Orthodb8-i5K-portal

OrthoDB8 clustering and mapping of i5K species

PRIVATE DATA: please contact i5K project leaders for usage permissions.
Please contact Evgeny Zdobnov with any questions (Evgeny dot Zdobnov at unige dot ch)

Species

10 i5K species included in OrthoDB8 clustering
18 i5K species later mapped to OrthoDB8
Many other arthropods from OrthoDB8
Selected outgroup species from OrthoDB8

Orthologous groups
Group ID and Gene ID text files for all species and all major radiations of the phylogeny
Metazoa, Arthropoda, Insecta, Endopterygota, Diptera, Lepidoptera, Coleoptera, Hymenoptera, etc.

Phylogenomics and Gene Families
Phylogenies of the major radiations with ultrametric trees and gene family evolution etc. View
Significantly different median gene counts per lineage View

Protein Alignment Data

1. Pairwise alignments: for each pair of species ::: SpeciesA_SpeciesB.align

2. Best-Reciprocal-Hits: for each pair of species ::: SpeciesA_SpeciesB.brh

Columns in .align and .brh files = protein_id1 protein_id2 score evalue percent_identity start1 end1 start2 end2

3. ID maps: OrthoDB protein ID to public protein ID mapping ::: SPECIES.idmap.txt

4. 97% paralogs: near-identical proteins from each species are identified before clustering/mapping
One representative (longest) is chosen for clustering/mapping, then its paralogs are added at the end
SPECIES.97pc.txt files give the representative protein ID followed by a comma-seperated list of its paralogs

# Order Code TaxonID Species & Name Mapped/Clustered

8 Arachnida CSCUL 218467 Centruroides sculpturatus Bark scorpion MAPPED
ISCAP 6945 Ixodes scapularis Black-legged deer tick CLUSTERED
LHESP 256737 Latrodectus hesperus Western black widow spider MAPPED
LRECL 6921 Loxosceles reclusa Brown recluse spider MAPPED
MOCCI 34638 Metaseiulus occidentalis Western predatory mite CLUSTERED
PTEPI 114398 Parasteatoda tepidariorum Common house spider MAPPED
SMIMO 407821 Stegodyphus mimosarum African social velvet spider CLUSTERED
TURTI 32264 Tetranychus urticae Two-spotted spider mite CLUSTERED

1 Blattodea BGERM 6973 Blattella germanica German cockroach MAPPED

6 Coleoptera AGLAB 217634 Anoplophora glabripennis Asian longhorned beetle CLUSTERED
APLAN 224129 Agrilus planipennis Emerald ash borer MAPPED
DPOND 77166 Dendroctonus ponderosae Mountain pine beetle CLUSTERED
LDECE 7539 Leptinotarsa decemlineata Colorado potato beetle CLUSTERED
OTAUR 166361 Onthophagus taurus Bull-headed dung beetle MAPPED
TCAST 7070 Tribolium castaneum Red flour beetle CLUSTERED

3 Crustacea DPULE 6669 Daphnia pulex Water flea CLUSTERED
EAFFI 88015 Eurytemora affinis Calanoid copepod MAPPED
HAZTE 294128 Hyalella azteca Freshwater epibenthic amphipod MAPPED

1 Diplura CAQUI 438503 Catajapyx aquilonaris Silvestris Northern Forcepstail MAPPED

14 Diptera AAEGY 7159 Aedes aegypti Yellowfever mosquito CLUSTERED
AALBI 7167 Anopheles albimanus New World malaria mosquito CLUSTERED
AFUNE 62324 Anopheles funestus African malaria mosquito CLUSTERED
AGAMB 7165 Anopheles gambiae African malaria mosquito CLUSTERED
CCAPI 7213 Ceratitis capitata Mediterranean fruit fly CLUSTERED
CQUIN 7176 Culex quinquefasciatus Southern house mosquito CLUSTERED
DGRIM 7222 Drosophila grimshawi Fruit fly CLUSTERED
DMELA 7227 Drosophila melanogaster Fruit fly CLUSTERED
DPSEU 7237 Drosophila pseudoobscura Fruit fly CLUSTERED
GMORS 7394 Glossina morsitans Savannah tsetse fly CLUSTERED
LCUP2 7375 Lucilia cuprina Sheep blowfly MAPPED
LLONG 7200 Lutzomyia longipalpis Sand Fly CLUSTERED
MDEST 39758 Mayetiola destructor Hessian fly CLUSTERED
MDOME 7370 Musca domestica House fly CLUSTERED

