Table S1 Taxa and sequences used in the phylogenetic analysis Additional file 5: Number of taxa and sequences used in the phylogenetic analysis. Protein Databases Num Taxa Num Seqs Nucleotide Databases Num Taxa Num Seqs Ciliophora 7 66,495 Perkinsea 2 24,884 Perkinsea 1 23,654 1 2,856 26 76,675 Alveolate Apicomplexa 1 1,844 Stramenopiles 32 171,687 Ciliophora* 22 287,638 2 22,919 * 22 614,141 Glaucocystophyceae 1 149 Stramenopiles 35 624,095 Plantae Rhodophyta 11 1,168 Rhizaria 7 9,472 167 590,694 Glaucocystophyceae 3 27,409 Haptophyceae 1 39,265 Plantae Rhodophyta 10 48,138 Cryptophyta 4 26,259 Viridiplantae 5 28,565 8 52,587 Haptophyceae 5 133,743 Fornicata 1 6,502 Cryptophyta* 3 60,187 Heterolobosea 1 15,801 Heterolobosea 3 37,017 Excavate Jakobida 1 67 Jakobida 5 34,041 1 49 Malawimonadidae 2 12,998 Excavate Parabasalia 1 59,679 Parabasalia 3 30,751 11 42,905 Euglenozoa 15 91,788 Choanoflagellida 1 18,399 Fornicata 3 36,304 Opistokont Fungi 113 459,222 Amoebozoa 11 184,511 Metazoa 1,856 759,023 Opistokont Choanoflagellida 3 73,213 Chlorobi 11 27,326 Chloroflexi 10 36,755 *New next-generation assemblies added to the NCBI TSA database Cyanobacteria 28 193,842 acuminata () GAIJ01000000; Alexandrium tamraense Group IV CCMP1598 (dinoflagellate) Deferribacteres 1 3,115 GAII01000000; Alexandrium tamarese Group I SPE10-03 Deinococci 5 13,118 (dinoflagellate) GAIK01000000; Alexandrium tamarese Group I Dictyoglomi 2 3,652 (dinoflagellate) GAIV01000000; Alexandrium tamarense Group III Acidobacteria 3 15,845 (dinoflagellate) GAIU01000000; catenatum GC744 Elusimicrobia 2 2,294 (dinoflagellate) GAIL01000000; Pyrodinium bahamense Fibrobacteres 1 3,081 CCFW293-B5 (dinoflagellate) GAIO01000000; Geminigera Firmicutes 243 932,573 cryophila CCMP2564 (cryptophyte) GAIM01000000; Myrionecta Actinobacteria 161 604,647 rubra CCMP2563 () GAIN01000000 Fusobacteria 12 45,397 Gemmatimonadetes 1 3,929 Bacteria Nitrospirae 2 2,044 Planctomycetes 6 36,770 Proteobacteria 526 2,341,088 Spirochaetes 18 39,221 Synergistetes 5 11,122 Tenericutes 29 20,021 Thermotogae 12 22,392 Thermus 3 5,258 Verrucomicrobia 8 38,409 Aquificae 9 18,801 Bacteria-other 7 19,118 Bacteroidetes 77 316,572 Chlamydiae 9 11,232 Archaea 84 174,912 Virus 2,372 66,922 Other 39 1,031

TABLE S3 Summary of KEGG annotated sequences in the A. tamarense Group IV transcriptome and 16 other eukaryotic genomes.

Species Total sequences Genes annotated KOs

Dinoflagellate A. tamarense Group IV 85,163 5,347 2,959

Apicomplexans B. bovis 3,706 1,085 998 C. parvum 3,805 1,002 950 P. falciparum 5,337 1,460 1,090 T. annulata 3,795 1,037 941 T. gondii 7,987 1,414 1,244

Ciliates P. tetraurelia 39,580 3,252 1,471 T. thermophila 24,770 2,439 1,532

Stramenopiles A. anophagefferens 11,501 3,075 2,195 E. siliculosus 16,580 3,404 2,651 P. tricornutum 10,402 2,194 1,818 T. pseudonana 11,776 2,381 1,899

Haptophyte E. huxleyi 39,125 5,060 2,705

Cryptophyte G. theta 24,840 3,768 2,749

Green Algae M. pusilla 10,672 2,824 2,356 O. lucimarinus 7,651 2,392 2,014 O. tauri 7,725 2,193 1,902 Total sequences: Total number of gene sequences per genome. Genes annotated: Number of genes with a KAAS assigned KEGG annotation per genome. KOs: Total number of unique KOs assigned per genome. SUPPLEMENTAL FIGURES

Supplementary Figure S1: Rarefaction curve assessment of de novo transcriptome assembly quality. Seven single kmer assemblies (23-47) were compared to a multi kmer merged assembly (orange). The merged assembly maximized assembly length (number of basepairs) while minimizing the number of contigs and Oases loci.

Supplementary Figure S2: Distribution of dinoflagellate-prokaryote associations recovered in the phylogenomic analysis. The number of gene trees that support dinoflagellate sequences grouping with each prokaryotic phyla is given in parenthesis. a Bacteria, the sister clade to contained more than one bacterial phyla. b Archaea, the sister subtree contained one or more archaeal phyla. cOther Bacteria, the sister clade to dinoflagellates consisted of bacteria not assigned to a bacterial phyla.

Supplementary Figure S3: Distribution of KEGG pathways in A. tamarense sequence sets.

Supplementary Figure S4: Color-coded KEGG pathway maps. Maps reflecting gene gain/loss transitions of A. tamarense, apicomplexans, and relative to the alveolate common ancestor using Dollo Parsimony. Genes that have been retained from the alveolate ancestor in one of the three major lineages (e.g. retained in A. tamarense) have been necessarily lost in the other two (e.g. lost in ciliates and apicomplexans). A) Photosynthesis, ko00195 B) Arginine and proline metabolism, ko00330 C) Phenylalanine, tyrosine, and tryptophan biosynthesis, ko00400 D) Histidine metabolism, ko00340 E) Fatty acid biosynthesis, ko00061 F) Fatty acid metabolism, ko00071 G) Oxidative phosphorylation, ko00190

Supplementary Figure S5: Phylogenetic trees of A. tamarense proteins. Taxa names are formatted as follows, Group-Genus_species_GeneID. Dinoflagellate taxa are bolded. Branch numbers indicate bootstrap support. When bootstrap numbers are <= 1, the tree was taken directly from the automated phylogenetic pipeline. Pipeline trees were constructed using fasttree with 1000 bootstrap replicates. When bootstrap numbers are >=50, the taxa and alignments were manually curated and the tree was built using RAxML with 100 bootstrap replicates. Numbers in parenthesis to the right of clade names indicate the number of taxa within the collapsed node. Trees S4B, S4F, S4H, S4I, S4L, S4M are rooted on bacteria; all other trees are midpoint rooted. A) Alternative NADH dehydrogenase. B) FAD-dependent glycerol-3-phosphate dehydrogenase. C) Malate:quinone oxidoreductase. D) Pyruvate dehydrogenase, AceE E) Pyruvate:NADP+oxidoreductase, PNO (N-terminal ) F) Pyruvate:NADP+oxidoreductase, PNO (C-terminal domain) G) Isocitrate dehydrogenase form 1 H) Isocitrate dehydrogenase form 2 I) Fumarase class I J) Fumarase class II K) Valine:pyruvate aminotransferase L) Branched-chain amino acid aminotransferase M) Molecular chaperone, grpE (alveolate-like) N) Molecular chaperone, grpE (algal-like) O) Molecular chaperone, grpE (bacterial-like) P) Phosphatidylserine synthase Q) Citrate lyase

Supplementary Figure S1: Rarefaction curve assessment of de novo transcriptome assembly quality.

Supplementary Figure S2: Distribution of dinoflagellate-prokaryote associations recovered in the phylogenomic analysis.

