Research - Institute of Biochemistry - Synthetic and Systems Biology Unit - Laboratory of Fungal Genomics and Evolution

László NAGY G.
senior research associate

picture
Krisztina KRIZSÁN research associate
Máté VIRÁGH research associate
Torda VARGA Ph.D. student
Enikő KISS Ph.D. student
Brigitta KISS laboratory assistant
Éva ALMÁSI undergraduate student

FUNGAL GENOMICS AND EVOLUTION

I. The evolution of complexity

We are interested in understanding general principles of genome evolution, in particular the genomic events behind the evolution of increasingly more complex organisms, starting from unicellular eukaryotes and resulting in complex multicellular organisms like mushroom-forming fungi, higher plants or humans. We are focusing on fungi, a group that evolved complex multicellularity in two steps: first, unicellular fungi gave rise to multi-celled filamentous fungi, which resemble fractals in their dimensions and include some of the most devastating pathogens. Subsequently, filamentous fungi evolved 3-dimensional multi-celled reproductive structures, called fruiting bodies.




We combine comparative genomics and transcriptomics with phylogenetics to trace back in time the gradual assembly of the genetic toolkit of complex multicellularity and understand the evolution of complexity. We are interested in the role of gene duplications, gene regulatory network rewiring, regulatory sRNAi, etc. To tackle these questions, we develop new bioinformatic approaches integrating phylogenetic theory into the calculations (see this paper why this is important).




II. Comparative genomics of fungi

Fungi are at the forefront of genomics. Over 60% of all eukaryotic genomes are fungal and there are >300 complete fungal genomes available and their number is rapidly increasing, providing a unique resource to understand genome evolution. We are involved in developing new bioinformatic tools and resources to understand general patterns of fungal genome evolution, such as gene duplication/loss dynamics, ancestral genome architecture of extinct ancestors or genomic diversification and its relation to species divergence. We are involved in developing new genomic resources within the Agaricomycetes clade of Fungi.




III. Phylogenomic inference

One way to leverage whole genome data is to reconstruct evolutionary relationships between organisms: genome-scale datasets are 10-100x the size of traditional phylogenetic datasets. However, there are many unresolved questions that make the use and interpretation of such data difficult. Through simulations and real-world datasets we investigate how different data collection strategies influence the resolution power of genome-scale phylogenetic datasets.


IV. Driving forces of fungal diversification

Biological evolution proceeds in an uneven fashion, there are long periods of slow change followed by shorter periods of explosive evolutionary change. This rate variation has profound impact on extant diversity and the evolutionary dynamics of economically important traits. During the ADiv Project, we examine rate variation in the largest group of mushroom forming fungi, the Agaricales. The aim is to test whether much of the extant diversity in this order is a result of explosive diversification events (adaptive radiations). See the ADiv website for more details. This project is done in collaboration with the Department of Microbiology at the University of Szeged.

Selected publications

Nagy GL, Ohm R, Kovacs GM, Floudas D, Riley R, Gacser A, Davis JM, Doty SL, de Hoog S, Spatafora J, Martin F, Grigoriev IV, Hibbett DS. (2014) Latent homology and convergent regulatory evolution underlies the repeated emergence of yeasts. Nat Comms 5:4471 DOI: 10.1038/ncomms5471.

Riley R, Salamov A, Brown D, Nagy GL, Floudas D, Held B, Levasseur A, Morin E, Otillar R, Linquist E, Baker S, Pisabarro A, Walton J, Blanchette R, Henrissat B, Martin F, Cullen D, Hibbett DS, Grigoriev IV (2014) Extensive sampling of basidiomycete genomes demonstrates inadequacy of the white rot/brown rot paradigm for wood decay fungi. Proc Natl Acad Sci U. S. A. doi/10.1073/pnas.1400592111.

Morin E, Kohler A, Baker AR, Foulongne-Oriol M, Lombard V, Nagy GL, Ohm RA, Patyshakuliyeva A, Brun A, Aerts AL, Bailey AM, Billette C, Coutinho PM, Deakin G, Doddapaneni H, Floudas D, Grimwood J, Hildén K, Kües U, LaButti KM, Lapidus A, Lindquist EA, Lucas SM, Murat C, Riley RW, Salamov AA, Schmutz J, Subramanian V, Wösten HAB, Xu J, Eastwood DC, Foster GD, Sonnenberg ASM, Cullen D, de Vries RP, Lundell T, Hibbett DS, Henrissat B, Burton KS, Kerrigan RW, Challen MP, Grigoriev IV, Martin F. (2013) Genome sequence of the button mushroom Agaricus bisporus reveals mechanisms governing adaptation to a humic-rich ecological niche. Proc Natl Acad Sci U. S. A. doi: 10.1073/pnas.1206847109

Floudas D, Binder M, Riley R, Barry K, Blanchette RA, Henrissat B, Martínez AT, Otillar R, Spatafora JW, Yadav JS, Aerts A, Benoit I, Boyd A, Carlson A, Copeland A, Coutinho PM, de Vries RP, Ferreira P, Findley K, Foster B, Gaskell J, Glotzer D, Górecki P, Heitman J, Hesse C, Hori C, Igarashi K, Jurgens JA, Kallen N, Kersten P, Kohler A, Kües U, Kumar TK, Kuo A, LaButti K, Larrondo LF, Lindquist E, Ling A, Lombard V, Lucas S, Lundell T, Martin R, McLaughlin DJ, Morgenstern I, Morin E, Murat C, Nagy GL, Nolan M, Ohm RA, Patyshakuliyeva A, Rokas A, Ruiz-Dueñas FJ, Sabat G, Salamov A, Samejima M, Schmutz J, Slot JC, St John F, Stenlid J, Sun H, Sun S, Syed K, Tsang A, Wiebenga A, Young D, Pisabarro A, Eastwood DC, Martin F, Cullen D, Grigoriev IV, Hibbett DS (2012) Paleozoic origin of enzymatic lignin decomposition reconstructed using 31 fungal genomes. Science 336: 1715-19.

Nagy GL, Házi J, Szappanos B, Kocsubé S, Bálint B, Rákhely G, Vágvölgyi Cs, Papp T. (2012) The Evolution of Defense Mechanisms Correlate with the Explosive Diversification of Autodigesting Coprinellus Mushrooms (Agaricales, Fungi). Systematic Biology, 61: 595-607.