| Genome Name | No of Superfamily |
| Oat blue dwarf virus | 1 |
| Oat chlorotic stunt virus | 1 |
| Obelia longissima | 1 |
| Obertrumia georgiana | 1 |
| Obuda pepper virus | 1 |
| Oceanobacillus iheyensis | 567 |
| Oceanobacter kriegii | 2 |
| Oceanospirillum beijerinckii | 2 |
| Oceanospirillum linum | 5 |
| Oceanospirillum maris | 3 |
| Oceanospirillum multiglobuliferum | 2 |
| Ochlerotatus ashworthi | 2 |
| Ochlerotatus atropalpus | 3 |
| Ochlerotatus australis | 5 |
| Ochlerotatus togoi | 1 |
| Ochlerotatus triseriatus | 7 |
| Ochlerotatus wardangensis | 1 |
| Ochna multiflora | 3 |
| Ochna serrulata | 2 |
| Ochotona collaris | 1 |
| Ochotona hyperborea | 2 |
| Ochotona princeps | 5 |
| Ochrobactrum anthropi | 9 |
| Ochrobactrum sp. 2FB10 | 1 |
| Ochrobactrum sp. 3CB4 | 1 |
| Ochrobactrum sp. 3CB5 | 1 |
| Ochrobactrum sp. 4FB13 | 1 |
| Ochrobactrum sp. 4FB14 | 1 |
| Ochroma pyramidale | 4 |
| Ochromonas danica | 13 |
| Ochropepla mourei | 1 |
| Ochrosphaera neapolitana | 5 |
| Ochthocosmus sp. 'Fay et al. 1997' | 2 |
| Ocimum basilicum | 5 |
| Octinodes sp. MFW-1997 | 1 |
| Octoblepharum albidum | 3 |
| Octodon degus | 1 |
| Octodon lunatus | 1 |
| Octomeles sumatrana | 2 |
| Octopus dofleini | 11 |
| Octopus vulgaris | 10 |
| Oculimacula acuformis | 1 |
| Oculimacula yallundae | 4 |
| Odiellus pictus | 2 |
| Odobenus rosmarus | 2 |
| Odocoileus adenovirus | 1 |
| Odocoileus hemionus | 4 |
| Odocoileus virginianus | 4 |
| Odonellia hirtiflora | 5 |
| Odontaspis ferox | 3 |
| Odontella sinensis | 71 |
| Odontella sp. | 1 |
| Odontesthes argentinensis | 1 |
| Odontodes aleuca | 1 |
| Odontoglossum ringspot virus | 1 |
| Odontosoria chinensis | 2 |
| Odontosoria scandens | 2 |
| Odontostomum hartwegii | 2 |
| Odontotermes formosanus | 1 |
| Oecetis avara | 3 |
| Oeconesus maori | 2 |
| Oedalea sp. NCSU-99071983 | 2 |
| Oedicarena latifrons | 1 |
| Oedipodium griffithianum | 3 |
| Oedistoma iliolophum | 2 |
| Oemleria cerasiformis | 1 |
| Oenanthe javanica | 3 |
| Oeneis chryxus | 1 |
| Oeneis ivallda | 1 |
| Oeneis nevadensis | 1 |
| Oenocarpus bataua | 2 |
| Oenococcus oeni | 335 |
| Oenothera ammophila | 1 |
| Oenothera arizonica | 1 |
| Oenothera berteriana | 11 |
| Oenothera biennis | 3 |
| Oenothera elata | 42 |
| Oenothera mexicana | 1 |
| Oenothera organensis | 1 |
| Oenothera villaricae | 4 |
| Oerskovia turbata | 2 |
| Oesophagostomum dentatum | 1 |
| Oesophagostomum quadrispinulatum | 1 |
| Oikopleura dioica | 8 |
| Oikopleura longicauda | 4 |
| Okamuraea hakoniensis | 2 |
| Okapia johnstoni | 2 |
| Okra mosaic tymovirus | 1 |
| Olavius algarvensis sulfate-reducing endosymbiont | 1 |
| Oldenlandia affinis | 2 |
| Oldenlandia goreensis | 2 |
| Olea europaea | 18 |
| Oleandra cumingii | 2 |
| Oleandra pistillaris | 2 |
| Oleispira antarctica | 4 |
| Oleomonas sagaranensis | 2 |
| Oliera sp. | 1 |
| Oligacanthorhynchus tortuosa | 1 |
| Oligarrhena micrantha | 2 |
| Oligella ureolytica | 4 |
| Oligella urethralis | 2 |
| Oligobrachia mashikoi | 1 |
| Oligotrichum parallelum | 3 |