!"#$%#&'($%")'*+,,-*Proteobacteria (55) a ./&'($%")'*+01-*Bacteria (27)

2)"3)(/$%4*+5,-*Firmicutes (15)

6(78#&'($%")'*+9-*Actinobacteria (8)

:%""/(#3)("#&)'*+;-*Verrucomicrobia (6)

<'($%"#)=%$%4*+,-*Bacteriodetes (5)

>?@#"#A%B)*+C-*Chloroblexi (3)

6"(?'%'*+5-*Archaea (1)b c <'($%")'*+5-*Other Bacteria (1)

2/4#&'($%")'*+5-*Fusobacteria (1)

!@'8($#3D(%$%4*+5-*Planctomycetes (1)

E%8%")(/$%4*+5-*Tenericutes (1)

E?%"3#$#F'%*+5-*Thermotogae (1)

Supplementary Figure S3: Distribution of KEGG pathways in A. tamarense sequence sets. All A. tamarense KOs KOs unique to A. tamarense

1 1 2 2 3 3 4 4 5 5 6 6 22 7 20 21 7 8 8 9 17 19 18 16 9 13 10 12 10 16 15 11 17 20 11 13 14 12 22 1415 21 18 19

A. tamarense KOs missing KOs of putative bacterial in other origin in A. tamarense

1 1 2

3

20 4 2 17 5 14 6 10 13 7 20 22 3 9 11 8 21 9 17 4 8 11 12 13 19 5 6 18 16 10 14 15 7

Metabolism 1 - Carbohydrate Metabolism 2 - Amino Acid Metabolism Genetic information 3 - Lipid Metabolism processing 4 - Energy Metabolism 5 - Nucleotide Metabolism Cellular processes 6 - Metabolism of Cofactors and Vitamins 7 - Glycan Biosynthesis and Metabolism Environmental information 8 - Xenobiotics Biodegradation and Metabolism processing 9 - Metabolism of Other Amino Acids 10 - Metabolism of Terpenoids and Polyketides Not mapped to pathway 11 - Biosynthesis of Other Secondary Metabolites 12 - Translation 13 - Folding, Sorting and Degradation 14 - Replication and Repair 15 - Transcription 16 - Cell Growth and Death 17 - Transport and Catabolism 18 - Cell Communication 19 - Cell Motility 20 - Signal Transduction 21 - Membrane Transport 22 - Signaling Molecules and Interaction Supplementary Figure S4A – Photosynthesis (ko00195) A. tamarense A. tamarense Lost in ciliates Gained in Retained in

Supplementary Figure S4B – Arginine and proline metabolism (ko00330) A. tamarense A. tamarense Lost in ciliates In all alveolates Retained in ciliates Lost in apicomplexans Gained in Retained in

Supplementary Figure S4C – Phenylalanine, tyrosine, and tryptophan biosynthesis (ko00400)

Gained in A. tamarense Lost in ciliates Retained in ciliates

Retained in A. tamarense Lost in apicomplexans In all alveolates

Supplementary Figure S4D – Histidine metabolism (ko00340) Retained in ciliates Lost in ciliates Lost in apicomplexans A. tamarense A. tamarense Gained in Retained in

Supplementary Figure S4E – Fatty acid biosynthesis (ko00061) Lost in ciliates In all alveolates A. tamarense A. tamarense Gained in Retained in

Supplementary Figure S4F – Fatty acid metabolism (ko00071)

In all alveolates Lost in apicomplexans A. tamarense A. tamarense Gained in Retained in

Supplementary Figure S4G – Oxidative phosphorylation (ko00190) A. tamarense In all alveolates Retained in ciliates Lost in Gained in DALCA Lost in ciliates A. tamarense A. tamarense Gained in Retained in

Supplementary Figure S5A – Alternative NADH dehydrogenase 75 Viridiplantae (19) 94 95 Euglenozoa−Leishmania_major_157877617 100 Euglenozoa−Leishmania_infantum_146104827 100 Euglenozoa−Leishmania_braziliensis_154346482 100 Euglenozoa−Trypanosoma_brucei_71748224 Euglenozoa−Trypanosoma_cruzi_71422638 61 stramenopiles−Phytophthora_parasitica_68418902est 62 stramenopiles−Phytophthora_capsici_PhycaF7_38066 54 stramenopiles−Phytophthora_sojae_Physo1_1_143510 88 stramenopiles−Phytophthora_ramorum_Phyra1_1_81150 100 99 stramenopiles−Phytophthora_capsici_PhycaF7_3648 stramenopiles−Phytophthora_ramorum_Phyra1_1_81153 stramenopiles−Pythium_ultimum_148600593est 82 88 Metazoa−Hydra_magnipapillata_221129462 Metazoa−Nematostella_vectensis_156372827 78 Metazoa−Ciona_intestinalis_198427647 Metazoa−Trichoplax_adhaerens_196011808 Dinophyceae−Alexandrium_tamarenseCCMP_Locus_87599 97 Dinophyceae−Alexandrium_tamarenseSP_Locus_2083est 100 Dinophyceae−Alexandrium_tamarenseG3_Locus_7411est Dinophyceae−Pyrodinium_bahamense_PbajaSW100_c2816est stramenopiles−Fragilariopsis_cylindrus_Fracy1_137231 67 Choanoflagellida−Monosiga_brevicollis_Monbr1_22868 Choanoflagellida−Monosiga_ovata_163044370est 57 stramenopiles−Thalassiosira_pseudonana_Thaps3_36673 81 stramenopiles−Fragilariopsis_cylindrus_Fracy1_191160 100 Haptophyceae−Emiliania_huxleyi_Emihu1_449901 77 78 Haptophyceae−Emiliania_huxleyi_Emihu1_463050 Haptophyceae−Isochrysis_galbana_106823873est stramenopiles−Phaeodactylum_tricornutum_Phatr2_11373 Malawimonadidae−Malawimonas_jakobiformis_110035753est stramenopiles−Ectocarpus_siliculosus_Esi0486_0005 100 Amoebozoa−Dictyostelium_discoideum_166240085 Amoebozoa−Dictyostelium_purpureum_Dicpu1_97816 Heterolobosea−Naegleria_gruberi_Naegr1_81197 70 Fungi (32) Amoebozoa−Physarum_polycephalum_152789898est 85 stramenopiles−Fragilariopsis_cylindrus_Fracy1_205063 96 stramenopiles−Phaeodactylum_tricornutum_Phatr2_26970 56 stramenopiles−Thalassiosira_pseudonana_Thaps3_687 68 stramenopiles−Ectocarpus_siliculosus_Esi0006_0133 100 Haptophyceae−Emiliania_huxleyi_Emihu1_428171 Haptophyceae−Emiliania_huxleyi_Emihu1_453801 stramenopiles−Aureococcus_anophagefferens_Auran1_10731 Rhodophyta−Porphyra_yezoensis_31933033est Cryptophyta−Guillardia_theta_117384562est 95 stramenopiles−Phaeodactylum_tricornutum_Phatr2_16430 100 stramenopiles−Thalassiosira_pseudonana_Thaps3_6361 stramenopiles−Aureococcus_anophagefferens_161651121est stramenopiles−Ectocarpus_siliculosus_Esi0005_0270 100 Dinophyceae−Alexandrium_tamarenseG3_Locus_29266est 76 Dinophyceae−Alexandrium_tamarenseCCMP_Locus_23902 65 Viridiplantae−Volvox_carteri_Volca1_63330 91 Viridiplantae−Volvox_carteri_Volca1_105834 55 Viridiplantae−Chlamydomonas_reinhardtii_159488552 100 Viridiplantae−Coccomyxa_sp._Coc_C169_1_66639 Viridiplantae−Chlorella_sp._ChlNC64A_1_143182 97 Fungi (35) 56 Dinophyceae−Alexandrium_tamarenseG3_Locus_8835est 100 Dinophyceae−Alexandrium_tamarenseCCMP_Locus_7449 100 Dinophyceae−Alexandrium_tamarenseSP_Locus_4317est 100 Dinophyceae−Alexandrium_tamarenseG3_Locus_34796est Dinophyceae−Alexandrium_tamarenseCCMP_Locus_74153 100 Viridiplantae−Chlamydomonas_reinhardtii_159491374 87 Viridiplantae−Volvox_carteri_Volca1_76599 Viridiplantae−Coccomyxa_sp._Coc_C169_1_19760 100 Viridiplantae−Ostreococcus_lucimarinus_Ost9901_3_12203 81 Viridiplantae−Ostreococcus_lucimarinus_145342040 99 Viridiplantae−Ostreococcus_sp._OstRCC809_1_46647 99 100 Viridiplantae−Ostreococcus_tauri_Ostta4_27768 83 Viridiplantae−Micromonas_pusilla_MicpuC2_32597 Viridiplantae−Micromonas_sp._MicpuN3_58414 89 Viridiplantae−Chlorella_sp._ChlNC64A_1_58189 Viridiplantae−Chlorella_sp._ChlNC64A_1_143930 Viridiplantae−Coccomyxa_sp._Coc_C169_1_36339 79 Viridiplantae (31) Heterolobosea−Naegleria_gruberi_Naegr1_72836 Alveolata−Perkinsus_marinus_XP_002784460 92 Fungi (55) Dinophyceae−Alexandrium_tamarenseCCMP_Locus_31037 Dinophyceae−Alexandrium_tamarenseG3_Locus_30644est 100 Dinophyceae−Alexandrium_tamarenseSP_Locus_29363est stramenopiles−Aureococcus_anophagefferens_161682951est stramenopiles−Aureococcus_anophagefferens_161699480est 100 Amoebozoa−Dictyostelium_discoideum_166240217 92 Amoebozoa−Dictyostelium_purpureum_Dicpu1_148767 Amoebozoa−Hartmannella_vermiformis_106816105est 51 Apicomplexa−Plasmodium_berghei_68062086 100 Apicomplexa−Plasmodium_yoelii_83318042 53 Apicomplexa−Plasmodium_chabaudi_70935187 69 Apicomplexa−Plasmodium_gallinaceum_387762377 100 Apicomplexa−Plasmodium_falciparum_124506849 Apicomplexa−Plasmodium_cynomolgi_389582988 100 Apicomplexa−Plasmodium_knowlesi_221054566 Apicomplexa−Plasmodium_vivax_156097306 100 Apicomplexa−Cryptosporidium_hominis_67624439 100 Apicomplexa−Cryptosporidium_parvum_66362802 Apicomplexa−Cryptosporidium_muris_209879834 100 Apicomplexa−Theileria_parva_71027847 100 Apicomplexa−Theileria_annulata_85001033 100 Apicomplexa−Theileria_orientalis_403222939 55 Apicomplexa−Babesia_bovis_156083326 Apicomplexa−Babesia_microti_399216064 Apicomplexa−Toxoplasma_gondii_221484413 100 Apicomplexa−Toxoplasma_gondii_78057337 96 100 Apicomplexa−Toxoplasma_gondii_237838043 Apicomplexa−Neospora_caninum_401401734 Apicomplexa−Toxoplasma_gondii_221482891 100 Apicomplexa−Toxoplasma_gondii_237840755 100 Apicomplexa−Toxoplasma_gondii_95007395 Apicomplexa−Neospora_caninum_401396786 Metazoa−Hydra_magnipapillata_221117548

