Supplementary Information

Palpitomonas bilix represents a basal cryptist lineage: insight into the character evolution in Cryptista.

Akinori Yabuki1,*, Ryoma Kamikawa2,3,*, Sohta A. Ishikawa4,5,, Martin Kolisko6,†, Eunsoo Kim7, Akifumi S. Tanabe5,‡, Keitaro Kume5, Ken-ichiro Ishida5, Yuji Inagki5,8

1 Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Kanagawa, Japan 2 Graduate School of Human and Environmental Studies, Kyoto University, Kyoto, Kyoto, Japan 3 Graduate School of Global Environmental Studies, Kyoto University, Kyoto, Kyoto, Japan 4 Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki, Japan 5 Graduate School of Systems and Information Engineering, University of Tsukuba, Tsukuba, Ibaraki, Japan 6 Departments of Biology, Dalhousie University, Halifax, Nova Scotia, Canada. 7 Sackler Institute for Comparative Genomics and Division of Invertebrate Zoology, American Museum of Natural History, New York, NY, USA 8 Center for Computational Sciences, University of Tsukuba, Tsukuba, Ibaraki, Japan

*A. Y. and R. K. contributed equally to this study. †Current address of MK: Canadian Institute for Advanced Research, Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada ‡Current address of AST: National Research Institute of Fisheries Science, Fisheries Research Agency, Yokohama, Kanagawa, Japan

1 Table S1. Data used in this work. ar21 arc20 arf3 arpc1 atp6 Alpha-tubulin Beta-tubulin calr capz cct-A Taxa Seq length Missing Seq length Missing Seq length Missing Seq length Missing Seq length Missing Seq length Missing Seq length Missing Seq length Missing Seq length Missing Seq length Missing Acanthamoeba castellanii 123 0 160 0 160 0 115 65.4 130 0 403 6.7 251 41.1 165 37.7 168 9.2 135 72.3 Amphimedon queenlandica 123 0 160 0 160 0 172 48.2 130 0 236 45.4 263 38.3 129 51.3 156 15.7 152 68.9 Andalucia incarcerata 123 0 128 20 160 0 0 100 130 0 214 50.5 426 0 0 100 0 100 385 21.1 Arabidopsis thaliana 123 0 160 0 160 0 332 0 130 0 432 0 426 0 265 0 185 0 488 0 Aureococcus anophagefferens 123 0 160 0 160 0 332 0 130 0 432 0 426 0 0 100 185 0 488 0 Bigelowiella natans 123 0 160 0 143 10.6 332 0 130 0 432 0 387 9.2 265 0 175 5.4 488 0 Capsaspora owczarzaki 123 0 160 0 160 0 332 0 130 0 432 0 426 0 265 0 185 0 488 0 Chlamydomonas reinharditii 121 1.6 160 0 160 0 332 0 130 0 432 0 426 0 265 0 0 100 416 14.8 Chondrus crispus 0 100 0 100 149 6.9 0 100 0 100 218 49.5 426 0 0 100 0 100 65 86.7 Collodictyon triciliatum 118 4.1 125 21.9 0 100 192 42.2 0 100 185 57.2 187 56.1 0 100 129 30.3 124 74.6 Cryptosporidium parvum 0 100 0 100 160 0 332 0 130 0 432 0 426 0 0 100 0 100 487 0.2 Cyanidioschyzon merolae 0 100 0 100 139 13.1 149 55.1 130 0 432 0 426 0 0 100 0 100 487 0.2 Cyanophora paradoxa 0 100 160 0 160 0 293 11.7 130 0 428 0.9 426 0 264 0.4 0 100 213 56.4 Dictyostelium discoideum 123 0 160 0 160 0 332 0 130 0 425 1.6 426 0 265 0 185 0 488 0 Diplonema papillatum 105 14.6 0 100 160 0 0 100 0 100 169 60.9 0 100 0 100 0 100 0 100 Diacronema (Pavlova) lutheri 0 100 0 100 160 0 154 53.6 130 0 401 7.2 402 5.6 165 37.7 0 100 0 100 Drosophila melanogaster 123 0 160 0 160 0 332 0 130 0 432 0 426 0 265 0 185 0 488 0 Ectocarpus siliculosus 87 29.3 160 0 160 0 332 0 130 0 432 0 426 0 265 0 185 0 486 0.4 Emiliania huxleyi 123 0 157 1.9 160 0 332 0 130 0 432 0 426 0 263 0.8 138 25.4 288 40.9 Euglena gracilis 0 100 0 100 160 0 0 100 119 8.5 432 0 426 0 184 30.6 0 100 0 100 Galdieria sulphlaria 0 100 0 100 160 0 332 0 130 0 432 0 426 0 259 2.3 0 100 488 0 Glaucocystis nostochinearum 0 100 0 100 160 0 0 100 130 0 330 23.6 265 37.8 110 58.5 0 100 0 100 Goniomonas sp. 0 100 109 31.9 160 0 38 88.6 130 0 385 10.9 204 52.1 39 85.3 0 100 0 100 Gracilaria changii 0 100 0 100 160 0 0 100 130 0 191 55.8 213 50 0 100 0 100 147 69.9 Guillardia theta 113 8.1 160 0 160 0 315 5.1 130 0 425 1.6 426 0 265 0 185 0 488 0 Homo sapiens 123 0 160 0 160 0 332 0 130 0 432 0 426 0 265 0 166 10.3 488 0 Isochrysis galbana 0 100 0 100 103 35.6 135 59.3 108 16.9 156 63.9 0 100 0 100 0 100 0 100 Jakoba bahamensis 0 100 0 100 107 33.1 152 54.2 126 3.1 432 0 426 0 0 100 0 100 181 62.9 Jakoba libera 0 100 106 33.8 160 0 173 47.9 130 0 432 0 426 0 0 100 0 100 0 100 Limnofila borokensis 0 100 0 100 160 0 0 100 0 100 125 71.1 0 100 0 100 0 100 130 73.4 Malawimonas californiensis 95 22.8 160 0 160 0 0 100 130 0 348 19.4 426 0 0 100 0 100 0 100 Malawimonas jakobiformis 0 100 160 0 160 0 135 59.3 130 0 378 12.5 387 9.2 110 58.5 182 1.6 374 23.4 Mastigamoeba balamthii 113 8.1 160 0 160 0 0 100 130 0 402 6.9 354 16.9 265 0 129 30.3 390 20.1 Micromonas sp. 0 100 0 100 160 0 0 100 130 0 289 33.1 426 0 265 0 0 100 482 1.2 Monosiga brevicolis 123 0 154 3.8 160 0 332 0 130 0 432 0 426 0 265 0 185 0 488 0 Naegleria gruberi 123 0 160 0 160 0 332 0 130 0 432 0 426 0 265 0 185 0 0 100 Oryza sativa 123 0 160 0 160 0 332 0 130 0 432 0 426 0 265 0 185 0 488 0 Ostreococcus tauli 121 1.6 160 0 160 0 332 0 130 0 432 0 426 0 0 100 0 100 488 0 Oxyrrhis marina 0 100 0 100 160 0 107 67.8 130 0 253 41.4 426 0 203 23.4 0 100 249 48.9 Palpitomonas bilix 0 100 106 33.8 160 0 55 83.4 130 0 272 37 426 0 168 36.6 158 14.6 203 58.4 Paramecium caudata 0 100 0 100 0 100 0 100 0 100 432 0 426 0 0 100 0 100 96 80.3 Paracercomonas marina 0 100 0 100 160 0 0 100 130 0 214 50.5 0 100 0 100 137 25.9 0 100 Perkinsus marinus 0 100 0 100 160 0 332 0 130 0 429 0.7 426 0 265 0 0 100 260 46.7 Phaeodactylum tricornatum 0 100 0 100 160 0 332 0 130 0 391 9.5 426 0 265 0 155 16.2 485 0.6 Physarum polycephalum 0 100 0 100 160 0 145 56.3 0 100 200 53.7 277 34.9 265 0 158 14.6 240 50.8 Phytophthora infestans 123 0 160 0 160 0 303 8.7 130 0 432 0 426 0 0 100 0 100 488 0 Uncultured picozoa (MS584-11)* 0 100 0 100 0 100 250 24.7 0 100 0 100 390 8.5 0 100 0 100 0 100 Polyplacocystis (Raphidiophrys) contractilis 0 100 0 100 160 0 130 60.8 130 0 378 12.5 387 9.2 265 0 185 0 169 65.4 Prymnesium parvum 0 100 0 100 160 0 0 100 130 0 273 36.8 273 35.9 218 17.7 0 100 173 64.5 Pyropia (Porphyra) yezoensis 0 100 0 100 155 3.1 128 61.4 130 0 173 59.9 176 58.7 0 100 0 100 145 70.3 Reclinomonas americana 123 0 158 1.3 160 0 255 23.2 130 0 432 0 426 0 157 40.8 185 0 228 53.3 Rhodmonas salina 0 100 0 100 160 0 0 100 0 100 249 42.4 364 14.6 0 100 0 100 0 100 Roombia truncata 0 100 0 100 160 0 0 100 130 0 429 0.7 426 0 265 0 142 23.2 283 42 Saccharomyces cereviceae 0 100 0 100 160 0 0 100 130 0 432 0 426 0 0 100 0 100 488 0 Seculamonas ecuadriensis 0 100 0 100 158 1.3 0 100 130 0 432 0 426 0 187 29.4 157 15.1 434 11.1 Stachyamoeba lipophora 0 100 91 43.1 0 100 0 100 0 100 178 58.8 0 100 0 100 0 100 0 100 Telonema subtilis 0 100 0 100 160 0 112 66.3 130 0 395 8.6 387 9.2 265 0 0 100 220 54.9 Tetrahymena pyriformis 0 100 0 100 159 0.6 172 48.2 116 10.8 432 0 375 11.9 0 100 174 5.9 488 0 Thalassiosira pseudonana 0 100 0 100 160 0 332 0 130 0 430 0.5 402 5.6 187 29.4 0 100 488 0 Thecamonas trahens 113 8.1 121 24.4 127 20.6 315 5.1 115 11.5 397 8.1 426 0 0 100 185 0 473 3.1 Toxoplasma gondii 0 100 0 100 160 0 332 0 130 0 432 0 426 0 0 100 185 0 430 11.9 Trimastix pyriformis 123 0 0 100 160 0 72 78.3 113 13.1 432 0 426 0 265 0 176 4.9 216 55.7 Tsukubamonas globosa 123 0 160 0 160 0 170 48.8 130 0 409 5.3 426 0 0 100 185 0 240 50.8 Ustilago maydis 123 0 160 0 160 0 0 100 130 0 430 0.5 425 0.2 0 100 0 100 488 0 Seq length and missing data are represented by bp and %, respectively. *only used for Supplementary file 2 Table S1. Data used in this work (continued). cct-B cct-D cct-E cct-G cct-N cct-T cct-Z cpn60 crfg ctsl1 Taxa Seq length Missing Seq length Missing Seq length Missing Seq length Missing Seq length Missing Seq length Missing Seq length Missing Seq length Missing Seq length Missing Seq length Missing Acanthamoeba castellanii 168 64.6 0 100 302 42.7 150 68.5 144 69.6 82 82.1 114 76.9 0 100 67 82.8 137 0 Amphimedon queenlandica 158 66.7 208 54.9 220 58.3 174 63.4 178 62.4 218 52.3 229 53.7 0 100 0 100 137 0 Andalucia incarcerata 150 68.4 0 100 0 100 168 64.7 0 100 177 61.3 390 21.2 226 53.8 0 100 137 0 Arabidopsis thaliana 474 0 461 0 527 0 457 3.9 474 0 457 0 495 0 489 0 390 0 137 0 Aureococcus anophagefferens 474 0 0 100 527 0 476 0 474 0 0 100 495 0 0 100 390 0 137 0 Bigelowiella natans 474 0 461 0 527 0 476 0 474 0 457 0 495 0 489 0 390 0 137 0 Capsaspora owczarzaki 474 0 461 0 527 0 476 0 474 0 457 0 495 0 295 39.7 390 0 137 0 Chlamydomonas reinharditii 472 0.4 461 0 527 0 459 3.6 474 0 457 0 494 0.2 443 9.4 390 0 137 0 Chondrus crispus 0 100 0 100 0 100 0 100 0 100 0 100 0 100 0 100 0 100 0 100 Collodictyon triciliatum 0 100 130 71.8 98 81.4 190 60.1 185 61.0 235 48.6 347 29.9 0 100 70 82.1 71 48.2 Cryptosporidium parvum 410 13.5 0 100 0 100 472 0.8 474 0 457 0 495 0 489 0 390 0 137 0 Cyanidioschyzon merolae 461 2.7 460 0.2 523 0.8 476 0 474 0 451 1.3 495 0 443 9.4 385 1.3 0 100 Cyanophora paradoxa 301 36.5 83 81.9 199 62.2 126 73.5 0 100 0 100 195 60.6 232 52.6 390 0 0 100 Dictyostelium discoideum 472 0.4 460 0.2 520 1.3 378 20.6 474 0 457 0 349 29.5 488 0.2 380 2.6 137 0 Diplonema papillatum 0 100 0 100 0 100 0 100 0 100 0 100 0 100 0 100 0 100 61 55.5 Diacronema (Pavlova) lutheri 138 70.9 0 100 213 59.6 248 47.9 0 100 83 0 72 85.5 0 100 102 73.8 0 100 Drosophila melanogaster 474 0 461 0 435 17.5 470 1.3 437 7.8 457 0 349 29.5 489 0 390 0 137 0 Ectocarpus siliculosus 474 0 461 0 527 0 476 0 474 0 457 0 495 0 489 0 390 0 137 0 Emiliania huxleyi 436 8 437 5.2 518 1.7 0 100 474 0 368 19.5 495 0 419 14.3 369 5.4 137 0 Euglena gracilis 238 49.8 0 100 264 49.9 181 61.9 201 57.6 202 55.8 0 100 489 0 0 100 74 45.9 Galdieria sulphlaria 474 0 459 0.4 527 0 459 3.6 473 0.2 456 0.2 495 0 488 0.2 377 3.3 0 100 Glaucocystis nostochinearum 0 100 0 100 0 100 0 100 0 100 0 100 0 100 0 100 0 100 0 100 Goniomonas sp. 0 100 92 80 0 100 0 100 0 100 0 100 0 100 172 64.8 0 100 111 Gracilaria changii 0 100 0 100 219 58.4 0 100 135 71.5 176 61.5 71 85.7 129 73.6 0 100 111 18.9 Guillardia theta 217 54.2 461 0 527 0 476 0 474 0 457 0 495 0 489 0 390 0 137 0 Homo sapiens 474 0 461 0 527 0 476 0 474 0 457 0 495 0 489 0 390 0 137 0 Isochrysis galbana 0 100 192 58.4 0 100 0 100 113 76.2 185 59.5 249 49.7 0 100 0 100 0 100 Jakoba bahamensis 0 100 243 47.3 0 100 0 100 160 66.2 0 100 186 62.4 0 100 0 100 137 0 Jakoba libera 190 59.9 0 100 214 59.4 0 100 160 66.2 0 100 0 100 0 100 0 100 137 0 Limnofila borokensis 0 100 0 100 0 100 0 100 0 100 0 100 165 66.7 0 100 0 100 114 16.8 Malawimonas californiensis 0 100 197 57.3 129 75.5 202 57.6 38 91.9 56 87.7 124 74.9 189 61.3 0 100 137 0 Malawimonas jakobiformis 197 58.4 0 100 0 100 0 100 0 100 0 57.9 0 100 0 100 0 100 74 45.9 Mastigamoeba balamthii 0 100 270 41.4 176 66.6 249 47.7 256 45.9 192 0 144 70.9 0 100 0 100 134 2.2 Micromonas sp. 165 65.2 461 0 527 0 455 4.4 474 0 457 0 495 0 462 5.5 390 0 137 0 Monosiga brevicolis 474 0 460 0.2 527 0 476 0 474 0 457 0 495 0 489 0 390 0 137 0 Naegleria gruberi 474 0 461 0 508 3.6 476 0 474 0 457 0 494 0.2 489 0 390 0 137 0 Oryza sativa 472 0.4 461 0 462 12.3 476 0 468 1.3 457 1.3 495 0 489 0 390 0 137 0 Ostreococcus tauli 461 2.7 461 0 527 0 476 0 474 0 451 24.3 495 0 477 2.5 390 0 137 0 Oxyrrhis marina 296 37.6 260 43.6 524 0.6 0 100 0 100 346 56 337 31.9 0 100 275 29.5 137 0 Palpitomonas bilix 251 47 211 54.2 231 56.2 197 58.6 178 62.4 209 54.3 217 56.2 45 90.8 67 82.8 137 0 Paramecium caudata 388 18.1 212 54 249 52.8 228 52.1 474 0 201 100 495 0 0 100 202 48.2 0 100 Paracercomonas marina 180 62 0 100 214 59.4 0 100 213 55.1 0 81.8 0 100 0 100 0 100 53 61.3 Perkinsus marinus 474 0 459 0.4 527 0 476 0 474 0 457 100 495 0 489 0 390 0 137 0 Phaeodactylum tricornatum 471 0.6 448 2.8 523 0.8 476 0 463 2.3 454 0.7 495 0 489 0 377 3.3 137 0 Physarum polycephalum 206 56.5 308 33.2 0 100 476 0 474 0 346 24.3 203 58.9 373 23.7 381 2.3 74 45.9 Phytophthora infestans 472 0.4 461 0 505 4.2 476 0 474 0 454 0.7 495 0 443 9.4 390 0 137 0 Uncultured picozoa (MS584-11)* 242 48.9 0 100 110 79.1 0 100 0 100 0 100 130 73.7 0 100 92 76.4 0 100 Polyplacocystis (Raphidiophrys) contractilis 203 57.2 247 46.4 143 72.9 0 100 200 57.8 0 100 79 84 0 100 124 68.2 126 8 Prymnesium parvum 241 49.2 246 46.6 206 60.9 0 100 0 100 0 100 0 100 243 50.3 0 100 63 54 Pyropia (Porphyra) yezoensis 0 100 146 68.3 110 79.1 154 67.6 0 100 126 72.4 145 70.7 159 67.5 174 55.4 0 100 Reclinomonas americana 0 100 0 100 224 57.5 0 100 0 100 194 57.5 155 68.7 129 73.6 0 100 137 0 Rhodmonas salina 0 100 0 100 0 100 0 100 0 100 0 100 0 100 0 100 0 100 135 1.5 Roombia truncata 474 0 0 100 0 100 0 