SOL 2007 - Jeju Island, Korea 14th September 2007 Chromosome Standards Discussion SOL 2007 - Jeju Island, Korea 14th September 2007 Wellcome Trust Medical Photographic Library

The need for chromosome standards What do we (the community/users) want? Wellcome Trust Medical Photographic Library

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 Wellcome Trust Medical Photographic Library

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. Wellcome Trust Medical Photographic Library

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 Wellcome Trust Medical Photographic Library

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 Wellcome Trust Medical Photographic Library

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 Wellcome Trust Medical Photographic Library

Wellcome Trust Medical Photographic Library

Finishing Standards Discussion http://docs.google.com/View.aspx?docid=dggs4r6k_1dd5p56 General Strategy Expected Steps Minimum Standard for HTGS Phase 3 clone Quality Control Contamination Reasonable attempts for repeats Misc_feature tags and wording Wellcome Trust Medical Photographic Library

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. Wellcome Trust Medical Photographic Library

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? Wellcome Trust Medical Photographic Library

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 Wellcome Trust Medical Photographic Library