Supplementary Table S1: Sequence completeness of 293 taxa shown in percentages of amino acid positions (AA) in the supermatrix. Taxa in bold (148) were selected for phylogenetic analyses. Highlights indicate taxa that have been combined in chimeric sequences resulting a final dataset of 109 operational taxonomic units (OTUs). AA positions in Operational taxonomic unit supermatrix Acanthamoeba castellanii Acastellanii_strNEFF_v1 78% Acanthamoeba castellanii N/A 2% Acanthocystis sp. N/A 90% Alexandrium monilatum CCMP3105 89% Amastigomonas sp. N/A 85% Amoebophrya sp. N/A 83% Amphidinium carterae CCMP1314 92% Ancoracysta twista TD 81% Aplanochytrium kerguelense N/A 84% Aplanochytrium sp. PBS07 75% Aplanochytrium stocchinoi GSBS06 68% Arabidopsis lyrata N/A 38% Arabidopsis thaliana N/A 23% Arabidopsis thaliana TAIR10 94% Aristerostoma sp. ATCC50986 65% Asterionellopsis glacialis CCMP134 88% Asterionellopsis glacialis CCMP1581 84% Asterionellopsis glacialis N/A 12% Astrolonche serrata N/A 46% Aurantiochytrium limacinum N/A 89% Aureococcus anophagefferens N/A 88% Aureoumbra lagunensis CCMP1510 75% Babesia bovis N/A 81% Batrachochytrium dendrobatidis N/A 94% Bigelowiella natans N/A 90% Blastocystis hominis N/A 82% Blastocystis sp. subtype_4 82% Bodo saltans N/A 85% Bolidomonas pacifica CCMP1866 92% Bolidomonas pacifica RCC208 85% Bolidomonas sp. RCC2347 85% Brachypodium distachyon N/A 90% Branchiostoma floridae N/A 95% Breviata anathema N/A 37% Cafeteria roenbergensis E4-10 65% Cafeteria sp. CaronLabIsolate 85% Calcidiscus leptoporus RCC1130 85% Capsaspora owczarzaki C_owczarzaki_V2 91% Capsaspora owczarzaki N/A 6% Chattonella subsalsa CCMP2191 90% Chlamydomonas reinhardtii N/A 92% Chlorarachnion reptans CCCM449 85% Chlorella vulgaris N/A 83% Choanocystis sp. N/A 90% Chondrus crispus N/A 83% Chromera velia CCMP2878 75% Chromera velia N/A 14% Chroomonas mesostigmatica CCMP1168 93% Chrysoculter rhomboideus RCC1486 77% Climacostomum virens StockW-24 64% Coccomyxa sp. N/A 92% Coleochaete scutata N/A 67% Collodictyon sp. N/A 40% Colpodella angusta N/A 35% Colpodella edax N/A 68% Colpodella sp. N/A 62% Compsopogon caeruleus SAG36.94 58% Crypthecodinium cohnii Seligo 91% Cryptococcus neoformans N/A 88% Cryptomonas curvata CCAP979_52 83% Cryptophyceae sp. CCMP2293 94% Cryptophyceae sp. N/A 94% Cryptosporidium muris N/A 82% Cunea sp. BSH-02190019_may 83% Cyanidioschyzon merolae N/A 76% Cyanophora paradoxa N/A 85% Cyanoptyche gloeocystis SAG4.97 71% Danio rerio N/A 92% Daphnia pulex N/A 90% Dictyocha speculum CCMP1381 91% Dictyostelium discoideum N/A 90% Dictyostelium lacteum ASM160615v1 91% Dictyostelium purpureum N/A 87% Ditylum brightwellii GSO103 83% Ditylum brightwellii GSO105 90% Drosophila melanogaster BDGP6 97% Ectocarpus siliculosus N/A 95% Elphidium margaritaceum N/A 85% Emiliania huxleyi 374 63% Emiliania huxleyi 379 73% Emiliania huxleyi CCMP370 76% Emiliania huxleyi PLYM219 79% Emiliania huxleyi N/A 6% Erythranthe guttata N/A 90% Erythrolobus australicus CCMP3124 57% Erythrolobus madagascarensis CCMP3276 56% Euplotes focardii TN1 71% Euplotes harpa FSP1.4 71% Eutreptiella gymnastica CCMP1594 44% Eutreptiella gymnastica NIES-381 44% Fibrocapsa japonica CCMP1661 