Supplementary material Table 2. Names of the 192 ... - Nature

Supplementary material Table 2. Names of the 192 sequences used for the test of the clustering levels in V4. AB080597.1.1745 Endomyxa;Ascetosporea;Haplosporida;Haplosporidium;;Haplosporidium nelsoni DQ356000.1.1762 Endomyxa;Ascetosporea;Haplosporida;Bonamia;;Bonamia perspora AY542903.1.1749 Endomyxa;Ascetosporea;Haplosporida;Bonamia;;Bonamia sp. ex Crassostrea ariakensis GQ366703.1.1746 Endomyxa;Ascetosporea;Haplosporida;Bonamia;;Bonamia sp. ex Ostrea chilensis AY449710.1.1747 Endomyxa;Ascetosporea;Haplosporida;Minchinia;;Minchinia tapetis FJ518816.1.1752 Endomyxa;Ascetosporea;Haplosporida;Minchinia;;Minchinia mercenariae U20320.1.1781 Endomyxa;Ascetosporea;Haplosporida;Minchinia;;Minchinia teredinis AY449711.1.1745 Endomyxa;Ascetosporea;Haplosporida;Minchinia;;Minchinia chitonis AF387122.1.1731 Endomyxa;Ascetosporea;Haplosporida;Haplosporidium;;Haplosporidium costale DQ458793.1.1744 Endomyxa;Ascetosporea;Haplosporida;Haplosporidium;;Haplosporidium edule AY449713.1.1789 Endomyxa;Ascetosporea;Haplosporida;Haplosporidium;;Haplosporidium lusitanicum AY452724.1.1635 Endomyxa;Ascetosporea;Haplosporida;Haplosporidium;;Haplosporidium pickfordi JN368430.1.1763 Endomyxa;Ascetosporea;Haplosporida;Haplosporidium;;Haplosporidium tuxtlensis DQ219484.1.1872 Endomyxa;Ascetosporea;Haplosporida;Haplosporidium;;Haplosporidium montforti gi|90652776|dbj|AB218766.1| Conchellium capsula gene for 18S rRNA partial sequence gi|90652777|dbj|AB218767.1| Protocystis xiphodon gene for 18S rRNA partial sequence gi|33089869|gb|AY266292.1| Aulosphaera trigonopa gi|33089871|gb|AY266294.1| Aulacantha scolymantha gi|33089870|gb|AY266293.1| Coelodendrum ramosissimum gi|90652775|dbj|AB218765.1| Challengeron diodon gene for 18S rRNA partial sequence AB558956.1.1768 Thecofilosea;uncultured;;Mataza hastifera gi|83367174|gb|DQ303924.1| Protaspa grandis 18S small subunit gi|225794700|gb|FJ824121.1| Protaspa obliqua isolate 1 small subunit ribosomal RNA gene, partial sequence AF290539.1.1815 Thecofilosea;Cryomonadida;Protaspidae;Cryothecomonas;;Cryothecomonas aestivalis gi|409971368|dbj|AB714270.1| Esquamula lacrimiformis gene for 18S ribosomal RNA partial sequence gi|82547951|gb|DQ211593.1| Peregrinia clavideferens gi|33309621|gb|AF411267.1| Cercomonas alexieffi 18S ribosomal RNA gene complete sequence gi|262262816|gb|FJ790709.1| Cercomonas parincurva strain IVY7A 18S gi|33309623|gb|AF411268.1| Cercomonas plasmodialis 18S ribosomal RNA gene complete sequence gi|262262809|gb|FJ790702.1| Cercomonas braziliensis strain B13 18S gi|262262818|gb|FJ790711.1| Cercomonas vacuolata strain Wyth3.8 18S gi|262262817|gb|FJ790710.1| Cercomonas celer strain C-51 18S gi|262262811|gb|FJ790704.1| Cercomonas clavideferens strain 17-12D 18S gi|48727881|gb|AY620256.1| Teretomonas rotunda gi|262262802|gb|FJ790695.1| Cercomonas kiaerdammane strain NY12 18S gi|262262792|gb|FJ790685.1| Cercomonas hiberna strain W70 18S gi|262262791|gb|FJ790684.1| Cercomonas mtoleri strain BuffaloH5 18S

