Supplementary Figure S1. Evolution of ammonium transporters/ammonia permeases.
Maximum likelihood analysis of 513 ammonium transporter/ammonia permease genes shows the presence of a eukaryotic clade
(AMT-Euk) representing vertical transmission of AMTs into eukaryotes and a well-supported predominantly prokaryotic clade (MEP) in which eukaryotic
lineages demonstrate horizontal gene transfer. AMT-Euk=eukaryotic ammonium transporters clade; MEP=methylammonium permease clade;
MEP grade=prokaryotic ammonium transporter/ammonia permease grade; Rh=Rhesus family (outgroup). Thickened branches show
bootstrap support of ≥ 70%.
Ciona intestinalis AMT2
Ciona savignyi “AMT2”
Ciona intestinalis AMT1
Ciona savignyi “AMT1”
Strongylocentrotus purpuratus Amt1
Strongylocentrotus purpuratus Amt1
Strongylocentrotus purpuratus Amt3
Caenorhabditis briggsae “amt-1”
Caenorhabditis elegans amt-1
Caenorhabditis briggsae “amt-4”
Caenorhabditis elegans amt-4
Chlamydomonas reinhardtii AMT1A
Volvox carteri 1.2
Chlamydomonas reinhardtii AMT1C
Chlamydomonas reinhardtii AMT1E
Volvox carteri 1.4
Chlamydomonas reinhardtii AMT1B
Volvox carteri 1.7
Volvox carteri 1.6
Volvox carteri 1.8
Chlamydomonas reinhardtii AMT1D
Volvox carteri 1.10
Volvox carteri 1.5
Lotus japonicus AMT1;1
Lotus corniculatus AMT1;1
Lotus japonicus AMT1;3
Populus trichocarpa AMT1;5
Populus trichocarpa AMT1;4
Arabidopsis thaliana AMT1;4
Solanum lycopersicum AMT1;3
Populus trichocarpa AMT1;6
Vitis vinifera 1.6
Arabidopsis thaliana AMT1;2
Populus trichocarpa AMT1;2
Solanum lyscopersicum AMT1;2
Populus trichocarpa AMT1;1
Populus trichocarpa AMT1;3
Solanum lycopersicum AMT1;1
Brassica napus AMT1;2
Arabidopsis thaliana AMT1;3
Arabidopsis thaliana AMT1;5
Arabidopsis thaliana AMT1;1
Vitis vinifera 1.1
Lotus japonicus AMT1;2
Lotus corniculatus AMT1;2
Selaginella moellendorfii 1.1
Selaginella moellendorfii 1.2
Physcomitrella patens 1.1
Physcomitrella patens 1.2
Physcomitrella patens 1.3
Physcomitrella patens 1.4
Physcomitrella patens 1.5
Physcomitrella patens 1.6
Oryza sativa AMT1;1
Oryza sativa AMT1;1
Oryza satva AMT1;3
Oryza sativa AMT1;2
Ostreococcus lucimarinus 1.1
Micromonas sp. RCC299 1.1
Coccomyxa sp. C-169 1.1
Asterochloris sp. amt1.1
Cyanidioschyzon merolae 2
Cyanidioscyzon merolae amt-1
Coccomyxa sp. C-169 1.2
Asterochloris sp. amt1.2
Chlorella sp. NC64A 1.1
Chlorella sp. NC64A 1.2
Ostreococcus lucimarinus 1.2
Aureococcus anophagefferens 1.1
Aureococcus anophagefferens 1.2
Aureococcus anophagefferens 1.3
Aureococcus anophagefferens 1.4
Aureococcus anophagefferens 1.5
Aureococcus anophagefferens 1.6
Aureococcus anophagefferens 1.7
Aureococcus anophagefferens 1.8
Aureococcus anophagefferens 1.9
Aureococcus anophagefferens 1.10
Aureococcus anophagefferens 1.11
Chlamydomonas reinhardtii AMT1G
Volvox carteri 1.9
