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Armillaria nabsnona
Fruiting bodies of Armillaria nabsnona. The largest fruiting bodies are up to 10 cm in length. [Photo credit: Laurel, used under the Creative Commons Attribution-Share Alike license via Mushroom Observer]

The Armillaria nabsnona genome was sequenced as part of the JGI CSP “1000 Fungal Genomes – Deep Sequencing of Ecologically-relevant Dikarya” project. Within the framework of this project, we are sequencing keystone lineages of saprophytic, mycorrhizal, and endophytic fungi that are of special ecological importance. Dozens of sequenced species were harvested from Long Term Observatories to serve as the foundation for a reference database for metagenomics of fungi and for a comprehensive survey of the soil fungal metatranscriptome.

Members of the genus Armillaria belong to the Physalacriaceae, a highly diverse family in the Agaricales containing white rot wood decayers and devastating tree pathogens. They cause shoestring root rot, which lead to significant losses in forest areas or woody plants, including forests, parks or vineyards, among others, mostly in the temperate zone. The infection is usually characterized by presence of rhizomorphs and mycelial mats between the bark and cambium layer of the host root. Rhizomorphs are shoestring-like multicellular structures, which are analogous to plant roots in appearance and forage for food by spreading inside the soil. Armillaria spp. produce macroscopic fruiting bodies that are edible and known as honey mushrooms. Many existing individuals of Armillaria are believed to be the largest and oldest terrestrial organisms known on earth.

We aim to sequence the genomes of several Armillaria strains representing both aggressive pathogens to white-rot saprotrophs. This will allow us to gain insights into the evolution of pathogenicity and the mechanisms of interaction between Armillaria and their host trees. It will further help understanding the biology of these species, including their strategies for host invasion, for wood decay, and the development of rhizomorphs and fruiting bodies. We hope these resources will open the door for developing efficient management strategies for limiting the spread and damage to forest ecosystems.

Armillaria nabsnona(Volk & Burdsall)5 is found in the west coast of North America, Hawaii, and Japan3,4,5. The fungus ranges to the Pacific Northwest region of North America, including the US states of Washington, Oregon, California, Idaho, Alaska, and the Canadian province British Columbia. It was also reported in Hawaii and Hokkaido Island in northern Japan. It can be distinguished from other related species by its orange coloration and narrow stipe in comparison to the size of the pileus. A. nabsnona produces gregarious fruiting bodies in groups. Phylogenetically, A. nabsnona clusters together with A. calvescens, A. cepistipes, A. gallica and A. altimontana1,2. It is a weakly pathogenic species compared to other related species. A. nabsnona causes white rot in dead and decaying wood, which can be recognized by the presence of branched black rhizomorphs and typical mycelial fans. Generally found fruiting on decaying hardwoods, mostly in riparian areas, on Alnus and Acer species and is often known to from association members of Orchidaceae such as Gastrodia and Galeola6.

The 1KFG project is a large collaborative effort aiming for master publication(s). Please do contact the PI for 1KFG - Deep Sequencing of Ecologically-relevant Dikarya (Dr. Francis Martin) for permission prior to the use of any data in publications.


1. Guo et.al., (2016). Phylogenetic analyses of Armillaria reveal at least 15 phylogenetic lineages in China, seven of which are associated with cultivated Gastrodia elata. PLoS ONE, 11(5), e0154794. doi:10.1371/journal.pone.0154794

2. Román et.al., (2013). Incidence and phylogenetic analyses of Armillaria spp. associated with root disease in peach orchards in the State of Mexico, Mexico. Forest Pathology. 2013; 43:390-401. doi:10.1111/efp.12043

3. Ota Y, Sotome K, Hasegawa E. (2009). Seven Armillaria species identified from Hokkaido Island, northern Japan. Mycoscience 50 (6): 442-47. doi:10.1007/s10267-009-0505-1

4. Hanna JW, Klopfenstein NB, Kim M-S. (2007). First report of the root-rot pathogen, Armillaria nabsnona, from Hawaii. Plant Disease 91 (5): 634. doi:10.1094/PDIS-91-5-0634B

5. Volk TJ, Burdsall HH, Banik MT. (1996). Armillaria nabsnona, a new species from western North America. Mycologia 88 (3): 484-91. doi:10.2307/3760888

6. Yuan et.al., (2018). The Gastrodia elata genome provides insights into plant adaptation to heterotrophy. Nat Commun. 2018; 9: 1615. doi:10.1038/s41467-018-03423-5