| Oligotropha carboxidovorans | 8 |
| Olimarabidopsis pumila | 4 |
| Olinga feredayi | 2 |
| Olinia cymosa | 2 |
| Olinia ventosa | 2 |
| Olisthodiscus luteus | 6 |
| Olive latent ringspot virus | 1 |
| Olive latent virus 1 | 1 |
| Olsynium filifolium | 1 |
| Ommastrephes sloani | 3 |
| Omphalogramma delavayi | 5 |
| Omphalogramma elwesiana | 2 |
| Omphalotus olearius | 1 |
| Omsk hemorrhagic fever virus | 2 |
| Onchidium sp. | 1 |
| Onchocerca gibsoni | 3 |
| Onchocerca ochengi | 2 |
| Onchocerca volvulus | 52 |
| Oncicola sp. WM-2001 | 1 |
| Oncidium ansiferum | 1 |
| Oncidium excavatum | 5 |
| Oncidium serratum | 2 |
| Oncifelis colocolo | 1 |
| Oncifelis geoffroyi | 1 |
| Oncinocalyx betchei | 2 |
| Oncoba spinosa | 2 |
| Oncocalamus mannii | 2 |
| Oncocnemis obscurata | 3 |
| Oncogenic virus E26 | 1 |
| Oncophorus wahlenbergii | 1 |
| Oncorhynchus gorbuscha | 1 |
| Oncorhynchus keta | 19 |
| Oncorhynchus kisutch | 6 |
| Oncorhynchus masou | 9 |
| Oncorhynchus mykiss | 134 |
| Oncorhynchus nerka | 10 |
| Oncorhynchus rhodurus | 1 |
| Oncorhynchus tshawytscha | 11 |
| Oncosperma tigillarium | 2 |
| Oncostemum sp. Villiers et al. 4937 | 2 |
| Oncotheca balansae | 6 |
| Oncothrips antennatus | 2 |
| Oncothrips morrisi | 1 |
| Oncothrips sterni | 1 |
| Oncothrips waterhousei | 2 |
| Ondatra zibethicus | 3 |
| Ondinea purpurea | 2 |
| Onesia tibialis | 1 |
| Onikusa foliacea | 2 |
| Onikusa japonicum | 2 |
| Onikusa pristoides | 3 |
| Onikusa sp. No103 | 2 |
| Onitis belial | 1 |
| Onobrychis arenaria | 1 |
| Onobrychis viciifolia | 3 |
| Onoclea sensibilis | 3 |
| Onocleopsis hintonii | 4 |
| Ononis spinosa | 2 |
| Ononis yellow mosaic virus | 1 |
| Onoseris sagittatis | 1 |
| Onslowia endophytica | 2 |
| Onthophagus coenobita | 1 |
| Onthophagus furcatus | 1 |
| Onthophagus grossepunctatus | 1 |
| Onthophagus latigena | 1 |
| Onthophagus lemur | 1 |
| Onthophagus maki | 1 |
| Onthophagus melitaeus | 1 |
| Onthophagus merdarius | 1 |
| Onthophagus nutans | 1 |
| Onthophagus ovatus | 1 |
| Onthophagus punctatus | 1 |
| Onthophagus ruficapillus | 1 |
| Onthophagus similis | 1 |
| Onthophagus stylocerus | 1 |
| Onthophagus vacca | 1 |
| Onychium japonicum | 3 |
| Onychium lucidum | 2 |
| Onychonema sp. UTEX LB 832 | 4 |
| O'nyong-nyong virus | 1 |
| Oopsacas minuta | 1 |
| Opephyllum martensii | 2 |
| Opephyllum sp. | 2 |
| Opercularia vaginata | 2 |
| Operculina pteripes | 5 |
| Operculina sp. Romero 1701 | 5 |
| Operculina turpethum | 5 |
| Opetia nigra | 2 |
| Ophelina sp. | 2 |
| Ophiderma evelyna | 2 |
| Ophiderma flavicephala | 2 |
| Ophiderma grisea | 2 |
| Ophiderma pubescens | 2 |
| Ophiocolea floribunda | 2 |
| Ophiocytium majus | 2 |
| Ophioglossum engelmannii | 1 |
| Ophioglossum pedunculosum | 2 |
| Ophioglossum reticulatum | 5 |
| Ophiophagus hannah | 5 |
| Ophiopogon jaburan | 2 |
| Ophiopogon japonicus | 2 |
| Ophiorrhiza mungos | 2 |
| Ophiostoma coronatum | 1 |
| Ophiostoma floccosum | 3 |
| Ophiostoma minus | 1 |
| Ophiostoma novo-ulmi | 9 |
| Ophiostoma piceae | 2 |
| Ophiostoma piliferum | 4 |