Chlamydomonas reinhardtii AMT1H
Volvox carteri 1.1
Asterochloris sp. amt1.3
Chlorella sp. NC64A 1.3
Chlorella sp. NC64A 1.4
Chlorella sp. NC64A 1.5
Cylindrotheca fusiformis amt1
Thalassiosira pseudonana 7
Thalassiosira pseudonana Amt4.1
Thalassiosira pseudonana Amt4.2
Thalassiosira pseudonana Amt4.3
Thalassiosira pseudonana Amt4.4
Thalassiosira pseudonana Amt4.5
Thalassiosira pseudonana Amt4.6
Thalassiosira pseudonana Amt4.7
Thalassiosira pseudonana THAPSDRAFT_36263
Thalassiosira pseudonana Amt3
Thalassiosira pseudonana Amt3
Thalassiosira pseudonana Amt6.1
Thalassiosira pseudonana Amt6.1
Thalassiosira pseudonana THAPSDRAFT_40537
Thalassiosira pseudonana THAPSDRAFT_40537
Thalassiosira pseudonana Amt2
Naegleria gruberi 1.1
Perkinsus marinus 1.1
Perkinsus marinus 1.2
Perkinsus marinus 1.3
Perkinsus marinus 1.4
Perkinsus marinus 1.5
Perkinsus marinus 1.6
Perkinsus marinus 1.7
Dictyostelium discoideum amtB
Dictyostelium discoideum amtA
Dictyostelium discoideum amtA
Paramecium tetraurelia amt1.1
Paramecium tetraurelia 1.2
Paramecium tetraurelia 1.3
Paramecium tetraurelia 1.4
Paramecium tetraurelia 1.5
Paramecium tetraurelia 1.6
Paramecium tetraurelia 1.7
Paramecium tetraurelia 1.8
Paramecium tetraurelia 1.9
Paramecium tetraurelia 1.10
Paramecium tetraurelia 1.11
Paramecium tetraurelia 1.12
Paramecium tetraurelia 1.13
Paramecium tetraurelia 1.14
Paramecium tetraurelia 1.15
Paramecium tetraurelia 1.16
Paramecium tetraurelia 1.17
Paramecium tetraurelia 1.18
Paramecium tetraurelia 1.19
Paramecium tetraurelia 1.20
Galdieria sulphuraria
Naegleria gruberi 1.2
Caenorhabditis briggsae “amt-2”
Caenorhabditis elegans amt-2
Caenorhabditis briggsae “amt-3”
Caenorhabditis elegans amt-3
Drosophila melanogaster CG6499
Drosophila melanogaster CG6499
Drosophila yakuba
Anopheles gambiae
Strongylocentrotus purpuratus Amt2
Nostoc sp. PCC 7120 1
Nostoc punctiforme 1
Ostreococcus lucimarinus 3
Microbulbifer degradans amtB1
Magnetococcus sp. MC-1 amtB
Azotobacter vinelandii amtB
Azotobacter vinelandii amtB
Pseudomonas putida amtB
Pseudomonas fluorescens 1
Pseudmonas fluorescens amt-1
Pseudomonas syringae var. syringae 1
Pseudomonas syringae var. tomato amt-2
Pseudomonas aeruginosa PAO1 amtB
Pseudomonas stutzeri amtB1
Azoarcus sp. BH72 amtB
Pseudomonas syringae var. syringae 2
Pseudomonas syringae pv. tomato amt-2
Azoarcus sp. BH72 .amtB
Xanthomonas citri amtB
Xanthomonas campestris amtB
Xyllela fastidiosa 9a5c
Xyllela fastidiosa M23
Xyllela fastidiosa Dixon
Yersinia pestis amtB
Photorhabdus luminescens amtB
Salmonella enterica amtB
Shigella flexneri amtB
Escherichi coli amtB
Bordetella bronchiseptica amtB
Bordetella parapertussis amtB
Dechloromonas aromatica 1
Ralstonia eutropha 1
Ralstonia metallidurans amtB
Ralstonia solanacearum amtB
Azorhizobium caulinodans amtB