100 474 0 456 0.2 0 100 0 100 164 57.9 128 6.6 Saccharomyces cereviceae 474 0 461 0 435 17.5 384 19.3 474 0 457 0 349 29.5 0 100 338 13.3 0 100 Seculamonas ecuadriensis 238 49.8 330 28.4 500 5.1 206 56.7 302 36.3 454 0.7 231 53.3 191 60.9 0 100 137 0 Stachyamoeba lipophora 0 100 116 74.8 0 100 0 100 0 100 0 100 0 100 0 100 0 100 113 17.5 Telonema subtilis 218 54 153 66.8 0 100 0 100 158 66.7 0 100 81 83.6 0 100 125 67.9 128 6.6 Tetrahymena pyriformis 456 3.8 461 0 451 14.4 476 0 425 10.3 457 0 428 13.5 489 0 335 14.1 137 0 Thalassiosira pseudonana 462 2.5 451 2.2 524 0.6 383 19.5 464 2.1 455 0.4 495 0 489 0 390 0 0 100 Thecamonas trahens 472 0.4 458 0.7 527 0 439 7.8 474 0 368 19.5 116 76.6 489 0 320 17.9 137 0 Toxoplasma gondii 451 4.9 461 0 523 0.8 476 0 463 2.3 457 0 495 0 489 0 316 18.9 137 0 Trimastix pyriformis 147 68.9 182 60.5 0 100 195 59 139 70.7 163 64.3 222 55.2 0 100 0 100 137 0 Tsukubamonas globosa 255 46.2 192 58.4 527 0 186 60.9 161 66 203 55.6 404 18.4 107 78.1 97 75.1 137 0 Ustilago maydis 474 0 461 0 527 0 476 0 474 0 454 0.7 495 0 489 0 389 0.3 0 100 Seq length and missing data are represented by bp and %, respectively. *only used for Supplementary file 3 Table S1. Data used in this work (continued). eif-5A fh fibri fpps gdi2 glcn gnb2l gnbpa grc5 Gamma-tubulin Taxa Seq length Missing Seq length Missing Seq length Missing Seq length Missing Seq length Missing Seq length Missing Seq length Missing Seq length Missing Seq length Missing Seq length Missing Acanthamoeba castellanii 122 0 288 36.1 230 0 0 100 381 3.3 148 41.7 0 100 85 64.7 204 0 0 100 Amphimedon queenlandica 122 0 0 100 186 19.1 0 100 212 46.2 141 44.5 207 20.7 0 100 204 0 0 100 Andalucia incarcerata 122 0 0 100 0 100 159 30.3 240 39.1 0 100 177 32.2 219 9.1 204 0 0 100 Arabidopsis thaliana 122 0 451 0 230 0 228 0 394 0 254 0 261 0 237 1.7 204 0 385 0 Aureococcus anophagefferens 122 0 451 0 0 100 0 100 368 6.6 0 100 261 0 241 0 204 0 384 0.3 Bigelowiella natans 122 0 451 0 230 0 228 0 392 0.5 254 0 261 0 241 0 202 0.9 348 9.6 Capsaspora owczarzaki 122 0 356 21.1 230 0 228 0 393 0.3 216 14.9 261 0 241 0 204 0 354 8.1 Chlamydomonas reinharditii 122 0 449 0.4 230 0 228 0 394 0 254 0 261 0 0 100 204 0 385 0 Chondrus crispus 122 0 0 100 33 85.7 0 100 169 57.1 0 100 113 56.7 0 100 183 10.3 0 100 Collodictyon triciliatum 79 35.2 0 100 133 42.2 0 100 109 72.3 0 100 213 18.4 0 100 139 31.9 0 100 Cryptosporidium parvum 122 0 0 100 230 0 217 4.8 394 0 254 0 260 0.4 0 100 204 0 385 0 Cyanidioschyzon merolae 122 0 451 0 230 0 228 0 393 0.3 252 0.8 261 0 0 100 204 0 385 0 Cyanophora paradoxa 122 0 0 100 97 57.8 190 16.7 276 29.9 0 100 261 0 0 100 204 0 0 100 Dictyostelium discoideum 122 0 451 0 228 0.9 228 0 394 0 254 0 261 0 241 0 204 0 385 0 Diplonema papillatum 122 0 0 100 0 100 0 100 0 100 0 100 0 100 0 100 198 2.9 0 100 Diacronema (Pavlova) lutheri 122 0 0 100 88 61.7 0 100 281 28.7 0 100 201 22.9 0 100 204 0 226 41.3 Drosophila melanogaster 122 0 450 0.2 230 0 228 0 394 0 254 0 261 0 241 0 204 0 385 0 Ectocarpus siliculosus 122 0 451 0 230 0 228 0 393 0.3 254 0 179 31.4 240 0.4 204 0 385 0 Emiliania huxleyi 122 0 418 7.3 230 0 0 100 373 5.3 254 0 261 0 241 0 204 0 385 0 Euglena gracilis 122 0 0 100 227 1.3 189 17.1 187 52.5 0 100 261 0 0 100 204 0 233 39.5 Galdieria sulphlaria 122 0 449 0.4 229 0.4 226 0.9 389 1.3 253 0.4 261 0 0 100 204 0 385 0 Glaucocystis nostochinearum 122 0 0 100 0 100 227 0.4 331 15.9 0 100 0 100 0 100 181 11.3 0 100 Goniomonas sp. 122 0 0 100 157 31.7 100 56.1 253 35.8 0 100 192 26.4 0 100 204 0 100 Gracilaria changii 122 0 0 100 125 45.7 0 100 0 100 0 100 201 22.9 0 100 204 0 0 100 Guillardia theta 122 0 311 31 230 0 197 13.6 393 0.3 254 0 261 0 0 100 200 1.9 385 0 Homo sapiens 122 0 451 0 230 0 228 0 394 0 254 0 261 0 241 0 204 0 344 10.6 Isochrysis galbana 0 100 118 73.8 0 100 0 100 0 100 0 100 120 54 84 65.1 0 100 194 49.6 Jakoba bahamensis 122 0 181 59.9 201 12.6 0 100 226 42.6 0 100 172 34.1 181 24.9 179 12.3 254 34 Jakoba libera 122 0 294 34.8 0 100 0 100 0 100 0 100 261 0 115 52.3 0 100 0 100 Limnofila borokensis 0 100 0 100 0 100 0 100 0 100 0 100 0 100 0 100 142 30.4 0 100 Malawimonas californiensis 122 0 171 62.1 83 63.9 0 100 237 39.8 0 100 261 0 0 100 204 0 0 100 Malawimonas jakobiformis 122 0 0 100 203 11.7 0 100 200 49.2 186 26.8 261 0 0 100 200 1.9 0 100 Mastigamoeba balamthii 122 0 0 100 145 36.9 0 100 221 43.9 254 0 261 0 215 10.8 204 0 0 100 Micromonas sp. 122 0 441 2.2 230 0 228 0 394 0 254* 0* 261 0 0 100 204 0 385 0 Monosiga brevicolis 122 0 433 3.9 230 0 228 0 393 0.3 254 0 261 0 241 0 204 0 382 0.8 Naegleria gruberi 122 0 451 0 226 1.7 228 0 394 0 254 0 261 0 241 0 204 0 385 0 Oryza sativa 122 0 451 0 230 0 225 1.3 394 0 254 0 261 0 232 3.7 204 0 385 0 Ostreococcus tauli 122 0 449 0.4 230 0 228 0 393 0.3 254 0 261 0 0 100 204 0 385 0 Oxyrrhis marina 122 0 0 100 165 28.3 0 100 160 59.4 0 100 261 0 0 100 133 34.8 0 100 Palpitomonas bilix 118 3.3 148 67.2 219 4.8 110 51.8 253 35.8 76 70.1 261 0 0 100 199 2.5 0 100 Paramecium caudata 0 100 0 100 165 28.3 0 100 0 100 0 100 0 100 0 100 185 9.3 385 0 Paracercomonas marina 0 100 182 59.6 166 27.8 0 100 0 100 0 100 117 55.2 168 30.3 0 100 188 51.2 Perkinsus marinus 122 0 0 100 230 0 228 0 394 0 254 0 261 0 0 100 204 0 385 0 Phaeodactylum tricornatum 122 0 442 1.9 230 0 228 0 394 0 254 0 261 0 241 0 204 0 384 0.3 Physarum polycephalum 0 100 128 71.6 190 17.4 228 0 250 36.5 0 100 228 12.6 241 0 204 0 0 100 Phytophthora infestans 122 0 451 0 230 0 228 0 393 0.3 254 0 261 0 241 0 204 0 385 0 Uncultured picozoa (MS584-11)* 43 64.8 0 100 0 100 0 100 202 48.7 0 100 0 100 0 100 0 100 0 100 Polyplacocystis (Raphidiophrys) contractilis 0 100 115 74.5 206 10.4 0 100 228 42.1 0 100 148 43.3 241 0 204 0 136 64.7 Prymnesium parvum 122 0 0 100 0 100 0 100 175 55.6 0 100 180 31 0 100 185 9.3 0 100 Pyropia (Porphyra) yezoensis 105 13.9 0 100 0 100 0 100 0 100 0 100 138 47.1 0 100 168 17.6 0 100 Reclinomonas americana 122 0 0 100 230 0 0 100 394 0 0 100 261 0 241 0 204 0 0 100 Rhodmonas salina 122 0 0 100 121 47.4 0 100 0 100 0 100 0 100 0 100 198 2.9 0 100 Roombia truncata 122 0 451 0 0 100 0 100 394 0 194 23.6 261 0 241 100 204 0 0 100 Saccharomyces cereviceae 122 0 451 0 230 0 228 0 394 0 0 100 0 100 0 100 204 0 384 0.3 Seculamonas ecuadriensis 121 0.8 400 11.3 230 0 228 0 243 38.3 0 100 261 0 0 100 204 0 0 100 Stachyamoeba lipophora 99 18.9 0 100 0 100 0 100 0 100 0 100 229 12.3 142 41.1 159 22.1 0 100 Telonema subtilis 0 100 51 88.7 158 31.3 0 100 118 70.1 0 100 260 0.4 77 68 103 49.5 106 72.5 Tetrahymena pyriformis 122 0 236 47.7 230 0 0 100 394 0 162 36.2 257 1.5 0 100 204 0 384 0.3 Thalassiosira pseudonana 105 13.9 451 0 207 10 228 0 394 0 254 0 261 0 241 0 204 0 385 0 Thecamonas trahens 113 7.4 451 0 230 0 228 0 350 11.2 245 3.5 97 62.8 0 100 200 1.9 350 9.1 Toxoplasma gondii 122 0 0 100 229 0.4 228 0 394 0 246 3.1 261 0 0 100 204 0 385 0 Trimastix pyriformis 122 0 0 100 230 0 0 100 239 39.3 0 100 261 0 190 21.2 198 2.9 0 100 Tsukubamonas globosa 122 0 0 100 230 0 131 42.5 314 20.3 83 67.3 261 0 67 72.2 204 0 155 59.7 Ustilago maydis 122 0 451 0 230 0 228 0 394 0 145 42.9 261 0 241 0 204 0 385 0 Seq length and missing data are represented by bp and %, respectively. *only used for Supplementary file 4 Table S1. Data used in this work (continued). h3 h4 hla-B hmt1 hsp70C hsp70E hsp70mt hsp90 if2b if2g Taxa Seq length Missing Seq length Missing Seq length Missing Seq length Missing Seq length Missing Seq length Missing Seq length Missing Seq length Missing Seq length Missing Seq length Missing Acanthamoeba castellanii 123 0.8 86 4.4 337 0 144 48 597 0.2 0 100 0 100 244 60.5 0 100 0 100 Amphimedon queenlandica 124 0 80 11.1 200 40.7 0 100 218 63.5 204 64.2 165 68.7 133 78.5 141 0 0 100 Andalucia incarcerata 124 0 90 0 0 100 0 100 291 51.3 0 100 334 36.6 390 36.9 0 100 186 51.3 Arabidopsis thaliana 124 0 0 100 337 0 277 0 598 0 570 0 0 100 618 0 141 0 382 0 Aureococcus anophagefferens 124 0 90 0 337 0 0 100 598 0 0 100 527 0 612 0.9 141 0 382 0 Bigelowiella natans 124 0 90 0 337 0 272 1.8 551 7.9 570 0 526 0.2 561 9.2 141 0 382 0 Capsaspora owczarzaki 124 0 86 4.4 337 0 277 0 597 0.2 570 0 527 0 618 0 141 0 382 0 Chlamydomonas reinharditii 123 0.8 90 0 337 0 277 0 598 0 570 0 527 0 612 0.9 141 0 340 10.9 Chondrus crispus 124 0 90 0 0 100 0 100 598 0 262 54 0 100 500 19.1 0 100 0 100 Collodictyon triciliatum 124 0 85 5.6 0 100 59 78.7 0 100 0 100 0 100 221 64.2 0 100 0 100 Cryptosporidium parvum 124 0 90 0 337 0 277 0 598 0 570 0 527 0 618 0 141 0 382 0 Cyanidioschyzon merolae 124 0 82 8.9 337 0 277 0 598 0 569 0.2 527 0 614 0.6 141 0 374 2.1 Cyanophora paradoxa 124 0 90 0 160 52.5 274 1.1 597 0.2 479 16.0 0 100 595 3.7 139 1.4 240 37.2 Dictyostelium discoideum 124 0 90 0 336 0.3 277 0 598 0 570 0 466 11.6 616 0.3 141 0 342 10.5 Diplonema papillatum 121 2.4 77 14.4 0 100 0 100 0 100 165 71.1 0 100 203 67.2 0 100 0 100 Diacronema (Pavlova) lutheri 56 54.8 90 0 150 55.5 0 100 598 0 0 100 0 100 532 13.9 0 100 240 37.2 Drosophila melanogaster 124 0 90 0 337 0 277 0 596 0.3 570 0 527 0 618 0 141 0 382 0 Ectocarpus siliculosus 124 0 90 0 306 9.2 277 0 598 0 570 0 527 0 612 0.9 141 0 341 10.7 Emiliania huxleyi 124 0 86 4.4 261 22.6 0 100 598 0 570 0 0 100 618 0 131 7.1 284 25.7 Euglena gracilis 124 0 0 100 337 0 0 100 598 0 0 100 0 100 618 0 0 100 177 53.7 Galdieria sulphlaria 124 0 86 4.4 337 0 0 100 597 0.2 570 0 527 100 614 0.6 141 0 381 0.3 Glaucocystis nostochinearum 124 0 90 0 189 43.9 129 53.4 0 100 0 100 0 100 59 90.5 0 100 136 64.4 Goniomonas sp. 82 33.9 0 100 113 66.5 0 100 166 72.2 103 81.9 97 81.6 293 52.6 84 40.4 60 84.3 Gracilaria changii 124 0 85 5.6 218 35.3 227 18.1 197 67.1 243 57.4 0 100 178 71.2 119 15.6 0 100 Guillardia theta 124 0 90 0 336 0.3 277 0 566 5.4 570 0 527 0 612 0.9 141 0 382 0 Homo sapiens 124 0 90 0 337 0 277 0 597 0.2 570 0 527 0 618 0 141 0 382 0 Isochrysis galbana 97 21.8 0 100 156 53.7 0 100 0 100 0 100 0 100 0 100 64 54.6 0 100 Jakoba bahamensis 0 100 64 28.9 305 9.5 0 100 0 100 0 100 0 100 251 59.4 0 100 126 67 Jakoba libera 0 100 0 100 0 100 0 100 0 100 0 100 0 100 389 37.1 0 100 201 47.4 Limnofila borokensis 0 100 0 100 0 100 183 33.9 0 100 0 100 0 100 0 100 0 100 0 100 Malawimonas californiensis 0 100 0 100 0 100 0 100 0 100 0 100 186 64.7 368 40.5 141 0 0 100 Malawimonas jakobiformis 0 100 90 0 0 100 0 100 572 4.3 0 100 0 100 521 15.7 108 23.4 79 79.3 Mastigamoeba balamthii 124 0 90 0 336 0.3 265 4.3 595 0.5 570 0 0 100 511 17.3 100 29.1 0 100 Micromonas sp. 123 0.8 90 0 166 50.7 254 8.3 598 0 570 0 527 0 612 0.9 141 0 0 100 Monosiga brevicolis 124 0 86 4.4 337 0 277 0 597 0.2 570 0 512 2.8 618 0 141 0 382 0 Naegleria gruberi 124 0 85 5.6 337 0 276 0.4 598 0 570 0 527 0 589 4.7 141 0 378 1 Oryza sativa 124 0 90 0 307 8.9 277 0 598 0 570 0 527 0 618 0 141 0 375 1.8 Ostreococcus tauli 124 0 90 0 305 9.5 259 6.5 598 0 570 0 527 0 618 0 141 0 382 0 Oxyrrhis marina 0 100 0 100 195 42.1 0 100 598 0 518 9.1 0 100 617 0.2 141 0 214 43.9 Palpitomonas bilix 106 14.5 86 4.4 172 49.0 195 29.6 213 64.4 0 100 0 100 293 52.6 141 0 66 82.7 Paramecium caudata 0 100 0 100 0 100 0 100 598 0 570 0 0 100 511 17.3 0 100 312 18.3 Paracercomonas marina 0 100 0 100 190 43.6 0 100 0 100 0 100 0 100 32 94.8 0 100 0 100 Perkinsus marinus 124 0 82 8.9 337 0 277 0 598 0 570 0 527 0 618 0 0 100 382 0 Phaeodactylum tricornatum 124 0 90 0 337 0 277 0 598 0 570 0 527 0 528 14.6 141 0 369 3.4 Physarum polycephalum 118 4.8 0 100 337 0 0 100 571 4.5 526 7.7 527 0 618 0 101 28.4 319 16.5 Phytophthora infestans 124 0 90 0 337 0 277 0 598 0 570 0 527 0 516 16.5 138 2.1 382 0 Uncultured picozoa (MS584-11)* 120 3.2 65 27.8 0 100 0 100 0 100 0 100 0 100 310 49.8 78 44.7 0 100 Polyplacocystis (Raphidiophrys) contractilis 123 0.8 86 4.4 172 48.9 117 57.8 596 0.3 0 100 0 100 546 11.7 120 14.9 119 68.8 Prymnesium parvum 124 0 0 100 254 24.6 0 100 268 55.2 256 55.1 264 49.9 272 55.9 107 24.1 0 100 Pyropia (Porphyra) yezoensis 124 0 85 5.6 171 49.3 0 100 175 70.7 0 100 178 66.2 185 70.1 0 100 161 57.9 Reclinomonas americana 124 0 90 0 0 100 193 30.3 0 100 256 55.1 0 100 618 0 139 1.4 120 68.6 Rhodmonas salina 0 100 0 100 157 53.4 0 100 598 0 0 100 0 100 0 100 0 100 0 100 Roombia truncata 124 0 90 100 305 9.5 274 1.1 589 1.5 570 0 527 0 618 0 141 0 382 0 Saccharomyces cereviceae 124 0 0 100 337 0 0 100 597 0.2 570 0 0 100 617 0.2 140 0.7 382 0 Seculamonas ecuadriensis 0 100 0 100 0 100 236 14.8 0 100 0 100 170 67.7 438 29.1 0 100 68 82.2 Stachyamoeba