0.3

Supplementary Figure S5B – FAD-dependent glycerol-3-phosphate dehydrogenase

77 56 Metazoa (41) 71 Fungi (31) 57 Stramenopiles−Fragilariopsis_cylindrus_Fracy1_276098 92 Stramenopiles−Phaeodactylum_tricornutum_Phatr2_1129 98 Stramenopiles−Thalassiosira_pseudonana_Thaps3_41505 100 Stramenopiles−Aureococcus_anophagefferens_Auran1_72359 Dinophyceae−Alexandrium_tamarenseCCMP_Locus_6606 73 50 Dinophyceae−Alexandrium_tamarenseG3_Locus_8348est 100 Dinophyceae−Alexandrium_tamarenseSP_Locus_229est Rhizaria−Bigelowiella_natans_89985 Amoebozoa−Physarum_polycephalum_152791705est 55 Apicomplexa−Plasmodium_berghei_68071805 96 Apicomplexa−Plasmodium_yoelii_82595178 62 Apicomplexa−Plasmodium_chabaudi_70954452 100 97 Apicomplexa−Plasmodium_knowlesi_221055683 Apicomplexa−Plasmodium_vivax_156094097 Apicomplexa−Plasmodium_falciparum_124504795 100 Apicomplexa−Theileria_annulata_85001393 100 Apicomplexa−Theileria_parva_71026355 Apicomplexa−Babesia_bovis_156087643 66 100 Ciliophora−Tetrahymena_thermophila_118361145 79 Ciliophora−Paramecium_tetraurelia_145521244 Apicomplexa−Toxoplasma_gondii_237832351 Perkinsea−Perkinsus_marinus_XP_002774011 96 Stramenopiles−Phytophthora_sojae_Physo1_1_109316 51 Stramenopiles−Phytophthora_capsici_PhycaF7_101913 53 80 Stramenopiles−Phytophthora_ramorum_Phyra1_1_74798 Phytophthora_infestans_301111270 100 Stramenopiles−Phytophthora_infestans_58151301est 92 Stramenopiles−Phytophthora_parasitica_68417779est 57 Stramenopiles−Pythium_ultimum_148599893est 64 Stramenopiles−Ectocarpus_siliculosus_Esi0117_0019 100 Cryptophyta−Guillardia_theta_84416 Cryptophyta−Geminigera_cryophila_GcryoSW10_c1393est Dinophyceae−Alexandrium_tamarenseCCMP_Locus_19915 99 Euglenozoa−Leishmania_major_157871506 100 Euglenozoa−Leishmania_infantum_146096003 100 Euglenozoa−Leishmania_braziliensis_154340205 94 Euglenozoa−Trypanosoma_cruzi_71422006 Euglenozoa−Trypanosoma_brucei_71755803 69 Viridiplantae−Ostreococcus_tauri_Ostta4_27797 100 Viridiplantae−Ostreococcus_lucimarinus_Ost9901_3_30486 99 Viridiplantae−Ostreococcus_sp._OstRCC809_1_31971 Viridiplantae−Micromonas_sp._MicpuN3_82879 100 Viridiplantae−Chlamydomonas_reinhardtii_Chlre4_413348 50 Viridiplantae−Volvox_carteri_Volca1_80593 99 Viridiplantae−Chlorella_sp._ChlNC64A_1_136099 Viridiplantae−Coccomyxa_sp._Coc_C169_1_27656 93 Viridiplantae−Zea_mays_212274307 99 100 Viridiplantae−Sorghum_bicolor_Sorbi1_4831786 56 Viridiplantae−Oryza_sativa_115457356 100 Viridiplantae−Arabidopsis_lyrata_Araly1_478367 51 Viridiplantae−Arabidopsis_thaliana_15228273 100 Viridiplantae−Populus_trichocarpa_Poptr1_1_822583 Viridiplantae−Ricinus_communis_255577446 100 Viridiplantae−Vitis_vinifera_225448978 Viridiplantae−Selaginella_moellendorffii_Selmo1_185263 Viridiplantae−Physcomitrella_patens_Phypa1_1_115350 Bacteria (12)

