With all the work I've been doing in metagenomics, it's nice to be reminded that I still do some of the non-meta type -- yes, I was involved in the P. chrysogenum project, and the paper (and supplemental) is now up in Nature Biotechnology's Advance Publications page prior to the print publication.We've actually gotten a little bit of press -- the BBC has a brief article here.
P. chrysogenum is one of those obvious genomes people are surprised to learn haven't been sequenced yet (well until now). While a "pure" biologist may yawn and say "it's just another filamentous fungus -- haven't we sequenced those already?", there is real practical potential for metabolic engineering of new antibiotics from this genome given that researchers have been doing work on the bug for over 60 years. Besides, the genome wasn't completely uninteresting even from the viewpoint of basic science -- we snuck in a fairly controversial fungal phylogeny in figure 2 -- and I stand by it as we used far more data in our alignments than in previous studies.
[updated links to final published version 10/14/08]
4 comments:
Not sure which part you are referring to as controversial? The A.nidulans/A.niger sister status? That controversial bit was also snuck in A.fumigatus A1163 paper (Fedora et al). I'm still confused why you aren't using an additional closer outgroup from the sister Onygenales clade (Histoplasma, Coccidioides, Uncinocarpus).
Yeah, that. Yes, the same sister status was shown in the trees in our previous paper as well. Both papers were being prepared at the same time, and there was a bit of disagreement among some of the authors on the earlier paper on including a phylogeny that "seemed weird", and we considered leaving it out entirely. We compromised by including it but not really drawing attention to it the way we did in the P. chrysogenum paper.
A closer outgroup would be nice, but at least when we doing the analysis, the genomes you suggest were still in fairly rough shape -- remember, we are using concatenated proteins, so we need gene models for all the proteins in question.
I guess I could look at it again -- do you think a closer outgroup could pull apart A.nidulans and niger?
I totally understand - these things have a way of taking a while to get through the pipeline. For the record the C.immitis data has been in genbank for a while, and TIGR sequenced the other species C.posadasii so the models have been around for a while.
Our 2006 tree used the C.immitis models based on concatenated proteins, but doesn't quite recover A.nidulans as basal (what is the currently accepted position) but it might have resolved better with more of the Eurotiomycete genomes we have now.
From the looks of your 2006 tree (as well as the newer one you sent me) it does look like the choice of species in the tree really does effect the topology, and I guess I shouldn't be that confident as to the sister status of nidulans/niger,
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