lipophora 0 100 0 100 0 100 151 45.5 0 100 0 100 0 100 200 67.6 0 100 0 100 Telonema subtilis 124 0 78 13.3 151 55.2 0 100 0 100 0 100 0 100 0 100 0 100 0 100 Tetrahymena pyriformis 124 0 90 0 0 100 219 20.9 415 30.6 569 0.2 527 0 618 0 93 34 306 19.9 Thalassiosira pseudonana 124 0 90 0 337 0 277 0 589 1.5 569 0.2 527 0 618 0 129 8.5 382 0 Thecamonas trahens 124 0 86 4.4 336 0.3 271 2.2 595 0.5 570 0 525 0.4 607 1.8 141 0 365 4.5 Toxoplasma gondii 124 0 90 0 337 0 277 0 598 0 570 0 527 0 618 0 141 0 382 0 Trimastix pyriformis 0 100 0 100 337 0 277 0 575 3.8 0 100 0 100 376 39.2 0 100 0 100 Tsukubamonas globosa 123 0.8 86 4.4 0 100 277 0 589 1.5 0 100 0 100 340 44.9 141 0 141 63.1 Ustilago maydis 124 0 90 0 336 0.3 277 0 597 0.2 542 4.9 527 0 578 6.5 141 0 382 0 Seq length and missing data are represented by bp and %, respectively. *only used for Supplementary file 5 Table S1. Data used in this work (continued). if2p if6 ino1 l10a mcm-A mcm-B mcm-C mcm-D metap2 mra1 Taxa Seq length Missing Seq length Missing Seq length Missing Seq length Missing Seq length Missing Seq length Missing Seq length Missing Seq length Missing Seq length Missing Seq length Missing Acanthamoeba castellanii 163 68 110 50.9 135 69 209 0 0 100 0 100 0 100 0 100 0 100 0 100 Amphimedon queenlandica 197 61.4 219 2.2 0 100 209 0 124 68.3 0 100 0 100 0 100 56 80.8 0 100 Andalucia incarcerata 89 82.5 0 100 436 0 209 0 0 100 0 100 0 100 0 100 291 0 0 100 Arabidopsis thaliana 510 0 224 0 436 0 0 100 391 0 545 0 370 0 452 0 291 0 163 0 Aureococcus anophagefferens 510 0 224 0 0 100 0 100 391 0 544 0.2 370 0 452 0 291 0 155 4.9 Bigelowiella natans 510 0 222 0.9 402 7.8 209 0 391 0 545 0 368 0.5 452 0 291 0 163 0 Capsaspora owczarzaki 510 0 224 0 422 3.2 209 0 391 0 545 0 370 0 452 0 291 0 163 0 Chlamydomonas reinharditii 464 9 224 0 436 0 206 1.4 389 0.5 545 0 365 1.4 452 0 291 0 163 0 Chondrus crispus 0 100 0 100 0 100 133 36.4 0 100 0 100 0 100 0 100 0 100 0 100 Collodictyon triciliatum 127 75.1 116 48.2 356 18.3 192 8.1 64 83.6 63 88.4 0 100 114 74.8 129 55.7 0 100 Cryptosporidium parvum 488 4.3 224 0 0 100 209 0 391 0 545 0 370 0 451 0.2 291 0 0 100 Cyanidioschyzon merolae 510 0 224 0 0 100 209 0 391 0 545 0 370 0 452 0 291 0 163 0 Cyanophora paradoxa 0 100 204 8.9 164 62.4 209 0 266 32.0 429 21.3 0 100 430 4.9 173 40.5 148 9.2 Dictyostelium discoideum 488 4.3 220 1.8 436 0 209 0 229 41.4 541 0.7 0 100 450 0.4 291 0 163 0 Diplonema papillatum 0 100 0 100 331 24.1 0 100 0 100 0 100 0 100 0 100 0 100 0 100 Diacronema (Pavlova) lutheri 0 100 0 100 0 100 52 75.1 114 70.8 0 100 0 100 0 100 211 27.5 49 69.9 Drosophila melanogaster 510 0 224 0 436 0 209 0 391 0 545 0 370 0 452 0 291 0 163 0 Ectocarpus siliculosus 500 1.9 0 100 436 0 209 0 391 0 545 0 370 0 452 0 290 0.3 163 0 Emiliania huxleyi 474 7.1 224 0 0 100 209 0 0 100 534 2 348 5.9 425 5.9 284 2.4 160 1.8 Euglena gracilis 218 57.3 224 0 0 100 209 0 0 100 0 100 0 100 0 100 126 56.7 0 100 Galdieria sulphlaria 509 0.2 224 0 434 0.5 209 0 372 4.9 545 0 370 0 452 0 290 0.3 160 1.8 Glaucocystis nostochinearum 0 100 192 14.3 0 100 209 0 0 100 0 100 0 100 0 100 0 100 0 100 Goniomonas sp. 0 100 124 44.6 135 69.0 209 0 0 100 0 100 0 100 0 100 117 59.8 112 31.3 Gracilaria changii 92 81.9 197 12.1 0 100 0 100 0 100 0 100 0 100 0 100 189 35.1 0 100 Guillardia theta 510 0 224 0 436 0 194 7.2 391 0 545 0 368 0.5 452 0 291 0 163 0 Homo sapiens 510 0 224 0 308 29.4 209 0 391 0 545 0 370 0 452 0 291 0 163 0 Isochrysis galbana 0 100 212 5.4 0 100 0 100 88 77.5 0 100 0 100 192 57.5 0 100 0 100 Jakoba bahamensis 204 60 0 100 394 9.6 209 0 0 100 146 73.2 0 100 0 100 206 29.2 0 100 Jakoba libera 0 100 0 100 436 0 116 44.5 0 100 198 63.7 173 53.2 0 100 288 1 0 100 Limnofila borokensis 0 100 0 100 0 100 0 100 0 100 0 100 0 100 0 100 0 100 0 100 Malawimonas californiensis 0 100 203 9.4 0 100 193 7.7 0 100 0 100 0 100 0 100 0 100 0 100 Malawimonas jakobiformis 161 68.4 223 0.4 0 100 209 0 0 100 0 100 0 100 0 100 0 100 139 14.7 Mastigamoeba balamthii 159 68.8 160 28.6 436 0 209 0 0 100 0 100 0 100 0 100 186 36.1 0 100 Micromonas sp. 510 0 224 0 436 0 209 0 0 100 545 0 368 0.5 452 0 290 0.3 163 0 Monosiga brevicolis 500 1.9 224 0 436 0 176 15.8 391 0 544 0.2 370 0 452 0 291 0 149 8.6 Naegleria gruberi 510 0 224 0 436 0 209 0 391 0 0 100 370 0 317 29.9 291 0 163 0 Oryza sativa 510 0 224 0 404 7.3 209 0 391 0 545 0 370 0 452 0 291 0 163 0 Ostreococcus tauli 510 0 215 4 436 0 209 0 391 0 538 1.3 370 0 451 0.2 291 0 163 0 Oxyrrhis marina 0 100 186 16.9 0 100 0 100 200 48.8 0 100 149 59.7 0 100 108 62.9 124 23.9 Palpitomonas bilix 159 68.8 140 37.5 173 60.3 209 0 0 100 74 86.4 0 100 0 100 240 17.5 0 100 Paramecium caudata 510 0 224 0 0 100 0 100 192 50.9 242 55.6 190 48.6 239 47.1 0 100 113 30.7 Paracercomonas marina 0 100 0 100 197 54.8 209 0 0 100 0 100 0 100 0 100 0 100 0 100 Perkinsus marinus 510 0 224 0 0 100 209 0 381 2.6 545 0 370 0 446 1.3 291 0 163 0 Phaeodactylum tricornatum 510 0 224 0 436 0 209 0 391 0 544 0.2 360 2.7 452 0 290 0.3 163 0 Physarum polycephalum 159 68.8 0 100 358 17.9 189 9.6 82 79 0 100 138 62.7 0 100 81 72.2 0 100 Phytophthora infestans 510 0 224 0 436 0 209 0 391 0 545 0 370 0 452 0 290 0.3 162 0.6 Uncultured picozoa (MS584-11)* 0 100 158 29.5 103 76.4 106 49.3 0 100 0 100 0 100 189 58.2 46 84.2 0 100 Polyplacocystis (Raphidiophrys) contractilis 0 100 131 41.5 98 77.5 209 0 0 100 0 100 0 100 0 100 130 55.3 0 100 Prymnesium parvum 0 100 78 65.2 186 57.3 209 0 0 100 79 85.5 0 100 0 100 0 100 0 100 Pyropia (Porphyra) yezoensis 151 70.4 93 58.5 150 65.6 157 24.9 0 100 0 100 0 100 0 100 158 45.7 0 100 Reclinomonas americana 302 40.8 221 1.3 436 0 209 0 0 100 0 100 0 100 0 100 193 33.7 156 4.3 Rhodmonas salina 0 100 39 82.6 0 100 0 100 0 100 0 100 0 100 0 100 0 100 0 100 Roombia truncata 0 100 224 0 91 79.1 209 0 0 100 0 100 0 100 0 100 224 23.0 0 100 Saccharomyces cereviceae 510 0 224 0 0 100 0 100 391 0 545 0 370 0 452 0 291 0 163 0 Seculamonas ecuadriensis 0 100 168 25 182 58.3 192 8.1 0 100 0 100 0 100 223 50.7 38 86.9 0 100 Stachyamoeba lipophora 0 100 0 100 0 100 209 0 0 100 0 100 0 100 0 100 0 100 0 100 Telonema subtilis 0 100 47 79 68 84.4 209 0 0 100 0 100 0 100 0 100 65 77.7 0 100 Tetrahymena pyriformis 507 0.6 207 7.6 0 100 133 36.4 0 100 247 54.7 0 100 235 48 291 0 163 0 Thalassiosira pseudonana 510 0 224 0 436 0 209 0 391 0 545 0 370 0 450 0.4 290 0.3 163 0 Thecamonas trahens 429 15.9 224 0 325 25.5 209 0 391 0 545 0 337 8.9 312 30.9 291 0 123 24.5 Toxoplasma gondii 510 0 195 12.9 0 100 209 0 391 0 544 0.2 370 0 418 7.5 291 0 0 100 Trimastix pyriformis 0 100 223 0.4 183 58 157 24.9 0 100 0 100 0 100 0 100 116 60.1 162 0.6 Tsukubamonas globosa 151 70.4 224 0 235 46.1 209 0 0 100 0 100 0 100 0 100 291 0 162 0.6 Ustilago maydis 505 0.9 224 0 157 63.9 0 100 391 0 545 0 241 34.9 452 0 291 0 163 0 Seq length and missing data are represented by bp and %, respectively. *only used for Supplementary file 6 Table S1. Data used in this work (continued). ndf1 nsf1-C nsf1-E nsf1-G nsf1-I nsf1-J nsf1-K nsf1-L nsf1-M nsf2-A Taxa Seq length Missing Seq length Missing Seq length Missing Seq length Missing Seq length Missing Seq length Missing Seq length Missing Seq length Missing Seq length Missing Seq length Missing Acanthamoeba castellanii 240 41.2 0 100 122 64.5 345 9.4 0 100 175 51.8 303 3.8 0 100 0 100 0 100 Amphimedon queenlandica 221 45.8 209 33.7 158 54.1 195 48.8 0 100 0 100 0 100 212 42.4 0 100 219 69.5 Andalucia incarcerata 0 100 0 100 0 100 0 100 0 100 0 100 159 49.5 0 100 0 100 391 45.6 Arabidopsis thaliana 408 0 315 0 344 0 354 7.1 397 0 339 6.6 315 0 341 7.3 379 0.5 719 0 Aureococcus anophagefferens 408 0 315 0 344 0 357 6.3 397 0 363 0 315 0 366 0.5 0 100 719 0 Bigelowiella natans 408 0 314 0.3 344 0 380 0.3 0 100 343 5.5 315 0 364 1.1 381 0 716 0.4 Capsaspora owczarzaki 408 0 315 0 344 0 380 0.3 397 0 363 0 315 0 368 0 381 0 719 0 Chlamydomonas reinharditii 408 0 314 0.3 344 0 370 2.9 397 0 363 0 315 0 368 0 381 0 719 0 Chondrus crispus 0 100 0 100 0 100 0 100 0 100 0 100 0 100 202 45.1 0 100 383 46.7 Collodictyon triciliatum 184 54.9 0 100 0 100 273 28.3 0 100 136 62.5 0 100 0 100 111 70.9 0 100 Cryptosporidium parvum 0 100 315 0 0 100 381 0 397 0 363 0 315 0 368 0 381 0 712 0.9 Cyanidioschyzon merolae 403 1.2 227 27.9 176 48.8 381 0 381 4 363 0 315 0 368 0 381 0 718 0.1 Cyanophora paradoxa 200 50.9 0 100 0 100 223 41.5 284 28.5 339 6.6 238 24.4 367 25.3 349 8.4 394 45.2 Dictyostelium discoideum 408 0 241 23.5 149 56.7 379 0.5 396 0.3 252 30.6 267 15.2 352 4.3 381 0 719 0 Diplonema papillatum 0 100 0 100 0 100 0 100 0 100 0 100 0 100 0 100 0 100 0 100 Diacronema (Pavlova) lutheri 180 55.9 0 100 0 100 0 100 170 57.2 0 100 275 12.7 0 100 282 25.9 163 77.3 Drosophila melanogaster 0 100 315 0 344 0 355 6.8 397 0 363 0 315 0 368 0 242 36.5 719 0 Ectocarpus siliculosus 408 0 315 0 0 100 380 0.3 0 100 363 0 315 0 366 0.5 381 0 719 0 Emiliania huxleyi 218 46.6 268 14.9 332 3.5 360 5.5 196 50.6 363 0 219 30.5 0 100 376 1.3 716 0.4 Euglena gracilis 198 51.5 206 34.6 0 100 225 40.9 211 46.9 218 39.9 191 39.4 253 31.3 194 49.1 414 42.4 Galdieria sulphlaria 408 0 315 0 344 0 361 5.2 397 0 363 315 0 368 0 381 0 719 0 Glaucocystis nostochinearum 267 34.6 0 100 0 100 0 100 362 8.8 0 100 0 100 206 44 381 0 0 100 Goniomonas sp. 0 100 0 100 0 100 0 100 136 65.7 0 100 0 100 0 100 0 100 86 88.0 Gracilaria changii 0 100 126 60 0 100 0 100 181 54.4 0 100 0 100 0 100 239 37.3 281 60.9 Guillardia theta 408 0 315 0 344 0 342 10.2 397 0 363 0 315 0 368 0 369 3.1 719 0 Homo sapiens 408 0 315 0 344 0 381 0 397 0 363 0 315 0 368 0 381 0 719 0 Isochrysis galbana 0 100 0 100 0 100 0 100 0 100 252 30.6 0 100 0 100 203 46.7 0 100 Jakoba bahamensis 106 74 0 100 0 100 187 50.9 0 100 0 100 216 31.4 286 22.3 381 0 197 72.6 Jakoba libera 200 50.9 0 100 0 100 0 100 132 66.8 141 61.2 81 74.3 199 45.9 0 100 229 68.2 Limnofila borokensis 0 100 0 100 0 100 0 100 174 56.2 0 100 0 100 0 100 0 100 0 100 Malawimonas californiensis 255 37.5 201 36.2 0 100 0 100 0 100 0 100 0 100 0 100 204 46.5 253 64.8 Malawimonas jakobiformis 0 100 0 100 0 100 201 47.2 0 100 219 39.7 137 56.5 218 40.8 195 48.8 0 100 Mastigamoeba balamthii 0 100 0 100 0 100 226 40.7 235 40.8 252 30.6 0 100 158 57.1 344 9.7 332 53.8 Micromonas sp. 408 0 315 0 344 0 381 0 397 0 0 100 315 0 368 0 381 0 719 0 Monosiga brevicolis 408 0 315 0 344 0 381 0 397 0 363 0 315 0 368 0 380 0.3 719 0 Naegleria gruberi 408 0 315 0 0 100 381 0 395 0.5 363 0 315 0 368 0 381 0 718 0.1 Oryza sativa 408 0 315 0 271 21.2 381 0 397 0 362 0.3 315 0 368 0 379 0.5 719 0 Ostreococcus tauli 408 0 266 15.6 344 0 309 18.9 397 0 354 2.5 315 0 368 0 380 0.3 719 0 Oxyrrhis marina 0 100 0 100 0 100 0 100 0 100 0 100 201 36.2 0 100 0 100 239 66.8 Palpitomonas bilix 66 83.8 0 100 0 100 244 36.0 202 49.1 178 51.0 0 100 220 0 0 100 144 80.0 Paramecium caudata 0 100 266 15.6 344 0 381 0 396 0.3 363 0 315 0 368 0 381 0 712 0.9 Paracercomonas marina 74 81.9 0 100 0 100 0 100 0 100 194 46.6 199 36.8 0 100 0 100 0 100 Perkinsus marinus 0 100 315 0 0 100 381 0 391 1.5 362 0.3 315 0 368 0 381 0 713 0.8 Phaeodactylum tricornatum 408 0 315 0 344 0 380 0.3 381 4 363 0 315 0 351 4.6 381 0 719 0 Physarum polycephalum 291 28.7 0 100 203 40.9 0 100 0 100 0 100 0 100 0 100 381 0 266 63 Phytophthora infestans 408 0 228 27.6 344 0 355 6.8 397 0 363 0 315 0 368 0 380 0.3 719 0 Uncultured picozoa (MS584-11)* 398 2.5 0 100 0 100 0 100 0 100 0 100 0 100 0 100 0 100 0 100 Polyplacocystis (Raphidiophrys) contractilis 64 84.3 0 100 0 100 0 100 0 100 153 57.9 0 100 0 100 0 100 236 67.2 Prymnesium parvum 35 91.4 0 100 0 100 195 48.8 243 38.8 0 100 0 100 0 100 0 100 234 67.5 Pyropia (Porphyra) yezoensis 178 56.4 164 47.9 0 100 173 54.6 171 56.9 178 50.9 138 56.2 169 54.1 178 53.3 162 77.5 Reclinomonas americana 157 61.5 315 0 0 100 0 100 0 100 363 0 195 38.1 0 100 0 100 0 100 Rhodmonas salina 0 100 0 100 0 100 0 100 0 100 0 100 0 100 0 100 0 100 0 100 Roombia truncata 407 0.2 191 39.4 0 100 182 52.2 397 0 0 100 315 0 348 5.4 0 100 307 57.3 Saccharomyces cereviceae 0 100 315 0 344 0 239 37.3 397 0 228 37.2 315 0 230 37.5 381 0 713 0.8 Seculamonas ecuadriensis 377 7.6 0 100 0 100 239 37.3 221 44.3 0 100 0 100 283 23.1 0 100 397 44.8 Stachyamoeba lipophora 0 100 0 100 0 100 0 100 0 100 0 100 218 30.8 164 55.4 0 100 0 100 Telonema subtilis 207 49.3 0 100 0 100 0 100 0 100 161 55.6 0 100 368 0 0 100 566 21.3 Tetrahymena pyriformis 240 41.2 0 100 169 50.9 381 0 382 3.8 363 0 315 0 368 0 380 0.3 689 4.2 Thalassiosira