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Home • Cyathus pallidus NK-01 v1.0
Field shot of Cyathus pallidus MES-3172 (scale bar = 5 mm) [Photo credit: Matthew E. Smith]
Field shot of Cyathus pallidus MES-3172 (scale bar = 5 mm) [Photo credit: Matthew E. Smith]

In the “1KFG: Deep Sequencing of Ecologically-relevant Dikarya” project (CSP1974), we are sequencing keystone lineages of plant-interacting fungi and saprophytic fungi that are of special ecological importance for understanding terrestrial ecosystems. In addition, comparative genome analysis with saprotrophic, mycorrhizal and pathogenic fungi will provide new insights into the specific and conserved adaptations associated with each fungal lifestyle.

Cyathus pallidus NK-01

Cyathus (family Nidulariaceae, class Agaricomycetes) is the most species-rich genus of bird’s nest fungi. Cyathus species are saprotrophic fungi that grow on woody debris and mulch. They also produce a diversity of secondary compounds, such as cyathin, even in the presence of other fungi (Allbutt et al. 1971). Cyathus species are phylogenetically distant from other genera of bird’s nest fungi and form a well-supported monophyletic clade (Kraisitudomsook et al. 2021). Morphologically, Cyathus species have cupulate peridia (an outer covering of the fruiting body), epiphragms (a lid on the peridium that covers the peridioles when young), and funiculi (specialized cords that attach the peridioles to the peridium) (Brodie 1975). They also produce relatively large peridioles (egg-like spore cases which contain basidiospores and basidia) that are usually dark (black, dark grey, or dark brown).

Cyathus pallidus was described from Cuba but is widespread in the tropics (Brodie 1950, Kraisitudomsook 2021). The genome strain NK-01 was isolated from a fruiting body of C. pallidus that grew on wood chips in Gainesville, Florida (USA).

This species is recognized by the small basidiospores and rigid hairs covering the peridia. Cyathus pallidus is the first species in the pallidum group (Zhao et al. 2007) whose genome has been sequenced. This genome will help clarify the phylogenetic relationships between Cyathus and other genera in the family. Because Cyathus species possess several features not found in other genera, the genome of C. pallidus could also help us understand the evolution of bird’s nest fungi morphology.

Researchers who wish to publish analyses using data from unpublished CSP genomes are respectfully required to contact the PI and JGI to avoid potential conflicts on data use and coordinate other publications with the CSP master paper(s).

Genome Reference(s)


  • Liu Y-J, Zhang K-Q. 2004. Antimicrobial activities of selected Cyathus species. Mycopathologia 157, 185-189.
  • Brodie HJ. 1950. Notes on two little known bird’s nest fungi from Southern United States. Mycologia 42:1, 186-190.
  • Brodie HJ, 1975. The Bird’s Nest Fungi. University of Toronto Press, Canada, pp. 1-199.
  • Kraisitudomsook N, Healy RA, Smith ME. 2021. Molecular systematics and taxonomic overview of the bird’s nest fungi (Nidulariaceae). Fungal Biology 125, 693-703.
  • Zhao RL, Jeewon R, Desjardin DE, Soytong K, Hyde KD. 2007. Ribosomal DNA phylogenies of Cyathus: Is the current infrageneric classification appropriate? Mycologia 99:3, 385-395.