1 Ephemeroptera EDANI 1049336 Ephemera danica Green drake mayfly CLUSTERED

7 Hemiptera APISU 7029 Acyrthosiphon pisum Pea aphid CLUSTERED
CLECT 79782 Cimex lectularius Bed bug CLUSTERED
GBUEN 56086 Gerris buenoi Water strider MAPPED
HHALY 286706 Halyomorpha halys Brown marmorated stink bug MAPPED
HVITR 197043 Homalodisca vitripennis Glassy winged sharpshooter MAPPED
OFAS2 77536 Oncopeltus fasciatus Milkweed bug MAPPED
PVENU 38123 Pachypsylla venusta Hackberry petiole gall psyllid MAPPED

24 Hymenoptera ACEPH 12957 Atta cephalotes Leafcutter ant CLUSTERED
AECHI 103372 Acromyrmex echinatior Panamanian leafcutter ant CLUSTERED
AFLOR 7463 Apis florea Little honey bee CLUSTERED
AMELL 7460 Apis mellifera Honey bee CLUSTERED
AROSA 37344 Athalia rosae Turnip sawfly CLUSTERED
BIMPA 132113 Bombus impatiens Common eastern bumble bee CLUSTERED
BTERR 30195 Bombus terrestris Buff-tailed bumble bee CLUSTERED
CCINC 211228 Cephus cinctus Wheat stem sawfly CLUSTERED
CFLOR 104421 Camponotus floridanus Florida carpenter ant CLUSTERED
COBSC 286306 Cardiocondyla obscurior Tramp ant CLUSTERED
COPFL 29053 Copidosoma floridanum Wasp MAPPED
DNOVA 178035 Dufourea novaeangliae Solitary univoltine bee CLUSTERED
EMEXI 516756 Eufriesea mexicana Orchid bee CLUSTERED
HLABO 597456 Habropoda laboriosa Southeastern blueberry bee CLUSTERED
HSALT 610380 Harpegnathos saltator Jerdons jumping ant CLUSTERED
LALBI 88501 Lasioglossum albipes Halictid bee CLUSTERED
LHUMI 83485 Linepithema humile Argentine ant CLUSTERED
MQUAD 166423 Melipona quadrifasciata Neotropical stingless bee CLUSTERED
MROTU 143995 Megachile rotundata Alfalfa leafcutting bee CLUSTERED
NVITR 7425 Nasonia vitripennis Parasitic jewel wasp CLUSTERED
OABIE 222816 Orussus abietinus Parasitic wood wasp CLUSTERED
PBARB 144034 Pogonomyrmex barbatus Red harvester ant CLUSTERED
SINVI 13686 Solenopsis invicta Red fire ant CLUSTERED
TPRET 7493 Trichogramma pretiosum Parasitic stingless wasp CLUSTERED

1 Isoptera ZNEVA 136037 Zootermopsis nevadensis Dampwood termite CLUSTERED

5 Lepidoptera BMORI 7091 Bombyx mori Domestic silkworm moth CLUSTERED
DPLEX 13037 Danaus plexippus Monarch butterfly CLUSTERED
HMELP 34740 Heliconius melpomene Postman butterfly CLUSTERED
MSEXT 7130 Manduca sexta Tobacco hornworm moth CLUSTERED
PXYLO 51655 Plutella xylostella Diamondback moth CLUSTERED

1 Myriapoda SMARI 126957 Strigamia maritima Geophilimorph centipede CLUSTERED

1 Odonata LFULV 123851 Ladona fulva Scarce chaser dragonfly CLUSTERED

13 Outgroups BTAUR 9913 Bos taurus Cattle CLUSTERED
CELEG 6239 Caenorhabditis elegans Nematode worm CLUSTERED
CINTE 7719 Ciona intestinalis Vase tunicate sea squirt CLUSTERED
CTELE 283909 Capitella teleta Polychaete annelid worm CLUSTERED
DRERI 7955 Danio rerio Zebrafish CLUSTERED
GGALL 9031 Gallus gallus Chicken CLUSTERED
HSAPI 9606 Homo sapiens Human CLUSTERED
LGIGA 225164 Lottia gigantea Owl limpet mollusc CLUSTERED
MMUSC 10090 Mus musculus House mouse CLUSTERED
NVECT 45351 Nematostella vectensis Starlet sea anemone CLUSTERED
OANAT 9258 Ornithorhynchus anatinus Duckbill platypus CLUSTERED
SPURP 7668 Strongylocentrotus purpuratus Purple sea urchin CLUSTERED
XTROP 8364 Xenopus tropicalis Western clawed frog CLUSTERED