gi|262262788|gb|FJ790681.1| Cercomonas media strain xt182 18S gi|262262789|gb|FJ790682.1| Cercomonas hederae strain IVY20 18S gi|262262794|gb|FJ790687.1| Cercomonas ricae strain IB3 18S gi|262262806|gb|FJ790699.1| Cercomonas elliptica strain N8 18S gi|262262808|gb|FJ790701.1| Cercomonas rotunda strain IVY9G 18S gi|262262807|gb|FJ790700.1| Cercomonas fastiga strain 18-3D 18S gi|262262801|gb|FJ790694.1| Cercomonas rapida strain 18-6E 18S gi|262262805|gb|FJ790698.1| Cercomonas paraglobosa strain 19-3E 18S gi|262262798|gb|FJ790691.1| Cercomonas lenta strain WA84 18S gi|262262797|gb|FJ790690.1| Cercomonas nebulosa strain xt164 18S AF411259.1.1822 Silicofilosea;Thaumatomonadida;Thaumatomonadidae;Thaumatomonas;;Thaumatomonas seravini gi|82547950|gb|DQ211592.1| Thaumatomonas coloniensis strain HFCC93 18S gi|336245474|gb|HM536165.1| Nucleocercomonas praelonga strain HFCC 920 18S gi|323652737|gb|HQ121434.1| Nudifila producta strain CCAP 1911/1 18S small subunit gi|225794707|gb|FJ824128.1| Ventrifissura foliiformis gi|225794706|gb|FJ824127.1| Ventrifissura artocarpoidea AY082998.1.1818 Thecofilosea;Cryomonadida;Rhizaspididae;Rhogostoma;;Rhogostoma minus gi|323652733|gb|HQ121430.1| Rhogostoma schuessleri strain CCAP 1966/1 18S small subunit gi|262262824|gb|FJ790717.1| Cavernomonas stercoris strain Cav-E 18S gi|262262825|gb|FJ790718.1| Cavernomonas mira strain Cav-A 18S gi|346983232|emb|FR846196.1| Thaumatomastix salina partial 18S rRNA gene isolate OF258 gi|262262810|gb|FJ790703.1| Cercomonas effusa strain Beaver-Creek 18S gi|83367172|gb|DQ303922.1| Ebria tripartita isolate 1 18S small subunit gi|225794705|gb|FJ824126.1| Botuliforma benthica gi|77994699|gb|DQ199662.1| Aurigamonas solis strain Glasgow 18S gi|194272461|gb|EU567254.1| Limnofila longa gi|194272463|gb|EU567256.1| Limnofila oxoniensis gi|38640506|gb|AF411284.1| Limnofila borokensis gi|194272462|gb|EU567255.1| Limnofila anglica gi|33309652|gb|AF411283.1| Mesofila limnetica gi|33309658|gb|AF411286.1| Massisteria marina 18S ribosomal RNA gene complete sequence gi|323652744|gb|HQ121441.1| Micrometopion nutans strain CCAP 1904/1 18S small subunit gi|262262820|gb|FJ790713.1| Eocercomonas uvella strain 11-7E 18S gi|262262821|gb|FJ790714.1| Eocercomonas minuscula strain C-73 18S gi|262262823|gb|FJ790716.1| Eocercomonas echina strain IVY19 18S gi|262262822|gb|FJ790715.1| Eocercomonas tribula strain IVY16A 18S AF411269.1.1773 Cercomonadidae;Cercomonas;;Cercomonas edax gi|262262800|gb|FJ790693.1| Cercomonas volcana strain C18 18S gi|262262799|gb|FJ790692.1| Cercomonas mutans strain W40a 18S gi|262262819|gb|FJ790712.1| Cercomonas radiata strain xt134 18S gi|33641923|gb|AY268040.1| Reckertia filosa gi|323652742|gb|HQ121439.1| Tremula longifila ATCC 50530 18S small subunit ribosomal RNA gene, partial sequence gi|262262835|gb|FJ790728.1| Paracercomonas ambulans strain W80 18S gi|262262834|gb|FJ790727.1| Paracercomonas astra strain W89 18S gi|262262830|gb|FJ790723.1| Paracercomonas compacta strain xt198 18S

