the funding to do the gold standard now. We will not get it again.

Comment: (Gerard Bishop): Every transcript sequenced should map to a genome sequence. That would be more important than finishing random gaps.

How many ESTs map to chromosome 0? -- A: chromosome 0 contains only very short pieces, so not very likely that much maps there.

Jim: We have tried to map chromosome 0 pieces... very difficult to map them (20 tried, only 2 successful).

Q: (Cornelius Barry): does chromosome 0 contain BACs? A: no full bACs, but there are BAC ends that map there.