Spreadsheet: 5f5beec4-4aba-4994-8e48-122404bd080a
Sheet: Sheet1

Supplementary Table 1. List of organisms in which FoxJ1 could not be identified either by reverse BLAST or phylogenetic analyses.
S.No. | Supergroup | Group | Phylum/subphylum | Organism | E-value | Reverse-BLAST | Annotation | Phylogenetic analyses
1 | Chromalveolata | Alveolate | Apicomplexa | Babesia bovis | No Hits
2 | Chromalveolata | Alveolate | Apicomplexa | Cryptosporidium hominis | No Hits
3 | Chromalveolata | Alveolate | Apicomplexa | Cryptosporidium parvum | No Hits
4 | Chromalveolata | Alveolate | Apicomplexa | [NAME] tenella | No Hits
5 | Chromalveolata | Alveolate | Apicomplexa | Neospora caninum | No Hits
6 | Chromalveolata | Alveolate | Apicomplexa | Plasmodium berghei | No Hits
7 | Chromalveolata | Alveolate | Apicomplexa | Plasmodium chabaudi | No Hits
8 | Chromalveolata | Alveolate | Apicomplexa | Plasmodium falciparum | No Hits
9 | Chromalveolata | Alveolate | Apicomplexa | Plasmodium gallinaceum | No Hits
10 | Chromalveolata | Alveolate | Apicomplexa | Plasmodium knowlesi | No Hits
11 | Chromalveolata | Alveolate | Apicomplexa | Plasmodium ovale | No Hits
12 | Chromalveolata | Alveolate | Apicomplexa | Plasmodium yoelii | No Hits
13 | Chromalveolata | Alveolate | Apicomplexa | Plasmodium reichenowi | No Hits
14 | Chromalveolata | Alveolate | Apicomplexa | Plasmodium vivax | No Hits
15 | Chromalveolata | Alveolate | Apicomplexa | Theileria annulata | No Hits
16 | Chromalveolata | Alveolate | Apicomplexa | Theileria parva | No Hits
17 | Chromalveolata | Alveolate | Apicomplexa | Toxoplasma gondii | No Hits
18 | Chromalveolata | Alveolate | Ciliophora | Tetrahymena thermophila | No Hits
19 | Chromalveolata | Alveolate | Ciliophora | Paramecium tetraurelia | No Hits
20 | Chromalveolata | Stramenopile | Haptophyta | Emiliania huxleyi | No Hits
21 | Chromalveolata | Stramenopile | Heterokontophyta | Aureococcus anophagefferens | No Hits
22 | Chromalveolata | Stramenopile | Heterokontophyta | Fragilariopsis cylindrus | No Hits
23 | Chromalveolata | Stramenopile | Heterokontophyta | Phaeodactylum tricornutum | No Hits
24 | Chromalveolata | Stramenopile | Heterokontophyta | Phytophthora ramorum | No Hits
25 | Chromalveolata | Stramenopile | Heterokontophyta | Phytophthora sojae | No Hits
26 | Chromalveolata | Stramenopile | Heterokontophyta | Thalassiosira pseudonana | No Hits
27 | Excavata | Discicristate | Euglenozoa | Crithidia deanei | No Hits
28 | Excavata | Discicristate | Euglenozoa | Leishmania braziliensis | No Hits
29 | Excavata | Discicristate | Euglenozoa | Leishmania infantum | No Hits
30 | Excavata | Discicristate | Euglenozoa | Leishmania major | No Hits
31 | Excavata | Discicristate | Euglenozoa | Leptomonas seymouri | No Hits
32 | Excavata | Discicristate | Euglenozoa | Trypanosoma brucei | No Hits