gi|262262836|gb|FJ790729.1| Paracercomonas elongata strain IVY11 18S gi|262262831|gb|FJ790724.1| Paracercomonas oxoniensis strain WA8 18S gi|262262828|gb|FJ790721.1| Paracercomonas producta strain WA42 18S gi|46393903|gb|AY496047.1| Paracercomonas ekelundi strain SCCAP C1 small subunit ribosomal RNA gene, partial sequence gi|262262832|gb|FJ790725.1| Paracercomonas crassicauda strain ATCC 50316 18S gi|33309627|gb|AF411270.1| Cercomonas longicauda 18S ribosomal RNA gene complete sequence gi|262262838|gb|FJ790731.1| Paracercomonas saepenatans strain CA5HKV 18S gi|262262837|gb|FJ790730.1| Paracercomonas paralaciniaegerens strain 31-1C 18S gi|82547955|gb|DQ211597.1| Cercomonas metabolicus strain HFCC88 18S gi|10644702|gb|AF289081.1| Nanofila marina AJ561116.1.1817 Silicofilosea;Marimonadida;Pseudopirsonia;;Pseudopirsonia mucosa gi|323652741|gb|HQ121438.1| Agitata vibrans ATCC 50407 18S small subunit ribosomal RNA gene, partial sequence gi|58414943|gb|AY748806.1| Agitata tremulans strain CCAP 1910/1 18S ribosomal RNA gene, partial sequence gi|18075907|emb|AJ418784.1| Euglypha rotunda 18S rRNA gene strain Teneriffa AJ418786.1.1786 Silicofilosea;Euglyphida;Euglyphidae;Euglypha;;Euglypha filifera gi|18075910|emb|AJ418787.1| Euglypha tuberculata 18S rRNA gene strain Millstream gi|18077598|emb|AJ418792.1| Trinema enchelys 18S rRNA gene gi|133902273|gb|EF456752.1| Trinema lineare small subunit ribosomal RNA gene, partial sequence gi|133902272|gb|EF456751.1| Corythion dubium small subunit ribosomal RNA gene, partial sequence gi|18075908|emb|AJ418785.1| Euglypha filifera 18S rRNA gene strain Costa Rica gi|18075911|emb|AJ418788.1| Euglypha acanthophora 18S rRNA gene strain Millstream gi|133902274|gb|EF456753.1| Euglypha penardi small subunit ribosomal RNA gene, partial sequence gi|18077596|emb|AJ418789.1| Trachelocorythion pulchellum 18S rRNA gene gi|18073055|emb|AJ418791.1| Assulina muscorum 18S rRNA gene gi|133902270|gb|EF456749.1| Assulina seminulum small subunit ribosomal RNA gene, partial sequence gi|133902267|gb|EF456748.1| Placocista spinosa small subunit ribosomal RNA gene, partial sequence gi|18073056|emb|AJ418793.1| Cyphoderia ampulla 18S rRNA gene gi|283777583|gb|GU228897.1| Cyphoderia major isolate Rila 1 small subunit ribosomal RNA gene, partial sequence gi|283777543|gb|GU228857.1| Cyphoderia compressa isolate Galata 1 small subunit ribosomal RNA gene, partial sequence gi|283777540|gb|GU228854.1| Cyphoderia littoralis isolate Galata 1 small subunit ribosomal RNA gene, partial sequence gi|283777572|gb|GU228886.1| Cyphoderia amphoralis isolate Rila 1 small subunit ribosomal RNA gene, partial sequence gi|283777555|gb|GU228869.1| Cyphoderia trochus palustris isolate Marchairuz 1 small subunit ribosomal RNA gene, partial sequence gi|283777538|gb|GU228852.1| Pseudocorythion acutum isolate Galata 1 small subunit ribosomal RNA gene, partial sequence gi|323652735|gb|HQ121432.1| Ovulinata parva strain CCAP 1554/1 18S small subunit gi|224549839|gb|FJ456918.1| Paulinella chromatophora strain FK01 18S