0.3

Supplementary Figure S5C – Malate:quinone oxidoreductase

97 Dinophyceae−Alexandrium_tamarenseSP_Locus_3026est Dinophyceae−Alexandrium_catenella_186961838est Dinophyceae−Alexandrium_tamarenseG3_Locus_2674est Dinophyceae−Alexandrium_tamarenseCCMP_Contig8913est 94 Dinophyceae−Alexandrium_tamarenseCCMP_Locus_7800 Dinophyceae−Alexandrium_tamarense_38453349est 62 Dinophyceae−Heterocapsa_triquetra_73768951est 99 Dinophyceae−Pyrodinium_bahamense_PbajaSW0_c11430est Dinophyceae−Karlodinium_micrum_106842736est 84 Dinophyceae−Gymnodinium_catenatum_F4S52ZS01D1901est 57 Dinophyceae−Karenia_brevis_158892731est 100 Haptophyceae−Emiliania_huxleyi_208409510est 100 Haptophyceae−Emiliania_huxleyi_Emihu1_442715 Cryptophyta−Geminigera_cryophila_FW1RJLL02GXCRPest 73 Actinobacteria−Beutenbergia_cavernae_229819313 75 51 Actinobacteria−Cellulomonas_flavigena_229242118 97 Actinobacteria−Xylanimonas_cellulosilytica_269957028 80 Actinobacteria−Sanguibacter_keddieii_269794622 15 Actinobacteria−Jonesia_denitrificans_256832796 Actinobacteria−marine_actinobacterium_88856408

74 Actinobacteria−Clavibacter_michiganensis_148272083 Actinobacteria−Leifsonia_xyli_50954180 Actinobacteria−Frankia_symbiont_289642204 Proteobacteria & Actinobacteria (16) 98 Actinobacteria (33) 52 88 Actinobacteria−Brachybacterium_faecium_257068474 Actinobacteria−Kineococcus_radiotolerans_152967657 Proteobacteria (17) 100 Proteobacteria−Gluconacetobacter_diazotrophicus_209542563 Proteobacteria−Acetobacter_pasteurianus_258542249 77 Firmicutes (22) Bacteroidetes (13) 99 Proteobacteria−Helicobacter_hepaticus_32267219 73 Proteobacteria−Helicobacter_cinaedi_224437784 Proteobacteria−Wolinella_succinogenes_34557176 Proteobacteria (50+) Proteobacteria (12) Proteobacteria−beta_proteobacterium_254468816 Proteobacteria−Candidatus_Carsonella_116335009 Proteobacteria−Methylophilales_bacterium_118594778 Viridiplantae−Ostreococcus_tauri_Ostta4_29969 Verrucomicrobia−Verrucomicrobium_spinosum_171912463 99 Apicomplexa−Plasmodium_vivax_156100981 77 Apicomplexa−Plasmodium_knowlesi_221057992

100 Apicomplexa−Plasmodium_falciparum_86171141 73 Apicomplexa−Plasmodium_yoelii_82595007 100 Apicomplexa−Plasmodium_berghei_68075787 Apicomplexa−Plasmodium_chabaudi_70944920 1 54 100 Apicomplexa−Theileria_annulata_85001458 100 Apicomplexa−Theileria_parva_71026417 53 Apicomplexa−Theileria_orientalis_403222720 98 Apicomplexa−Babesia_bovis_156087573 96 Apicomplexa−Babesia_microti_399219219 100Apicomplexa−Toxoplasma_gondii_92399525 100 Apicomplexa−Toxoplasma_gondii_221505584 98 Apicomplexa−Neospora_caninum_401401618 76 Apicomplexa−Eimeria_tenella_118490754 Apicomplexa−Cryptosporidium_muris_209876664 87 Proteobacteria−Methylophaga_sp_387131402 100 Proteobacteria−Methylophaga_sp_387128078 Proteobacteria−Methylophaga_thiooxidans_254491979 Proteobacteria−Allochromatium_vinosum_288942433 62 Archaea−Halomicrobium_mukohataei_257386752 52 Archaea−Halorhabdus_utahensis_257054047 100 Archaea−Haloterrigena_turkmenica_284166392 100 Archaea−Halorubrum_lacusprofundi_222478864 Perkinsea−Perkinsus_marinus_XP_002781001 58 Cyanobacteria−Cyanobium_sp_254431517 Cyanobacteria−Cyanothece_sp_220908999 80 Proteobacteria (18)

0.6

Supplementary Figure S5D – Pyruvate dehydrogenase

0.98 Deinococci−Deinococcus_deserti_226355150 1 Deinococci−Deinococcus_radiodurans_15805289 Deinococci−Deinococcus_geothermalis_94985987 1 1 Thermus−Thermus_thermophilus_161611241 0.93 Thermus−Thermus_aquaticus_218295971 0.85 Deinococci−Meiothermus_silvanus_227990321

0.93 0.99 Acidobacteria−Candidatus_Koribacter_94969819 Proteobacteria−Nitrosococcus_oceani_77164760 Bacteroidetes−Gramella_forsetii_120436033

0.73 Planctomycetes−Pirellula_staleyi_283781656 0.72 1 Planctomycetes−Rhodopirellula_baltica_32472508 Planctomycetes−Blastopirellula_marina_87311705 0.95 0.95 Planctomycetes−Planctomyces_maris_149175160 0.66 0.81 Planctomycetes−Planctomyces_limnophilus_229537527 Verrucomicrobia−bacterium_Ellin514_223938989 Acidobacteria−Candidatus_Solibacter_116624469 1 1 Acidobacteria−Acidobacterium_capsulatum_225872044 Planctomycetes−Gemmata_obscuriglobus_168703333 1 0.98 Proteobacteria (212) Dinophyceae−Alexandrium_tamarenseG3_Locus_3766est 1 Dinophyceae−Alexandrium_tamarenseSP_Locus_22285est 1 Dinophyceae−Alexandrium_tamarenseCCMP_Locus_27996 Dinophyceae−Amphidinium_carterae_39543524est 0.87 Actinobacteria (95)

0.3

Supplementary Figure S5E – Pyruvate:NADP+oxidoreductase (N-terminal domain)

100 Perkinsea−Perkinsus_marinus_294866647 Perkinsea−Perkinsus_marinus_294887311

100 Perkinsea−Perkinsus_marinus_294886221 Perkinsea−Perkinsus_marinus_294936201

100 Apicomplexa−Cryptosporidium_parvum_33112419 Apicomplexa−Cryptosporidium_parvum_209879035 100

100 Perkinsea−Perkinsus_marinus_294889633 Perkinsea−Perkinsus_marinus_294867467

100 Perkinsea−Perkinsus_marinus_294889635

Perkinsea−Perkinsus_marinus_294867463

Dinophyceae−Alexandrium_tamarenseG3_Locus_771est

100 Dinophyceae−Alexandrium_tamarenseSP_Locus_4475est

Dinophyceae−Alexandrium_tamarenseCCMP_Locus_2028

100 Amoebozoa−Entamoeba_histolytica_183230217 Amoebozoa−Entamoeba_dispar_167376288

Stramenopiles−Blastocystis_hominis

Euglenozoa−Euglena_gracilis_9909124

Stramenopiles−Blastocystis_hominis

93 Viridiplantae−Chlamydomonas_reinhardtii_159486358

Fornicata−Giardia_lamblia_159117456

95 95 Bacteria (195) Firmicutes−Moorella_thermoacetica_83588937

100 Bacteria−Candidatus_Cloacamonas_218960661 Bacteria−Victivallis_vadensis_281356167 100 Bacteria (123)

0.3

Supplementary Figure S5F – Pyruvate:NADP+oxidoreductase (C-terminal domain)

88 75 Metazoa (23) Choanoflagellida−Monosiga_brevicollis_Monbr1_16143 85 100 Fungi−Vanderwaltozyma_polyspora_156841693 100 Fungi−Clavispora_lusitaniae_260950699 100 Fungi−Aspergillus_terreus_115397301 100 Viridiplantae (12) 64 100 Stramenopiles−Phaeodactylum_tricornutum_Phatr2_9283 89 Stramenopiles−Thalassiosira_pseudonana_Thaps3_264678 100 Stramenopiles−Ectocarpus_siliculosus_Esi0000_0401 Rhizaria−Bigelowiella_natans_146442 100 Metazoa (9) 77 100 Amoebozoa−Dictyostelium_purpureum_Dicpu1_155023 59 64 Amoebozoa−Dictyostelium_discoideum_66806397 99 Heterolobosea−Naegleria_gruberi_Naegr1_36877 100 100 Viridiplantae (10) 97 Stramenopiles−Ectocarpus_siliculosus_Esi0101_0066 Stramenopiles−Phytophthora_ramorum_Phyra1_1_52148 98 Perkinsea−Perkinsus_marinus_294889633 100 Perkinsea−Perkinsus_marinus_294867467 100 Perkinsea−Perkinsus_marinus_294889635 69 Perkinsea−Perkinsus_marinus_294867463

