| Organism | Common name | Organism Abbrev | Organism ID | Genes |
|---|
| Acorus americanus | sweetflag | ACOAM | 99 | 6 |
| Aegilops speltoides | goatgrass | AEGSP | 79 | 3 |
| Agapanthus praecox | African-lily | AGAPR | 126 | 1 |
| Allium cepa | garden onion | ALLCE | 142 | 11 |
| Allium sativum | cultivated garlic | ALLSA | 111 | 1 |
| Anopheles gambiae str. PEST | African malaria mosquito | ANOGA | 153 | 64 |
| Antirrhinum majus | garden snapdragon | ANTMA | 109 | 29 |
| Apis mellifera | honey bee | APIME | 156 | 27 |
| Apium graveolens | wild celery | APIGR | 144 | 2 |
| Aquilegia alpina | | AGUAL | 155 | 5 |
| Aquilegia formosa x Aquilegia pubescens | columbine | AQUFO | 19 | 80 |
| Arabidopsis thaliana | mouse-ear cress | ARATH | 0 | 517 |
| Arachis hypogaea | peanut | ARAHY | 105 | 2 |
| Aranda deborah | vanda orchid | ARADE | 132 | 1 |
| Ashbya gossypii ATCC 10895 | | ASHGO | 28 | 136 |
| Asparagus officinalis | garden asparagus | ASPOF | 80 | 8 |
| Asparagus virgatus | | ASPVI | 86 | 2 |
| Aspergillus fumigatus | | ASPFU | 41 | 143 |
| Aspergillus nidulans FGSC A4 | | ASPNI | 27 | 134 |
| Avena sativa | oat | AVESA | 154 | 1 |
| Beta vulgaris | common beet | BETVU | 114 | 6 |
| Brassica napus | rape | BRANA | 108 | 32 |
| Brassica oleracea | asparagus broccoli | BRAOL | 169 | 1 |
| Brassica rapa | field mustard | BRARA | 197 | 2 |
| Caenorhabditis elegans | nematode | CAEEL | 3 | 254 |
| Callitropsis nootkatensis | Sitka cypress | CALNO | 147 | 1 |
| Canavalia gladiata | sword jackbean | CANGLA | 127 | 2 |
| Candida albicans | | CANAL | 32 | 131 |
| Candida glabrata CBS 138 | | CANGL | 31 | 146 |
| Capsicum annuum | cayenne pepper | CAPAN | 195 | 9 |
| Ceratopteris richardii | | CERRI | 43 | 6 |
| Chlamydomonas reinhardtii | | CHLRE | 34 | 168 |
| Cicer arietinum | chick pea | CICAR | 120 | 2 |
| Citrus sinensis | sweet orange | CITSI | 194 | 15 |
| Coffea canephora | robusta coffee | COFCA | 166 | 1 |
| Cryptococcus neoformans var. neoformans JEC21 | | CRYNE | 29 | 135 |
| Cucumis sativus | garden cucumber | CUCSA | 97 | 5 |
| Cycas rumphii | | CYCRU | 68 | 5 |
| Danio rerio | zebrafish | DANRE | 160 | 303 |
| Debaryomyces hansenii CBS767 | | DEBHA | 40 | 126 |
| Dendrobium grex Madame Thong-In | Dendrobium hybrid | DENGR | 135 | 3 |
| Dictyostelium discoideum AX4 | | DICDI | 44 | 58 |
| Drosophila melanogaster | fruit fly | DROME | 4 | 211 |
| Elaeis guineensis | African oil palm | ELAGU | 133 | 2 |
| Eschscholzia californica | California poppy | ESCCAL | 84 | 5 |
| Eucalyptus globulus subsp. globulus | Tasmanian bluegum | EUCGL | 121 | 2 |
| Eucalyptus grandis | grand eucalyptus | EUCGR | 131 | 3 |
| Eucalyptus occidentalis | flat-top yate | EUCOC | 143 | 1 |
| Euphorbia esula | leafy spurge | EUPSU | 171 | 8 |
| Fragaria x ananassa | strawberry | FRAANA | 96 | 2 |
| Fritillaria agrestis | stinkbells | FRIAG | 67 | 2 |
| Fritillaria liliacea | stinkbells | FRILIL | 170 | 2 |
| Gerbera hybrid cultivar | | GERHY | 134 | 5 |
| Gibberella zeae PH-1 | | GIBZE | 39 | 156 |
| Glycine soja | wild soybean | GLYSO | 48 | 4 |
| Gossypium arboreum | tree cotton | GOSAR | 101 | 10 |
| Gossypium hirsutum | upland cotton | GOSHI | 33 | 6 |
| Gossypium raimondii | cotton | GOSRA | 89 | 13 |
| Helianthus annuus | common sunflower | HELAN | 192 | 9 |
| Homo sapiens | human | HOMSA | 5 | 410 |
| Hordeum vulgare | common barley | HORVU | 10 | 187 |
| Hyacinthus orientalis | garden hyacinth | HYAOR | 66 | 4 |
| Ipomoea batatas | sweetpotato | IPOBA | 49 | 4 |
| Ipomoea nil | whiteedge morning-glory | IPONI | 71 | 12 |
| Kluyveromyces lactis NRRL Y-1140 | | KLULA | 60 | 137 |
| Laccaria bicolor | | LACBI | 162 | 137 |
| Lactuca sativa | garden lettuce | LACSA | 193 | 16 |
