[Gramene] Inconsistency between list of 18,000 SSR's

[Susan McCouch]

Hi Melissa,

The positions of the SSRs in Gramene are based on the current rice  
pseudomolecules, as assemblies from TIGR.  We re-run the pipeline  
that positions these SSRs on the rice genome (based on e-PCR with the  
primer pairs) with every build of Gramene.  Thus, as the assemblies  
of the rice pseudomolecules are updated in Gramene, the bp positions  
of the SSRs change, reflecting their current positions on the latest  
assembly of the pseudomolecules.  Thus, with each build of Gramene,  
the positions of the SSRs may change slightly.

In addition, you will find that the positions of the SSRs published  
in 2005 (and downloaded as a supplemental file that I shared with you  
at that time) were based on the 2005 assembly of the rice  
pseudomolecule by the IRGSP.  That assembly differs from the TIGR  
pseudomolecules, even though the underlying sequence information is  
the same.

I hope this answers your questions.  I would suggest that you use the  
most recent positions of the SSRs as published in Gramene, but please  
cite the version of the pseudomolecules (i.e., TIGR v. 5) so that as  
they continue to change, it is clear where you referenced your  
positions.

Best regards,
Susan




On Sep 19, 2007, at 11:52 AM, Melissa Jia wrote:

> About two years ago, Dr. McCouch provided me with an excel file  
> listing the 18,000 Class I SSR's.  The location and sequence listed  
> in gramene are different from this one.  I assume gramene lists  
> correct one.  Is this so?  For reference I've attached the original  
> table Dr. McCouch gave me.
> <18000_Class1_SSrs.xls>
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