CultivariumFungal research tools

Fungal research @ Cultivarium

Explore tools and data for the fungal biology program at Cultivarium.

Data from our lab

Experimental data generated at Cultivarium labs

Culture Image Atlas

Browse time-lapse videos, growth images, and growth curves for fungal species on diverse carbon, nitrogen, and standard media panels.

Explore strains →
Line drawing of three Petri dishes with fungal colonies at increasing growth stages

Electroporation

Browse electroporation conditions tested across fungal strains, including electrical parameters, media, culture preparation, and qualitative outcomes for each experiment.

Explore results →
Line drawing of an electroporation cuvette beside an exponential-decay pulse trace

Fungal DNA Methylation

Browse 5mC, 5hmC, and 6mA methylation calls across four fungal genomes. Interactive genome browser with per-contig tracks built from Nanopore sequencing, Dorado basecalling, and modkit thresholded BEDs.

Browse methylation →
Line drawing of a DNA double helix with methylation marks along the backbone

Software tools

Online tools for fungal research

Codon Explorer

Explore codon usage patterns across 2,100+ fungal species, optimize gene sequences for heterologous expression, and compare codon adaptation indices.

Explore codons →
Line drawing of a codon track above a codon-frequency bar chart

Ku Annotation

Annotation and literature curation of non-homologous end joining (NHEJ) genes and knockouts across Fungi. Browse characterized Ku70/Ku80 homologs identified via HMM-based search across fungal genomes.

Browse genes →
Line drawing of Ku protein rings encircling a DNA double helix

PRISM AI-Powered Protocols

PRISM is an AI-assisted laboratory protocol platform through which we are sharing protocols for fungal biology, helping researchers create reproducible, detailed experimental procedures.

Visit PRISM →
Line drawing of lab glassware linked in a protocol sequence

Cultivarium Portal

A general resource for information and user discussion on microbial species and strains, including 72,948 species of Fungi. Sign up for access.

Visit Portal →
Line drawing of a magnifier over a network of linked species records

Species in our lab54

Fungal species in the Cultivarium collection

Ascomycota34

  • Aspergillus flavus
  • Aspergillus fumigatus
  • Aspergillus nidulans
  • Aspergillus niger
  • Aspergillus sydowii
  • Aureobasidium pullulans
  • Botrytis cinerea
  • Candidozyma auris
  • Cladosporium cladosporioides
  • Emergomyces africanus
  • Epicoccum nigrum
  • Exophiala dermatitidis
  • Falciformispora senegalensis
  • Fusarium falciforme
  • Fusarium venenatum
  • Hortaea werneckii
  • Knufia petricola
  • Komagataella phaffii
  • Nakaseomyces glabratus
  • Neurospora crassa
  • Penicillium chrysogenum
  • Penicillium polonicum
  • Pseudogymnoascus appendiculatus
  • Pseudogymnoascus pannorum
  • Pyrenophora teres
  • Saccharomyces cerevisiae
  • Scedosporium apiospermum
  • Sclerotinia sclerotiorum
  • Scopulariopsis brevicaulis
  • Sporothrix schenckii
  • Trematosphaeria grisea
  • Trichoderma reesei
  • Verticillium dahliae
  • Yarrowia lipolytica

Basidiomycota13

  • Coprinopsis cinerea
  • Cryptococcus gattii
  • Ganoderma lucidum
  • Ganoderma sessile
  • Malassezia pachydermatis
  • Moesziomyces aphidis
  • Mycosarcoma maydis
  • Phaffia rhodozyma
  • Phanerodontia chrysosporium
  • Pleurotus ostreatus
  • Rhodotorula dairenensis
  • Wallemia ichthyophaga
  • Wallemia mellicola

Mucoromycota7

  • Cunninghamella bertholletiae
  • Lichtheimia corymbifera
  • Mucor circinelloides
  • Mucor lusitanicus
  • Phycomyces blakesleeanus
  • Rhizopus arrhizus
  • Rhizopus microsporus