1. SOL 2007 - Jeju Island, Korea 14th September 2007
Chromosome Standards Discussion
SOL Jeju Island, Korea 14th September 2007
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2. The need for chromosome standards
What do we (the community/users) want?
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3. The need for chromosome standards
Helps to direct each centre’s approach for the project.
Parity across final product - important when project is worked on by a consortium.
The final genome needs to appear cohesive and be of equal quality.
Quality of tomato genome as a reference will be essential for future initiatives eg SOL-100
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4. The need for chromosome standards (cont.)
Essential for good annotation and subsequent analysis.
Important for the community to be able to understand the product they are given.
All members of the consortium need to be in agreement about these basic principles.
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5. Key Areas - Chromosomes
TPF files
Benefit that each centre can control their current minimal tile path set.
BAC Registry and Public databases will contain more than the non-redundant clone set by the end of the project.
Inevitable changes will be represented with each monthly submission.
Allows for representation of heterochromatic blocks both in position and size if known.
Files will also become a resource for the community.
AGP files
Data sets can be assessed whilst the project is in progress
AGP files and similar can be used to make perform an assembly of the current sequence on genome. Used in Medicago.
Good method for quality control of content of genome
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6. Key Areas (cont.) - Clones
Finishing Standards
Finishing mail alias has been set up - some discussion but limited traffic currently
Finishing Standards Document Updated in April 07
Finishing Workshop held in UK in April 2007
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7. Workshop Delegates – Not all chromosomes represented
Chrm 1, 10 and 11
Lukas Mueller
SGN/Cornell
Chrm 4
Karen McLaren, Helen Beasley, Jo Collins
WTSI
Chrm 6
Marjo van Staveren, Marleen Henkens, Elio Schijlen, René Klein-Lankhorst
Plant Research International, Wageningen
Chrm 7
Farid Regad, Mohamed Zouine, Mondher Bouzayen
INRA/INP-ENSAT
Chrm 9
Sheila Zuñiga
Sistemas Genómicos
Chrm 12
Alessandro Vezzi
University of Padua
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8. Wellcome Trust Medical Photographic Library

9. Finishing Standards Discussion
General Strategy
Expected Steps
Minimum Standard for HTGS Phase 3 clone
Quality Control
Contamination
Reasonable attempts for repeats
Misc_feature tags and wording
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10. Conclusions from workshop
Use of restriction digest data is essential for the clones
Contamination screen is essential – with both the centres and SGN checking
There was agreement that TPF and AGP files would be submitted by all by end of June.
Have you submitted yours?
Minimum expectation and Phase 3 standards document is still under discussion.
Requirement for a QA exercise for the tomato genome.
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11. On-going issues
Do we have general agreement that we need a standard to which all chromosomes and clones will be completed?
Discussion regarding the details of the finishing standards document requires all chromosomes taking part.
What is the best mechanism for this?
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12. Possible mechanisms Let’s get the data out there.
Publish version 1 of the sequencing status.
Perhaps accompanied as a submission to a journal?
Help identify the key issues to be addressed.
I.e. sequence standards, publication of data at EMBL/GENBANK/DDBJ and SGN
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