| Lactuca serriola | | LACSE | 119 | 2 |
| Lathyrus aphaca | yellow pea | LATAP | 50 | 1 |
| Lathyrus sativus | white pea | LATSA | 55 | 1 |
| Lens culinaris | lentil | LENCU | 56 | 1 |
| Lilium longiflorum | Easter lily | LILLO | 54 | 6 |
| Linum usitatissimum | common flax | LINUS | 53 | 3 |
| Liriodendron tulipifera | tuliptree | LIRTU | 94 | 1 |
| Lolium multiflorum | ryegrass | LOLMU | 95 | 2 |
| Lolium perenne | perennial ryegrass | LOLPE | 115 | 3 |
| Lolium temulentum | Darnel ryegrass | LOLTE | 136 | 2 |
| Lotus japonicus | birdfoot deervetch | LOTJA | 17 | 19 |
| Lupinus albus | white lupine | LUPAL | 82 | 1 |
| Lycopersicon chilense | tomato | LYCCH | 51 | 1 |
| Lycopersicon hirsutum | tomato | LYCHI | 52 | 1 |
| Lycopodium annotinum | | LYCAN | 104 | 2 |
| Magnaporthe grisea 70-15 | rice blast fungus | MAGGR | 30 | 159 |
| Magnolia praecocissima | | MAGPR | 117 | 10 |
| Malus x domestica | apple | MALUSD | 70 | 181 |
| Manihot esculenta | tapioca | MANES | 85 | 2 |
| Medicago sativa | alfalfa | MEDSA | 72 | 3 |
| Medicago truncatula | barrelclover | MEDTR | 13 | 179 |
| Mesembryanthemum crystallinum | common iceplant | MESCR | 106 | 7 |
| Mus musculus | house mouse | MUSMU | 37 | 384 |
| Musa acuminata | banana | MUSAC | 128 | 1 |
| Nectria haematococca | | NECHA | 21 | 171 |
| Neurospora crassa OR74A | red bread mold | NEUCR | 20 | 164 |
| Nicotiana benthamiana | tobacco | NICBE | 73 | 13 |
| Nicotiana tabacum | cultivated tobacco | NICTA | 23 | 29 |
| Oryza sativa (indica cultivar-group) | indica rice | ORYSAI | 22 | 362 |
| Oryza sativa ssp. japonica | rice | ORYSA | 7 | 514 |
| Ostreococcus lucimarinus | | OSTLU | 35 | 158 |
| Ostreococcus tauri | | OSTTA | 36 | 135 |
| Panicum virgatum | switchgrass | PANVI | 125 | 1 |
| Paulownia kawakamii | empress tree | PAUKA | 116 | 1 |
| Petroselinum crispum | parsley | PETCR | 98 | 1 |
| Petunia hybrid | petunia | PETHY | 74 | 36 |
| Phaeodactylum tricornutum | | PHATR | 152 | 165 |
| Phaseolus coccineus | scarlet runner | PHACO | 78 | 7 |
| Physcomitrella patens | moss | PHYPA | 15 | 378 |
| Phytophthora sojae | | PHYSO | 65 | 96 |
| Picea abies | Norway spruce | PICAB | 123 | 3 |
| Picea glauca | spruce | PICGL | 75 | 7 |
| Picea sitchensis | Sitka spruce | PICSI | 76 | 3 |
| Pimpinella brachycarpa | saxifrage | PIMBR | 129 | 1 |
| Pinus pinaster | maritime pine | PINPI | 57 | 6 |
| Pinus radiata | Monterey pine | PINRA | 124 | 6 |
| Pinus taeda | loblolly pine | PINTA | 18 | 29 |
| Pisum fulvum | tawny pea | PISFU | 59 | 1 |
| Pisum sativum | pea | PISSA | 107 | 16 |
| Poncirus trifoliata | hardy orange | PONTR | 90 | 7 |
| Populus trichocarpa | poplar | POPTR | 9 | 601 |
| Prunus persica | peach | PRUPE | 58 | 3 |
| Saccharomyces cerevisiae | baker's yeast | SACCE | 2 | 155 |
| Saccharum officinarum | sugarcane | SACOF | 25 | 19 |
| Schizosaccharomyces pombe 972h- | fission yeast | SCHPO | 6 | 159 |
| Secale cereale | cereal rye | SECCE | 62 | 3 |
| Silene diclinis | Catchfly | SILDI | 91 | 1 |
| Sinapis alba | white mustard | SINAL | 122 | 4 |
| Solanum lycopersicum | garden tomato | SOLLY | 11 | 52 |
| Solanum tuberosum | potato | SOLTU | 14 | 29 |
| Sorghum bicolor | sorghum | SORBI | 26 | 20 |
| Sorghum propinquum | sorghum | SORPR | 61 | 2 |
| Sphagnum sp. JL-2005 | | SPHSP | 146 | 1 |
| Strongylocentrotus purpuratus | purple sea urchin | STRPU | 149 | 217 |
| Theobroma cacao | cacao | THECA | 63 | 2 |
| Triticum aestivum | common wheat | TRIAE | 8 | 164 |
| Triticum monococcum | wheat | TRIMO | 77 | 11 |
| Ustilago maydis 521 | | USTMA | 38 | 124 |
| Vicia species | vetch | VICSP | 100 | 3 |
| Yarrowia lipolytica CLIB122 | | YARLI | 81 | 132 |
| Zea mays | corn | ZEAMA | 1 | 428 |