33 | Excavata | Discicristate | Euglenozoa | Trypanosoma congolense | No Hits
34 | Excavata | Discicristate | Euglenozoa | Trypanosoma vivax | No Hits
35 | Excavata | Discicristate | Metamonada | Giardia intestinalis | No Hits
36 | Excavata | Discicristate | Metamonada | Giardia lamblia | No Hits
37 | Excavata | Discicristate | Metamonada | Trichomonas vaginalis | No Hits
38 | Excavata | Discicristate | Percolozoa | Naegleria gruberi | 2e-08 | FoxN2 | Predicted protein | sister to FoxN1-N4; FoxR1-R2
39 | [NAME] | Green Algae | [NAME] | Chlamydomonas reinhardtii | No Hits
40 | [NAME] | Green Algae | [NAME] | Chlorella sp. NC64A | No Hits
41 | [NAME] | Green Algae | [NAME] | Micromonas pusilla | No Hits
42 | [NAME] | Green Algae | [NAME] | Micromonas sp. RCC299 | No Hits
43 | [NAME] | Green Algae | [NAME] | Ostreococcus lucimarinus | No Hits
44 | [NAME] | Green Algae | [NAME] | Ostreococcus tauri | No Hits
45 | [NAME] | Green Algae | [NAME] | Volvox [NAME] | No Hits
46 | [NAME] | Red Algae | Cryptophyta | [NAME] theta | No Hits
47 | [NAME] | Red Algae | [NAME] | Cyanidioschyzon merolae | No Hits
48 | [NAME] | Red Algae | Cryptophyta | Hemiselmis andersenii | No Hits
49 | [NAME] | Streptophyte | Bryophyta | Physcomitrella patens | No Hits
50 | [NAME] | Streptophyte | Anthophyta | Arabidopsis thaliana | No Hits
51 | [NAME] | Streptophyte | Anthophyta | Oryza sativa | No Hits
52 | [NAME] | Streptophyte | Anthophyta | Sorghum bicolor | No Hits
53 | [NAME] | Streptophyte | Lycopodiophyta | Selaginella moellendorffii | No Hits
54 | [NAME] | Streptophyte | Magnoliophyta | Populus trichocarpa | No Hits
55 | Rhizaria | Rhizaria | Cercozoa | Bigelowiella natans | No Hits
56 | [NAME] | [NAME] | Acanthopodia | Acanthamoeba castellani Neff | No Hits
57 | [NAME] | [NAME] | Archamoebae | Entamoeba dispar | No Hits
58 | [NAME] | [NAME] | Archamoebae | Entamoeba histolytica | No Hits
59 | [NAME] | [NAME] | Archamoebae | Entamoeba invadens | No Hits
60 | [NAME] | [NAME] | Archamoebae | Entamoeba moshkovskii | No Hits
61 | [NAME] | [NAME] | Archamoebae | Entamoeba terrapinae | No Hits
62 | [NAME] | [NAME] | Mycetozoa | Dictyostelium discoideum | No Hits
63 | [NAME] | [NAME] | Mycetozoa | Physarum polycephalum | No Hits
64 | [NAME] | [NAME] | Mycetozoa | Dictyostelium purpureum [NAME] | No Hits
65 | Opisthokonta | [NAME] | [NAME] | Helobdella robusta | 6e-31 | FoxK1 | e_gw1.20.242.1 | sister to FoxK1-K2
66 | Opisthokonta | [NAME] | Arthropoda | Acyrthosiphon pisum | 2e-28 | FoxK1 | FoxK1 | sister to FoxK1-K2
67 | Opisthokonta | [NAME] | Arthropoda | Anopheles gambiae | 8e-27 | FoxK2 | AGAP000662-PA | sister to FoxK1-K2
68 | Opisthokonta | [NAME] | Arthropoda | Apis mellifera | 4e-29 | FoxK2 | similar to forkhead box [NAME] | sister to FoxK1-K2
