[ensembl-dev] Dev Digest, Vol 39, Issue 19

[Dan Staines]

Hi Sam,

> After a bit of digging, I reached a conclusion:
> 
> The version of the Chlamydomonas genome installed at EnsemblPlants is
> actually version 3.1, whilst the version installed at the JGI (note,
> not Phytozome itself) is version 3.0, you can see a separate set of
> files in this page:
> 
> http://genome.jgi-psf.org/Chlre3/Chlre3.download.ftp.html [17]
> 
> (it took me a while to realize that there was actually two different
> sub-versions available)
> 
> The problem was exacerbated by the fact that some of the genes are
> almost identical in both versions, but have different gene ids, so
> some recent data I downloaded, containing Chlamydomonas annotation,
> was using gene ids not found in version 3.1.

Yes, we reached a similar conclusion here ourselves. We actually loaded 
the data from the annotations submitted by JGI to GenBank/ENA/DDBJ, 
where the assembly is recorded as v3.0 (with a second version with some 
minor versions called v3.0(2)). We'll change to using v3.1 in the next 
version of Ensembl Plants.

> On a related note, I see that Phytozome is planning on releasing
> v5.0, does EnsemblPlants have plans to include this version?

JGI are currently in the process of submitting this new data to the 
GenBank/ENA/DDBJ archives, after which we will schedule an update to 
Ensembl Plants.

Thanks,

DAn.

-- 
Dan Staines, PhD               Ensembl Genomes Technical Coordinator
EMBL-EBI                       Tel: +44-(0)1223-492507
Wellcome Trust Genome Campus   Fax: +44-(0)1223-494468
Cambridge CB10 1SD, UK         http://www.ensemblgenomes.org/