Bradyrhizobium japonicum amtB
Rhodopseudomonas palustris amtB
Caulobacter cresentus
Rhizobium etli amtB
Rhodobacter sphaeroides amtB
Sinorhizobium meliloti amtB
Agrobacterium tumifaciens
Methylobacillus flagellatus 1
Methylobacillus flagellatus 2
Azospirillum brasilense amtB
Haemophillus somnus amtB
Neisseria meningitidis (MC58) amtB
Neisseria meningitidis (Z2491) amtB
Brevibacterium linens 1
Burkholderia cepacia 1
Burkholderia fungorum 1
Chromobacterium violaceum amtB
Brucella suis 1330
Brucella melitensis
Brucella suis ATCC 23445
Mesorhizobium loti amtB
Gluconacetobacter diazotrophicus amtB1
Rhodospirillum rubrum
Rhodopseudomonas palustris amtB1
Acidithiobacillus ferroxidans amt-2
Acidithiobacillus ferroxidans amt-2
Novosphingobium aromaticivorans
Ostreococcus lucimarinus 4
Micromonas sp. RCC299 2
Phytophthora infestans 1
Phytophthora infestans 2
Phytophthora infestans 3
Deinococcus radiodurans
Gloeobacter violaceus 1
Brevibacterium linens 2
Corynebacterium efficiens amtP
Corynebacterium glutamicum 1
Bifidobacterium longum amtB
Bifidobacterium longum amtP
Mycobacterium tuberculosis amt
Streptomyces coelicolor 1
Streptomyces avermitilis 1
Thermobifida fusca
Streptomyces avermitilis 2
Corynebacterium efficiens 2
Corynebacterium glutamicum 2
Methanosarcina barkeri amtB
Methanosarcina mazei 1
Methanosarcina mazei 1
Methanosarcina acetivorans amtB (1)
Geobacter metallireducens 1
Geobacter sulfurreducens 1
Chlorobium tepidum amt-3
Chlorobium chlorochromatii
Desulfuromonas acetoxidans 1
Desulfococcus oleovorans 1
Rhodopirellula sp. amtB
Desulfovibrio desulfuricans 1
Desulfovibrio desulfuricans 2
Synechococcus elongatus PCC 7942 1
Nostoc sp. PCC7120 1
Nostoc punctiforme PCC73102 1
Cyanothece sp. PCC7822
Desulfitobacterium hafniense DCB-2
Carboxydothermus hydrogenoformans amt
Listeria monocytogenes EGD
Listeria innocua Clip11262
Bacillus subtilis subsp. subtilis amtB
Bacillus cereus ATTC 14579
Clostridium acetobutylicum nrgA
Lactobacillus plantarum amtB
Lactobacillus casei amtB
Oenococcus oeni
MEP β
Streptococcus mutans UA159 nrgA
Lactococcus lactis amtB
Lactococcus lactis subsp. cremoris amtB
Leuconostoc mesenteroides subsp mesenteroides
Staphylococcus aureus MSSA476 nrgA
Staphylococcus aureus 04-0281 nrgA
Staphylococcus epidermis ATCC 12228
Lotus japonicus AMT2
Medicago truncatula AMT2
Vitis vinifera 2.1
Populus trichocarpa AMT2;2
Populus trichocarpa AMT2;1
Arabidopsis thaliana AMT2
Vitis vinifera 2.2
Cryptomeria japonica
Picea sitchensis
Populus trichocarpa AMT3;1
Selaginella moellendorfi 2.1
Vitis vinifera 2.3
Populus trichocarpa AMT4;2
Vitis vinifera 2.4
Populus trichocarpa AMT4;1
Populus trichocarpa AMT4;3
Vitis vinifera 2.5
Populus trichocarpa AMT4;4
Vitis vinifera 2.6
Populus trichocarpa AMT4;5
Physcomitrella patens subsp. patens 2.1