100 63 Perkinsea−Perkinsus_marinus_294886221 100 Perkinsea−Perkinsus_marinus_294866647 61 Perkinsea−Perkinsus_marinus_294887311 Perkinsea−Perkinsus_marinus_294936201 Stramenopiles−Blastocystis_hominis_300175205 100 Apicomplexa−Cryptosporidium_parvum_33112419 100 Apicomplexa−Cryptosporidium_hominis_67588070 Apicomplexa−Cryptosporidium_muris_209879035 100 59 Euglenozoa−Euglena_gracilis_9909124 Cryptophyta−Guillardia_theta_159505 Choanoflagellida−Monosiga_brevicollis_167518083 Dinophyceae−Alexandrium_tamarenseCCMP_Locus_2028 Dinophyceae−Dinophysis_acuminata_GNV6H5201ELEZL 100 Bacteria (16)

0.3

Supplementary Figure S5G – Isocitrate dehydrogenase form 1

0.9 0.67 Metazoa (16) 0.74 Amoebozoa−Dictyostelium_purpureum_253824377est Amoebozoa−Polysphondylium_pallidum_110075517est 0.95 Amoebozoa−Dictyostelium_purpureum_Dicpu1_154640 Amoebozoa−Physarum_polycephalum_110074197est Amoebozoa−Hyperamoeba_dachnaya_110160199est Glaucocystophyceae−Cyanophora_paradoxa_109767940est 0.97 0.81 Ciliophora−Paramecium_tetraurelia_145537055 0.86 Ciliophora−Anophryoides_haemophila_269110254est 0.95 Ciliophora−Paramecium_tetraurelia_134010324est 0.87 Ciliophora−Tetrahymena_thermophila_47049324est 0.92 0.77 Amoebozoa−Hartmannella_vermiformis_106815385est 0.98 Euglenozoa−Trypanosoma_cruzi_71659757 Metazoa (28) Jakobida−Jakoba_libera_109800647est Dinophyceae−Alexandrium_tamarenseCCMP_Locus_54686 Dinophyceae−Alexandrium_tamarenseSP_Locus_2799est 0.95 Dinophyceae−Alexandrium_tamarenseG3_Locus_37815est 0.99 Dinophyceae−Alexandrium_tamarense_38453006est 0.86 0.82 Dinophyceae−Pyrocystis_lunula_32332193est 0.92 Dinophyceae−Pyrodinium_bahamense_PbajaSW100_c2320est Dinophyceae−Karlodinium_micrum_106840021est Perkinsea−Perkinsus_marinus_XP_002782165 0.86 Apicomplexa−Plasmodium_yoelii_82594625 0.98 0.95 Apicomplexa−Plasmodium_berghei_68075339 0.62 Apicomplexa−Plasmodium_chabaudi_70937961 1 0.99 Apicomplexa−Plasmodium_knowlesi_221058503 0.88 0.86 0.87 Apicomplexa−Plasmodium_vivax_156096404 Apicomplexa−Plasmodium_falciparum_124513630 Apicomplexa−Toxoplasma_gondii_237830457 Amoebozoa−Mastigamoeba_balamuthi_110022433est 0.91 0.97Euglenozoa−Leishmania_infantum_146079062 0.96 Euglenozoa−Leishmania_major_157865307 0.76 Euglenozoa−Leishmania_chagasi_60317313est 1 Euglenozoa−Leishmania_braziliensis_154333083 Euglenozoa−Phytomonas_serpens_58333573est Euglenozoa−Trypanosoma_brucei_72392799 0.62 Stramenopiles−Phytophthora_ramorum_Phyra1_1_71685 0.56 Stramenopiles−Phytophthora_brassicae_144588059est 0.64 Stramenopiles−Phytophthora_sojae_38059680est 0.75 Stramenopiles−Phytophthora_sojae_Physo1_1_109565 0.90.88 0.99 0.87 Stramenopiles−Phytophthora_infestans_239856382est Stramenopiles−Phytophthora_parasitica_222396041est 0.82 Stramenopiles−Pythium_ultimum_148601380est 0.96 1 Stramenopiles−Ectocarpus_siliculosus_241960587est 0.82 Stramenopiles−Ectocarpus_siliculosus_Esi0048_0101 Malawimonadidae−Malawimonas_californiana_110030969est 0.95 Viridiplantae−Chlorella_sp._ChlNC64A_1_55969_0.750656167979003/1−377 1 Viridiplantae−Volvox_carteri_Volca1_77629 0.9 Viridiplantae−Chlamydomonas_reinhardtii_159481269 0.75 Viridiplantae−Coccomyxa_sp._Coc_C169_1_57881 Jakobida−Histiona_aroides_110157884est 0.77 1 Heterolobosea−Naegleria_gruberi_168538674est Heterolobosea−Naegleria_gruberi_Naegr1_82731 1 Jakobida−Seculamonas_ecuadoriensis_110123006est Bacteria (100+) 0.95 0.9 Apicomplexa−Cryptosporidium_muris_209879746 0.81 0.88 Bacteroidetes−Blattabacterium_sp._262341048 1 Amoebozoa−Acanthamoeba_castellanii_106792723est Viridiplantae (10) 0.99 Stramenopiles−Phytophthora_capsici_186713042est 0.98 0.73 Stramenopiles−Phytophthora_capsici_PhycaF7_107227 Stramenopiles−Aphanomyces_cochlioides_144586423est 0.71 Jakobida−Reclinomonas_americana_110105986est 0.81 0.84 Ciliophora−Tetrahymena_thermophila_118368129 0.94 Ciliophora−Ichthyophthirius_multifiliis_133878935est Fungi (48) 0.92 0.85 Ciliophora−Sterkiella_histriomuscorum_209370884est Perkinsea−Perkinsus_marinus_161754221est 1 Apicomplexa−Theileria_parva_71029224 1 Apicomplexa−Theileria_annulata_84997081 0.9 Apicomplexa−Babesia_bovis_156088897 1 Amoebozoa−Dictyostelium_discoideum_19403184est 1 Amoebozoa−Dictyostelium_discoideum_66823859 Bacteria (100+)

0.2

Supplementary Figure S5H – Isocitrate dehydrogenase form 2

100 Viridiplantae−Micromonas_pusilla_MicpuC2_70903 84 Viridiplantae−Micromonas_sp._MicpuN3_60441 100 Haptophyceae−Emiliania_huxleyi_208401438est Haptophyceae−Emiliania_huxleyi_Emihu1_450594

73 Cryptophyta−Geminigera_cryophila_Contig5495est Cryptophyta−Guillardia_theta_84453

77 Rhizaria−Bigelowiella_natans_57271 100 Stramenopiles−Fragilariopsis_cylindrus_282261242est 91 Stramenopiles−Fragilariopsis_cylindrus_Fracy1_277597 Stramenopiles−Phaeodactylum_tricornutum_144643794est 100 100 Stramenopiles−Phaeodactylum_tricornutum_Phatr2_45017 Stramenopiles−Thalassiosira_pseudonana_Thaps3_1456

100 Dinophyceae−Alexandrium_tamarenseG3_Locus_4988est 100 Dinophyceae−Alexandrium_tamarenseSP_Locus_726est Dinophyceae−Alexandrium_tamarenseCCMP_Locus_537 Dinophyceae−Pyrodinium_bahamense_Contig7447est

