Postia placenta genome is now published in early edition of PNAS. Brown rotting fungi are import part of the cellulose degrading ecology of the forest as well (hopefully) providing some enzymes that will help in the ligin to biofuels process. Brown rotters break down cellulose but cannot break down lignin or lignocellulose while white rotters (like the previously sequenced Phanerochaete chrysosporium) are able to break down the lignin. This fungus was chosen for sequencing as it is another potentially helpful fungus in the war on sugars (turning them into fuels) including recently published Trichoderma reesei and 1st basidiomycete genome Phanerochaete (all incidentally with the Diego Martinez as first author – go Diego!). It is also helpful to contrast the white and brown rotters to understand how their enzyme capabilities have changed and how these different lifestyles evolved. There had been some issues with the initial assembly of this genome which is basically twice as big as one would expect because the dikaryon genome was sequenced – this is where two nuclei with different genomes are present as the result of fusion between two parents of opposite mating types. When genome sequenced is performed it is hard to assemble these into a single assembly since there are really two haplotypes present. So these haplotypes have to be sorted out to obtain the gene ‘count’ for the organism for those who like simple numbers. This is a similar situation to the Candida albicans genome, although those haplotypes are much more similar. The main problem is that one has to generate twice as much sequence to get the same coverage of each haplotype without playing some tricks to collapse them into a consensus and them afterwards separate the haplotypes back out. At any rate, this sequenced provided a good summary of the gene content and thus metabolic and enzymatic capabilities to match up functional data collected from LC/MS and transcriptional profiling.
There are several other rotting fungi that are nearly done at JGI (but the task of writing and coordinating the analyses for the papers are ongoing!) include Schizophyllum commune and Pleurotus ostreatus. There are also several more mycorrhizal and plant pathogenic basidiomycete fungi as well as some classic model systems that have finished genomes and are in the process of finalizing papers. It is an exciting time that is just beginning as these genome and transcriptional data are integrated and compared for their different ecological, morphological, and metabolic capabilities.
The article is unfortunately not Open Access so I haven’t even read it from home yet, but pass along this news to you, dear reader. Will get a chance to read through more than the abstract to see what glistening gems have been extracted from this genomic endeavor.
D. Martinez, J. Challacombe, I. Morgenstern, D. Hibbett, M. Schmoll, C. P. Kubicek, P. Ferreira, F. J. Ruiz-Duenas, A. T. Martinez, P. Kersten, K. E. Hammel, A. V. Wymelenberg, J. Gaskell, E. Lindquist, G. Sabat, S. S. BonDurant, L. F. Larrondo, P. Canessa, R. Vicuna, J. Yadav, H. Doddapaneni, V. Subramanian, A. G. Pisabarro, J. L. Lavin, J. A. Oguiza, E. Master, B. Henrissat, P. M. Coutinho, P. Harris, J. K. Magnuson, S. E. Baker, K. Bruno, W. Kenealy, P. J. Hoegger, U. Kues, P. Ramaiya, S. Lucas, A. Salamov, H. Shapiro, H. Tu, C. L. Chee, M. Misra, G. Xie, S. Teter, D. Yaver, T. James, M. Mokrejs, M. Pospisek, I. V. Grigoriev, T. Brettin, D. Rokhsar, R. Berka, D. Cullen (2009). Genome, transcriptome, and secretome analysis of wood decay fungus Postia placenta supports unique mechanisms of lignocellulose conversion Proceedings of the National Academy of Sciences DOI: 10.1073/pnas.0809575106