77% Galdieria sulphuraria N/A 83% Geminigera cryophila CCMP2564 95% Geminigera sp. N/A 93% Gloeochaete wittrockiana SAG46.84 89% Goniomonas pacifica CCMP1869 91% Goniomonas pacifica N/A 8% Goniomonas sp. m 78% Gromia sphaerica N/A 52% Gromia sphaerica SRR2003399 32% Guillardia theta N/A 96% Hammondia hammondi HHA1_v02 91% Haptolina brevifila UTEXLB985 87% Hematodinium sp. N/A 69% Hematodinium sp. SG-2015 2% Hemiselmis andersenii CCMP1180 22% Hemiselmis andersenii CCMP439 22% Hemiselmis andersenii CCMP441 10% Hemiselmis andersenii CCMP644 40% Hemiselmis rufescens PCC563 91% Heterosigma akashiwo CCMP2393 82% Homo sapiens N/A 99% Ichthyophthirius multifiliis N/A 83% Isochrysis galbana CCMP1323 91% Isochrysis galbana N/A 3% Jakoba bahamiensis N/A 27% Jakoba libera N/A 24% Karenia brevis CCMP2229 40% Karenia brevis SP1 17% Karenia brevis SP3 7% Karenia brevis Wilson 31% Karlodinium veneficum CCMP2283 94% Karlodinium veneficum N/A 18% Leptocylindrus danicus B650 90% Leptocylindrus danicus CCMP1856 87% Leptomonas pyrrhocoris ASM129339v1 95% Litonotus pictus P1 56% Lottia gigantea N/A 91% Madagascaria erythrocladoides CCMP3234 60% Malawimonas californiana N/A 34% Malawimonas jakobiformis N/A 44% Mallomonas sp. CCMP3275 81% Mantoniella antarctica SL-175 85% Mantoniella sp. CCMP1436 78% Mesostigma viride n/a 58% Mesostigma viride N/A 29% Micromonas sp. CCMP2099 72% Micromonas sp. N/A 73% Micromonas sp. NEPCC29 54% Micromonas sp. RCC472 54% Moneuplotes crassus CT5 71% Monosiga brevicollis N/A 88% Mus musculus N/A 99% Naegleria gruberi N/A 79% Nannochloropsis gaditana ASM24072v1 19% Nannochloropsis gaditana N/A 26% Nannochloropsis gaditana NagaB31_1 83% Nematostella vectensis N/A 95% Neobodo designis CCAP1951_1 90% Nephroselmis pyriformis CCMP717 83% Neurospora crassa N/A 87% Noctiluca scintillans N/A 86% Nuclearia sp. SRR1617645 89% Nutomonas longa SRR1617398 78% Ochromonas sp. BG-1 81% Ochromonas sp. CCMP1393 92% Ochromonas sp. CCMP1899 82% Odontella aurita isolate1302-5 91% Oryza sativa N/A 92% Ostreococcus lucimarinus clade-A-BCC118000 68% Ostreococcus lucimarinus N/A 46% Ostreococcus mediterraneus clade-D-RCC1107 72% Ostreococcus mediterraneus clade-D-RCC1621 69% Ostreococcus mediterraneus clade-D-RCC2572 73% Ostreococcus mediterraneus clade-D-RCC2573 69% Ostreococcus mediterraneus clade-D-RCC2593 72% Ostreococcus mediterraneus clade-D-RCC2596 77% Oxyrrhis marina CCMP1795 26% Oxyrrhis marina LB1974 90% Oxyrrhis marina n/a 85% Oxyrrhis marina N/A 20% Oxytricha trifallax oxytricha_asm_v1.1 93% Oxytricha trifallax Oxytricha_MIC_v2.0 0% Palpitomonas bilix NIES-2562 78% Paramecium tetraurelia N/A 82% Paraphysomonas bandaiensis N/A 97% Paraphysomonas imperforata PA2 85% Pavlovales sp. N/A 92% Undescribed Pavlovaceae CCMP2436 90% Pelagomonas calceolata CCMP1756 92% Pelagomonas calceolata RCC969 81% Percolomonas cosmopolitus AE-1 68% Percolomonas cosmopolitus WS 81% Perkinsela sp. ASM123584v1 77% Perkinsus marinus N/A 84% Phaeocystis antarctica CaronLabIsolate 60% Phaeocystis antarctica CCMP1374 35% Phaeocystis sp. CCMP2710 77% Phaeodactylum tricornutum N/A 89% Phaeomonas parva CCMP2877 73% Pinguiococcus pyrenoidosus CCMP2078 60% Phycomyces blakesleeanus N/A 90% Physcomitrella patens