1 Phthiraptera PHUMA 121225 Pediculus humanus Body louse CLUSTERED

1 Thysanoptera FOCCI 133901 Frankliniella occidentalis Western flower thrip CLUSTERED

1 Trichoptera LLUNA 1218281 Limnephilus lunatus Caddisfly MAPPED

# Order	Code	TaxonID	Species & Name	Mapped/Clustered

8 Arachnida	CSCUL	218467	Centruroides sculpturatus Bark scorpion	MAPPED
	ISCAP	6945	Ixodes scapularis Black-legged deer tick	CLUSTERED
	LHESP	256737	Latrodectus hesperus Western black widow spider	MAPPED
	LRECL	6921	Loxosceles reclusa Brown recluse spider	MAPPED
	MOCCI	34638	Metaseiulus occidentalis Western predatory mite	CLUSTERED
	PTEPI	114398	Parasteatoda tepidariorum Common house spider	MAPPED
	SMIMO	407821	Stegodyphus mimosarum African social velvet spider	CLUSTERED
	TURTI	32264	Tetranychus urticae Two-spotted spider mite	CLUSTERED

1 Blattodea	BGERM	6973	Blattella germanica German cockroach	MAPPED

6 Coleoptera	AGLAB	217634	Anoplophora glabripennis Asian longhorned beetle	CLUSTERED
	APLAN	224129	Agrilus planipennis Emerald ash borer	MAPPED
	DPOND	77166	Dendroctonus ponderosae Mountain pine beetle	CLUSTERED
	LDECE	7539	Leptinotarsa decemlineata Colorado potato beetle	CLUSTERED
	OTAUR	166361	Onthophagus taurus Bull-headed dung beetle	MAPPED
	TCAST	7070	Tribolium castaneum Red flour beetle	CLUSTERED

3 Crustacea	DPULE	6669	Daphnia pulex Water flea	CLUSTERED
	EAFFI	88015	Eurytemora affinis Calanoid copepod	MAPPED
	HAZTE	294128	Hyalella azteca Freshwater epibenthic amphipod	MAPPED

1 Diplura	CAQUI	438503	Catajapyx aquilonaris Silvestris Northern Forcepstail	MAPPED

14 Diptera	AAEGY	7159	Aedes aegypti Yellowfever mosquito	CLUSTERED
	AALBI	7167	Anopheles albimanus New World malaria mosquito	CLUSTERED
	AFUNE	62324	Anopheles funestus African malaria mosquito	CLUSTERED
	AGAMB	7165	Anopheles gambiae African malaria mosquito	CLUSTERED
	CCAPI	7213	Ceratitis capitata Mediterranean fruit fly	CLUSTERED
	CQUIN	7176	Culex quinquefasciatus Southern house mosquito	CLUSTERED
	DGRIM	7222	Drosophila grimshawi Fruit fly	CLUSTERED
	DMELA	7227	Drosophila melanogaster Fruit fly	CLUSTERED
	DPSEU	7237	Drosophila pseudoobscura Fruit fly	CLUSTERED
	GMORS	7394	Glossina morsitans Savannah tsetse fly	CLUSTERED
	LCUP2	7375	Lucilia cuprina Sheep blowfly	MAPPED
	LLONG	7200	Lutzomyia longipalpis Sand Fly	CLUSTERED
	MDEST	39758	Mayetiola destructor Hessian fly	CLUSTERED
	MDOME	7370	Musca domestica House fly	CLUSTERED

1 Ephemeroptera	EDANI	1049336	Ephemera danica Green drake mayfly	CLUSTERED

7 Hemiptera	APISU	7029	Acyrthosiphon pisum Pea aphid	CLUSTERED
	CLECT	79782	Cimex lectularius Bed bug	CLUSTERED
	GBUEN	56086	Gerris buenoi Water strider	MAPPED
	HHALY	286706	Halyomorpha halys Brown marmorated stink bug	MAPPED
	HVITR	197043	Homalodisca vitripennis Glassy winged sharpshooter	MAPPED
	OFAS2	77536	Oncopeltus fasciatus Milkweed bug	MAPPED
	PVENU	38123	Pachypsylla venusta Hackberry petiole gall psyllid	MAPPED