pseudonana 408 0 315 0 344 0 354 7.1 397 0 363 0 315 0 366 0.5 381 0 679 5.6 Thecamonas trahens 408 0 266 15.6 299 13.1 344 9.7 397 0 221 39.1 315 0 292 20.7 381 0 455 36.7 Toxoplasma gondii 0 100 304 3.5 344 0 346 9.2 315 20.7 363 0 315 0 355 3.5 381 0 719 0 Trimastix pyriformis 0 100 184 41.6 0 100 376 1.3 192 51.6 0 100 0 100 0 100 0 100 0 100 Tsukubamonas globosa 0 100 92 70.8 0 100 152 60.1 111 72 0 100 0 100 188 48.9 177 53.5 225 68.7 Ustilago maydis 0 100 315 0 0 100 337 11.5 397 0 252 30.6 315 0 339 7.9 353 7.3 719 0 Seq length and missing data are represented by bp and %, respectively. *only used for Supplementary file 7 Table S1. Data used in this work (continued). nsf2-F orf2 osgep pace2A pace2B pace2C pace5 pp2A psmaA psmaB Taxa Seq length Missing Seq length Missing Seq length Missing Seq length Missing Seq length Missing Seq length Missing Seq length Missing Seq length Missing Seq length Missing Seq length Missing Acanthamoeba castellanii 0 100 169 0 227 22.3 0 100 142 34.3 0 100 0 100 272 1.4 181 11.3 180 6.7 Amphimedon queenlandica 0 100 0 100 0 100 137 38.6 173 19.9 0 100 39 74.5 191 30.8 194 4.9 169 12.4 Andalucia incarcerata 0 100 0 100 0 100 0 100 0 100 0 100 0 100 0 100 0 100 193 0 Arabidopsis thaliana 396 0 167 1.2 292 0 223 0 216 0 184 0 153 0 276 0 204 0 193 0 Aureococcus anophagefferens 324 18.2 169 0 292 0 223 0 214 0.9 184 0 153 0 0 100 204 0 193 0 Bigelowiella natans 396 0 169 0 280 4.1 223 0 216 0 184 0 153 0 276 0 204 0 193 0 Capsaspora owczarzaki 396 0 152 10.1 292 0 220 1.3 216 0 184 0 153 0 276 0 204 0 193 0 Chlamydomonas reinharditii 396 0 168 0.6 0 100 215 3.6 216 0 184 0 134 12.4 276 0 204 0 192 0.5 Chondrus crispus 0 100 0 100 0 100 0 100 0 100 0 100 140 8.5 129 53.3 0 100 0 100 Collodictyon triciliatum 231 41.7 0 100 0 100 0 100 0 100 0 100 0 100 0 100 0 100 0 100 Cryptosporidium parvum 396 0 169 0 292 0 215 3.6 215 0.5 184 0 153 0 276 0 204 0 193 0 Cyanidioschyzon merolae 396 0 169 0 292 0 223 0 207 4.2 184 0 153 0 276 0 204 0 193 0 Cyanophora paradoxa 300 24.2 167 1.2 109 62.7 178 20.2 0 100 159 13.6 133 13.1 272 1.4 197 3.4 147 23.8 Dictyostelium discoideum 396 0 169 0 292 0 223 0 216 0 0 100 153 0 276 0 108 47.1 193 0 Diplonema papillatum 0 100 0 100 0 100 0 100 0 100 0 100 0 100 0 100 0 100 0 100 Diacronema (Pavlova) lutheri 0 100 0 100 0 100 0 100 0 100 0 100 0 100 0 100 146 28.4 156 19.2 Drosophila melanogaster 396 0 169 0 292 0 223 0 216 0 155 15.8 153 0 276 0 204 0 193 0 Ectocarpus siliculosus 396 0 169 0 209 28.4 223 0 153 29.2 184 0 153 0 276 0 204 0 193 0 Emiliania huxleyi 368 7.1 168 0.6 0 100 215 3.6 209 3.2 178 3.3 153 0 253 8.3 0 100 193 0 Euglena gracilis 0 100 0 100 0 100 0 100 0 100 0 100 0 100 276 0 204 0 193 0 Galdieria sulphlaria 379 4.3 169 0 292 0 219 1.8 0 100 0 100 145 5.2 276 0 204 0 193 0 Glaucocystis nostochinearum 0 100 142 15.9 0 100 0 100 0 100 0 100 0 100 187 32.2 101 50.5 0 100 Goniomonas sp. 0 100 122 27.8 0 100 0 100 0 100 57 69.0 0 100 120 56.5 0 100 85 56.0 Gracilaria changii 0 100 0 100 0 100 0 100 0 100 90 51.1 140 8.5 0 100 164 19.6 142 26.4 Guillardia theta 396 0 156 7.7 292 0 223 0 216 0 184 0 0 100 0 100 204 0 193 0 Homo sapiens 396 0 169 0 292 0 223 0 216 0 184 0 153 0 276 0 204 0 193 0 Isochrysis galbana 164 58.6 125 26 0 100 0 100 0 100 131 28.8 0 100 187 32.2 0 100 181 6.2 Jakoba bahamensis 0 100 0 100 94 67.8 122 45.3 0 100 0 100 0 100 0 100 0 100 189 2.1 Jakoba libera 195 50.8 0 100 0 100 0 100 0 100 0 100 0 100 0 100 0 100 131 32.1 Limnofila borokensis 0 100 0 100 0 100 0 100 0 100 0 100 0 100 0 100 0 100 0 100 Malawimonas californiensis 165 58.3 167 1.2 0 100 0 100 0 100 0 100 0 100 0 100 154 24.5 0 100 Malawimonas jakobiformis 0 100 0 100 138 52.7 123 44.8 0 100 0 100 0 100 191 30.8 204 0 191 1 Mastigamoeba balamthii 0 100 0 100 0 100 0 100 0 100 0 100 0 100 0 100 191 6.4 0 100 Micromonas sp. 396 0 169 0 286 2.1 223 0 216 0 184 0 153 0 276 0 176 13.7 193 0 Monosiga brevicolis 396 0 169 0 292 0 215 3.6 216 0 184 0 153 0 276 0 204 0 193 0 Naegleria gruberi 396 0 169 0 292 0 223 0 216 0 184 0 153 0 276 0 204 0 193 0 Oryza sativa 396 0 169 0 292 0 223 0 216 0 184 0 153 0 276 0 204 0 193 0 Ostreococcus tauli 396 0 144 14.8 292 0 223 0 216 0 184 0 134 12.4 276 0 204 0 193 0 Oxyrrhis marina 0 100 0 100 0 100 0 100 0 100 0 100 0 100 0 100 204 0 154 20.2 Palpitomonas bilix 0 100 68 59.8 0 100 0 100 0 100 39 78.8 0 100 0 100 165 19.1 180 6.7 Paramecium caudata 396 0 0 100 0 100 0 100 0 100 77 58.2 0 100 0 100 145 28.9 63 67.4 Paracercomonas marina 162 59.1 0 100 0 100 0 100 0 100 0 100 0 100 106 61.6 0 100 0 100 Perkinsus marinus 265 33.1 169 0 0 100 223 0 192 11.1 184 0 153 0 276 0 204 0 193 0 Phaeodactylum tricornatum 396 0 169 0 291 0.3 223 0 215 0.5 181 1.6 152 0.7 276 0 204 0 193 0 Physarum polycephalum 396 0 0 100 0 100 145 34.9 0 100 0 100 0 100 247 10.5 0 100 0 100 Phytophthora infestans 377 4.8 169 0 278 4.8 223 0 215 0.5 184 0 153 0 275 0.4 204 0 193 0 Uncultured picozoa (MS584-11)* 0 100 0 100 0 100 62 72.2 0 100 0 100 0 100 0 100 0 100 0 100 Polyplacocystis (Raphidiophrys) contractilis 0 100 113 33.1 0 100 223 0 0 100 0 100 0 100 147 46.7 0 100 0 100 Prymnesium parvum 0 100 0 100 0 100 0 100 0 100 0 100 0 100 247 10.5 109 46.6 0 100 Pyropia (Porphyra) yezoensis 0 100 0 100 0 100 0 100 138 36.1 0 100 153 0 176 36.2 144 29.4 145 24.9 Reclinomonas americana 0 100 0 100 194 33.6 0 100 0 100 0 100 0 100 276 0 111 45.6 193 0 Rhodmonas salina 0 100 0 100 0 100 0 100 0 100 0 100 0 100 0 100 0 100 0 100 Roombia truncata 0 100 169 0 0 100 148 33.6 43 80.1 0 100 144 5.9 166 39.9 204 0 192 0.5 Saccharomyces cereviceae 396 0 169 0 292 0 221 0.9 216 0 184 0 153 0 276 0 204 0 193 0 Seculamonas ecuadriensis 202 48.9 0 100 0 100 0 100 0 100 0 100 0 100 0 100 204 0 0 100 Stachyamoeba lipophora 0 100 0 100 0 100 0 100 0 100 0 100 0 100 0 100 0 100 0 100 Telonema subtilis 260 34.3 75 55.6 0 100 67 69.9 0 100 0 100 0 100 201 27.2 0 100 184 4.7 Tetrahymena pyriformis 395 0.3 0 100 92 68.5 203 8.9 203 6 145 21.2 152 0.7 276 0 56 72.5 193 0 Thalassiosira pseudonana 368 7.1 169 0 292 0 223 0 215 0.5 184 0 153 0 276 0 204 0 193 0 Thecamonas trahens 396 0 169 0 292 0 204 8.5 216 0 175 4.9 153 0 0 100 178 12.7 138 28.5 Toxoplasma gondii 396 0 169 0 292 0 223 0 216 0 184 0 0 100 276 0 203 0.5 193 0 Trimastix pyriformis 0 100 169 0 0 100 143 35.9 0 100 0 100 146 4.6 140 49.3 201 1.5 182 5.7 Tsukubamonas globosa 0 100 105 37.9 92 68.5 0 100 0 100 0 100 143 6.5 0 100 160 21.6 193 0 Ustilago maydis 369 6.8 169 0 0 100 223 0 216 0 184 0 153 0 276 0 197 3.4 193 0 Seq length and missing data are represented by bp and %, respectively. *only used for Supplementary file 8 Table S1. Data used in this work (continued). psmaC psmaE psmaF psmaG psmaH psmaJ psmbK psmbL psmbM psmbN Taxa Seq length Missing Seq length Missing Seq length Missing Seq length Missing Seq length Missing Seq length Missing Seq length Missing Seq length Missing Seq length Missing Seq length Missing Acanthamoeba castellanii 203 0 207 0 156 20 204 4.7 89 49.1 193 0 197 0 161 6.4 188 0 0 100 Amphimedon queenlandica 203 0 167 19.3 195 0 0 100 175 0 145 24.9 186 5.6 172 0 188 0 0 100 Andalucia incarcerata 152 25.1 0 100 0 100 166 22.4 0 100 0 100 0 100 172 0 0 100 0 100 Arabidopsis thaliana 203 0 207 0 195 0 214 0 175 0 193 0 197 0 172 0 188 0 141 0 Aureococcus anophagefferens 201 0.9 182 12.1 195 0 214 0 175 0 143 25.9 197 0 172 0 188 0 141 0 Bigelowiella natans 203 0 191 7.7 191 2.1 0 100 167 4.6 193 0 197 0 161 6.4 188 0 141 0 Capsaspora owczarzaki 203 0 207 0 195 0 214 0 175 0 193 0 197 0 172 0 178 5.3 141 0 Chlamydomonas reinharditii 202 0.5 207 0 195 0 214 0 175 0 0 100 197 0 155 9.9 164 12.8 141 0 Chondrus crispus 131 35.5 0 100 0 100 0 100 0 100 0 100 188 4.6 96 44.2 116 38.3 74 47.5 Collodictyon triciliatum 160 21.2 0 100 0 100 140 34.6 0 100 0 100 0 100 156 9.3 83 55.9 0 100 Cryptosporidium parvum 203 0 207 0 195 0 214 0 174 0.6 193 0 196 0.5 172 0 159 15.4 141 0 Cyanidioschyzon merolae 203 0 206 0.5 195 0 214 0 175 0 193 0 197 0 172 0 188 0 141 0 Cyanophora paradoxa 193 4.9 183 11.6 187 4.1 214 0 175 0 192 0.5 188 4.6 169 1.7 188 0 140 0.7 Dictyostelium discoideum 203 0 207 0 195 0 212 0.9 174 0.6 182 5.7 135 31.5 171 0.6 188 0 141 0 Diplonema papillatum 0 100 0 100 0 100 0 100 0 100 0 100 0 100 0 100 0 100 0 100 Diacronema (Pavlova) lutheri 0 100 0 100 0 100 172 19.6 0 100 0 100 100 49.2 110 36 157 16.5 123 12.8 Drosophila melanogaster 202 0.5 207 0 195 0 214 0 175 0 193 0 197 0 172 0 188 0 141 0 Ectocarpus siliculosus 203 0 207 0 195 0 214 0 175 0 193 0 185 6.1 172 0 188 0 141 0 Emiliania huxleyi 95 53.2 138 33.3 134 31.3 214 0 175 0 192 0.5 197 0 172 0 184 2.1 125 11.3 Euglena gracilis 0 100 207 0 195 0 0 100 0 100 112 41.9 197 0 172 0 188 0 0 100 Galdieria sulphlaria 203 0 207 0 195 0 214 0 175 0 193 0 197 0 172 0.0 188 0 141 0 Glaucocystis nostochinearum 107 47.3 0 100 187 4.1 214 0 175 0 177 8.3 194 1.5 172 0 0 100 0 100 Goniomonas sp. 141 30.5 139 0 100 0 100 123 29.7 0 100 45 77.2 0 100 188 0 0 100 Gracilaria changii 157 22.7 0 100 0 100 0 100 50 71.4 158 18.1 0 100 132 23.3 0 100 0 100 Guillardia theta 203 0 207 0 183 6.2 205 4.2 0 100 193 0 197 0 172 0 188 0 141 0 Homo sapiens 203 0 207 0 195 0 214 0 175 0 193 0 197 0 172 0 188 0 141 0 Isochrysis galbana 0 100 0 100 195 0 0 100 175 0 138 28.5 185 6.1 134 22.1 0 100 111 21.3 Jakoba bahamensis 119 41.4 0 100 0 100 0 100 0 100 193 0 162 17.8 142 17.4 0 100 0 100 Jakoba libera 203 0 174 15.9 193 1 0 100 0 100 0 100 166 15.7 0 100 0 100 0 100 Limnofila borokensis 0 100 0 100 0 100 0 100 0 100 0 100 166 15.7 0 100 0 100 0 100 Malawimonas californiensis 203 0 0 100 194 0.5 0 100 0 100 0 100 0 100 172 0 0 100 141 0 Malawimonas jakobiformis 203 0 0 100 187 4.1 205 4.2 0 100 177 8.3 156 20.8 172 0 188 0 141 0 Mastigamoeba balamthii 184 9.4 174 15.9 195 0 0 100 0 100 0 100 0 100 172 0 188 0 0 100 Micromonas sp. 203 0 0 100 195 0 202 5.6 171 2.3 193 0 197 0 172 0 139 26.1 141 0 Monosiga brevicolis 203 0 207 0 194 0.5 214 0 175 0 107 44.6 135 31.5 172 0 188 0 141 0 Naegleria gruberi 203 0 194 6.3 0 100 214 0 175 0 193 0 197 0 172 0 186 1.1 141 0 Oryza sativa 203 0 194 6.3 195 0 214 0 175 0 193 0 197 0 172 0 188 0 141 0 Ostreococcus tauli 203 0 0 100 178 8.7 214 0 175 0 193 0 195 1 168 2.3 188 0 141 0 Oxyrrhis marina 148 27.1 0 100 149 23.6 0 100 0 100 0 100 0 100 0 100 0 100 0 100 Palpitomonas bilix 203 0 148 28.5 119 39.0 214 0 123 29.7 169 12.4 185 6.1 111 35.5 182 3.2 141 0 Paramecium caudata 0 100 66 68.1 0 100 98 54.2 0 100 119 38.3 132 32.9 0 100 142 24.5 0 100 Paracercomonas marina 0 100 0 100 128 34.4 0 100 0 100 178 7.8 17 91.4 0 100 0 100 112 20.6 Perkinsus marinus 203 0 207 0 195 0 214 0 175 0 193 0 197 0 172 0 188 0 141 0 Phaeodactylum tricornatum 203 0 207 0 195 0 211 1.4 169 3.4 118 38.9 197 0 172 0 188 0 141 0 Physarum polycephalum 0 100 0 100 0 100 0 100 0 100 0 100 0 100 0 100 0 100 0 100 Phytophthora infestans 203 0 207 0 195 0 214 0 175 0 193 0 197 0 172 0 188 0 141 0 Uncultured picozoa (MS584-11)* 0 100 0 100 0 100 0 100 0 100 0 100 0 100 0 100 0 100 0 100 Polyplacocystis (Raphidiophrys) contractilis 0 100 0 100 195 0 0 100 0 100 0 100 121 38.6 126 26.7 149 20.7 0 100 Prymnesium parvum 153 24.6 185 10.6 0 100 214 0 170 2.9 86 55.4 0 100 172 0 0 100 141 0 Pyropia (Porphyra) yezoensis 157 22.7 118 42.9 159 18.5 136 36.4 156 10.9 159 17.6 134 31.9 117 31.9 0 100 97 31.2 Reclinomonas americana 203 0 207 0 194 0.5 214 0 175 0 186 3.6 176 10.7 172 0 0 100 141 0 Rhodmonas salina 0 100 0 100 0 100 0 100 0 100 0 100 0 100 0 100 0 100 0 100 Roombia truncata 203 0 207 0 195 0 214 0 175 0 73 62.2 177 10.2 172 0 188 0 141 0 Saccharomyces cereviceae 203 0 207 0 195 0 214 0 175 0 193 0 197 0 172 0 188 0 141 0 Seculamonas ecuadriensis 0 100 194 6.3 190 2.6 191 10.7 0 100 0 100 0 100 0 100 0 100 141 0 Stachyamoeba lipophora 0 100 0 100 59 69.7 0 100 0 100 0 100 69 64.9 0 100 0 100 0 100 Telonema subtilis 0 100 183 11.6 178 8.7 0 100 0 100 0 100 197 0 0 100 188 0 0 100 Tetrahymena pyriformis 203 0 168 18.8 187 4.1 199 7 114 34.9 130 32.6 185 6.1 172 0 164 12.8 141 0 Thalassiosira pseudonana 203 0 207 0 194 0.5 214 0 144 17.7 193 0 197 0 172 0 188 0 141 0 Thecamonas trahens 181 10.8 143 30.9 188 3.6 0 100 134 23.4 186 3.6 187 5.1 171 0.6 188 0 121 14.2 Toxoplasma gondii 203 0 207 0 195 0 214 0 175 0 193 0 197 0 172 0 188 0 141 0 Trimastix pyriformis 201 0.9 0 100 191 2.1 151 29.4 164 6.3 158 18.1 185 6.1 172 0 188 0 141 0 Tsukubamonas globosa 203 0 207 0 195 0 214 0 175 0 193 0 197 0 172 0 188 0 72 48.9 Ustilago