[ensembl-dev] Use of Coelomata in NCBI Taxonomy

[Matthieu Muffato]

Hi Sébastien

By default, the gene-tree pipeline is building a species tree from the NCBI taxonomy. This stands for Ensembl (vertebrates) and some divisions of Ensembl Genomes (for other divisions, the feature is overridden by a custom species tree).

The NCBI has recently updated the taxonomy at the base of the animal kingdom between e68 and e69. The tree now looks like:
(Metazoa > ... > Bilateria > ) Coelomata
  > Deuterostomia ( > Chordata > ... > Homo sapiens)
  > Protostomia > Ecdysozoa
           > Panarthropoda ( > ... > Drosophila melanogaster)
           > Nematoda ( > ... > Caenorhabditis elegans)
instead of:
(Metazoa > ... >) Bilateria
  > Pseudocoelomata > Nematoda ( > ... > Caenorhabditis elegans)
  > Coelomata
           > Protostomia ( > Panarthropoda > ... > Drosophila melanogaster)
           > Deuterostomia ( > Chordata > ... > Homo sapiens)

In the e69 Compara database, you can see homologies linked to "Coelomata" and "Ecdysozoa", but not to "Metazoa" or "Bilateria". In Ensembl Genomes, the change has also been included between versions 15 and 16, but there are more species covering this part of the tree of life. As a result, you can still find homologies linked to "Bilateria", "Metazoa", etc.

We thought about publishing a blog post about that, but did not find any exciting consequence

Best regards,
Matthieu

On 17/12/12 13:55, Moretti Sébastien wrote:
> Hi
>
> The documentation links towards
> http://www.phylowidget.org/full/index.html?tree=http://tinyurl.com/ensembltree&useBranchLengths=true&minTextSize=7,
> but this does not seem to be the tree used. You seem to be using the
> NCBI Taxonomy.
>
> Moreover, NCBI taxonomy includes Bilateria and Metazoa, which we do not
> find in Ensembl Vertebrata. We do find them in Ensembl Metazoa.
>
> Could you please clarify these points for Ensembl Compara users?
>