Physcomitrella patens subsp. patens 2.2
Physcomitrella patens subsp. patens 2.3
Physcomitrella patens subsp. patens 2.4
Physcomitrella patens subsp. patens 2.5
Physcomitrella patens subsp. patens 2.6
Physcomitrella patens subsp. patens 2.7
Vitis vinifera 2.7
Vitis vinifera 2.8
Oryza sativa AMT2;1
Oryza sativa AMT2;3
Oryza sativa AMT3;1
Oryza sativa AMT3;2
Oryza sativa AMT2;2
Selaginella moellendorfi 2.2
Oryza sativa AMT3;3
Selaginella moellendorfii 2.3
Talaromyces stipitatus 5
Penicillium marneffei 5
Pyrenula pseudobufonia B
Cladonia grayi mep1b
Cladonia grayi mep1a
Stereocaulon tennesseense A
Parmotrema michauxiana A
Usnea mutabilis A
Ramalina sp. A
Usnea mutabilis B
Laurera megasperma A
Gibberella moniliformis 4
Fusarium oxysporum 5
Trypethelium virens A
Laurera megasperma B
Ramalina sp. B
Acidithiobacillus ferrooxidans ATCC amt-1
Acidithiobacillus ferrooxidans ATCC amt-1
Acidithiobacillus caldus 436 amt-1
Leptospirillum rubarum 1
MEP α
Acidimicrobium ferrooxidans
Caldivirga macquilingensis
Ferroplasma acidarmanus
Picrophilus torridus
Sulfolobus solfataricus
Sulfolobus tokodaii 1
Sulfolobus tokodaii 1
Methanothermobacter thermoautotrophicus 1
Methanothermobacter thermoautotrophicus 2
Methanosohaera stadtmanae
Wolinella succinogenes
Desulfococcus oleovorans HxD3 2
Nautilia profundicola AmH 1
Sulfurihydrogenibium sp. YO3AOP1
Aquifex aeolicus VF5
Archaeoglobus fulgidus amt-1
Archaeoglobus fulgidus amt-3
Cladonia grayi mep2
Tuber borchii AMT1
Sclerotinia sclerotiorum 2
Magnaporthe grisea 1
Fusarium graminearum 1
Giberella moniliformis 1
Fusarium oxysporum 1
Pyrenophora tritici-repentis 1
Aspergillus nidulans mepA
Aspergillus fumigatus mep2
Coccidioides immitis 1
Penicillium marneffei 1
Talaromyces stipitatus 1
Penicllium chrysogenum 1
Neurospora crassa 1
Magnaporthe grisea 2
Fusarium graminearum 2
Fusarium oxysporum 2
Giberella moniliformis 2
Neurospora crassa 2
Pyrenophora tritic-repentis 2
Talaromyces stipitatus 2
Penicillium marneffei 2
Cryptococcus neoformans AMT2
Hebeloma cylindrosporum AMT2
Laccaria bicolor AMT1.1a
Laccaria bicolor AMT1.1b
Coprinopsis cinerea 1
Hebeloma cylindrosporum AMT1
Coprinopsis cinerea 2
Coprinopsis cinerea 3
Laccaria bicolor AMT1.2
Ustilago maydis ump2
Schizosaccharomyces pombe amt1
Neurospora crassa 3
Magnaporthe grisea 3
Fusarium graminearum 3
Aspergillus nidulans meaA
Aspergillus fumigatus meaA
Penicillium chrysogenum 2
Penicillium marneffei 3
Talaromyces stipitatus 3
Coccidioides immitis 2
Ajellomyces dermatitidis mep3
Pyrenophora tritici-repentis 3
Cladonia grayi mep3
Sclerotinia sclerotiorum 1
Saccharomyces cereviseae MEP3
Sacharomyces cereviseae MEP1
Candida albicans MEP1
Hebeloma cylindrosporum AMT3
Laccaria bicolor AMT2.1
Laccaria bicolor AMT2.2
Laccaria bicolo AMT2.3b
Laccaria bicolor AMT2.3a
Laccaria bicolor AMT2.3c