69 | Opisthokonta | [NAME] | Arthropoda | Drosophila melanogaster | 5e-25 | FoxG1 | RE11345p | FoxG1
70 | Opisthokonta | [NAME] | Arthropoda | Nasonia vitripennis | 3e-28 | FoxK2 | similar to Forkhead box [NAME] | sister to FoxK1-K2
71 | Opisthokonta | [NAME] | Chordata | Ciona intestinalis | 3e-26 | FoxJ3 | transcription factor protein | FoxJ3
72 | Opisthokonta | [NAME] | Nematoda | Caenorhabditis elegans | 2e-23 | FoxG1 | ForKHead transcription factor family member (fkh-2) | FoxG1
73 | Opisthokonta | [NAME] | Ascomycota | [NAME] brassicicola | 1e-22 | FoxI1 | AB07947.1 | sister to FoxJ1-J3; FoxK1-K2
74 | Opisthokonta | [NAME] | Ascomycota | Aspergillus fumigatus | 3e-28 | FoxI3 | forkhead transcription factor (Sep1) | sister to FoxJ1-J3; FoxK1-K2
75 | Opisthokonta | [NAME] | Ascomycota | Cochliobolus heterostrophus C5 | 4e-25 | FoxK1 | estExt_Genewise1Plus.C_11317 | sister to FoxJ1, FoxK1-K2
76 | Opisthokonta | [NAME] | Ascomycota | Cryphonectria parasitica | 1e-21 | Foxk2 | estExt_fgenesh1_pg.C_10757 | sister to FoxK1-K2
77 | Opisthokonta | [NAME] | Ascomycota | Debaryomcyces hansenii | 6e-24 | FoxI2 | DEHA2F11308p | sister to FoxJ1-J3; FoxK1-K2
78 | Opisthokonta | [NAME] | Ascomycota | Gibberella zeae | 2e-23 | FoxI1 | hypothetical protein FG06944.1 | sister to FoxJ1-J3; FoxK1-K2
79 | Opisthokonta | [NAME] | Ascomycota | Kluyveromyces lactis | 1e-22 | FoxK1 | hypothetical protein | sister to FoxK1-K2
80 | Opisthokonta | [NAME] | Ascomycota | Magnaporthe grisea | No Hits
81 | Opisthokonta | [NAME] | Ascomycota | Mycosphaerella fijiensis | 4e-28 | FoxI3 | e_gw1.15.387.1 | sister to FoxJ1-J3; FoxK1-K2
82 | Opisthokonta | [NAME] | Ascomycota | Mycosphaerella graminicola | 3e-29 | FoxG1 | e_gw.7.605.1 | sister to FoxJ1, FoxK1-K2
83 | Opisthokonta | [NAME] | Ascomycota | Nectria haematococca | 7e-24 | FoxI1 | hypothetical protein NECHADRAFT_104145 | sister to FoxJ1-J3; FoxK1-K2
84 | Opisthokonta | [NAME] | Ascomycota | Neurospora crassa | 1e-23 | FoxI3 | hypothetical protein [NAME] | sister to FoxJ1-J3; FoxK1-K2
85 | Opisthokonta | [NAME] | Ascomycota | Pichia stipitis | 8e-24 | FoxJ3 | transcription factor | sister to FoxJ2-J3
86 | Opisthokonta | [NAME] | Ascomycota | [NAME] | 4e-21 | FoxI1 | forkhead box protein J2 | sister to FoxJ1-J3; FoxK1-K2
87 | Opisthokonta | [NAME] | Ascomycota | Trichoderma atroviride | 4e-29 | FoxI1 | fgenesh1_pm.C_scaffold_10000331 | sister to FoxJ1-J3; FoxK1-K2
88 | Opisthokonta | [NAME] | Ascomycota | Trichoderma virens | 3e-29 | FoxI1 | e_gw1.2.100.1 | sister to FoxJ1-J3; FoxK1-K2
89 | Opisthokonta | [NAME] | Ascomycota | Yarrowia lipolytica | 2e-26 | FoxJ3 | [NAME] | sister to FoxJ1-J3; FoxK1-K2
90 | Opisthokonta | [NAME] | Basidiomycota | Cryptococcus neoformans | 6e-15 | FoxK1 | hypothetical protein CNBK2900 | sister to [NAME], [NAME], O4, O6
