International team including Maynooth researchers sequence the Humongous Fungus

Monday, November 20, 2017 - 12:15

The blue whale may be the largest living animal on the planet but the world’s largest living organism is actually a mushroom, called Armillaria ostoyae. The largest known Armillaria specimen, discovered over twenty years ago in Oregon, USA, is thought to be thousands of years old and covers an area of over ten square kilometers. Armillaria species are amongst the most devastating fungal pathogens, causing root rot disease in more than 500 plant species, which may cause severe deforestation and impact on climate change. They are known as white rot fungi, meaning they are capable of breaking down all components of plant cell walls, a capability that also interests bioenergy researchers.
Now an international group of scientists including researchers from the Hungarian Academy of Sciences, the U.S. Department of Energy Joint Genome Institute (DOE JGI) and five researchers from the Department of Biology at Maynooth University (Dr. David Fitzpatrick & Professor Sean Doyle along with PhD students Nicola Moloney, Eoin O’Connor and Rose Waldron) have recently sequenced and analysed the complete genomes of four Armillaria species, published in Nature Ecology and Evolution (1), the team uncovered a number of genetic mechanisms that help Armillaria species develop their unusual rhizomorphs, shoestring-like structures that spread through soil in search of new food sources, to grow so big and get so good at killing host plants.
Aside from A. ostoyae, the team also sequenced and analyzed the genomes of A. cepistipes, A. gallica and A. solidipes. This genome work builds on earlier work (2) by Professor Doyle and Dr. Fitzpatrick who along with PhD student Cindy Collins and colleagues at the Wellcome Trust Sanger Institute sequenced the first Armillaria genome (A. mellea, the honey fungus) in 2013.
Comparing the newly sequenced Armillaria genomes against 22 related fungal genomes, the team were able to catalogue 20 gene families related to pathogenicity in Armillaria, and identified plant cell degrading wall enzyme families, that allow Armillaria efficiently break down and access nutrients in dead wood, which has major biotechnological potential. To help explain the unusually large fungal genomes in Armillaria species, they also located many duplicated genes, suggesting Armillaria evolved primarily through gene family expansion.
Using comparative genomics, transcriptomics and proteomic data generated from Science Foundation Ireland funded protein mass spectrometry facilities, the team generated information that suggests that the development of rhizomorphs have a lot in common with that of the fungal fruiting bodies (mushroom cap) indicating that rhizomorphs may be multicellular structures, a discovery of great interest to evolutionary mycologists.

1: Sipos G, Prasanna AN, Walter MC, O'Connor E, Bálint B, Krizsán K, Kiss B, Hess J, Varga T, Slot J, Riley R, Bóka B, Rigling D, Barry K, Lee J, Mihaltcheva S, LaButti K, Lipzen A, Waldron R, Moloney NM, Sperisen C, Kredics L, Vágvölgyi C, Patrignani A, Fitzpatrick D, Nagy I, Doyle S, Anderson JB, Grigoriev IV, Güldener U, Münsterkötter M, Nagy LG. Genome expansion and lineage-specific genetic innovations in the forest pathogenic fungi Armillaria. Nat Ecol Evol. 2017 Oct 30. doi: 10.1038/s41559-017-0347-8. [Epub ahead of print] PubMed PMID: 29085064.
2: Collins C, Keane TM, Turner DJ, O'Keeffe G, Fitzpatrick DA, Doyle S. Genomic and proteomic dissection of the ubiquitous plant pathogen, Armillaria mellea: toward a new infection model system. J Proteome Res. 2013 Jun 7;12(6):2552-70.  doi: 10.1021/pr301131t. Epub 2013 May 28. PubMed PMID: 23656496; PubMed Central PMCID: PMC3679558.