All genomes
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Genome names in green represent completed genomes
| Genome Name | No of Superfamily |
| Zabrotes subfasciatus | 1 |
| Zaira arrisor | 1 |
| Zaire ebolavirus | 1 |
| Zalophus californianus | 4 |
| Zaluzianskya katharinae | 3 |
| Zamia floridana | 4 |
| Zamia furfuracea | 8 |
| Zamia inermis | 3 |
| Zamia pumila | 4 |
| Zamioculcas zamiifolia | 2 |
| Zannichellia palustris | 2 |
| Zantedeschia aethiopica | 13 |
| Zanthoxylum monophyllum | 3 |
| Zanthoxylum sp. Chase 1348 | 5 |
| Zaocys dhumnades | 3 |
| Zaprionus tuberculatus | 7 |
| Zapus princeps | 1 |
| Zea diploperennis | 2 |
| Zea luxurians | 2 |
| Zea mays | 322 |
| Zea perennis | 3 |
| Zelkova serrata | 6 |
| Zellera tawallina | 2 |
| Zelometeorium patulum | 1 |
| Zenia insignis | 2 |
| Zenobia pulverulenta | 2 |
| Zenopsis nebulosus | 1 |
| Zephyra elegans | 3 |
| Zephyranthes candida | 1 |
| Zephyranthes filifolia | 2 |
| Zercon sp. 'Zer' | 2 |
| Zerene cesonia | 1 |
| Zerynthia rumina | 1 |
| Zeus faber | 1 |
| Zingiber gramineum | 5 |
| Zingiber officinale | 1 |
| Zinnia elegans | 18 |
| Ziphius cavirostris | 6 |
| Zizania latifolia | 1 |
| Zizania texana | 2 |
| Ziziphus sp. | 2 |
| Zizyphomyia crescentis | 1 |
| Zoanthus sp. | 1 |
| Zoanthus sp. SAL-2001 | 1 |
| Zoarces viviparus | 1 |
| Zobellia galactanivorans | 1 |
| Zobellia uliginosa | 1 |
| Zonosemata electa | 1 |
| Zoogloea ramigera | 4 |
| Zoogloea resiniphila | 1 |
| Zootoca vivipara | 1 |
| Zophobas atratus | 1 |
| Zornia cantoniensis | 2 |
| Zostera marina | 4 |
| Zostera mucronata | 2 |
| Zostera muelleri | 2 |
| Zostera noltii | 5 |
| Zosterograptus sp. | 2 |
| Zosterops nigrorum | 1 |
| Zosterops senegalensis | 2 |
| Zucchini green mottle mosaic virus | 1 |
| Zucchini yellow mosaic virus | 1 |
| Zu cristatus | 1 |
| Zychaea mexicana | 2 |
| Zygnema peliosporum | 4 |
| Zygodon intermedius | 3 |
| Zygodon obtusifolius | 2 |
| Zygodon pungens | 2 |
| Zygodon reinwardtii | 2 |
| Zygodon viridissimus | 2 |
| Zygogonium tunetanum | 2 |
| Zygogynum pauciflorum | 3 |
| Zygogynum sp. Qiu 90024 | 2 |
| Zygopetalum maculatum | 2 |
| Zygophyllum album | 2 |
| Zygophyllum billardierei | 2 |
| Zygophyllum coccineum | 2 |
| Zygophyllum cylindrifolium | 2 |
| Zygophyllum decumbens | 2 |
| Zygophyllum fabago | 2 |
| Zygophyllum fruticulosum | 2 |
| Zygophyllum hildebrandtii | 2 |
| Zygophyllum hirticaule | 2 |
| Zygophyllum simplex | 2 |
| Zygophyllum spinosum | 2 |
| Zygophyllum xanthoxylum | 2 |
| Zygorhynchus heterogamus | 2 |
| Zygosaccharomyces bailii | 6 |
| Zygosaccharomyces bisporus | 3 |
| Zygosaccharomyces fermentati | 1 |
| Zygosaccharomyces rouxii | 19 |
| Zymobacter palmae | 2 |
| Zymomonas mobilis | 161 |
| Zyras collaris | 1 |
| Zyras haworthi | 1 |