maydis 203 0 207 0 195 0 155 27.6 175 0 177 8.3 197 0 172 0 188 0 141 0 Seq length and missing data are represented by bp and %, respectively. *only used for Supplementary file 9 Table S1. Data used in this work (continued). psmd rac rad23 rad51A ran rf1 rla2a rla2b rpl2 rpl3 Taxa Seq length Missing Seq length Missing Seq length Missing Seq length Missing Seq length Missing Seq length Missing Seq length Missing Seq length Missing Seq length Missing Seq length Missing Acanthamoeba castellanii 0 100 150 0 89 50.3 80 72.9 167 8.2 153 58.8 0 100 0 100 192 22.3 285 16.2 Amphimedon queenlandica 0 100 150 0 92 48.6 0 100 182 0 103 72.2 65 0 52 0 209 15.4 212 37.6 Andalucia incarcerata 0 100 150 0 0 100 0 100 0 100 0 100 65 0 52 0 180 27.1 185 45.6 Arabidopsis thaliana 259 0 150 0 179 0 295 0 182 0 371 0 65 0 0 100 247 0 340 0 Aureococcus anophagefferens 210 18.9 150 0 179 0 0 100 182 0 371 0 65 0 0 100 247 0 340 0 Bigelowiella natans 259 0 150 0 179 0 295 0 182 0 371 0 65 0 52 0 247 0 340 0 Capsaspora owczarzaki 259 0 150 0 137 23.5 295 0 181 0.5 371 0 0 100 52 0 247 0 340 0 Chlamydomonas reinharditii 259 0 0 100 179 0 295 0 182 0 371 0 65 0 52 0 247 0 340 0 Chondrus crispus 160 38.2 88 41.3 0 100 0 100 0 100 143 61.5 0 100 0 100 246 0.4 128 62.4 Collodictyon triciliatum 200 22.8 98 34.7 0 100 0 100 161 11.5 63 83.0 65 0 0 100 142 42.5 175 48.5 Cryptosporidium parvum 259 0 0 100 179 0 295 0 181 0.5 371 0 65 0 52 0 247 0 340 0 Cyanidioschyzon merolae 259 0 148 1.3 179 0 295 0 182 0 321 13.5 65 0 52 0 246 0.4 340 0 Cyanophora paradoxa 138 46.7 0 100 0 100 93 68.5 182 0 369 0.5 65 0 52 0 247 0 223 34.4 Dictyostelium discoideum 259 0 150 0 179 0 284 3.7 182 0 371 0 63 3.1 52 0 247 0 340 0 Diplonema papillatum 0 100 0 100 0 100 0 100 0 100 0 100 0 100 0 100 0 100 78 77.1 Diacronema (Pavlova) lutheri 138 46.7 0 100 0 100 0 100 0 100 150 59.6 0 100 52 0 179 27.5 185 45.6 Drosophila melanogaster 259 0 150 0 179 0 295 0 182 0 371 0 65 0 52 0 247 0 340 0 Ectocarpus siliculosus 259 0 150 0 179 0 295 0 182 0 371 0 0 100 52 0 247 0 340 0 Emiliania huxleyi 259 0 150 0 0 100 0 100 182 0 361 2.7 65 0 50 3.8 246 0.4 213 37.4 Euglena gracilis 0 100 0 100 0 100 202 31.5 182 0 371 0 0 100 52 0 247 0 340 0 Galdieria sulphlaria 259 0 150 0 179 0 295 0 175 3.8 370 0.3 65 0 52 0 244 340 0 Glaucocystis nostochinearum 0 100 0 100 0 100 137 53.6 182 0 159 57.1 65 0 51 1.9 247 0 217 36.2 Goniomonas sp. 0 100 0 100 0 100 0 100 128 29.7 0 100 65 0 52 0 247 0 214 37.1 Gracilaria changii 121 53.3 0 100 90 49.7 0 100 101 44.5 0 100 65 0 52 0 246 0.4 150 55.9 Guillardia theta 239 7.7 150 0 179 0 295 0 182 0 362 2.4 65 0 51 1.9 233 5.7 340 0 Homo sapiens 259 0 150 0 179 0 295 0 182 0 371 0 65 0 52 0 247 0 340 0 Isochrysis galbana 125 51.7 0 100 0 100 141 52.2 0 100 217 41.5 0 100 0 100 223 9.7 0 100 Jakoba bahamensis 233 10 150 0 0 100 243 17.6 0 100 145 60.9 0 100 0 100 0 100 311 8.5 Jakoba libera 173 33.2 0 100 0 100 0 100 0 100 0 100 0 100 0 100 196 20.6 340 0 Limnofila borokensis 148 42.9 0 100 0 100 0 100 0 100 0 100 0 100 0 100 0 100 0 100 Malawimonas californiensis 195 24.7 0 100 0 100 0 100 182 0 0 100 62 4.6 52 0 247 0 340 0 Malawimonas jakobiformis 203 21.6 150 0 0 100 237 19.7 182 0 0 100 65 0 51 1.9 237 4 340 0 Mastigamoeba balamthii 0 100 150 0 0 100 0 100 182 0 184 50.4 65 0 52 0 246 0.4 340 0 Micromonas sp. 259 0 150 0 179 0 295 0 175 3.8 171 53.9 65 0 52 0 247 0 340 0 Monosiga brevicolis 259 0 150 0 179 0 0 100 182 0 371 0 0 100 0 100 247 0 340 0 Naegleria gruberi 259 0 150 0 0 100 0 100 182 0 371 0 65 0 0 100 246 0.4 340 0 Oryza sativa 259 0 150 0 179 0 295 0 175 3.8 371 0 65 0 51 1.9 247 0 340 0 Ostreococcus tauli 259 0 150 0 124 30.7 295 0 182 0 363 2.2 65 0 52 0 247 0 340 0 Oxyrrhis marina 188 27.4 0 100 0 100 146 50.5 170 6.6 0 100 0 100 0 100 247 0 223 34.4 Palpitomonas bilix 205 20.8 127 15.3 89 50.3 90 69.5 182 0 51 86.3 65 0 52 0 244 1.2 213 37.4 Paramecium caudata 0 100 0 100 0 100 287 2.7 0 100 0 100 0 100 0 100 242 2 339 0.3 Paracercomonas marina 0 100 150 0 81 54.7 70 76.3 166 8.8 66 82.2 0 100 0 100 0 100 95 72.1 Perkinsus marinus 259 0 0 100 0 100 0 100 174 4.4 371 0 0 100 0 100 247 0 340 0 Phaeodactylum tricornatum 259 0 0 100 165 7.8 295 0 182 0 371 0 0 100 0 100 247 0 340 0 Physarum polycephalum 0 100 0 100 90 49.7 181 38.6 124 31.9 209 43.7 0 100 0 100 234 5.3 340 0 Phytophthora infestans 259 0 109 27.3 140 21.8 289 2 182 0 371 0 65 0 52 0 246 0.4 340 0 Uncultured picozoa (MS584-11)* 232 10.4 0 100 0 100 0 100 0 100 0 100 0 100 0 100 0 100 299 12.1 Polyplacocystis (Raphidiophrys) contractilis 144 44.4 150 0 0 100 0 100 156 14.3 195 47.4 0 100 0 100 247 0 181 46.8 Prymnesium parvum 0 100 0 100 88 50.8 0 100 182 0 0 100 0 100 52 0 244 1.2 218 35.9 Pyropia (Porphyra) yezoensis 113 56.4 0 100 0 100 153 48.1 158 13.2 195 47.4 0 100 52 0 187 24.3 161 52.6 Reclinomonas americana 259 0 150 0 0 100 0 100 172 5.5 167 54.9 0 100 0 100 186 24.7 340 0 Rhodmonas salina 0 100 0 100 0 100 0 100 0 100 0 100 0 100 0 100 244 1.2 0 100 Roombia truncata 259 0 150 0 0 100 0 100 161 11.5 369 0.5 65 0 0 100 233 5.7 340 0 Saccharomyces cereviceae 0 100 0 100 173 3.4 295 0 182 0 371 0 64 1.5 52 0 247 0 340 0 Seculamonas ecuadriensis 160 38.2 150 0 0 100 0 100 182 0 0 100 0 100 0 100 247 0 319 6.2 Stachyamoeba lipophora 81 68.7 84 44 89 50.3 0 100 0 100 0 100 0 100 52 0 237 4 237 30.3 Telonema subtilis 259 0 0 100 0 100 63 78.6 182 0 322 13.2 0 100 0 100 247 0 340 0 Tetrahymena pyriformis 238 8.1 149 0.7 0 100 295 0 182 0 0 100 0 100 0 100 247 0 340 0 Thalassiosira pseudonana 259 0 0 100 124 30.7 295 0 182 0 371 0 65 0 52 0 245 0.8 340 0 Thecamonas trahens 259 0 150 0 157 12.3 243 17.6 182 0 356 4 0 100 0 100 206 16.6 340 0 Toxoplasma gondii 259 0 0 100 179 0 295 0 182 0 371 0 65 0 52 0 247 0 340 0 Trimastix pyriformis 115 55.6 0 100 0 100 0 100 182 0 235 36.7 0 100 0 100 247 0 337 0.9 Tsukubamonas globosa 0 100 150 0 89 50.3 0 100 182 0 371 0 65 0 52 0 247 0 340 0 Ustilago maydis 222 14.3 150 0 179 0 295 0 182 0 371 0 65 0 52 0 247 0 340 0 Seq length and missing data are represented by bp and %, respectively. *only used for Supplementary file 10 Table S1. Data used in this work (continued). rpl4b rpl5 rpl6 rpl7a rpl9 rpl11 rpl12 rpl13A rpl13e rpl14e Taxa Seq length Missing Seq length Missing Seq length Missing Seq length Missing Seq length Missing Seq length Missing Seq length Missing Seq length Missing Seq length Missing Seq length Missing Acanthamoeba castellanii 0 100 207 0 41 57.3 92 52.3 156 0 166 0 156 0 153 0 110 0 104 0 Amphimedon queenlandica 215 19.5 201 2.9 96 0 193 0 156 0 166 0 156 0 153 0 110 0 104 0 Andalucia incarcerata 185 30.7 207 0 96 0 171 11.4 156 0 166 0 107 31.4 153 0 110 0 0 100 Arabidopsis thaliana 267 0 207 0 96 0 193 0 156 0 166 0 156 0 152 0.7 110 0 104 0 Aureococcus anophagefferens 267 0 207 0 96 0 193 0 156 0 166 0 0 100 153 0 110 0 104 0 Bigelowiella natans 267 0 207 0 96 0 193 0 0 100 166 0 156 0 153 0 0 100 99 4.8 Capsaspora owczarzaki 0 100 207 0 96 0 193 0 156 0 166 0 156 0 153 0 110 0 104 0 Chlamydomonas reinharditii 267 0 207 0 96 0 193 0 156 0 164 1.2 156 0 153 0 110 0 104 0 Chondrus crispus 0 100 104 49.8 87 9.4 100 48.2 0 100 111 33.1 0 100 95 37.9 0 100 0 100 Collodictyon triciliatum 187 30.0 188 9.2 54 43.8 132 31.6 91 41.7 162 2.4 156 0 120 21.6 90 18.2 103 1.0 Cryptosporidium parvum 267 0 207 0 96 0 193 0 156 0 166 0 156 0 153 0 110 0 98 5.8 Cyanidioschyzon merolae 267 0 207 0 96 0 193 0 155 0.6 165 0.6 156 0 153 0 110 0 104 0 Cyanophora paradoxa 228 14.6 207 0 96 0 193 0 156 0 166 0 156 0 153 0 110 0 104 0 Dictyostelium discoideum 267 0 207 0 96 0 193 0 156 0 166 0 156 0 153 0 110 0 104 0 Diplonema papillatum 0 100 0 100 0 100 136 29.5 156 0 149 10.2 156 0 96 37.3 0 100 102 1.9 Diacronema (Pavlova) lutheri 140 47.6 146 29.5 40 58.3 163 15.5 156 0 47 71.7 0 100 0 100 0 100 104 0 Drosophila melanogaster 267 0 207 0 96 0 193 0 156 0 166 0 156 0 153 0 110 0 104 0 Ectocarpus siliculosus 267 0 207 0 96 0 193 0 156 0 166 0 156 0 153 0 110 0 104 0 Emiliania huxleyi 234 12.4 207 0 0 100 193 0 156 0 165 0.6 97 37.8 153 0 110 0 104 0 Euglena gracilis 258 3.4 207 0 0 100 192 0.5 156 0 166 0 156 0 153 0 110 0 103 0.9 Galdieria sulphlaria 267 0 207 0 96 0 191 1 152 2.6 0 100 153 1.9 153 0 104 5.5 104 0 Glaucocystis nostochinearum 0 100 201 2.9 96 0 193 0 156 0 166 0 156 0 153 0 110 0 104 0 Goniomonas sp. 33 87.6 172 16.9 96 0 193 0 156 0 133 19.9 156 0 153 0 0 100 96 7.7 Gracilaria changii 179 32.9 207 0 93 3.1 120 37.8 0 100 166 0 156 0 138 9.8 110 0 104 0 Guillardia theta 267 0 207 0 62 35.4 193 0 155 0.6 166 0 153 1.9 153 0 110 0 102 1.9 Homo sapiens 267 0 207 0 96 0 193 0 156 0 166 0 156 0 153 0 110 0 104 0 Isochrysis galbana 138 48.3 194 6.3 0 100 0 100 0 100 0 100 0 100 0 100 0 100 0 100 Jakoba bahamensis 143 46.4 161 22.2 96 0 193 0 156 0 100 39.8 156 0 153 0 0 100 104 0 Jakoba libera 267 0 207 0 0 100 193 0 0 100 0 100 0 100 0 100 110 0 104 0 Limnofila borokensis 58 78.3 0 100 0 100 193 0 156 0 0 100 150 3.8 0 100 0 100 104 0 Malawimonas californiensis 192 28.1 180 13 45 53.1 193 0 156 0 166 0 153 1.9 153 0 110 0 104 0 Malawimonas jakobiformis 225 15.7 171 17.4 96 0 193 0 156 0 166 0 156 0 153 0 110 0 104 0 Mastigamoeba balamthii 267 0 207 0 96 0 193 0 153 1.9 166 0 156 0 153 0 110 0 104 0 Micromonas sp. 267 0 205 0.9 96 0 193 0 156 0 166 0 156 0 153 0 110 0 104 0 Monosiga brevicolis 0 100 201 2.9 96 0 193 0 156 0 166 0 156 0 153 0 110 0 104 0 Naegleria gruberi 0 100 207 0 96 0 193 0 156 0 166 0 156 0 153 0 110 0 0 100 Oryza sativa 267 0 207 0 96 0 193 0 156 0 166 0 156 0 153 0 110 0 104 0 Ostreococcus tauli 267 0 205 0.9 96 0 193 0 156 0 164 1.2 156 0 153 0 110 0 103 0.9 Oxyrrhis marina 200 25.1 207 0 0 100 193 0 0 100 0 100 0 100 153 0 110 0 0 100 Palpitomonas bilix 96 64.0 207 0 96 0 193 0 156 0 166 0 156 0 153 0 110 0 94 9.6 Paramecium caudata 267 0 159 23.2 0 100 175 9.3 0 100 0 100 0 100 141 7.8 0 100 0 100 Paracercomonas marina 0 100 172 16.9 62 35.4 171 11.4 0 100 151 9 156 0 0 100 0 100 102 1.9 Perkinsus marinus 0 100 207 0 96 0 193 0 156 0 166 0 156 0 153 0 110 0 104 0 Phaeodactylum tricornatum 267 0 207 0 96 0 193 0 0 100 166 0 156 0 153 0 110 0 104 0 Physarum polycephalum 266 0.4 95 54.1 0 100 0 100 156 0 161 3 148 5.1 153 0 0 100 0 100 Phytophthora infestans 267 0 207 0 96 0 193 0 156 0 0 100 153 1.9 153 0 110 0 104 0 Uncultured picozoa (MS584-11)* 0 100 144 30.4 0 100 0 100 0 100 0 100 0 100 89 41.8 0 100 0 100 Polyplacocystis (Raphidiophrys) contractilis 0 100 119 42.5 0 100 193 0 128 17.9 0 100 156 0 0 100 0 100 0 100 Prymnesium parvum 236 11.6 207 0 95 1 0 100 155 0.6 0 100 0 100 0 100 0 100 0 100 Pyropia (Porphyra) yezoensis 168 37.1 141 31.9 62 35.4 0 100 156 0 140 15.7 0 100 153 0 110 0 104 0 Reclinomonas americana 267 0 182 12.1 96 0 193 0 156 0 166 0 96 38.5 153 0 110 0 100 3.8 Rhodmonas salina 189 29.2 0 100 0 100 171 11.4 0 100 0 100 0 100 134 12.4 0 100 0 100 Roombia truncata 261 2.2 207 0 96 0 192 0.5 153 1.9 166 0 156 0 153 0 110 0 101 2.9 Saccharomyces cereviceae 267 0 207 0 0 100 193 0 0 100 0 100 0 100 153 0 110 0 104 0 Seculamonas ecuadriensis 267 0 207 0 96 0 193 0 156 0 166 0 0 100 153 0 74 32.7 104 0 Stachyamoeba lipophora 140 47.6 193 6.8 96 0 193 0 156 0 149 10.2 68 56.4 116 24.2 79 28.2 93 10.6 Telonema subtilis 265 0.7 119 42.5 0 100 177 8.3 153 1.9 0 100 151 3.2 0 100 0 100 0 100 Tetrahymena pyriformis 267 0 185 10.6 96 0 144 25.4 156 0 166 0 0 100 153 0 110 0 98 5.8 Thalassiosira pseudonana 266 0.4 207 0 96 0 193 0 156 0 166 0 154 1.3 153 0 110 0 104 0 Thecamonas trahens 261 2.2 0 100 96 0 193 0 153 1.9 163 1.8 145 7.1 153 0 79 28.2 88 15.4 Toxoplasma gondii 267 0 207 0 96 0 193 0 0 100 166 0 156 0 153 0 110 0 104 0 Trimastix pyriformis 267 0 0 100 89 7.3 193 0 156 0 166 0 150 3.8 153 0 106 3.6 86 17.3 Tsukubamonas globosa 266 0.4 207 0 96 0 193 0 155 0.6 0 100 156 0 0 100 110 0 104 0 Ustilago maydis 266 0.4 207 0 96 0 193 0 156 0 166 0 156 0 153 0 110 0 104 0 Seq length and missing data are represented by bp and %, respectively. *only used for Supplementary file 11 Table S1. Data used in this work (continued). rpl15 rpl17 rpl18 rpl19 rpl20 rpl21 rpl24A rpl26 rpl27 rpl30 Taxa Seq length Missing Seq length Missing Seq length Missing Seq length Missing Seq length Missing Seq length Missing Seq length Missing Seq length Missing Seq length Missing Seq length Missing Acanthamoeba castellanii 173 11.3 109 24.8 101 32.2 167 2.9 146 0 126 0 89 0 114 0 128 0 101 0 Amphimedon queenlandica 195 0 145 0 149 0 172 0 146 0 124 1.6 89 0 114 0 128 0 101 