73 100 Dinophyceae−Alexandrium_tamarenseSP_Contig2210est Dinophyceae−Alexandrium_catenella_186953245est 100 Dinophyceae−Karenia_brevis_158892069est Dinophyceae−Alexandrium_tamarenseCCMP_Locus_19508

100 Stramenopiles−Aureococcus_anophagefferens_161664701est Stramenopiles−Aureococcus_anophagefferens_Auran1_59240

100 Proteobacteria−Francisella_tularensis_56708560 100 Proteobacteria−Francisella_novicida_254373363 78 Proteobacteria−Francisella_philomiragia_254876571 61 Bacteroidetes−Psychroflexus_torquis_91214546 Proteobacteria−Bermanella_marisrubri_94499668

100 Proteobacteria−Psychromonas_sp._90408078 50 Proteobacteria−Psychromonas_ingrahamii_119944742 Cyanobacteria−Synechococcus_sp._170077460 82 100 Cyanobacteria−Acaryochloris_marina_158338841 Planctomycetes−Rhodopirellula_baltica_32471503 Proteobacteria−Sorangium_cellulosum_162455100

0.1

Supplementary Figure S5I – Fumarase class I

Apicomplexa − Plasmodium_vivax_156097554 Apicomplexa − Plasmodium_knowlesi_221054818 Apicomplexa − Plasmodium_yoelii_82594864 Apicomplexa − Plasmodium_falciparum_124507093 Apicomplexa − Plasmodium_berghei_68073759 Apicomplexa − Plasmodium_chabaudi_70952487 100 Apicomplexa − Cryptosporidium_muris_209877192 94 Dinophyceae − Alexandrium_tamarenseCCMP_Locus_59440_fs 88 87 Apicomplexa − Babesia_bovis_156082840 Apicomplexa − Theileria_annulata_85000145 Apicomplexa − Theileria_parva_71026907 100 Perkinsea − Perkinsus_marinus_161739362est Perkinsea − Perkinsus_marinus_XP_002766476 100 Euglenozoa − Leishmania_braziliensis_154341168 Dinophyceae − Alexandrium_catenella_186961380est Euglenozoa − Leishmania_major_73536886 Euglenozoa − Leishmania_chagasi_60318161est Euglenozoa − Leishmania_infantum_146093223 Dinophyceae − Alexandrium_tamarenseCCMP_Locus_17954_x Euglenozoa − Trypanosoma_brucei_72387235 Euglenozoa − Trypanosoma_cruzi_71658956 62 Apicomplexa − Toxoplasma_gondii_237839007 Dinophyceae − Alexandrium_tamarenseG3_Locus_6849est Dinophyceae − Alexandrium_tamarenseCCMP_Locus_8813_x 100 Dinophyceae − Karenia_brevis_159010520est 0.2 Stramenopiles − Aureococcus_anophagefferens_Auran1_23252 Stramenopiles − Aureococcus_anophagefferens_161678937est Euglenozoa − Trypanosoma_congolense_225623032est 100 100 Stramenopiles − Phaeodactylum_tricornutum_144647695est 100 Stramenopiles − Phaeodactylum_tricornutum_Phatr2_19708 Stramenopiles − Fragilariopsis_cylindrus_Fracy1_209986 Stramenopiles − Thalassiosira_pseudonana_162395348est Stramenopiles − Thalassiosira_pseudonana_Thaps3_22464 89 100 Glaucocystophyceae − Cyanophora_paradoxa_138228064est Viridiplantae − Ostreococcus_lucimarinus_Ost9901_3_86934 Choanoflagellida − Monosiga_ovata_163067100est 100 Viridiplantae − Ostreococcus_sp._OstRCC809_1_45492 Viridiplantae − Ostreococcus_tauri_Ostta4_16948 Viridiplantae − Chlamydomonas_reinhardtii_Chlre4_195953 Viridiplantae − Chlamydomonas_reinhardtii_159477070 Cryptophyta − Geminigera_cryophila_GcryoSW10_c2559est Ciliophora − Myrionecta_rubra_Contig1187est Viridiplantae − Volvox_carteri_Volca1_77105 Heterolobosea − Naegleria_gruberi_168536676est Heterolobosea − Naegleria_gruberi_Naegr1_34693 100 Proteobacteria − Granulibacter_bethesdensis_114328471 100 Stramenopiles − Ectocarpus_siliculosus_Esi0173_0060 Proteobacteria − Rhodospirillum_rubrum_83593541 Proteobacteria − Acidiphilium_cryptum_148260340 Viridiplantae − Micromonas_pusilla_MicpuC2_46951 Haptophyceae − Prymnesium_parvum_76568964est Cryptophyta − Guillardia_theta_101390 Metazoa − Schistosoma_mansoni_256071735 100 Viridiplantae − Micromonas_sp._MicpuN3_58123 Metazoa − Trichoplax_adhaerens_196007192 Euglenozoa − Euglena_gracilis_109788825est 80 Haptophyceae − Emiliania_huxleyi_208424792est Haptophyceae − Emiliania_huxleyi_Emihu1_438455 100 Metazoa − Branchiostoma_floridae_260839820 Rhizaria − Bigelowiella_natans_57804 Proteobacteria − Azospirillum_sp._288960498 86 100 98 Choanoflagellida − Monosiga_brevicollis_170635341est Choanoflagellida − Monosiga_brevicollis_Monbr1_37063 Proteobacteria − Magnetospirillum_magneticum_83310430 71 Amoebozoa − Physarum_polycephalum_152799438est 53 100 100 99 100 100 79 61 100 98 100 100 51 89 99 59 96 94 76 92 88