| Ophiostoma setosum | 1 |
| Ophiostoma sp. 412T | 1 |
| Ophiostoma ulmi | 3 |
| Ophlitaspongia tenuis | 3 |
| Ophrestia hedysaroides | 2 |
| Ophrestia radicosa | 2 |
| Ophrys apifera | 2 |
| Ophyiulus pilosus | 2 |
| Opilia amentacea | 2 |
| Opilia sp. Chase 1902 | 4 |
| Opisthiolepis heterophylla | 3 |
| Opisthocomus hoazin | 3 |
| Opisthonecta henneguyi | 2 |
| Opisthonecta matiensis | 2 |
| Opisthorchis felineus | 1 |
| Opisthorchis sinensis | 1 |
| Opodiphthera eucalypti | 3 |
| Opsanus beta | 7 |
| Opsanus tau | 3 |
| Opthalmopsylla volgensis | 3 |
| Opuntiella californica | 2 |
| Orangutan hepadnavirus | 1 |
| Orania lauterbachiana | 2 |
| Orania trispatha | 5 |
| Oraniopsis appendiculata | 2 |
| Orasturmia vallicola | 1 |
| Orbignya barbosiana | 5 |
| Orchesella villosa | 1 |
| Orchidantha fimbriata | 5 |
| Orchidantha maxillarioides | 2 |
| Orchidantha siamensis | 5 |
| Orchis quadripunctata | 3 |
| Orcinus orca | 2 |
| Orconectes limosus | 8 |
| Oreas martiana | 1 |
| Orectanthe sceptrum | 2 |
| Oreobolus kuekenthalii | 2 |
| Oreobolus obtusangulus | 2 |
| Oreobolus pectinatus | 2 |
| Oreochromis aureus | 5 |
| Oreochromis mossambicus | 18 |
| Oreochromis niloticus | 20 |
| Oreophoetes peruana | 1 |
| Oreopolus glacialis | 2 |
| Oreortyx pictus | 1 |
| Oreostylidium subulatum | 2 |
| Oreotragus oreotragus | 1 |
| Orf virus | 12 |
| Orgyia leucostigma | 2 |
| Orgyia pseudotsugata multicapsid nucleopolyhedrovirus | 16 |
| Orgyia pseudotsugata single capsid nuclopolyhedrovirus | 2 |
| Orientia tsutsugamushi | 3 |
| Origanum laevigatum | 2 |
| Oriolus larvatus | 2 |
| Orites lancifolia | 3 |
| Orithyia edulis | 2 |
| Ormosia emarginata | 2 |
| Ornithoboea wildeana | 2 |
| Ornithoctonus huwena | 1 |
| Ornithodoros moubata | 5 |
| Ornithodoros savignyi | 1 |
| Ornithogalum caudatum | 3 |
| Ornithogalum longibracteatum | 2 |
| Ornithogalum mosaic virus | 1 |
| Ornithorhynchus anatinus | 11 |
| Orobanche caryophyllacea | 1 |
| Orobanche cernua | 3 |
| Orobanche corymbosa | 3 |
| Orobanche fasciculata | 3 |
| Orobanche hederae | 1 |
| Orobanche minor | 2 |
| Orobanche ramosa | 2 |
| Orobanche uniflora | 1 |
| Orontium aquaticum | 5 |
| Oroperipatus corrodai | 1 |
| Orothamnus zeyheri | 2 |
| Oroxylum indicum | 2 |
| Orpinomyces joyonii | 2 |
| Orpinomyces sp. PC-2 | 7 |
| Ortalis vetula | 2 |
| Orthiopteris kingii | 2 |
| Orthoceras strictum | 2 |
| Orthochirus scrobiculosus | 1 |
| Orthocricus sp. 'Spi1' | 2 |
| Orthodes crenulata | 3 |
| Orthodicranum flagellare | 1 |
| Orthodicranum fulvum | 3 |
| Orthodontium lineare | 3 |
| Orthonyx spaldingii | 2 |
| Orthopodomyia alba | 1 |
| Orthoporus ornata | 2 |
| Orthostichopsis tetragona | 1 |
| Orthothecium chryseum | 1 |
| Orthothecium intricatum | 1 |
| Orthothecium rufescens | 3 |
| Orthotomicus caelatus | 2 |
| Orthotrichum alpestre | 1 |
| Orthotrichum anomalum | 3 |
| Orthotrichum lyelli | 3 |
| Orthotrichum obtusifolium | 3 |
| Orthotrichum pumilum | 2 |
| Orthrosanthus chimboracensis | 1 |
| Orthrosanthus polistachus | 5 |
