TABLE 1.
Overview of proteomes investigated.
| Eukaryotic super group | Kingdom | Other labels | Species | Uniprot | Description | Note |
| Opisthokonta | Metazoa (animals) | Vertebrate, mammalian | Homo sapiens | HUMAN | Human | |
| Vertebrate, mammalian | Mus musculus | MOUSE | House mouse | |||
| Vertebrate | Danio rerio | DANRE | Zebrafish | |||
| Drosophila melanogaster | DROME | Fruit fly | ||||
| Caenorhabditis elegans | CAEEL | Nematode | ||||
| Fungi | Yeasts* | Saccharomyces cerevisiae | YEAST | Baker’s yeast | ||
| Komagataella phaffiia | KOMPG | Yeast | Methylotropic | |||
| Candida albicans | CANAL | Opportunistic pathogenic yeast/fungus | Causes candidiasis | |||
| Ogataea polymorphab | PICAN | Yeast | Methylotropic | |||
| Other Fungi | Penicillium rubens | PENRW | Filamentous fungus | Produces penicillin | ||
| Aspergillus niger | ASPNC | Filamentous fungus | Causes black mold | |||
| Colletotrichum higginsianum | COLHI | Plant pathogen | ||||
| Gibberella fujikuroi | GIBF5 | Plant pathogen | Causes bakanae disease in rice | |||
| Neurospora crassa | NEUCR | Red bread mold | ||||
| Schizosaccharomyces pombe | SCHPO | Fission yeast | Smallest known genome sequence for eukaryote | |||
| Schizophyllum commune | SCHCM | Split gill (mushroom) | Edible | |||
| Cryptococcus neoformans | CRYNJ | Filamentous, encapsulated, pathogenic yeast and obligate aerobe | Can live in plants/animals. Causes cryptococcosis | |||
| Amoebozoa | Amoebozoa | Protist | Dictyostelium discoideum | DICDI | Amoeba | Slime mold |
| Entamoeba histolytica | ENTHI | Parasitic anaerobic amoeba | Causes amoebiasis, lacks peroxisomes | |||
| Archaeplastida | Viridiplantae | Plant | Arabidopsis thaliana | ARATH | Mouse-ear cress (plant) | Relatively small genome, diploid |
| Physcomitrella patens | PHYPA | Moss | Highly efficient homologous recombination (good for creating knock-outs) | |||
| Protist | Ostreococcus tauri | OSTTA | Green algae | Compact genome | ||
| Rhodophyta | Galdieria sulphuraria | GALSU | Red algae | Horizontal gene transfer from archaea and bacteria (5% of genome). Extremophile | ||
| SARc | Alveolata | Toxoplasma gondii | TOXGV | Parasite, protozoa | Causes toxoplasmosis | |
| Tetrahymena thermophila | TETTS | Ciliate | Nuclear dimorphism | |||
| Stramenopiles | Phytophthora infestans | PHYIT | Water mold | Causes potato blight | ||
| Thalassiosira pseudonana | THAPS | Marine diatom | Relatively small genome | |||
| Excavata | Heterolobosea | Naegleria gruberi | NAEGR | Amoebo-flagellate | Can change from amoeba to flagellate | |
| Euglenozoa | Euglena gracilis | EGRACILISd | Single-celled alga | Has chloroplasts | ||
| Trypanosoma brucei | TRYB2 | Parasitic kinetoplastid | Causes sleeping sickness in animals. kinetoplast (organelle) | |||
| Leishmania major | LEIMA | Parasite, trypanosomatid | Causes zoonotic cutaneous leishmaniasis | |||
| Bodo saltans | BODSA | Non-parasitic kinetoplastid protozoa | ||||
*These four species belong to the order of Saccharomycetales and are sometimes referred to as “true yeasts.” They are hereafter referred to in the text as “yeasts.”
aPreviously named Pichia pastoris.
bPreviously named Hansenula polymorpha.
cSAR, Stramenopiles, Alveolates and Rhizaria.
dProteome not from Uniprot, but from recently identified proteome described by Ebenezer et al. (2019).