74

Supplementary Figure S5J – Fumarase class II

51 Metazoa (16) 100 Ciliophora−Tetrahymena_thermophila_118394845 89 Ciliophora−Tetrahymena_thermophila_47044882est 80 Ciliophora−Ichthyophthirius_multifiliis_133879575est 90 Ciliophora−Anophryoides_haemophila_269106417est 100 Ciliophora−Paramecium_tetraurelia_145513837 Ciliophora−Paramecium_tetraurelia_133941995est Ciliophora−Sterkiella_histriomuscorum_209373773est 100 Amoebozoa−Dictyostelium_discoideum_66814056 97 Amoebozoa−Dictyostelium_discoideum_19312343est Amoebozoa−Dictyostelium_purpureum_Dicpu1_158228 Amoebozoa−Acanthamoeba_castellanii_106787696est Rhizaria−Paracercomonas_marina_156132155est 52 Metazoa (28) 100 Stramenopiles−Fragilariopsis_cylindrus_282256426est 69 Stramenopiles−Fragilariopsis_cylindrus_Fracy1_208253 100 Stramenopiles−Phaeodactylum_tricornutum_144644893est 92 Stramenopiles−Phaeodactylum_tricornutum_Phatr2_36139 100 Stramenopiles−Thalassiosira_pseudonana_Thaps3_24123 Stramenopiles−Thalassiosira_pseudonana_162365108est Stramenopiles−Schizochytrium_sp._148526293est Haptophyceae−Emiliania_huxleyi_261431074est 100 Stramenopiles−Aureococcus_anophagefferens_Auran1_18365 Stramenopiles−Aureococcus_anophagefferens_161697041est Cryptophyta−Geminigera_cryophila_Contig2289est Cryptophyta−Guillardia_theta_47205 94Stramenopiles−Phytophthora_capsici_186865672est Stramenopiles−Phytophthora_capsici_PhycaF7_94497 Stramenopiles−Phytophthora_infestans_58124014est 81 Stramenopiles−Phytophthora_parasitica_222388255est 86Stramenopiles−Phytophthora_sojae_Physo1_1_109373 100 Stramenopiles−Phytophthora_sojae_38066959est Stramenopiles−Phytophthora_ramorum_Phyra1_1_71712 Stramenopiles−Saprolegnia_parasitica_76445226est 100 Stramenopiles−Ectocarpus_siliculosus_Esi0128_0027 Stramenopiles−Ectocarpus_siliculosus_242180970est 100 Heterolobosea−Naegleria_gruberi_168555045est Heterolobosea−Naegleria_gruberi_Naegr1_83307 Rhizaria−Bigelowiella_natans_35288 Rhizaria−Reticulomyxa_filosa_113376107est Fungi (48) Proteobacteria−Candidatus_Pelagibacter_71082721 Rhizaria−Quinqueloculina_sp._158072195est Amoebozoa−Hartmannella_vermiformis_106815110est Amoebozoa−Physarum_polycephalum_152798087est Malawimonadidae−Malawimonas_californiana_110028676est 95 Viridiplantae (10) 100 Proteobacteria−Campylobacterales_bacterium_254458049 67 Proteobacteria−Desulfotalea_psychrophila_51246239 Proteobacteria−Erythrobacter_sp._85709828 68 Proteobacteria−Rhodospirillum_centenum_209965159 Proteobacteria−Azospirillum_sp._288958592 Bacteria (50+) Dinophyceae−Alexandrium_tamarenseCCMP_Locus_39511 70 Dinophyceae−Alexandrium_tamarense_42750154est Dinophyceae−Alexandrium_tamarenseG3_Locus_28774est Dinophyceae−Alexandrium_tamarenseSP_Locus_73862est 100 Dinophyceae−Alexandrium_tamarenseSP_SpatSW0_c9432est 76 98 Dinophyceae−Pyrodinium_bahamense_PbajaSW0_c6809est Dinophyceae−Karlodinium_micrum Proteobacteria−alpha_proteobacterium_163796972 100 Viridiplantae−Chlamydomonas_reinhardtii_159463442 Viridiplantae−Volvox_carteri_Volca1_62042 100 Viridiplantae−Ostreococcus_lucimarinus_145397055est 78 Viridiplantae−Ostreococcus_lucimarinus_Ost9901_3_46735 100 Viridiplantae−Ostreococcus_tauri_Ostta4_35119 100 Viridiplantae−Ostreococcus_sp._OstRCC809_1_33273 100 Viridiplantae−Micromonas_sp._MicpuN3_96474 Viridiplantae−Micromonas_pusilla_MicpuC2_43834 Jakobida−Jakoba_bahamiensis_109795185est Proteobacteria−Bdellovibrio_bacteriovorus_42522839 Jakobida−Seculamonas_ecuadoriensis_110122075est Jakobida−Jakoba_libera_109798456est Rhodophyta−Porphyra_haitanensis_61665484est 88 Proteobacteria−Ehrlichia_canis_73667253 100 Proteobacteria−Ehrlichia_chaffeensis_88657861 79 Proteobacteria−Ehrlichia_ruminantium_57239362 100 Proteobacteria−Anaplasma_marginale_56417024 83 97 Proteobacteria−Anaplasma_centrale_269958561 Proteobacteria−Anaplasma_phagocytophilum_88607036 Proteobacteria−Wolbachia_endosymbiont_190570666

0.2

Supplementary Figure S5K – Valine:pyruvate aminotransferase

Proteobacteria−Neisseria_cinerea_269213788

0.97 Proteobacteria−Neisseria_gonorrhoeae_268685848

0.95 Proteobacteria−Neisseria_meningitidis_15677659

Proteobacteria−Neisseria_lactamica_261401661 1 0.99 Proteobacteria−Neisseria_flavescens_241759184 Proteobacteria−Neisseria_subflava_261381296

0.90 Proteobacteria−Neisseria_mucosa_261365726 1 Proteobacteria−Neisseria_sicca_255068200

1 Proteobacteria−Psychrobacter_cryohalolentis_93007264 0.98 Proteobacteria−Psychrobacter_arcticus_71066672

0.93 Proteobacteria−Psychrobacter_sp._148651906

Proteobacteria−Enhydrobacter_aerosaccus_257454344

0.83 Dinophyceae−Alexandrium_tamarenseSP_Locus_74741est 0.97 Dinophyceae−Alexandrium_tamarenseSP_SpatSW0_c149est

0.51 Dinophyceae−Alexandrium_tamarenseG3_Locus_86585est 1 Dinophyceae−Alexandrium_tamarenseCCMP_Locus_16211 0.83 0.97 Dinophyceae−Alexandrium_tamarenseCCMP_AtamSW10_c5469est

Dinophyceae−Oxyrrhis_marina_117403531est

0.96 Spirochaetes−Leptospira_interrogans_161484957

0.87 0.52 Spirochaetes−Leptospira_biflexa_189910227 0.91 Proteobacteria−marine_gamma_119504804

1 Proteobacteria−Alteromonadales_bacterium_119470141 0.95 Proteobacteria−Pseudoalteromonas_haloplanktis_77360644 0.99 Proteobacteria (90)

Verrucomicrobia−Verrucomicrobium_spinosum_171910487 0.98 0.91 Planctomycetes−Planctomyces_limnophilus_229539648

Verrucomicrobia−Akkermansia_muciniphila_187735978 0.97 1 Cyanobacteria (15) Firmicutes−Bacillus_licheniformis_52082518

0.87 Synergistetes−Pyramidobacter_piscolens_282857181 0.99 Synergistetes−Thermanaerovibrio_acidaminovorans

Archaea−Pyrobaculum_arsenaticum_145591615

0.5

Supplementary Figure S5L – Branched-chain amino acid aminotransferase

79 Viridiplantae−Populus_trichocarpa_Poptr1_1_578099 67 Stramenopiles−Phytophthora_infestans_58156096est 74 Viridiplantae−Ricinus_communis_255551024 90 Viridiplantae−Vitis_vinifera_225430001 100 Viridiplantae−Arabidopsis_thaliana_22327924 Viridiplantae−Arabidopsis_lyrata_Araly1_332076 82 98 Viridiplantae−Sorghum_bicolor_Sorbi1_142823 59 Viridiplantae−Zea_mays_212274781 99 96 Viridiplantae−Oryza_sativa_115462827 59 Stramenopiles−Phytophthora_parasitica_222395647est Viridiplantae−Selaginella_moellendorffii_Selmo1_117604 50 Viridiplantae−Physcomitrella_patens_Phypa1_1_216935 72 Viridiplantae−Ostreococcus_tauri_Ostta4_36541 100 Viridiplantae−Ostreococcus_lucimarinus_Ost9901_3_43558 97 Viridiplantae−Ostreococcus_sp._OstRCC809_1_43353 55 78 Viridiplantae−Micromonas_sp._MicpuN3_87938 Viridiplantae−Micromonas_pusilla_MicpuC2_65271 100 Viridiplantae−Chlamydomonas_reinhardtii 83 Viridiplantae−Volvox_carteri_Volca1_73975 61 Viridiplantae−Coccomyxa_sp._Coc_C169_1_30869 Viridiplantae−Chlorella_sp._ChlNC64A_1_52990 98 Dinophyceae−Alexandrium_tamarenseCCMP_Locus_21069 Dinophyceae−Alexandrium_tamarenseG3_Locus_6029est 51 Dinophyceae−Alexandrium_tamarenseCCMP_Contig9603est 58 Dinophyceae−Alexandrium_tamarenseSP_Locus_14799est 98 83 Dinophyceae−Karlodinium_micrum_106837836est 81 Dinophyceae−Pyrodinium_bahamense_PbajaSW100_c2769est Dinophyceae−Crypthecodinium_cohnii_120466696est 74 Haptophyceae−Emiliania_huxleyi_Emihu1_112960 Euglenozoa−Euglena_gracilis_109788692est 100 Cryptophyta−Guillardia_theta_75808 Cryptophyta−Geminigera_cryophila_Contig3127est 70 87 Rhizaria−Bigelowiella_natans_77442 Stramenopiles−Ectocarpus_siliculosus_Esi0002_0203 100 Perkinsea−Perkinsus_marinus_161749351est 76 Perkinsea−Perkinsus_marinus_XP_002776089 100 Ciliophora−Paramecium_tetraurelia_145528496 83 Ciliophora−Paramecium_tetraurelia_133937925est 100 Ciliophora−Tetrahymena_thermophila_118373150 Ciliophora−Sterkiella_histriomuscorum_198393744est 100 Bacteria (13)