gi|225794709|gb|FJ824130.1| Verrucomonas longifila gi|225794708|gb|FJ824129.1| Verrucomonas bifida CC-2009e small subunit ribosomal RNA gene, partial sequence AF411276.1.1857 Glissomonadida;Bodomorpha;;Bodomorpha minima gi|82547952|gb|DQ211594.1| Bodomorpha minima strain HFCC55 18S gi|33309617|gb|AF411265.1| Allapsa vibrans gi|33309637|gb|AF411275.1| Proleptomonas faecicola 18S ribosomal RNA gene, complete sequence gi|33309647|gb|AF411280.1| Spongomonas minima strain ATCC 50404 18S ribosomal RNA gene complete sequence gi|219524790|gb|EU709153.1| Sandona ubiquita gi|219524799|gb|EU709162.1| Sandona afra 18S ribosomal RNA gene, partial sequence gi|205361657|gb|EU734844.1| Sandona aporians 18S ribosomal RNA gene, partial sequence gi|219524779|gb|EU709142.1| Sandona tetramutans WA46ap86t11LS 18S ribosomal RNA gene, partial sequence gi|219524777|gb|EU709140.1| Sandona dimutans G11 18S ribosomal RNA gene, partial sequence gi|219524780|gb|EU709143.1| Sandona trimutans 18S ribosomal RNA gene, partial sequence gi|219524784|gb|EU709147.1| Sandona pentamutans 18S ribosomal RNA gene, partial sequence gi|219524775|gb|EU709138.1| Sandona mutans 18S ribosomal RNA gene, partial sequence gi|219524810|gb|EU709173.1| Sandona similis 18S ribosomal RNA gene, partial sequence gi|219524811|gb|EU709174.1| Sandona trisimilis 18S ribosomal RNA gene, partial sequence gi|219524809|gb|EU709172.1| Sandona disimilis 18S ribosomal RNA gene, partial sequence gi|219524812|gb|EU709175.1| Sandona tetrasimilis 18S ribosomal RNA gene, partial sequence gi|205361658|gb|EU734845.1| Neoheteromita caudratti KV-Pc 18S ribosomal RNA gene, partial sequence gi|219524826|gb|EU709189.1| Flectomonas lenta 18S ribosomal RNA gene, partial sequence gi|46393899|gb|AY496043.1| Flectomonas ekelundi(Heteromita globosa) strain SCCAP H251 small subunit ribosomal RNA gene, partial sequence gi|219524848|gb|EU709211.1| Neoheteromita hederae 18S ribosomal RNA gene, partial sequence gi|323652736|gb|HQ121433.1| Neoheteromita tolerans gi|219524849|gb|EU709212.1| Neoheteromita soli 18S ribosomal RNA gene, partial sequence gi|1695785|gb|U42447.1|HGU42447 Neoheteromita globosa 18S ribosomal RNA gene, complete sequence gi|219524792|gb|EU709155.1| Sandona aestiva 18S ribosomal RNA gene, partial sequence gi|62632909|gb|AY905499.1| Sandona campae PRA-74 18S ribosomal RNA gene, partial sequence gi|262262814|gb|FJ790707.1| Cercomonas pigra strain CASphII 18S gi|262262813|gb|FJ790706.1| Cercomonas magna strain IVY8C 18S gi|262262815|gb|FJ790708.1| Cercomonas sphagnicola strain CASphI 18S gi|194272499|gb|EU567292.1| Filoreta turcica gi|33641927|gb|AY268044.1| Filoreta marina AJ418794.1.1798 Thecofilosea;Phaeodarea;Incertae Sedis;Pseudodifflugia;;Pseudodifflugia cf. gracilis gi|336245476|gb|HM536167.1| Metabolomonas insania strain HFCC 922 18S gi|323652743|gb|HQ121440.1| Paracercomonas baikali B148 18S small subunit ribosomal RNA gene, partial sequence gi|33309631|gb|AF411272.1| Paracercomonas anaerobica sp. ATCC 50367 18S ribosomal RNA gene, complete sequence gi|237846377|gb|FJ919772.1| Clautriavia biflagellata gi|187438878|gb|EU484393.1| Auranticordis quadriverberis isolate 1