N/A 93% Phytophthora capsici N/A 77% Phytophthora infestans ASM14294v1 96% Phytophthora ramorum ASM14973v1 96% Phytophthora ramorum N/A 2% Phytophthora sojae N/A 13% Phytophthora sojae P_sojae_V3_0 95% Picobiliphyte sp. MS584-11 23% Picocystis salinarum CCMP1897 64% Plasmodiophora brassicae N/A 9% Plasmodiophora brassicae pbe3.h15 94% Plasmodium chabaudi N/A 28% Plasmodium chabaudi PCHAS01 87% Plasmodium falciparum N/A 15% Plasmodium falciparum Plas_falc_7G8_V1 84% Platyophrya macrostoma WH 85% Pleurochrysis carterae CCMP645 95% Polysphondylium pallidum N/A 90% Populus trichocarpa N/A 92% Porphyra purpurea N/A 64% Porphyra umbilicalis 4086291 81% Porphyra umbilicalis N/A 63% Porphyridium aerugineum SAG1380-2 62% Porphyridium purpureum N/A 83% Prasinoderma singulare RCC927 78% Protocruzia adherens Boccale 71% Prymnesium parvum N/A 2% Prymnesium parvum Texoma1 93% Prymnesium polylepis CCMP1757 84% Prymnesium polylepis UIO037 8% Pseudokeronopsis sp. Brazil 61% Pseudokeronopsis sp. OXSARD2 59% Pseudopedinella elastica CCMP716 93% Pycnococcus sp. CCMP1998 62% Undescribed Chlorophyta RCC1871 66% Undescribed Chlorophyta RCC2335 54% Pygsuia biforma N/A 90% Pyramimonas sp. CCMP2087 90% Raineriophrys erinaceoides N/A 92% Raphidiophrys ambigua N/A 46% Raphidiophrys heterophryoidea N/A 92% Reclinomonas americana N/A 52% Reticulomyxa filosa N/A 93% Rhizochromulina marina CCMP1243 87% Rhizopus delemar RO3 91% Rhodella violacea CCMP736 71% Rhodomonas abbreviata CaronLabIsolate 84% Rhodomonas sp. CCMP768 86% Rhodosorus marinus CCMP769 75% Rhodosorus marinus UTEXLB2760 75% Roombia truncata N/A 69% Salpingoeca rosetta Proterospongia_sp_ATCC50818 93% Salpingoeca sp. N/A 16% Saprolegnia diclina Sap_diclina_VS20_V1 98% Saprolegnia parasitica N/A 91% Sawyeria marylandensis N/A 38% Schizochytrium aggregatum N/A 89% Schizosaccharomyces pombe ASM294v2 90% Schizosaccharomyces pombe N/A 5% Schmidingerella taraikaensis FeNarragansettBay 65% Scyphosphaera apsteinii RCC1455 86% Seculamonas ecuadoriensis N/A 35% Selaginella moellendorffii N/A 92% Sexangularia sp. ATCC50979 64% Spizellomyces punctatus S_punctatus_V1 96% Spumella elongata CCAP955_1 95% Stereomyxa ramosa Chinc5 79% Sterkiella histriomuscorum N/A 82% Strombidinopsis acuminatum SPMC142 65% Strombidinopsis sp. SopsisLIS2011 52% Strombidium inclinatum S3 72% Strombidium rassoulzadegani ras09 73% Symbiodinium sp. C1 93% Symbiodinium sp. C15 88% Synchroma pusillum CCMP3072 79% Telonema sp. P1 58% Telonema sp. P2 98% Telonema subtile N/A 56% Telonema subtile Tel-1 99% Tetrahymena thermophila N/A 89% Tetraselmis astigmatica CCMP880 91% Thalassiosira pseudonana N/A 90% Thalassiosira rotula CCMP3096 92% Thalassiosira rotula GSO102 87% Thecamonas trahens N/A 79% Thraustochytrium sp. LLF1b 88% Toxoplasma gondii N/A 85% Trichoplax adhaerens ASM15027v1 96% Trichosphaerium sp. Am-I-7wt 72% Tsukubamonas globosa N/A 67% Undescribed Rhizaria D1 92% Undescribed Stramenopila-Sagenista MAST4 42% Ustilago maydis N/A 83% Vannella sp. DIVA3517_6_12 82% Vaucheria litorea CCMP2940 70% Vitrella brassicaformis CCMP3155 69% Vitrella brassicaformis Vbrassicaformis 96% Volvox carteri N/A 93% Voromonas pontica GG 60% Voromonas pontica N/A 18% Zea mays AGPv4 92%