91 | Opisthokonta | [NAME] | Basidiomycota | Heterobasidion annosum | 2e-19 | FoxJ2 | e_gw1.4.2249.1 | sister to FoxN1-N4; FoxR1-R2
92 | Opisthokonta | [NAME] | Basidiomycota | [NAME] laricis-populina | 1e-26 | FoxK2 | fgenesh1_pg.C_scaffold_28000065 | sister to FoxK1-K2
93 | Opisthokonta | [NAME] | Basidiomycota | Phanerochaete chrysosporium | 3e-21 | FoxJ2 | fgenesh1_pg.C_scaffold_2000701 | sister to FoxN1-N4; FoxR1-R2
94 | Opisthokonta | [NAME] | Basidiomycota | Pleurotus ostreatus | 9e-20 | FoxJ3 | e_gw1.4.269.1 | sister to FoxN1-N4; FoxR1-R2
95 | Opisthokonta | [NAME] | Basidiomycota | Postia placenta | 4e-21 | FoxJ2 | estExt_Genewise1Plus.C_1000102 | sister to FoxN1-N4; FoxR1-R2
96 | Opisthokonta | [NAME] | Basidiomycota | Sporobolomyces roseus | 2e-22 | FoxK1 | estExt_fgenesh1_pg.C_30269 | sister to FoxN1-N4; FoxR1-R2; FoxP1-P4; [NAME], [NAME], O4, O6
97 | Opisthokonta | [NAME] | Basidiomycota | Ustilago maydis | 1e-20 | FoxL2 | hypothetical protein UM01042.1 | sister to [NAME], [NAME], O4, O6
98 | Opisthokonta | [NAME] | Chytridiomycota | Batrachochytrium dendrobatidis | 3e-24 | FoxJ2 | estExt_fgenesh1_pg.C_40396 | sister to FoxN1-N4; FoxR1-R2
99 | Opisthokonta | [NAME] | Zygomycota | [NAME] circinelloides | 9e-30 | FoxK2 | e_gw1.1.1225.1 | sister to FoxJ1-J3; FoxK1-K2
100 | Opisthokonta | [NAME] | Zygomycota | Phycomyces blakesleeanus | 2e-29 | FoxJ3 | estExt_fgeneshPB_pg.C_490005 | sister to FoxJ2-J3
101 | Opisthokonta | [NAME] | Arthropoda | Aedes aegypti | 9e-27 | FoxK2 | forkhead box protein (AaegFOXK1) | sister to FoxK1-K2
102 | Opisthokonta | [NAME] | Chordata | Anolis carolinensis | No Hits
103 | Opisthokonta | [NAME] | Ascomycota | Aspergillus flavus | 7e-28 | FoxI3 | forkhead transcription factor (Sep1) | sister to FoxJ1-J3; FoxK1-K2
104 | Opisthokonta | [NAME] | Ascomycota | Aspergillus nidulans | 6e-27 | FoxI3 | hypothetical protein AN8858.2 | sister to FoxJ1-J3; FoxK1-K2
105 | Opisthokonta | [NAME] | Arthropoda | Bombyx mori | 2e-25 | FoxG1 | forkfead transcription factor [NAME] | FoxG1
106 | Opisthokonta | fungi | Ascomycota | Botrytis cinerea | 1e-22 | FoxJ3 | hypothetical protein BC1G_06590 | sister to FoxJ1-J3; FoxK1-K2
107 | Opisthokonta | [NAME] | Nematoda | Brugia malayi | 4e-25 | FoxG1 | Forkhead transcription factor family protein 2, isoform b, putative | FoxG1
108 | Opisthokonta | [NAME] | Nematoda | [NAME] | 6e-18 | [NAME] | hypothetical protein Cbre_JD13.008 | FoxG1
109 | Opisthokonta | [NAME] | Nematoda | Caenorhabditis briggsae | 5e-23 | FoxG1 | CBR-FKH-2 protein | FoxG1
110 | Opisthokonta | [NAME] | Nematoda | Caenorhabditis japonica | 1e-23 | FoxD2 | CJA16219 | sister to FoxD1-D4
111 | Opisthokonta | [NAME] | Nematoda | Caenorhabditis remanei | 3e-23 | FoxD3 | CRE-UNC-130 protein | sister to FoxD1-D4
