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

[Pankaj Jaiswal]

Dear Mary,

Thanks for your update and considering my question. I really appreciate this. I
am including my comments ### next to yours 

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)
### In this issue please consider that the indica Tax ID 39946 / japonica Tax ID
39947 are the two major  subspecies of the species O. sativa used world wide.
These are not the cultivars as represented in the EMBL and GenBank records.
People should be using the indica/japonica Tax ID and not the Tax ID 4530 for O.
sativa under organism field.  The cultivars are for examples Nipponbare, Lamont
(ssp japonica) and IR36, 93-11 (ssp indica).I am mentioning these four cultivars
specially because IRGSP (rice sequencing consortium) is generating sequences
from Nipponbare CV and Chines institutions are shortly going to submit a first
draft sequence for the cultivar 93-11.   

> 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.

### that will be great. Will it include the same feature in SEQUIN.


> 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.
### There are about 120000, cultivars that represent these two sub species and
the hybrids. The International Crop Information System
(http://www.cgiar.org/icis/) database hosts International Rice Information
System (IRIS), which carries the information on these cultivars and assigns a
Germplasm ID to them. This way I guess we make the system more intact and cover
the issue of SP and CV more precisely. I am attaching a file carrying the
cultivars listed in SWALL records and the subspecies they belong to. The
subspecies association is not yet complete, but will give you an idea of it. The
IRIS database is going to release this CV-SSP info soon in their new release.

> The curator who communicates with submitters of long term sequencing projects
> will be contacting them to inform them of the changes.
### That's an ideal situation

> I hope this improves the situation.

> Please do not hesitate to contact me should you have further questions.
> 
> Yours sincerely
> 
> Mary Ann Tuli

Best wishes

Pankaj




> --------------------------------------------------------------------------------
> 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)

-- 

******************************************
Pankaj Jaiswal, Ph.D.                                   
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   
******************************************