gi|378735000|emb|HE609039.1| Leptophrys vorax partial 18S rRNA gene strain LV.04 gi|194272501|gb|EU567294.1| Arachnula impatiens strain BaikalA155 18S gi|62903120|gb|AY941200.1| Platyreta germanica strain Fritzlar-Werkel 18S gi|378734996|emb|HE609035.1| Vampyrella pendula partial 18S rRNA gene strain VP.01 gi|378735001|emb|HE609040.1| Vampyrella lateritia partial 18S rRNA gene strain VL.01 gi|148514622|gb|EF405665.1| Minimassisteria diva strain HFCC380 18S ribosomal RNA gene, partial sequence gi|262262829|gb|FJ790722.1| Paracercomonas filosa strain 17-1F 18S gi|48727879|gb|AY620254.1| Metromonas simplex clone TC-S small subunit ribosomal RNA gene, complete sequence AF411281.1.1803 Silicofilosea;Spongomonadida;Spongomonas;;Spongomonas minima gi|323652738|gb|HQ121435.1| Spongomonas solitaria AB452995.1.1694 Silicofilosea;Chlorarachniophyta;Partenskyella;;Partenskyella glossopodia AF054832.1.1762 Silicofilosea;Chlorarachniophyta;Bigelowiella;;Bigelowiella natans gi|424124|gb|U03477.1|CRU03477 Chlorarachnion reptans CCMP 238 clones pF55 and pF56 18S rRNA small subunit gi|397310687|gb|JX272635.1| Minorisa minuta isolate 6C1 18S AB526843.1.3105 Endomyxa;Phytomyxea;Plasmodiophora;;Plasmodiophora brassicae gi|15088523|gb|AF310901.1| Spongospora subterranea f. sp. nasturtii AF310902.1.1841 Endomyxa;Phytomyxea;Polymyxa;;Polymyxa betae gi|15088520|gb|AF310898.1| Polymyxa graminis 18S small subunit gi|15088522|gb|AF310900.1| Sorosphaera veronicae 18S small subunit gi|15088526|gb|AF310904.1| Phagomyxa odontellae 18S small subunit gi|15088525|gb|AF310903.1| Phagomyxa bellerocheae 18S small subunit AF405547.1.1802 Endomyxa;Phytomyxea;Maullinia;;Maullinia ectocarpi gi|18077597|emb|AJ418790.1| Tracheleuglypha dentata 18S rRNA gene U47851.1.1702 Endomyxa;Ascetosporea;Haplosporida;Haplosporidium;;Haplosporidium louisiana AJ457811.1.1891 Endomyxa;Gromia;;Gromia oviformis AY305009.1.2157 Clathrulinidae;Hedriocystis;;Clathrulina elegans AY305010.1.2094 Clathrulinidae;Hedriocystis;;Hedriocystis reticulata gi|33309660|gb|AF411287.1| Sainouron acronematica 18S ribosomal RNA gene complete sequence gi|419066668|gb|KC109665.1| Reticulamoeba gemmipara strain 7 18S small subunit ribosomal RNA gene complete sequence gi|419066664|gb|KC109661.1| Reticulamoeba minor strain 3 18S small subunit ribosomal RNA gene complete sequence gi|238617589|gb|FJ973364.1| Cholamonas cyrtodiopsidis strain ATCC 50325 18S gi|237687967|gb|FJ410915.1| Helkesimastix sp. ATCC 50328 18S AF054889.1.1794 Silicofilosea;Chlorarachniophyta;Lotharella;;Lotharella vacuolata AF076178.1.1710 Silicofilosea;Chlorarachniophyta;Lotharella;;Lotharella globosa AF076175.1.1732 Silicofilosea;Chlorarachniophyta;Gymnochlora;;Gymnochlora stellata gi|424123|gb|U03275.1|CRU03275 Chlorarachnion reptans CCMP 238 clone pF54 18S rRNA small subunit