0 Andalucia incarcerata 195 0 145 0 140 6 172 0 146 0 126 0 89 0 76 33.3 128 0 101 0 Arabidopsis thaliana 195 0 0 100 149 0 172 0 146 0 126 0 89 0 114 0 128 0 101 0 Aureococcus anophagefferens 195 0 145 0 149 0 172 0 146 0 126 0 89 0 114 0 89 30.5 101 0 Bigelowiella natans 188 3.6 143 1.4 149 0 172 0 132 9.6 126 0 89 0 113 0.9 126 1.6 101 0 Capsaspora owczarzaki 195 0 145 0 149 0 170 1.2 146 0 122 3.2 87 2.2 114 0 128 0 101 0 Chlamydomonas reinharditii 195 0 145 0 149 0 172 0 146 0 126 0 89 0 114 0 128 0 101 0 Chondrus crispus 96 50.8 145 0 116 22.1 131 23.8 108 26 0 100 0 100 114 0 113 11.7 0 100 Collodictyon triciliatum 165 15.4 135 6.9 125 16.1 92 46.5 140 4.1 120 4.8 52 57.4 93 18.4 97 24.2 101 0 Cryptosporidium parvum 195 0 145 0 149 0 170 1.2 146 0 122 3.2 89 0 111 2.6 128 0 0 100 Cyanidioschyzon merolae 195 0 144 0.7 149 0 140 18.6 146 0 0 100 89 0 82 28.1 128 0 101 0 Cyanophora paradoxa 195 0 145 0 148 0.7 172 0 146 0 126 0 89 0 113 0.9 128 0 101 0 Dictyostelium discoideum 195 0 145 0 140 6 172 0 146 0 126 0 89 0 114 0 128 0 101 0 Diplonema papillatum 195 0 50 65.5 0 100 172 0 103 29.5 0 100 89 0 106 7 105 17.9 0 100 Diacronema (Pavlova) lutheri 195 0 145 0 136 8.7 172 0 146 0 0 100 0 100 0 100 128 0 101 0 Drosophila melanogaster 195 0 145 0 149 0 172 0 146 0 126 0 89 0 114 0 128 0 101 0 Ectocarpus siliculosus 195 0 145 0 149 0 172 0 146 0 0 100 89 0 114 0 128 0 101 0 Emiliania huxleyi 0 100 50 65.5 149 0 56 67.4 146 0 122 3.2 89 0 114 0 128 0 101 0 Euglena gracilis 195 0 137 5.5 149 0 172 0 146 0 122 3.2 89 0 114 0 127 0.8 101 0 Galdieria sulphlaria 195 0 142 2.1 149 0 158 8.1 136 6.8 120 4.8 58 52.5 86 24.6 128 0 101 0 Glaucocystis nostochinearum 0 100 144 0.7 148 0.7 172 0 146 0 126 0 0 100 0 100 128 0 101 0 Goniomonas sp. 185 5.1 145 0 116 22.1 172 0 146 0 122 3.2 89 0 86 24.6 126 1.6 101 0 Gracilaria changii 195 0 145 0 148 0.7 172 0 0 100 126 0 89 0 114 0 0 100 0 100 Guillardia theta 195 0 145 0 149 0 172 0 146 0 100 20.6 89 0 86 24.6 128 0 101 0 Homo sapiens 195 0 145 0 149 0 172 0 146 0 126 0 89 0 114 0 128 0 101 0 Isochrysis galbana 0 100 0 100 149 0 0 100 0 100 0 100 89 0 0 100 0 100 0 100 Jakoba bahamensis 172 11.8 145 0 144 3.4 0 100 146 0 126 0 0 100 0 100 0 100 0 100 Jakoba libera 170 12.8 0 100 146 2 172 0 146 0 126 0 0 100 114 0 128 0 101 0 Limnofila borokensis 0 100 0 100 0 100 0 100 0 100 0 100 0 100 0 100 0 100 0 100 Malawimonas californiensis 195 0 145 0 149 0 153 11 0 100 118 6.3 0 100 114 0 128 0 101 0 Malawimonas jakobiformis 190 2.6 145 0 149 0 153 11 146 0 126 0 89 0 114 0 128 0 101 0 Mastigamoeba balamthii 195 0 145 0 148 0.7 112 34.9 146 0 126 0 83 6.7 114 0 127 0.8 101 0 Micromonas sp. 173 11.3 145 0 149 0 172 0 146 0 126 0 75 15.7 114 0 128 0 101 0 Monosiga brevicolis 193 1 145 0 149 0 172 0 146 0 126 0 89 0 113 0.9 128 0 101 0 Naegleria gruberi 194 0.5 145 0 148 0.7 170 1.2 131 10.3 122 3.2 84 5.6 114 0 128 0 99 1.9 Oryza sativa 195 0 145 0 149 0 172 0 146 0 126 0 89 0 114 0 128 0 101 0 Ostreococcus tauli 173 11.3 145 0 149 0 171 0.6 146 0 126 0 89 0 114 0 128 0 97 3.9 Oxyrrhis marina 195 0 0 100 149 0 0 100 0 100 0 100 66 25.8 0 100 0 100 0 100 Palpitomonas bilix 195 0 143 1.4 149 0 172 0 146 0 126 0 89 0 114 0 128 0 101 0 Paramecium caudata 195 0 0 100 39 73.8 0 100 0 100 0 100 0 100 0 100 0 100 0 100 Paracercomonas marina 165 15.4 92 36.6 144 3.4 0 100 139 4.8 126 0 0 100 108 5.3 128 0 101 0 Perkinsus marinus 195 0 145 0 149 0 172 0 146 0 126 0 89 0 114 0 128 0 101 0 Phaeodactylum tricornatum 195 0 0 100 148 0.7 172 0 146 0 126 0 89 0 108 5.3 127 0.8 0 100 Physarum polycephalum 195 0 131 9.7 149 0 168 2.3 140 4.1 0 100 85 4.5 110 3.5 120 6.3 44 56.4 Phytophthora infestans 195 0 145 0 149 0 172 0 146 0 122 3.2 88 1.1 114 0 128 0 100 0.9 Uncultured picozoa (MS584-11)* 134 31.3 0 100 41 72.5 0 100 0 100 97 23.0 0 100 0 100 0 100 0 100 Polyplacocystis (Raphidiophrys) contractilis 107 45.1 92 36.6 149 0 168 2.3 146 0 114 9.5 0 100 109 4.4 128 0 0 100 Prymnesium parvum 186 4.6 0 100 132 11.4 169 1.7 0 100 116 7.9 89 0 0 100 128 0 101 0 Pyropia (Porphyra) yezoensis 149 23.6 145 0 149 0 163 5.2 146 0 126 0 89 0 107 6.1 128 0 101 0 Reclinomonas americana 195 0 145 0 149 0 172 0 146 0 126 0 79 11.2 114 0 128 0 101 0 Rhodmonas salina 195 0 0 100 86 42.3 0 100 0 100 0 100 85 4.5 0 100 0 100 0 100 Roombia truncata 188 3.6 141 2.8 125 16.1 172 0 145 0.7 107 15.1 52 57.4 83 27.2 128 0 101 0 Saccharomyces cereviceae 195 0 0 100 149 0 0 100 0 100 0 100 89 0 0 100 0 100 0 100 Seculamonas ecuadriensis 195 0 0 100 0 100 0 100 0 100 126 0 88 1.1 114 0 0 100 0 100 Stachyamoeba lipophora 182 6.7 145 0 131 12.1 144 16.3 125 14.4 106 15.9 0 100 46 59.6 97 24.2 97 3.9 Telonema subtilis 195 0 110 24.1 116 22.1 172 0 146 0 126 0 0 100 109 4.4 107 16.4 0 100 Tetrahymena pyriformis 195 0 0 100 148 0.7 172 0 146 0 122 3.2 89 0 114 0 128 0 0 100 Thalassiosira pseudonana 195 0 145 0 148 0.7 172 0 146 0 126 0 87 2.2 114 0 127 0.8 0 100 Thecamonas trahens 188 3.6 138 4.8 149 0 55 68 146 0 126 0 89 0 86 24.6 127 0.8 94 6.9 Toxoplasma gondii 195 0 145 0 149 0 170 1.2 146 0 126 0 88 1.1 114 0 127 0.8 101 0 Trimastix pyriformis 193 1 139 4.1 144 3.4 172 0 88 39.7 126 0 79 11.2 110 3.5 124 3.1 100 0.9 Tsukubamonas globosa 195 0 145 0 149 0 170 1.2 146 0 126 0 86 3.4 114 0 127 0.8 101 0 Ustilago maydis 195 0 145 0 149 0 172 0 146 0 121 3.9 89 0 109 4.4 128 0 101 0 Seq length and missing data are represented by bp and %, respectively. *only used for Supplementary file 12 Table S1. Data used in this work (continued). rpl31 rpl32 rpl33 rpl35 rpl43 rpl44 rpoA rpoB rpoC rppO Taxa Seq length Missing Seq length Missing Seq length Missing Seq length Missing Seq length Missing Seq length Missing Seq length Missing Seq length Missing Seq length Missing Seq length Missing Acanthamoeba castellanii 97 0 124 0 92 0 112 0 87 0 88 0 0 100 0 100 0 100 234 0.4 Amphimedon queenlandica 97 0 124 0 92 0 112 0 87 0 88 0 0 100 158 84.6 99 89.5 181 22.9 Andalucia incarcerata 94 3.1 124 0 49 46.7 112 0 35 59.8 0 100 0 100 0 100 0 100 235 0 Arabidopsis thaliana 97 0 124 0 92 0 112 0 87 0 88 0 626 0.3 1026 0 943 0 235 0 Aureococcus anophagefferens 97 0 124 0 92 0 112 0 87 0 88 0 576 8.3 994 3.1 935 0.8 0 100 Bigelowiella natans 97 0 124 0 92 0 112 0 0 100 88 0 571 9.1 1015 1.1 943 0 216 8.1 Capsaspora owczarzaki 97 0 124 0 92 0 112 0 87 0 87 1.1 628 0 1026 0 943 0 235 0 Chlamydomonas reinharditii 97 0 124 0 92 0 112 0 87 0 88 0 490 21.9 1026 0 0 100 235 0 Chondrus crispus 97 0 124 0 64 30.4 0 100 0 100 0 100 0 100 0 100 0 100 0 100 Collodictyon triciliatum 0 100 110 11.3 92 0 59 47.3 87 0 88 0 0 100 212 79.3 173 81.7 195 17.0 Cryptosporidium parvum 97 0 124 0 92 0 112 0 80 8 87 1.1 0 100 1025 0 943 0 235 0 Cyanidioschyzon merolae 97 0 110 11.3 92 0 84 25 60 31 88 0 628 0 1026 0 888 5.8 235 0 Cyanophora paradoxa 97 0 124 0 92 0 112 0 87 0 88 0 0 100 0 100 0 100 235 0 Dictyostelium discoideum 97 0 124 0 92 0 112 0 87 0 0 100 497 20.9 1026 0 915 2.9 232 1.3 Diplonema papillatum 59 39.2 118 4.8 72 21.7 112 0 41 52.9 88 0 0 100 0 100 0 100 0 100 Diacronema (Pavlova) lutheri 97 0 112 9.7 92 0 0 100 0 100 52 40.9 0 100 0 100 0 100 0 100 Drosophila melanogaster 97 0 124 0 92 0 112 0 87 0 88 0 628 0 1026 0 942 0.1 235 0 Ectocarpus siliculosus 97 0 124 0 92 0 112 0 87 0 88 0 492 21.7 1024 0.2 943 0 0 100 Emiliania huxleyi 97 0 124 0 92 0 88 21.4 87 0 0 100 596 5.1 1007 1.9 887 5.9 234 0.4 Euglena gracilis 97 0 119 4 92 0 112 0 0 100 88 0 0 100 0 100 0 100 235 0 Galdieria sulphlaria 96 1.0 118 4.8 92 0 112 0 87 0 88 0 614 2.2 560 45.4 941 0.2 233 0.9 Glaucocystis nostochinearum 97 0 124 0 92 0 112 0 87 0 88 0 0 100 0 100 0 100 0 100 Goniomonas sp. 97 0 124 0 92 0 112 0 87 0 88 0 0 100 0 100 34 96.4 153 34.9 Gracilaria changii 97 0 119 4 92 0 112 0 87 0 87 1.1 0 100 70 93.2 86 90.9 198 15.7 Guillardia theta 97 0 124 0 92 0 112 0 87 0 88 0 587 6.5 1004 2.1 830 11.9 235 0 Homo sapiens 97 0 124 0 92 0 112 0 87 0 0 100 627 0.2 1026 0 943 0 235 0 Isochrysis galbana 0 100 0 100 0 100 0 100 0 100 0 100 0 100 196 80.9 0 100 0 100 Jakoba bahamensis 97 0 124 0 0 100 112 0 87 0 0 100 0 100 0 100 0 100 0 100 Jakoba libera 97 0 122 1.6 92 0 0 100 0 100 0 100 0 100 0 100 0 100 206 12.3 Limnofila borokensis 0 100 122 1.6 0 100 0 100 0 100 0 100 0 100 0 100 0 100 0 100 Malawimonas californiensis 96 1 124 0 0 100 112 0 0 100 88 0 0 100 0 100 77 91.8 0 100 Malawimonas jakobiformis 97 0 124 0 92 0 112 0 87 0 88 0 0 100 0 100 0 100 137 41.7 Mastigamoeba balamthii 97 0 119 4 92 0 112 0 87 0 88 0 0 100 992 3.3 32 96.6 235 0 Micromonas sp. 97 0 124 0 92 0 112 0 87 0 88 0 620 1.3 1026 0 943 0 235 0 Monosiga brevicolis 97 0 124 0 0 100 112 0 72 17.2 88 0 627 0.2 671 34.6 931 1.3 235 0 Naegleria gruberi 0 100 124 0 92 0 112 0 0 100 87 1.1 554 11.8 992 3.3 943 0 235 0 Oryza sativa 97 0 124 0 92 0 112 0 87 0 88 0 0 100 1026 0 943 0 235 0 Ostreococcus tauli 97 0 99 20.2 92 0 112 0 87 0 88 0 626 0.3 1026 0 943 0 235 0 Oxyrrhis marina 0 100 0 100 0 100 0 100 0 100 0 100 0 100 79 92.3 0 100 235 0 Palpitomonas bilix 97 0 124 0 92 0 112 0 87 0 87 1.1 95 84.9 122 88.1 138 85.4 235 0 Paramecium caudata 0 100 0 100 0 100 0 100 0 100 0 100 335 46.7 363 64.6 325 65.5 105 55.3 Paracercomonas marina 72 25.8 124 0 91 1.1 0 100 0 100 88 0 0 100 0 100 0 100 87 62.9 Perkinsus marinus 0 100 122 1.6 92 0 112 0 87 0 88 0 628 0 1026 0 870 7.7 235 0 Phaeodactylum tricornatum 97 0 124 0 92 0 112 0 87 0 87 1.1 628 0 994 3.1 920 2.4 234 0.4 Physarum polycephalum 97 0 124 0 0 100 102 8.9 85 2.3 88 0 0 100 0 100 82 91.3 235 0 Phytophthora infestans 97 0 124 0 92 0 112 0 87 0 0 100 628 0 1026 0 943 0 235 0 Uncultured picozoa (MS584-11)* 0 100 0 100 0 100 0 100 0 100 0 100 0 100 183 82.2 264 72.0 0 100 Polyplacocystis (Raphidiophrys) contractilis 0 100 124 0 0 100 0 100 0 100 0 100 0 100 0 100 0 100 0 100 Prymnesium parvum 0 100 0 100 92 0 0 100 0 100 88 0 0 100 0 100 0 100 147 37.4 Pyropia (Porphyra) yezoensis 0 100 118 4.8 92 0 112 0 87 0 87 1.1 0 100 166 83.8 148 84.3 160 31.9 Reclinomonas americana 97 0 124 0 92 0 112 0 79 9.2 88 0 41 93.5 0 100 0 100 0 100 Rhodmonas salina 0 100 0 100 0 100 0 100 0 100 0 100 0 100 0 100 0 100 194 17.4 Roombia truncata 97 0 124 0 92 0 86 23.2 87 0 87 1.1 0 100 0 100 0 100 234 0.4 Saccharomyces cereviceae 0 100 0 100 0 100 0 100 0 100 0 100 628 0 1026 0 943 0 235 0 Seculamonas ecuadriensis 97 0 124 0 69 25 0 100 87 0 83 5.7 0 100 0 100 0 100 235 0 Stachyamoeba lipophora 0 100 112 9.7 0 100 0 100 53 39.1 51 42 0 100 0 100 0 100 235 0 Telonema subtilis 0 100 124 0 0 100 0 100 0 100 0 100 0 100 0 100 0 100 0 100 Tetrahymena pyriformis 97 0 124 0 92 0 112 0 87 0 88 0 548 12.7 151 85.3 0 100 235 0 Thalassiosira pseudonana 97 0 124 0 92 0 112 0 86 1.1 88 0 628 0 1026 0 943 0 235 0 Thecamonas trahens 93 4.1 81 34.7 89 3.3 112 0 86 1.1 51 42 585 6.8 1026 0 941 0.2 235 0 Toxoplasma gondii 97 0 124 0 92 0 112 0 87 0 88 0 0 100 1026 0 943 0 235 0 Trimastix pyriformis 96 1 120 3.2 91 1.1 104 7.1 87 0 88 0 0 100 0 100 184 80.5 234 0.4 Tsukubamonas globosa 97 0 122 1.6 92 0 112 0 87 0 0 100 57 90.9 0 100 102 89.2 234 0.4 Ustilago maydis 97 0 123 0.8 92 0 112 0 87 0 83 5.7 628 0 1012 1.4 0 100 235 0 Seq length and missing data are represented by bp and %, respectively. *only used for Supplementary file 13 Table S1. Data used in this work (continued). rps2 rps3 rps4 rps5 rps6 rps8 rps10 rps11 rps12 rps14 Taxa Seq length Missing Seq length Missing Seq length Missing Seq length Missing Seq length Missing Seq length Missing Seq length Missing Seq length Missing Seq length Missing Seq length Missing Acanthamoeba castellanii 191 0 189 0 230 0.4 115 35 183 0 166 0 77 0 114 0 95 0 0 100 Amphimedon queenlandica 185 3.1 189 0 214 7.4 177 0 183 0 164 1.2 77 0 114 0 95 0 115 0 Andalucia incarcerata 191 0 189 0 227 1.7 0 100 119 34.9 166 0 77 0 114 0 95 0 115 0 Arabidopsis thaliana 191 0 189 0 231 0 177 0 182 0.5 166 0 77 0 114 0 95 0 115 0 Aureococcus anophagefferens 191 0 189 0 231 0 177 0 183 0 166 0 77 0 114 0 95 0 115 0 Bigelowiella natans 176 7.9 180 4.8 231 0 177 0 0 100 166 0 77 0 114 0 95 0 115 0 Capsaspora owczarzaki 191 0 188 0.5 231 0 177 0 183 0 166 0 77 0 114 0 95 0 115 0 Chlamydomonas reinharditii 191 0 189 0 231 0 177 0 183 0 166 0 77 0 114 0 95 0 115 0 Chondrus crispus 0 100 136 28 200 13.4 0 100 127 30.6 166 0 77 0 0 100 95 0 0 100 Collodictyon triciliatum 191 0 163 13.8 228 1.3 160 9.6 142 22.4 120 27.7 75 2.6 114 0 87 8.4 114 6.6 Cryptosporidium parvum 191 0 189 0 231 0 177 0 183 0 166 0 77 0 0 100 95 0 115 0 Cyanidioschyzon merolae 191 0 189 0 231 0 