[Fwd: subspecies information in submitted DNA sequences (tuli) (SUB#117690)]

[Pankaj Jaiswal]

datasubs at ebi.ac.uk wrote:
> 
> >Date: Thu, 14 Feb 2002 14:40:26 -0500
> >From: pj37 at cornell.edu
> >Reply-to:
> >To: Robin Buell <rbuell at tigr.org>, tsasaki at nias.affrc.go.jp,
> gb-admin at ncbi.nlm.nih.gov, DATASUBS at ebi.ac.uk, ddbjsub at ddbj.nig.ac.jp
> >Subject: subspecies information in submitted DNA sequences
> 
> >
> > Dear All,
> >
> > I have two suggestions and probably they are addressed to the Databases EBI,
> > GenBank and DDBJ and also to IRGSP members. This is in relation to the
> > subspecies for rice Oryza.
> >
> > The two groups doing rice genome sequencing are
> >
> > The IRGSP is doing for Japonica subspecies (Cultivar: Nipponbare) of O.sativa
> > and Chinese are doing it for Indica Subspecies (Cultivar: 93-11) of O.sativa.
> >
> > However there are several others who are not part of the above two but does it
> > in some small way for either the same cultivars or for the cultivars coming
> from
> > same sub species.
> >
> > Take a look at the GenBank Statistics
> > 210302 nucleotide sequences from O.sativa
> > 398 from indica
> > 287 from japonica
> >
> > We at Gramene are trying to populate the database with Rice sequences and its
> > really hard to classify according to the subspecies information in the
> database.
> > This way we may loose some important information. Is it possible for these
> > databases to make sure when a person submits the sequence he/she mentions the
> > subspecies info (preferred as mandatory) and wherever possible the cultivar
> > also. At least the rice community can get together and make sure that they
> > always report this information.
> >
> > With best wishes
> >
> > Pankaj
> >
> >
> Dear Pankaj,
> Thank you for your message. I apologise for the delay in my reply.
> 
> I discussed your question with the both GenBank and DDBJ aswell as the
> taxonomists at the NCBI (whose taxonomy the three database of the collaboration
> use).
> 
> We have agreed to encourage submitters of either japonica or indica to use the
> unique taxonomic node which reflects these "cultivar-groups".
> So we have either:
> Oryza sativa (japonica cultivar-group)
> 
> Oryza sativa (indica cultivar-group)
> 
> If submitters select either of these when submitting using Webin (our WWW
> submission tool) they will have to enter something other than japonica or indica
> (accordingly) in the cultivar field.
> 
> We are working on creating a list of most common cultivated plants so that it
> becomes mandatory for submitters to include a cultivar where we feel there
> should be one.
> 
> The curator who communicates with submitters of long term sequencing projects
> will be contacting them to inform them of the changes.
> 
> I hope this improves the situation.
> 
> Please do not hesitate to contact me should you have further questions.
> 
> Yours sincerely
> 
> Mary Ann Tuli
> 
> --------------------------------------------------------------------------------
> Mary Ann Tuli
> WEBIN Administrator and
> Nucleotide Sequence Database Curator Co-ordinator
> 
> EMBL Outstation Hinxton, The European Bioinformatics Institute,
> Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, U.K.
> Tel: +44 1223 494444. Fax: +44 1223 494468
> 
> Internet electronic addresses:
> datasubs at ebi.ac.uk (data submissions), update at ebi.ac.uk (updates)
> datalib at ebi.ac.uk (general enquiries)
> http://www.ebi.ac.uk/ (world wide web submissions, updates, services, info)

-- 

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Pankaj Jaiswal, Ph.D.                                   
Postdoctoral Associate
Dept. of Plant Breeding                             
Cornell University                                   
Ithaca, NY-14853, USA   

Tel:+1-607-255-3103 / Fax:+1-607-255-6683
E mail: pj37 at cornell.edu
http://www.gramene.org   
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