SAP paper published in Science

Our paper from the Saprotrophic Agaricomycotina Project was published this week in Science. This project has been a major focus of our lab’s work for over two years, and it is very gratifying to finally have it out. For a snapshot of the work, see the Perspective by Chris Hittinger that accompanied our article.

This was a complicated project, reporting twelve new genomes and involving 71 authors from 13 countries. Ten of the authors are from Clark, including Dimitris Floudas and Manfred Binder, who were the first and second authors, respectively. Other Clark-based coauthors include Masters students Darcy Young and Dylan Glotzer ; Post-doctoral fellow Laszlo Nagy; and undergraduates Nathan Kallen, Alexis Carlson, Albee Ling, and Rachael Martin. Two former PhD students also joined us on this paper, Jason Slot (now in the Rokas lab at Vanderbilt) and Ingo Morgenstern (now in the Tsang lab at Concordia).

I have always enjoyed working in collaborative groups, whether in a leading or supporting role, and this was no exception. The cool thing about collaborations, like mutualistic symbioses, is that the different partners bring unique skills, which allows one to address big problems synthetically. This project required expertise in basic mycology (i.e., collecting, culturing and identifying fungal species), genome and transcriptome sequencing, genome annotation, biochemistry and structural biology of CAZYmes and decay-related oxidoreductases, wood decay chemistry, carbon utilization, and phylogenetics and comparative methods (including molecular clock analyses, ancestral state reconstruction, and gene tree/species tree reconciliation). All of this is packed into less than five pages! The main article is really an extended abstract; to understand the work in detail, one really has to read the 97-page supplement.

Anyway, it is a great relief to finally have this in print (and great to see Bob Blanchette’s SEM of white rot decay on the NSF homepage). Now I am looking forward to additional studies with new genomes that will let us further investigate the early origin of white rot in Agaricomycetes, the genetic bases of substrate-switching, and the evolution of ectomycorrhizae.

Article: Dimitrios Floudas et al. The Paleozoic Origin of Enzymatic Lignin Decomposition Reconstructed from 31 Fungal Genomes. Science 336: 1715-1719. 2012.

Perspective: Chris Todd Hittinger. Endless Rots Most Beautiful. Science 336: 1649-1650. 2012.

Other commentaries and press releases:

Scientific American: White Rot Fungi Slowed Coal Formation.

ABC Science: Fungi may have ended coal era

Clark: Findings point to fungi as prime suspects in fossil fuel mystery

NSF: Study on Fungi Evolution Answers Questions About Ancient Coal Formation and May Help Advance Future Biofuels Production

JGI: Tracking the Remnants of the Carbon Cycle: How an Ancestral Fungus May Have Influenced Coal Formation

INRA: Évolution : un champignon préhistorique serait à l’origine de l’arrêt de la formation du charbon

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