112 | Opisthokonta | [NAME] | Chordata | Callorhinchus milii | 7e-18 | FoxN4 | forkhead box N4 | FoxN4
113 | Opisthokonta | fungi | Ascomycota | Candida albicans | 2e-24 | FoxJ3 | forkhead-like transcriptional regulator | sister to FoxJ2-J3
114 | Opisthokonta | fungi | Ascomycota | Candida guilliermondii | 1e-22 | FoxJ3 | hypothetical protein PGUG_02044 | sister to FoxJ2-J3
115 | Opisthokonta | fungi | Ascomycota | Candida lusitaniae | 6e-23 | FoxJ3 | hypothetical protein CLUG_01333 | sister to FoxJ2-J3
116 | Opisthokonta | fungi | Ascomycota | Candida parapsilosis | No Hits
117 | Opisthokonta | fungi | Ascomycota | Candida tropicalis | 1e-23 | FoxJ3 | hypothetical protein CTRG_05718 | sister to FoxJ2-J3
118 | Opisthokonta | fungi | Ascomycota | Chaetomium globosum | 4e-24 | FoxJ3 | hypothetical protein CHGG_03283 | sister to FoxJ2-J3
119 | Opisthokonta | [NAME] | Chordata | Ciona savignyi | 2e-38 | FoxJ3 | ENSCSAVP00000002491 | FoxJ3
120 | Opisthokonta | fungi | Ascomycota | Cochliobolus heterostrophus | 3.67e-24 | FoxK1 | fgenesh1_pg.C_scaffold_1000548 | sister to FoxJ1, FoxK1-K2
121 | Opisthokonta | [NAME] | Basidiomycota | Coprinus cinerea | 6e-16 | FoxJ2 | hypothetical protein CC1G_00050 | sister to FoxN1-N4; FoxR1-R2
122 | Opisthokonta | [NAME] | Arthropoda | [NAME] | 5e-27 | FoxK2 | conserved hypothetical protein | sister to FoxK1-K2
123 | Opisthokonta | [NAME] | Chordata | Dasypus novemcinctus | 6.4e-41 | FoxJ3 | forkhead box J3 | FoxJ3
124 | Opisthokonta | [NAME] | Chordata | Dipodomys ordii | 7.5e-41 | FoxJ3 | forkhead box J3 | FoxJ3
125 | Opisthokonta | [NAME] | Arthropoda | Drosophila ananassae | 3e-25 | FoxG1 | GF15039 | FoxG1
126 | Opisthokonta | [NAME] | Arthropoda | Drosophila erecta | 2e-25 | FoxG1 | GG24972 | FoxG1
127 | Opisthokonta | [NAME] | Arthropoda | Drosophila grimshawi | 7e-26 | FoxG1 | GH11194 | FoxG1
128 | Opisthokonta | [NAME] | Arthropoda | Drosophila mojavensis | 8e-26 | FoxG1 | GI18115 | FoxG1
129 | Opisthokonta | [NAME] | Arthropoda | Drosophila persimilis | 8e-26 | FoxG1 | GL18683 | FoxG1
130 | Opisthokonta | [NAME] | Arthropoda | Drosophila pseudoobscura | 8e-26 | FoxG1 | GA15533 | FoxG1
131 | Opisthokonta | [NAME] | Arthropoda | Drosophila sechellia | 2e-25 | FoxG1 | GM18443 | FoxG1
132 | Opisthokonta | [NAME] | Arthropoda | Drosophila simulans | 1e-24 | foxD3 | GD11717 | sister to FoxD1-D4
133 | Opisthokonta | [NAME] | Arthropoda | Drosophila virilis | 7e-26 | FoxG1 | GJ18555 | FoxG1
134 | Opisthokonta | [NAME] | Arthropoda | Drosophila willistoni | 2e-25 | FoxG1 | GK25667 | FoxG1
135 | Opisthokonta | [NAME] | Arthropoda | Drosophila yakuba | 2e-25 | FoxG1 | GE18263 | FoxG1
136 | Opisthokonta | [NAME] | Chordata | Echinops telfairi | 7.8e-41 | FoxJ3 | forkhead box J3 | FoxJ3
137 | Opisthokonta | [NAME] | Ascomycota | Fusarium graminearum | 2e-23 | FoxI1 | hypothetical protein FG06944.1 | sister to FoxJ1-J3; FoxK1-K2