177 0 183 0 166 0 77 0 114 0 95 0 113 1.7 Cyanophora paradoxa 191 0 189 0 231 0 177 0 183 0 162 2.4 77 0 114 0 95 0 115 0 Dictyostelium discoideum 191 0 187 1.1 231 0 177 0 183 0 166 0 77 0 114 0 95 0 115 0 Diplonema papillatum 178 6.8 189 0 172 25.5 121 31.6 53 71 153 7.8 52 32.5 114 0 95 0 115 0 Diacronema (Pavlova) lutheri 191 0 127 32.8 212 8.2 128 27.7 124 32.2 166 0 77 0 0 100 34 64.2 115 0 Drosophila melanogaster 191 0 189 0 231 0 177 0 183 0 166 0 77 0 114 0 95 0 115 0 Ectocarpus siliculosus 191 0 189 0 231 0 177 0 183 0 166 0 77 0 114 0 95 0 115 0 Emiliania huxleyi 39 79.6 189 0 140 39.4 177 0 183 0 166 0 77 0 112 1.8 95 0 115 0 Euglena gracilis 191 0 189 0 231 0 177 0 183 0 162 2.4 77 0 114 0 95 0 115 0 Galdieria sulphlaria 191 0 189 0 230 0.4 177 0 183 0 166 0 77 0 114 0 95 0 115 0 Glaucocystis nostochinearum 175 8.4 189 0 200 13.4 177 0 183 0 166 0 77 0 114 0 95 0 115 0 Goniomonas sp. 191 0 189 0 231 0 177 0 182 0.5 166 0 64 16.9 114 0 89 6.3 115 0 Gracilaria changii 124 35.1 189 0 121 47.6 177 0 177 3.3 162 2.4 77 0 71 37.7 95 0 115 0 Guillardia theta 191 0 189 0 231 0 177 0 183 0 164 1.2 77 0 114 0 95 0 115 0 Homo sapiens 191 0 189 0 231 0 177 0 183 0 166 0 77 0 114 0 95 0 115 0 Isochrysis galbana 191 0 0 100 0 100 0 100 0 100 0 100 0 100 0 100 0 100 0 100 Jakoba bahamensis 191 0 0 100 219 5.2 165 6.8 138 24.6 0 100 0 100 114 0 0 100 0 100 Jakoba libera 185 3.1 189 0 189 18.2 154 12.9 183 0 0 100 0 100 0 100 94 1.1 115 0 Limnofila borokensis 0 100 0 100 0 100 0 100 0 100 0 100 77 0 0 100 0 100 20 82.6 Malawimonas californiensis 0 100 0 100 231 0 145 18.1 0 100 166 0 0 100 114 0 95 0 115 0 Malawimonas jakobiformis 153 19.9 0 100 231 0 177 0 183 0 166 0 77 0 114 0 95 0 115 0 Mastigamoeba balamthii 191 0 185 2.1 231 0 177 0 183 0 144 13.3 77 0 114 0 95 0 115 0 Micromonas sp. 191 0 189 0 219 5.2 177 0 183 0 165 0.6 77 0 114 0 95 0 115 0 Monosiga brevicolis 191 0 189 0 231 0 176 0.6 183 0 166 0 77 0 114 0 95 0 115 0 Naegleria gruberi 191 0 189 0 231 0 177 0 168 8.2 166 0 77 0 114 0 0 100 115 0 Oryza sativa 191 0 189 0 231 0 177 0 183 0 166 0 77 0 114 0 95 0 115 0 Ostreococcus tauli 191 0 184 2.6 231 0 177 0 182 0.5 164 1.2 77 0 104 8.8 95 0 115 0 Oxyrrhis marina 191 0 189 0 231 0 177 0 124 32.2 166 0 0 100 0 100 0 100 0 100 Palpitomonas bilix 191 0 184 2.6 231 0 118 33.3 143 21.9 166 0 77 0 114 0 95 0 115 0 Paramecium caudata 191 0 188 0.5 82 64.5 177 0 167 8.7 166 0 0 100 0 100 0 100 0 100 Paracercomonas marina 0 100 0 100 187 19 172 2.8 0 100 0 100 0 100 114 0 95 0 0 100 Perkinsus marinus 191 0 189 0 231 0 177 0 183 0 166 0 0 100 114 0 95 0 115 0 Phaeodactylum tricornatum 191 0 189 0 231 0 177 0 183 0 166 0 0 100 114 0 90 5.3 115 0 Physarum polycephalum 191 0 158 16.4 231 0 177 0 183 0 0 100 77 0 114 0 95 0 115 0 Phytophthora infestans 191 0 189 0 231 0 177 0 183 0 166 0 77 0 0 100 95 0 115 0 Uncultured picozoa (MS584-11)* 148 22.5 0 100 183 20.8 0 100 0 100 59 64.5 0 100 47 58.8 0 100 66 42.6 Polyplacocystis (Raphidiophrys) contractilis 191 0 149 21.2 219 5.2 177 0 0 100 166 0 77 0 114 0 0 100 115 0 Prymnesium parvum 191 0 188 0.5 122 47.2 177 0 181 1.1 166 0 75 2.6 0 100 0 100 115 0 Pyropia (Porphyra) yezoensis 92 51.8 161 14.8 159 31.2 0 100 142 22.4 137 17.5 77 0 114 0 95 0 115 0 Reclinomonas americana 191 0 189 0 231 0 177 0 162 11.5 166 0 77 0 114 0 94 1.1 115 0 Rhodmonas salina 86 54.9 188 0.5 0 100 0 100 133 27.3 0 100 0 100 0 100 0 100 0 100 Roombia truncata 191 0 189 0 230 0.4 177 0 170 7.1 163 1.8 77 0 114 0 95 0 114 6.6 Saccharomyces cereviceae 191 0 189 0 231 0 177 0 183 0 166 0 0 100 0 100 0 100 0 100 Seculamonas ecuadriensis 152 20.4 189 0 231 0 177 0 181 1.1 166 0 0 100 114 0 95 0 115 0 Stachyamoeba lipophora 191 0 189 0 231 0 177 0 183 0 76 54.2 52 32.5 104 8.8 72 24.2 0 100 Telonema subtilis 191 0 189 0 231 0 154 12.9 0 100 133 19.9 77 0 0 100 95 0 115 0 Tetrahymena pyriformis 189 1 161 14.8 192 16.9 177 0 142 22.4 166 0 0 100 88 22.8 0 100 115 0 Thalassiosira pseudonana 191 0 189 0 231 0 177 0 182 0.5 165 0.6 77 0 114 0 95 0 115 0 Thecamonas trahens 176 7.9 185 2.1 156 32.5 159 10.2 183 0 61 63.3 52 32.5 114 0 95 0 115 0 Toxoplasma gondii 191 0 189 0 231 0 177 0 183 0 166 0 77 0 114 0 95 0 115 0 Trimastix pyriformis 191 0 188 0.5 139 39.8 177 0 183 0 164 1.2 77 0 104 8.8 95 0 115 0 Tsukubamonas globosa 191 0 189 0 231 0 177 0 183 0 162 2.4 77 0 114 0 95 0 115 0 Ustilago maydis 191 0 189 0 231 0 177 0 183 0 166 0 77 0 113 0.9 95 0 115 0 Seq length and missing data are represented by bp and %, respectively. *only used for Supplementary file 14 Table S1. Data used in this work (continued). rps15 rps16 rps17 rps18 rps20 rps23 rps26 rps27 s15a s15p Taxa Seq length Missing Seq length Missing Seq length Missing Seq length Missing Seq length Missing Seq length Missing Seq length Missing Seq length Missing Seq length Missing Seq length Missing Acanthamoeba castellanii 118 0 107 17.1 104 0 144 0 93 1.1 133 0 73 13.1 77 0 130 0 151 0 Amphimedon queenlandica 118 0 129 0 104 0 144 0 94 0 133 0 84 0 77 0 130 0 151 0 Andalucia incarcerata 118 0 97 24.8 104 0 144 0 78 17 106 20.3 84 0 39 49.4 130 0 151 0 Arabidopsis thaliana 118 0 129 0 104 0 144 0 94 0 133 0 84 0 77 0 130 0 151 0 Aureococcus anophagefferens 118 0 129 0 103 0.9 144 0 94 0 133 0 84 0 77 0 130 0 151 0 Bigelowiella natans 114 3.4 129 0 104 0 144 0 94 0 110 17.3 0 100 77 0 130 0 151 0 Capsaspora owczarzaki 118 0 129 0 104 0 144 0 94 0 133 0 84 0 77 0 130 0 151 0 Chlamydomonas reinharditii 118 0 129 0 104 0 144 0 94 0 133 0 84 0 77 0 130 0 151 0 Chondrus crispus 0 100 0 100 104 0 0 100 94 0 0 100 0 100 77 0 0 100 147 2.6 Collodictyon triciliatum 117 0.8 129 0 60 42.3 125 13.2 61 35.1 126 5.3 72 14.3 77 0 129 0.8 106 29.8 Cryptosporidium parvum 118 0 129 0 104 0 144 0 94 0 133 0 84 0 77 0 130 0 151 0 Cyanidioschyzon merolae 118 0 129 0 104 0 144 0 94 0 133 0 0 100 77 0 0 100 151 0 Cyanophora paradoxa 118 0 129 0 104 0 144 0 94 0 133 0 84 0 77 0 130 0 151 0 Dictyostelium discoideum 118 0 129 0 104 0 144 0 90 4.3 133 0 84 0 77 0 130 0 151 0 Diplonema papillatum 110 6.8 115 10.9 85 18.3 143 0.7 93 1.1 133 0 84 0 77 0 112 13.8 146 3.3 Diacronema (Pavlova) lutheri 118 0 45 65.1 0 100 0 100 94 0 133 0 0 100 0 100 0 100 56 62.9 Drosophila melanogaster 118 0 129 0 104 0 144 0 94 0 133 0 84 0 77 0 130 0 151 0 Ectocarpus siliculosus 0 100 129 0 103 0.9 144 0 94 0 133 0 84 0 77 0 130 0 151 0 Emiliania huxleyi 88 25.4 129 0 101 2.9 144 0 94 0 133 0 0 100 77 0 105 19.2 151 0 Euglena gracilis 118 0 128 0.8 104 0 144 0 94 0 133 0 84 0 77 0 130 0 151 0 Galdieria sulphlaria 0 100 129 0 102 1.9 144 0 94 0 0 100 84 0 77 0 130 0 151 0 Glaucocystis nostochinearum 118 0 129 0 104 0 143 0.7 94 0 133 0 84 0 77 0 130 0 151 0 Goniomonas sp. 118 0 108 16.3 98 5.8 144 0 94 0 132 0.8 84 0 77 0 130 0 151 0 Gracilaria changii 115 2.5 129 0 104 0 144 0 92 2.1 133 0 77 8.3 0 100 129 0.8 141 6.6 Guillardia theta 118 0 129 0 104 0 144 0 89 5.3 133 0 84 0 77 0 129 0.8 150 0.7 Homo sapiens 118 0 129 0 104 0 144 0 94 0 133 0 84 0 77 0 130 0 151 0 Isochrysis galbana 0 100 0 100 0 100 0 100 0 100 0 100 0 100 0 100 0 100 0 100 Jakoba bahamensis 0 100 0 100 0 100 0 100 0 100 133 0 0 100 0 100 0 100 151 0 Jakoba libera 118 0 129 0 104 0 0 100 0 100 133 0 84 0 0 100 0 100 52 65.6 Limnofila borokensis 0 100 100 22.5 0 100 0 100 0 100 0 100 0 100 0 100 0 100 0 100 Malawimonas californiensis 118 0 129 0 104 0 144 0 94 0 133 0 84 0 77 0 125 3.8 0 100 Malawimonas jakobiformis 118 0 129 0 104 0 144 0 94 0 133 0 84 0 77 0 130 0 151 0 Mastigamoeba balamthii 118 0 129 0 104 0 144 0 93 1.1 133 0 84 0 67 12.9 129 0.8 151 0 Micromonas sp. 116 1.7 129 0 104 0 141 2.1 94 0 133 0 84 0 75 2.6 130 0 151 0 Monosiga brevicolis 118 0 129 0 104 0 144 0 94 0 0 100 84 0 0 100 129 0.8 151 0 Naegleria gruberi 102 13.6 129 0 104 0 144 0 92 2.1 133 0 84 0 77 0 130 0 148 1.9 Oryza sativa 118 0 129 0 104 0 144 0 94 0 133 0 84 0 77 0 130 0 151 0 Ostreococcus tauli 116 1.7 129 0 104 0 141 2.1 92 2.1 133 0 84 0 77 0 130 0 151 0 Oxyrrhis marina 0 100 0 100 0 100 144 0 0 100 0 100 0 100 0 100 0 100 0 100 Palpitomonas bilix 118 0 129 0 104 0 144 0 94 0 133 0 0 100 77 0 130 0 151 0 Paramecium caudata 0 100 0 100 0 100 136 5.6 0 100 0 100 0 100 0 100 0 100 0 100 Paracercomonas marina 69 41.5 129 0 0 100 142 1.4 94 0 133 0 0 100 77 0 96 26.2 151 0 Perkinsus marinus 118 0 129 0 104 0 141 2.1 94 0 133 0 84 0 77 0 130 0 151 0 Phaeodactylum tricornatum 117 0.8 129 0 103 0.9 140 2.8 94 0 133 0 84 0 77 0 130 0 151 0 Physarum polycephalum 118 0 129 0 93 10.6 144 0 0 100 133 0 84 0 77 0 130 0 151 0 Phytophthora infestans 118 0 129 0 103 0.9 144 0 94 0 0 100 84 0 77 0 124 4.6 151 0 Uncultured picozoa (MS584-11)* 38 67.8 0 100 38 63.5 0 100 48 48.9 0 100 0 100 35 54.5 0 100 0 100 Polyplacocystis (Raphidiophrys) contractilis 118 0 115 10.9 0 100 144 0 0 100 133 0 0 100 0 100 130 0 82 45.7 Prymnesium parvum 118 0 0 100 0 100 0 100 94 0 60 54.9 0 100 77 0 0 100 151 0 Pyropia (Porphyra) yezoensis 118 0 129 0 0 100 144 0 92 2.1 133 0 0 100 77 0 130 0 143 5.3 Reclinomonas americana 118 0 129 0 104 0 144 0 94 0 133 0 84 0 77 0 130 0 151 0 Rhodmonas salina 0 100 0 100 0 100 119 17.4 0 100 0 100 0 100 0 100 0 100 0 100 Roombia truncata 0 100 129 0 103 0.9 140 2.8 94 0 133 0 72 14.3 77 0 130 0 150 0.7 Saccharomyces cereviceae 0 100 0 100 0 100 142 1.4 0 100 0 100 0 100 0 100 0 100 0 100 Seculamonas ecuadriensis 118 0 129 0 104 0 0 100 94 0 133 0 84 0 0 100 127 2.3 0 100 Stachyamoeba lipophora 95 19.5 116 10.1 0 100 78 45.8 71 24.5 122 8.3 84 0 47 38.9 91 30 83 45 Telonema subtilis 118 0 129 0 0 100 142 1.4 0 100 133 0 0 100 0 100 130 0 63 58.3 Tetrahymena pyriformis 118 0 129 0 104 0 144 0 94 0 133 0 84 0 77 0 130 0 0 100 Thalassiosira pseudonana 117 0.8 129 0 103 0.9 140 2.8 94 0 133 0 84 0 77 0 130 0 151 0 Thecamonas trahens 117 0.8 115 10.9 103 0.9 144 0 77 18.1 133 0 56 33.3 77 0 130 0 146 3.3 Toxoplasma gondii 118 0 129 0 104 0 144 0 94 0 133 0 84 0 77 0 130 0 150 0.7 Trimastix pyriformis 118 0 129 0 104 0 144 0 92 2.1 133 0 80 4.8 77 0 130 0 151 0 Tsukubamonas globosa 118 0 129 0 104 0 144 0 94 0 133 0 84 0 77 0 130 0 151 0 Ustilago maydis 118 0 129 0 104 0 144 0 94 0 133 0 84 0 77 0 130 0 144 4.6 Seq length and missing data are represented by bp and %, respectively. *only used for Supplementary file 15 Table S1. Data used in this work (continued). sap40 sra srp54 srs suca tfiid topo1 trs ubc ubq Taxa Seq length Missing Seq length Missing Seq length Missing Seq length Missing Seq length Missing Seq length Missing Seq length Missing Seq length Missing Seq length Missing Seq length Missing Acanthamoeba castellanii 186 0.5 0 100 0 100 157 52.6 272 0 0 100 43 87.2 169 65.3 0 100 0 100 Amphimedon queenlandica 187 0 0 100 72 77.5 0 100 0 100 0 100 65 80.6 0 100 139 0 76 0 Andalucia incarcerata 187 0 0 100 0 100 163 50.8 205 24.6 71 51.7 0 100 220 54.8 139 0 76 0 Arabidopsis thaliana 187 0 259 0 320 0 331 0 272 0 147 0 335 0 486 0.2 139 0 76 0 Aureococcus anophagefferens 187 0 259 0 320 0 331 0 272 0 147 0 335 0 487 0 139 0 76 0 Bigelowiella natans 187 0 259 0 317 0.9 165 50.2 272 0 147 0 335 0 487 0 139 0 76 0 Capsaspora owczarzaki 187 0 221 14.7 320 0 331 0 272 0 147 0 335 0 486 0.2 139 0 76 0 Chlamydomonas reinharditii 187 0 258 0.4 320 0 330 0.3 272 0 147 0 335 0 463 4.9 139 0 76 0 Chondrus crispus 0 100 121 53.3 132 58.8 0 100 0 100 0 100 80 76.1 0 100 119 14.4 76 0 Collodictyon triciliatum 160 14.4 0 100.0 0 100 227 31.4 0 100 61 58.5 0 100 0 100 0 100 76 0 Cryptosporidium parvum 187 0 259 0 320 0 331 0 0 100 147 0 335 0 479 1.6 139 0 76 0 Cyanidioschyzon merolae 187 0 259 0 320 0 331 0 272 0 145 1.4 335 0 486 0.2 139 0 0 100 Cyanophora paradoxa 187 0 144 44.4 291 9.1 284 14.2 212 22.1 117 100 0 100 246 49.5 139 0 76 0 Dictyostelium discoideum 187 0 259 0 320 0 331 0 272 0 147 0 333 0.6 393 19.3 139 0 76 0 Diplonema papillatum 0 100 0 100 0 100 0 100 0 100 0 100 0 100 0 100 60 56.8 76 0 Diacronema (Pavlova) lutheri 0 100 0 100 0 100 0 100 0 100 0 100 156 53.4 0 100 139 0 76 0 Drosophila melanogaster 187 0 259 0 320 0 331 0 272 0 147 0 335 0 486 0.2 139 0 76 0 Ectocarpus siliculosus 187 0 259 0 320 0 327 1.2 272 0 147 0 320 4.5 390 19.9 139 0 76 0 Emiliania huxleyi 187 0 256 1.2 290 9.4 320 3.3 269 1.1 0 100 335 0 423 13.1 139 0 76 0 Euglena gracilis 187 0 0 100 0 100 0 100 272 0 0 100 43 87.2 139 71.5 139 0 76 0 Galdieria sulphlaria 0 100 259 0 320 0 331 0 271 0.4 146 0.7 335 0 477 2.1 139 0 76 0 Glaucocystis nostochinearum 0 100 175 32.4 0 100 0 100 0 100 0 100 43 87.2 90 81.5 139 0 76 0 Goniomonas sp. 