| Orychophragmus violaceus | 3 |
| Orycteropus afer | 7 |
| Oryctes rhinoceros | 1 |
| Oryctolagus cuniculus | 265 |
| Orygma luctuosum | 2 |
| Oryx gazella | 1 |
| Oryx leucoryx | 1 |
| Oryza longistaminata | 2 |
| Oryza meyeriana | 2 |
| Oryza officinalis | 1 |
| Oryza rufipogon | 1 |
| Oryza sativa | 696 |
| Oryzias curvinotus | 3 |
| Oryzias javanicus | 2 |
| Oryzias latipes | 74 |
| Oryzias luzonensis | 2 |
| Oryzias sp. | 1 |
| Osbeckia chinensis | 2 |
| Osbeckia stellata | 2 |
| Oscheius brevesophaga | 1 |
| Oscheius tipulae | 2 |
| Oscillatoria brevis | 2 |
| Oscillatoria chalybea | 2 |
| Oscillatoria limnetica | 1 |
| Oscillatoria sp. NKBG091600 | 4 |
| Oscillatoria sp. PCC 6304 | 1 |
| Oscillatoria sp. PCC 7515 | 1 |
| Osculotes curta | 1 |
| Oserya coulteriana | 2 |
| Osgoodomys banderanus | 1 |
| Osmadenia tenella | 1 |
| Osmaronia cerasiformis | 2 |
| Osmerus mordax | 2 |
| Osmorhiza aristata | 2 |
| Osmunda banksiifolia | 3 |
| Osmunda cinnamomea | 4 |
| Osmunda claytoniana | 2 |
| Osmunda japonica | 2 |
| Osmunda javanica | 2 |
| Osmunda regalis | 2 |
| Osmunda vachellii | 2 |
| Osmundea hybrida | 2 |
| Osmundea osmunda | 2 |
| Osmundea pinnatifida | 3 |
| Osmundea ramosissima | 2 |
| Osmundea truncata | 2 |
| Osteoglossum bicirrhosum | 3 |
| Ostericum sieboldii | 2 |
| Ostertagia ostertagi | 13 |
| Ostiophyllum sonderopeltidis | 2 |
| Ostiophyllum sonderopeltis | 2 |
| Ostodes paniculata | 2 |
| Ostrea edulis | 4 |
| Ostreobium quekettii | 2 |
| Ostrinia furnacalis | 2 |
| Ostrinia latipennis | 1 |
| Ostrinia nubilalis | 4 |
| Ostrinia palustralis | 1 |
| Ostrya virginiana | 1 |
| Ostryopsis davidiana | 2 |
| Osyris lanceolata | 5 |
| Otholobium sericeum | 2 |
| Otidoecus houbarae | 2 |
| Otiophora cupheoidea | 2 |
| Otolemur crassicaudatus | 2 |
| Otolemur garnettii | 1 |
| Otomeria oculata | 2 |
| Otomys angoniensis | 1 |
| Otostegia tomentosa | 2 |
| Ottelia alismoides | 2 |
| Ottelia ulvifolia | 2 |
| Oubanguia alata | 2 |
| Oubanguia sp. Breteler 13096 | 2 |
| Ouratea duparquetiana | 2 |
| Ovibos moschatus | 2 |
| Ovidia andina | 2 |
| Ovine adenovirus A | 5 |
| Ovine adenovirus D | 4 |
| Ovine enzootic nasal tumour virus | 2 |
| Ovine lentivirus | 3 |
| Ovine papillomavirus 1 | 3 |
| Ovine papillomavirus 2 | 3 |
| Ovine pulmonary adenocarcinoma virus | 3 |
| Ovis aries | 134 |
| Ovis sp. | 7 |
| Ovophis okinavensis | 1 |
| Owenia fusiformis | 4 |
| Oxalis dillenii | 2 |
| Oxalis regnellii | 2 |
| Oxalis tuberosa | 1 |
| Oxalobacter formigenes | 1 |
| Oxidus gracilus | 2 |
| Oxyanthus pyriformis | 2 |
| Oxyanthus sp. 'Andreasen 1997' | 2 |
| Oxycaryum cubense | 2 |
| Oxyceros sp. Ridsdale 2235 | 2 |
| Oxychloe andina | 3 |
| Oxydendrum arboreum | 3 |
| Oxylipeurus chiniri | 1 |
| Oxypoda longipes | 1 |
| Oxyrhynchus volubilis | 2 |
| Oxytricha granulifera | 5 |
| Oxytricha longa | 1 |
| Oxytropis pilosa | 1 |
| Oxyuranus scutellatus | 2 |
| Ozodiceromyia sp. | 2 |
| Ozopemon brownei | 1 |
| Ozopemon uniseriatus | 1 |
| Ozophora clevelandii | 2 |
| Onion yellows phytoplasm | 277 |
