Thursday, December 15, 2011

Very nice new #PLoSGenetics paper on "Functional Phylogenomics" of Seed Plants

Update2 - 12/22 - Data available here.  Thanks to the authors for clearing things up quickly.

Update1 -  12/19 - Data for this paper seems to be unavailable - not sure why - but looking into this after a TWEET from Karen Cranston. The paper says data is available at: http://nypg.bio.nyu.edu/main/ but I could not find any there.  Note - this is one reason that all data sets should be made available at the journal or third party sites.

Original post:

OK never mind that the terminology of "functional phylogenomics" is a tiny bit vexing to me (long story - some other time perhaps). The paper behind it - PLoS Genetics: A Functional Phylogenomic View of the Seed Plants is very cool.

Here's what the authors did (a very coarse summary)

1. Identified sets of orthologs between plant species using the OrthologID system (which has a phylogenetic underpinning) (the data input for this appeared to have mostly been Unigene EST clusters)

2. Constructed a "total evidence" phylogeny for these taxa (using a few approaches) 


3. Use this phylogeny to reinterpret some general features of the evolution of plants 

4. Searched for gene ontology categories (in annotated genes from these organisms) that agreed with the phylogeny. In essence, this seems to be a search for shared-derived traits (i.e., synapomorphies) in particular clades. 




5. Generated hypothesis about functional evolution in particular clades.

Overall, there is a lot that is really fascinating in here and this approach seems very powerful (though I note - I think something akin to this though not as comprehensive or as careful has been done for other groups but not sure).  Check out the paper for more detail ...
Lee EK, Cibrian-Jaramillo A, Kolokotronis S-O, Katari MS, Stamatakis A, et al. (2011) A Functional Phylogenomic View of the Seed Plants. PLoS Genet 7(12): e1002411. doi:10.1371/journal.pgen.1002411

1 comment:

  1. Thanks for alerting us about this! The URL with the data was given to the reviewers and I guess we didn't reveal it in time. :-/ It is now linked through that same website cited in the paper (see Data page).

    As for the "registration" it was just a Drupal CMS thing during the review process. Removed now. Let me know if not the case.

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