187 0 0 100 64 80 88 73.4 0 100 144 2.0 0 100 0 100 139 0 76 0 Gracilaria changii 187 0 140 45.9 0 100 86 74 0 100 63 57.1 41 87.8 0 100 139 0 76 0 Guillardia theta 187 0 239 7.7 320 0 318 3.9 271 0.4 147 0 335 0 487 0 139 0 76 0 Homo sapiens 187 0 259 0 320 0 331 0 272 0 147 0 335 0 486 0.2 139 0 76 0 Isochrysis galbana 65 65.2 164 36.7 168 47.5 0 100 0 100 117 20.4 0 100 0 100 0 100 0 100 Jakoba bahamensis 0 100 147 43.2 269 15.9 0 100 0 100 0 100 0 100 343 29.6 139 0 0 100 Jakoba libera 114 39 0 100 0 100 62 81.3 0 100 0 100 0 100 97 80.1 139 0 76 0 Limnofila borokensis 0 100 0 100 0 100 0 100 0 100 0 100 0 100 0 100 0 100 74 2.6 Malawimonas californiensis 187 0 0 100 70 78.1 140 57.7 179 34.2 0 100 0 100 89 81.7 134 3.6 76 0 Malawimonas jakobiformis 187 0 0 100 39 87.8 157 52.6 178 34.6 147 0 126 62.4 0 100 139 0 76 0 Mastigamoeba balamthii 187 0 197 23.9 64 80 319 3.6 0 100 0 100 0 100 189 61.2 121 12.9 76 0 Micromonas sp. 187 0 259 0 320 0 331 0 272 0 147 0 335 0 486 0.2 139 0 76 0 Monosiga brevicolis 187 0 259 0 228 28.8 315 4.8 272 0 147 0 322 3.9 458 5.9 139 0 76 0 Naegleria gruberi 187 0 259 0 315 1.6 331 0 261 4 145 1.4 335 0 487 0 139 0 69 9.2 Oryza sativa 187 0 259 0 320 0 331 0 272 0 147 0 335 0 486 0.2 139 0 76 0 Ostreococcus tauli 187 0 259 0 320 0 329 0.6 272 0 147 0 291 13.1 463 4.9 139 0 76 0 Oxyrrhis marina 187 0 0 100 160 50 129 61 232 14.7 0 100 0 100 0 100 108 22.3 76 0 Palpitomonas bilix 187 0 115 55.6 64 80 152 54.1 0 100 0 100 43 87.2 129 73.5 139 0 76 0 Paramecium caudata 0 100 133 48.6 320 0 331 0 272 0 147 0 183 45.4 456 6.4 0 100 76 0 Paracercomonas marina 0 100 167 35.5 0 100 0 100 0 100 0 100 107 68.1 0 100 115 17.3 76 0 Perkinsus marinus 187 0 250 3.5 320 0 331 0 272 0 147 0 334 0.3 487 0 139 0 76 0 Phaeodactylum tricornatum 186 0.5 258 0.4 318 0.6 331 0 272 0 135 8.2 335 0 487 0 139 0 76 0 Physarum polycephalum 181 3.2 0 100 170 46.9 100 69.8 179 34.2 0 100 0 100 0 100 0 100 76 0 Phytophthora infestans 187 0 259 0 320 0 329 0.6 272 0 145 1.4 313 6.6 487 0 139 0 76 0 Uncultured picozoa (MS584-11)* 0 100 0 100 0 100 0 100 0 100 37 74.8 0 100 0 100 0 100 67 11.8 Polyplacocystis (Raphidiophrys) contractilis 130 30.5 74 71.4 125 60.9 0 100 85 68.8 67 54.4 158 52.8 113 76.8 134 3.6 76 0 Prymnesium parvum 56 70.1 0 100 134 58.1 0 100 116 57.4 0 100 0 100 0 100 108 22.3 76 0 Pyropia (Porphyra) yezoensis 174 6.9 0 100 98 69.4 131 60.4 0 100 0 100 157 53.1 0 100 139 0 76 0 Reclinomonas americana 187 0 259 0 312 2.5 212 35.9 192 29.4 0 100 0 100 149 69.4 139 0 76 0 Rhodmonas salina 0 100 0 100 0 100 0 100 0 100 0 100 0 100 0 100 0 100 76 0 Roombia truncata 187 0 0 100 320 0 322 2.7 235 13.6 147 0 0 100 100 79.5 139 0 76 0 Saccharomyces cereviceae 187 0 187 27.8 320 0 331 0 272 0 147 0 335 0 487 0 0 100 76 0 Seculamonas ecuadriensis 187 0 0 100 147 54.1 161 51.4 194 28.7 147 0 55 83.6 185 62 139 0 76 0 Stachyamoeba lipophora 187 0 0 100 0 100 146 55.9 0 100 0 100 0 100 149 69.4 0 100 76 0 Telonema subtilis 187 0 123 52.5 70 78.1 59 82.2 268 1.5 0 100 0 100 42 91.4 138 0.7 0 100 Tetrahymena pyriformis 126 32.6 259 0 320 0 322 2.7 272 0 147 0 334 0.3 82 83.2 139 0 76 0 Thalassiosira pseudonana 187 0 251 3.1 320 0 330 0.3 266 2.2 140 4.8 335 0 484 0.6 139 0 76 0 Thecamonas trahens 123 34.2 259 0 276 13.8 283 14.5 216 20.6 118 19.7 335 0 487 0 110 20.9 76 0 Toxoplasma gondii 187 0 259 0 320 0 316 4.5 272 0 116 21.1 335 0 487 0 139 0 76 0 Trimastix pyriformis 187 0 0 100 0 100 327 1.2 0 100 146 0.7 0 100 221 54.6 139 0 0 100 Tsukubamonas globosa 187 0 101 61 20 93.8 138 58.3 272 0 35 76.2 0 100 199 59.1 139 0 76 0 Ustilago maydis 185 1.1 259 0 320 0 302 8.8 270 0.7 147 0 335 0 487 0 139 0 76 0 Seq length and missing data are represented by bp and %, respectively. *only used for Supplementary file 16 Table S1. Data used in this work (continued). vata vatb vatc vate wd wrs xpd Total Taxa Seq length Missing Seq length Missing Seq length Missing Seq length Missing Seq length Missing Seq length Missing Seq length Missing Seq length Missing Acanthamoeba castellanii 212 59.6 338 23.9 189 0 160 0 0 100 179 44.9 102 77.9 19420 53.1 Amphimedon queenlandica 210 60 178 59.9 155 17.9 160 0 142 21.1 175 46.2 22 95.2 19167 53.7 Andalucia incarcerata 298 43.2 444 0 0 100 124 22.5 109 39.4 0 100 0 100 15938 61.5 Arabidopsis thaliana 525 0 444 0 189 0 160 0 180 0 325 0 461 0 40239 2.7 Aureococcus anophagefferens 525 0 444 0 189 0 0 100 167 7.2 325 0 461 0 35528 14.1 Bigelowiella natans 515 1.9 444 0 186 1.6 160 0 141 21.7 293 9.8 217 52.9 39140 5.4 Capsaspora owczarzaki 525 0 444 0 189 0 160 0 160 11.1 325 0 355 22.9 40413 2.3 Chlamydomonas reinharditii 525 0 431 2.9 189 0 160 0 0 100 325 0 0 100 38218 7.6 Chondrus crispus 0 100 0 100 0 100 0 100 0 100 0 100 0 100 8765 78.8 Collodictyon triciliatum 246 53.1 114 74.3 0 100 0 100 139 22.8 71 78.2 0 100 13996 66.2 Cryptosporidium parvum 525 0 444 0 182 3.7 160 0 0 100 325 0 277 39.9 35788 13.5 Cyanidioschyzon merolae 524 0.2 444 0 105 44.4 160 0 0 100 325 0 461 0 38303 7.4 Cyanophora paradoxa 37 92.9 195 56.1 0 100 104 35 151 16.1 53 83.7 203 56.0 25629 38.1 Dictyostelium discoideum 525 0 444 0 189 0 160 0 180 0 324 0.3 461 0 39251 5.1 Diplonema papillatum 0 100 0 100 73 61.4 0 100 0 100 0 100 0 100 6444 84.4 Diacronema (Pavlova) lutheri 320 39 300 32.4 115 39.2 160 0 122 32.2 163 49.8 0 100 13563 67.2 Drosophila melanogaster 525 0 444 0 189 0 160 0 180 0 325 0 461 0 40483 2.1 Ectocarpus siliculosus 525 0 435 2 189 0 160 0 154 14.4 324 0.3 0 100 38739 6.4 Emiliania huxleyi 525 0 444 0 189 0 0 100 178 1.1 325 0 461 0 34175 17.4 Euglena gracilis 341 35 232 47.7 184 2.6 151 5.6 180 0 0 100 0 100 20509 50.4 Galdieria sulphlaria 513 2.3 432 2.7 187 1.1 155 3.1 0 100 294 9.5 460 0.2 38241 7.6 Glaucocystis nostochinearum 0 100 85 80.9 126 33.3 151 5.6 0 100 0 100 0 100 13353 67.7 Goniomonas sp. 194 63.0 0 100 0 100 0 100 0 100 106 67.4 0 100 12866 68.9 Gracilaria changii 0 100 158 64.4 0 100 153 4.4 0 100 0 100 0 100 13513 67.3 Guillardia theta 525 0 444 0 154 18.5 160 0 180 0 0 100 451 2.2 39192 5.3 Homo sapiens 525 0 444 0 189 0 160 0 180 0 325 0 461 0 41093 0.7 Isochrysis galbana 221 57.9 144 67.6 189 0 0 100 133 26.1 0 100 0 100 7611 81.6 Jakoba bahamensis 0 100 0 100 115 39.2 160 0 180 0 0 100 0 100 13926 66.3 Jakoba libera 233 55.6 183 58.8 114 39.7 129 19.4 109 39.4 118 63.7 0 100 13078 68.4 Limnofila borokensis 0 100 0 100 0 100 0 100 0 100 0 100 0 100 2561 93.8 Malawimonas californiensis 0 100 123 72.3 0 100 160 0 0 100 92 71.7 0 100 13923 66.3 Malawimonas jakobiformis 106 79.8 300 32.4 130 31.2 160 0 124 31.1 0 100 0 100 18224 56.0 Mastigamoeba balamthii 523 0.4 442 0.5 189 0 160 0 138 23.3 88 72.9 34 92.6 22704 45.1 Micromonas sp. 525 0 444 0 189 0 160 0 180 0 325 0 461 0 37895 8.4 Monosiga brevicolis 525 0 444 0 160 15.3 159 0.6 170 5.6 325 0 452 1.9 39533 4.4 Naegleria gruberi 525 0 444 0 189 0 157 1.9 180 0 325 0 460 0.2 38203 7.7 Oryza sativa 525 0 444 0 189 0 160 0 180 0 325 0 461 0 40492 2.1 Ostreococcus tauli 525 0 443 0.2 189 0 160 0 180 0 325 0 461 0 39955 3.4 Oxyrrhis marina 223 57.5 416 6.3 119 37 160 0 0 100 0 100 0 100 14282 65.5 Palpitomonas bilix 0 100 245 44.8 189 0 53 66.9 0 100 138 57.5 0 100 19514 52.8 Paramecium caudata 241 54.1 321 27.7 189 0 160 0 0 100 325 0 427 7.4 20263 51.0 Paracercomonas marina 0 100 0 100 69 63.5 0 100 0 100 0 100 0 100 8820 78.7 Perkinsus marinus 525 0 444 0 189 0 160 0 164 8.9 325 0 461 0 36872 10.9 Phaeodactylum tricornatum 525 0 440 0.9 189 0 160 0 180 0 295 9.2 461 0 39833 3.7 Physarum polycephalum 525 0 213 52 189 0 0 100 0 100 112 65.5 0 100 20065 51.5 Phytophthora infestans 525 0 444 0 189 0 160 0 180 0 325 0 461 0 39933 3.5 Uncultured picozoa (MS584-11)* 39 92.6 0 100 0 100 0 100 0 100 239 26.5 110 76.1 #REF! #REF! Polyplacocystis (Raphidiophrys) contractilis 204 61.1 115 74.1 0 100 0 100 84 53.3 0 100 0 100 14279 65.5 Prymnesium parvum 230 56.2 248 44.1 126 33.3 160 0 159 11.7 0 100 0 100 13022 68.5 Pyropia (Porphyra) yezoensis 161 69.3 166 62.6 101 46.6 102 36.3 0 100 71 78.2 148 67.9 15528 62.5 Reclinomonas americana 221 57.9 0 100 0 100 160 0 180 0 184 43.4 0 100 20806 49.7 Rhodmonas salina 0 100 0 100 0 100 0 100 0 100 0 100 0 100 4043 90.2 Roombia truncata 510 2.9 444 0 0 100 160 0 150 16.7 0 100 0 100 25283 38.9 Saccharomyces cereviceae 523 0.4 444 0 189 0 160 0 155 13.9 325 0 461 0 31986 22.7 Seculamonas ecuadriensis 508 3.2 435 2 188 0.5 0 100 0 100 0 100 0 100 18877 54.4 Stachyamoeba lipophora 202 61.5 95 78.6 66 65.1 0 100 0 100 0 100 0 100 8767 78.8 Telonema subtilis 385 26.7 302 31.9 0 100 0 100 0 100 0 100 0 100 13939 66.3 Tetrahymena pyriformis 515 1.9 196 55.9 130 31.2 160 0 147 18.3 324 0.3 130 71.8 30825 25.5 Thalassiosira pseudonana 454 13.5 429 3.4 175 7.4 137 14.4 178 1.1 320 1.5 461 0 39859 3.7 Thecamonas trahens 293 44.2 421 5.2 189 0 100 37.5 153 15 325 0 461 0 36280 12.3 Toxoplasma gondii 525 0 393 11.5 189 0 160 0 177 1.7 325 0 461 0 37548 9.2 Trimastix pyriformis 383 27 215 51.6 184 2.6 129 19.4 0 100 0 100 0 100 19381 53.2 Tsukubamonas globosa 515 1.9 444 0 189 0 160 0 27 85 211 35.1 0 100 22718 45.1 Ustilago maydis 525 0 444 0 188 0.5 160 0 0 100 325 0 461 0 37047 10.5 Seq length and missing data are represented by bp and %, respectively. *only used for Supplementary file 17 Table S2. Akaike Information Criterion (AIC)-based model selection for the maximum-likelihood phylogenetic analysis of a 157-gene alignment. Model AIC Model AIC DAYHOFF + Γ 3210548.96 DAYHOFF + Γ + F 3202054.47 DCMUT + Γ 3210476.36 DCMUT + Γ + F 3202257.90 JTT + Γ 3200475.75 JTT + Γ + F 3199897.08 MTREV + Γ 3363588.41 MTREV + Γ + F 3246024.01 WAG + Γ 3171504.90 WAG + Γ + F 3169115.19 RTREV + Γ 3169167.33 RTREV + Γ + F 3148634.71 CPREV + Γ 3203469.97 CPREV + Γ + F 3200192.17 VT + Γ 3186233.87 VT + Γ + F 3183740.35 BLOSUM62 + Γ 3193272.57 BLOSUM62 + Γ + F 3195658.42 MTMAM + Γ 3452763.75 MTMAM + Γ + F 3344027.21 MTART + Γ 3337837.64 MTART + Γ + F 3232312.96 MTZOA + Γ 3268646.92 MTZOA + Γ + F 3200005.69 PMB + Γ 3201844.21 PMB + Γ + F 3202497.38 HIVB + Γ 3306850.93 HIVB + Γ + F 3299903.49 HIVW + Γ 3482858.27 HIVW + Γ + F 3437951.33 JTTDCMUT + Γ 3199493.75 JTTDCMUT + Γ + F 3198185.12 FLU + Γ 3279882.21 FLU + Γ + F 3271134.95 DUMMY + Γ 3489935.60 DUMMY + Γ + F 3391055.37 DUMMY2 + Γ 3351772.73 DUMMY2 + Γ + F 3337288.87 LG + Γ 3140743.96 LG + Γ + F 3139948.37 LG4M 3108012.20 LG4X 3102958.65

18 Thecamonas trahens Apusozoa Homo sapiens Drosophila melanogaster Amphimedon queenslandica Monosiga brevicollis Capsaspora owczarzaki Opisthokonts Saccharomyces cerevisiae Ustilago maydis Blastocladiella emersonii Physarum polycephalum 76 Dictyostelium discoideum Mastigamoeba balamuthi Amoebozoa Acanthamoeba castellanii 67 Bigelowiella natans Limnofila borokensis Paracercomonas marina Rhizaria Thalassiosira pseudonana 83 Phaeodactylum tricornutum Aureococcus anophagefferens Ectocarpus siliculosus Stramenopiles Phytophthora infestans Paramecium caudatum Tetrahymena pyriformis Oxyrrhis marina Perkinsus marinus Alveolata Cryptosporidium parvum Toxoplasma gondii Isochrysis galbana Emiliania huxleyi Prymnesium parvum Haptophyta 46 Diacronema (Pavlova) lutheri 32 Polyplacocystis (Raphidiophrys) contractilis Heliozoa uncultured picozoa (MS584-11) Guillardia theta 91 Rhodomonas salina Cryptophyceae Goniomonas sp. Goniomonada 81 Roombia truncata Leucocrypta Cryptista 27 Palpitomonas bilix Palpitia Telonema subtilis Telonemea Micromonas sp. Ostreococcus tauri Chlamydomonas reinhardtii Oryza sativa Arabidopsis thaliana Glaucocystis nostochinearum Cyanophora paradoxa Archaeplastida 50 Chondrus crispus Gracilaria changii Pyropia (Porphyra) yezoensis Cyanidioschyzon merolae Galdieria sulphuraria Euglena gracilis Diplonema papillatum Naegleria gruberi Stachyamoeba lipophora Tsukubamonas globosa 68 ‘Seculamonas ecuadoriensis’ Reclinomonas americana Jakoba libera Excavata ‘Jakoba bahamensis’ Andalucia incarcerata Trimastix pyriformis ‘Malawimonas californiensis’ Malawimonas jakobiformis Collodictyon triciliatum Diphyllatea 0.1 substitutions/site

Figure S1 19 Figure S1.

Phylogenetic position of Palpitomonas bilix inferred from the maximum-likelihood

(ML) analysis of a 157-gene dataset (41,372 amino acid positions) containing picozoan sequences. The 157-protein dataset was analyzed by both maximum-likelihood (ML).

ML bootstrap percentage values (MLBPs) >60 % were only shown. The values for the position of Telonema and Picozoa were exceptionally shown, although they are less than 60 %. Dots correspond to MLBP >95%.

20