138 | Opisthokonta | [NAME] | Ascomycota | Fusarium oxysporum | 3.38801e-22 | FoxI1 | hypothetical protein | sister to FoxJ1-J3; FoxK1-K2
139 | Opisthokonta | [NAME] | Ascomycota | Fusarium verticillioides | 3.38801e-22 | FoxI1 | hypothetical protein | sister to FoxJ1-J3; FoxK1-K2
140 | Opisthokonta | fungi | Ascomycota | Lodderomyces elongisporus | 1e-22 | FoxJ3 | conserved hypothetical protein | sister to FoxJ2-J3
141 | Opisthokonta | Choanozoa | Choanozoa | Monosiga ovata | No Hits
142 | Opisthokonta | [NAME] | Ascomycota | Neosartorya fischeri | 2e-28 | FoxI3 | forkhead transcription factor (Sep1) | sister to FoxJ1-J3; FoxK1-K2
143 | Opisthokonta | [NAME] | Chordata | Oryzias latipes | 4.3e-40 | FoxJ3 | forkhead box J3 | FoxJ3
144 | Opisthokonta | [NAME] | Chordata | [NAME] garnettii | 1.3e-37 | FoxK2 | forkhead box K2 | FoxK2
145 | Opisthokonta | [NAME] | Nematoda | Pristionchus pacificus | No Hits
146 | Opisthokonta | [NAME] | Zygomycota | Rhizopus oryzae | 6.61748e-25 | FoxJ3 | hypothetical protein | sister to FoxJ2-J3
147 | Opisthokonta | [NAME] | Ascomycota | Saccharomyces bayanus | No Hits
148 | Opisthokonta | [NAME] | Ascomycota | Saccharomyces castellii | No Hits
149 | Opisthokonta | [NAME] | Ascomycota | Saccharomyces kluyveri | No Hits
150 | Opisthokonta | [NAME] | Ascomycota | Saccharomyces kudriavzevii | No Hits
151 | Opisthokonta | [NAME] | Ascomycota | Saccharomyces mikatae | No Hits
152 | Opisthokonta | [NAME] | Ascomycota | Saccharomyces paradoxus | No Hits
153 | Opisthokonta | [NAME] | Ascomycota | Schizosaccharomyces octosporus | No Hits
154 | Opisthokonta | [NAME] | Ascomycota | Sclerotinia sclerotiorum | 5e-23 | FoxI1 | hypothetical protein SS1G_00580 | sister to FoxJ1-J3; FoxK1-K2
155 | Opisthokonta | [NAME] | Chordata | Sorex araneus | 1.1e-37 | FoxK2 | forkhead box K2 | FoxK2
156 | Opisthokonta | [NAME] | Chordata | Spermophilus tridecemlineatus | 6.8e-41 | FoxJ3 | forkhead box J3 | FoxJ3
157 | Opisthokonta | [NAME] | Chordata | Tarsius syrichta | 1.3e-37 | FoxK2 | forkhead box K2 | FoxK2
158 | Opisthokonta | [NAME] | Ascomycota | Trichoderma reesei | 2.29e-29 | FoxI1 | estExt_fgenesh1_pm.C_10175 | sister to FoxJ1-J3; FoxK1-K2
159 | Opisthokonta | [NAME] | Chordata | [NAME] pacos | 3.3e-31 | FoxA1 | forkhead box A1 | FoxA1
The following databases were used to conduct the searches: NCBI non-redundant protein sequences database (http://blast.ncbi.nlm.nih.gov/Blast.cgi), Joint Genomes Institute, Department of Energy (genome.jgi-psf.org), Human Genome Sequencing Center, Baylor College of Medicine (http://www.hgsc.bcm.tmc.edu), Broad Institute (www.broadinstitute.org), Ensembl Genome Browser (http://www.ensembl.org) and Saccharomyces Genome Database (www.yeastgenome.org).