0.3 Supplementary Figure S5M – Molecular chaperone (grpE)

0.95 Dinophyceae−Alexandrium_tamarenseCCMP 0.86 Dinophyceae−Alexandrium_tamarenseG3_Locus_36253est 0.98 Dinophyceae−Alexandrium_tamarenseSP_Locus_29427est 0.94 Dinophyceae−Gymnodinium_catenatum_F4S52ZS01C26JJest 0.85 Perkinsea−Perkinsus_marinus_161759845est Perkinsea−Perkinsus_marinus_XP_002781987 1 0.78 Apicomplexans and Chromera (13) 0.82 0.73 Ciliates (4) 0.89 Fungi (41) 0.99 Metazoa (40) 0.85 Rhizaria−Bigelowiella_natans_43108 0.9 0.81 Stramenopiles (15) 0.92 Excovates (9) 0.88 1 Amoebozoa (5) 0.93 Viridiplantae (17) 0.87 0.71 0.84 (4) 0.8 Jakobida−Histiona_aroides_110156902est 0.78 Amoebozoa−Acanthamoeba_castellanii_106792928est 0.79 Cryptophyta−Guillardia_theta_152067 Choanoflagellida−Monosiga_brevicollis_Monbr1_28513 Malawimonadidae−Malawimonas_jakobiformis_110040066est Rhizaria−Reticulomyxa_filosa_113375184est 0.79 Bacteria (200+)

0.3 Supplementary Figure S5N – Molecular chaperone (grpE)

1 Stramenopiles−Thalassiosira_pseudonana_162381613est 0.8 Stramenopiles−Thalassiosira_pseudonana_Thaps3_23278 0.93 Stramenopiles−Phaeodactylum_tricornutum_186991678est 1 Stramenopiles−Phaeodactylum_tricornutum_Phatr2_12188 0.96 Stramenopiles−Fragilariopsis_cylindrus_282259653est 0.91 Stramenopiles−Fragilariopsis_cylindrus_Fracy1_219337 Stramenopiles−Fucus_serratus_229035762est

0.98 Haptophyceae−Isochrysis_galbana_106823415est 0.89Haptophyceae−Emiliania_huxleyi_208420832est 0.5 Haptophyceae−Emiliania_huxleyi_Emihu1_444320 Dinophyceae−Gymnodinium_catenatum_GcatSW0_c12277est 0.97 0.92 Dinophyceae−Alexandrium_tamarenseSP_Locus_35750est 0.7 0.91 Dinophyceae−Alexandrium_tamarenseCCMP_Locus_23653 Dinophyceae−Alexandrium_tamarenseG3_Locus_70390est Dinophyceae−Alexandrium_tamarense_42749353est 0.96 0.99 Cryptophyta−Guillardia_theta_153595 Ciliophora−Myrionecta_rubra_Contig4683est 0.98 0.86 Rhodophyta−Gracilaria_changii_120461020est Rhodophyta−Porphyra_yezoensis_31939324est 0.98 0.87 Viridiplantae (20) 0.78 Cyanobacteria (22) 0.98 Bacteria (500+)

0.3 Supplementary Figure S5O – Molecular chaperone (grpE)

0.76Dinophyceae−Alexandrium_tamarenseG3_Locus_54660est 0.74 Dinophyceae−Alexandrium_tamarenseSP_Locus_66332est Dinophyceae−Alexandrium_tamarenseCCMP_Locus_15730 0.98 0.72 Dinophyceae−Alexandrium_tamarense_42749353est 0.66 Dinophyceae−Gymnodinium_catenatum_Contig2347est

0.94 Dinophyceae−Karlodinium_micrum_106842714est Dinophyceae−Karenia_brevis_194491382est 0.93 Tenericutes−Mycoplasma_gallisepticum_31544539 0.98 Proteobacteria−Anaeromyxobacter_dehalogenans_86158197 0.98 Proteobacteria−Anaeromyxobacter_sp._197122474 0.65 0.97 Proteobacteria−Stigmatella_aurantiaca_115374464 Proteobacteria−Myxococcus_xanthus_108761636 0.6 0.84 Actinobacteria (62) 0.83 Firmicutes−Coprothermobacter_proteolyticus_206896184 0.89 Synergistetes−Pyramidobacter_piscolens_282857128 0.92 Synergistetes−Dethiosulfovibrio_peptidovorans_288572918 0.88 Synergistetes−Thermanaerovibrio_acidaminovorans_269792235 Firmicutes−Desulfotomaculum_acetoxidans_258515240 0.83 Bacteria and (500+)

0.3 Supplementary Figure S5P – Phosphatidylserine synthase

1 Fungi−Candida_albicans_68484479 Fungi−Candida_dubliniensis_241949949 0.95 0.91Fungi−Botryotinia_fuckeliana_154300290 Fungi−Aspergillus_fumigatus_70993232 Fungi−Schizosaccharomyces_pombe_19075826 0.98 Fungi−Malassezia_globosa_164659036 0.78 Fungi−Cryptococcus_neoformans_58265794 0.66 1 Firmicutes (13) 0.96 0.83 Bacteriodetes and Chlorobi (127) 0.9 0.71 Firmicutes (121) Archaea (35) 0.87 0.78 Bacteria misc. (29) Proteobacteria (258) 0.88 0.97 Bacteria misc. (8) 0.87 0.62 Bacteria misc. (5) 0.91 Actinobacteria (10) 0.63 Dinophyceae−Alexandrium_tamarenseCCMP_Locus_74147 Dinophyceae−Alexandrium_tamarenseCCMP_AtamSW0_c4711est 0.96 Dinophyceae−Alexandrium_tamarenseG3_Locus_2935est 0.66 Dinophyceae−Alexandrium_tamarenseSP_Locus_19967est 1 0.64 Dinophyceae−Pyrodinium_bahamense_PbajaSW100_c2832est 0.81 0.56 Dinophyceae−Pyrodinium_bahamense_PbajaSW100_c7493est Dinophyceae−Gymnodinium_catenatum_F4S52ZS01EL5OPest 0.92 Proteobacteria−Roseobacter_sp._149912875 0.9 0.76 Proteobacteria (19) 0.99 Proteobacteria (27) 0.98 Actinobacteria (24) 0.84 0.58 Proteobacteria (36) 0.7 Proteobacteria (3) 0.81 0.87 Proteobacteria (23) 0.99 Bacteria misc. (3) 0.81 Bacteria misc. (6)

0.5

Supplementary Figure S5Q – Citrate lyase

Dinophyceae−Alexandrium_tamarenseG3_Locus_12003est 0.73 Dinophyceae−Alexandrium_tamarenseSP_Locus_18931est 1 Dinophyceae−Alexandrium_tamarenseCCMP_Locus_1536 Dinophyceae−Alexandrium_tamarenseSP_Locus_19469est 1 Dinophyceae−Symbiodinium_sp._145310576est 0.74 Dinophyceae−Gymnodinium_catenatum_Contig146est 0.99 Proteobacteria−Rhodospirillum_rubrum_83591557 0.98 Proteobacteria (8) 0.86 0.95 Proteobacteria (15) 1 0.98 Proteobacteria (10) 1 0.92 Proteobacteria (32) 1 Proteobacteria−Verminephrobacter_eiseniae_121608550 0.92 0.87 Proteobacteria−Cupriavidus_taiwanensis_194292473 Actinobacteria−Frankia_sp._158318641 0.98 Proteobacteria−Syntrophobacter_fumaroxidans_116749987 Chloroflexi−Sphaerobacter_thermophilus_269838088

0.98 Actinobacteria−Streptomyces_sp._256771983 Actinobacteria−Rubrobacter_xylanophilus_108805617 0.4