24 Hymenoptera	ACEPH	12957	Atta cephalotes Leafcutter ant	CLUSTERED
	AECHI	103372	Acromyrmex echinatior Panamanian leafcutter ant	CLUSTERED
	AFLOR	7463	Apis florea Little honey bee	CLUSTERED
	AMELL	7460	Apis mellifera Honey bee	CLUSTERED
	AROSA	37344	Athalia rosae Turnip sawfly	CLUSTERED
	BIMPA	132113	Bombus impatiens Common eastern bumble bee	CLUSTERED
	BTERR	30195	Bombus terrestris Buff-tailed bumble bee	CLUSTERED
	CCINC	211228	Cephus cinctus Wheat stem sawfly	CLUSTERED
	CFLOR	104421	Camponotus floridanus Florida carpenter ant	CLUSTERED
	COBSC	286306	Cardiocondyla obscurior Tramp ant	CLUSTERED
	COPFL	29053	Copidosoma floridanum Wasp	MAPPED
	DNOVA	178035	Dufourea novaeangliae Solitary univoltine bee	CLUSTERED
	EMEXI	516756	Eufriesea mexicana Orchid bee	CLUSTERED
	HLABO	597456	Habropoda laboriosa Southeastern blueberry bee	CLUSTERED
	HSALT	610380	Harpegnathos saltator Jerdons jumping ant	CLUSTERED
	LALBI	88501	Lasioglossum albipes Halictid bee	CLUSTERED
	LHUMI	83485	Linepithema humile Argentine ant	CLUSTERED
	MQUAD	166423	Melipona quadrifasciata Neotropical stingless bee	CLUSTERED
	MROTU	143995	Megachile rotundata Alfalfa leafcutting bee	CLUSTERED
	NVITR	7425	Nasonia vitripennis Parasitic jewel wasp	CLUSTERED
	OABIE	222816	Orussus abietinus Parasitic wood wasp	CLUSTERED
	PBARB	144034	Pogonomyrmex barbatus Red harvester ant	CLUSTERED
	SINVI	13686	Solenopsis invicta Red fire ant	CLUSTERED
	TPRET	7493	Trichogramma pretiosum Parasitic stingless wasp	CLUSTERED

1 Isoptera	ZNEVA	136037	Zootermopsis nevadensis Dampwood termite	CLUSTERED

5 Lepidoptera	BMORI	7091	Bombyx mori Domestic silkworm moth	CLUSTERED
	DPLEX	13037	Danaus plexippus Monarch butterfly	CLUSTERED
	HMELP	34740	Heliconius melpomene Postman butterfly	CLUSTERED
	MSEXT	7130	Manduca sexta Tobacco hornworm moth	CLUSTERED
	PXYLO	51655	Plutella xylostella Diamondback moth	CLUSTERED

1 Myriapoda	SMARI	126957	Strigamia maritima Geophilimorph centipede	CLUSTERED

1 Odonata	LFULV	123851	Ladona fulva Scarce chaser dragonfly	CLUSTERED

13 Outgroups	BTAUR	9913	Bos taurus Cattle	CLUSTERED
	CELEG	6239	Caenorhabditis elegans Nematode worm	CLUSTERED
	CINTE	7719	Ciona intestinalis Vase tunicate sea squirt	CLUSTERED
	CTELE	283909	Capitella teleta Polychaete annelid worm	CLUSTERED
	DRERI	7955	Danio rerio Zebrafish	CLUSTERED
	GGALL	9031	Gallus gallus Chicken	CLUSTERED
	HSAPI	9606	Homo sapiens Human	CLUSTERED
	LGIGA	225164	Lottia gigantea Owl limpet mollusc	CLUSTERED
	MMUSC	10090	Mus musculus House mouse	CLUSTERED
	NVECT	45351	Nematostella vectensis Starlet sea anemone	CLUSTERED
	OANAT	9258	Ornithorhynchus anatinus Duckbill platypus	CLUSTERED
	SPURP	7668	Strongylocentrotus purpuratus Purple sea urchin	CLUSTERED
	XTROP	8364	Xenopus tropicalis Western clawed frog	CLUSTERED

1 Phthiraptera	PHUMA	121225	Pediculus humanus Body louse	CLUSTERED

1 Thysanoptera	FOCCI	133901	Frankliniella occidentalis Western flower thrip	CLUSTERED

1 Trichoptera	LLUNA	1218281	Limnephilus lunatus Caddisfly	MAPPED

LINKS: Zdobnov's Computational Evolutionary Genomics Group CEGG and the Hierarchical Catalog of Orthologs OrthoDB