Coprinopsis cinerea 4
Schizosaccaromyces pombe amt2
Ustilago maydis mep1
Cryptococcus neoformans AMT1
Neurospora crassa 4
Fusarium oxysporum 3
Fusarium graminearum 4
Pyrenophora tritici-repentis 4
Schizosaccharomyces pombe amt3
Talaromyces stipitatus 4
Penicillium marneffei 4
Aspergillus fumigatus mepA
Penicillium chrysogenum 3
Sclerotinia sclerotiorum 3
Pyrenophora tritici-repentis 5
Microbotryum violaceum mepA
Saccharomyces cereviseae MEP2
MEP γ
Candida albicans MEP2
Rhizopus oryzae 4
Rhizopus oryzae 1
Rhizopus oryzae 3
Glomus intraradices
Batracochytrium dendrobatitis
Rhizopus oryzae 5
Rhizopus oryzae 2
Cytophaga hutchinsonii amtB (1)
Leptospirillum rubarum 2
Dictyostelium discoideum amtC
Naegleria gruberi amtA
Trypanosoma cruzi
Methanosarcina barkerii 2
Methanosarcina acetivorans amtB (2 )
Ureaplasma urealyticum amt-1
Ureaplasma urealyticum amt-2
Enterococcus faecium
Ferroplasma acidarmanus
Nautilia profundicola amt
Bacillus halodurans
Exiguobacterium sibiricum
Cytophaga hutchinsonii amtB (2)
Cytophaga hutchinsonii amtB (3)
Cytophga hutchinsonii amtB (4)
Synechocystis sp. amt-3
Oceanobacillus iheyensis
Clostridium thermocellum ATCC 27405
Thermosynechococcus elongatus 1
Synechococcus sp. PCC7002 amtA
Trichodesmium erythraeum 1
Nostoc sp. PCC712 3
Anabaena variabilis
Thermosynechococcus elongatus 2
Synechocystis sp. amt1
Cyanothece sp. ATCC 51142 amt1
Trichodesmium erythraeum IMS101 2
Prochlorococcus marinus str. MIT 9313 amt1
Synechococcus sp. strain WH8102 amt1
Synechococcus sp. strain WH8102 amt1
Prochlorococcus marinus amtB
Prochlorococcus marinus amtB
Synechococcus sp. PCC7942 amt1
Synechococcus sp. PCC7942 amt1
Bacterioides thetaiotaomicron
Methanosarcina barkeri 3
MEP grade
Methanosarcina mazei 2
Methanosarcina acetivorans amt
Archaeoglobus fulgidus amt-2
Methylobacillus flagellatus 3
Desulfococcus oleovorans HxD3 3
Desulfovibrio desulfuricans amtB
Chlorobium tepidum amt-1
Thermotoga maritima
Chloroflexus aurantiacus amtB
Rhodospirillum rubrum 2
Desulfuromonas acetoxidans 2
Desulfuromonas acetoxidans 3
Saccharophagus degradans 2
Psychrobacter sp. amtB
Vibrio vulnifiicus 1
Vibrio vulnificus 1
Vibrio parahaemolyticus 1
Shewanella oneidensis amt
Pseudomonas stutzeri amtB2
Chlorobium tepidum amt-2
Synechocystis sp. amt2
Rhodopirellula sp. 2
Methanopyrus kandlerii amtB
Vibrio vulnificus 2
Vibrio vulnificus 2
Vibrio parahaemolyticus 2
Dechloromonas aromatica 2
Ralstonia eutropha 2
Ralstonia metallidurans 2
Burkholderia cepacia 2
Brevibacterium linens 2
Burkholderia fungorum 2
Pseudomonas putida 2
Pseudomonas aeruginosa 2
Pseudomonas fluorescens 2
Pseudomonas fluorescens 2
Acidithiobacillus ferrooxidans ATCC 53993 amtB
Acidithiobacillus ferrooxidans ATCC 23270 amtB
Acidithiobacillus caldus amtB
Magnetospirillum magnetotacticum amb-1
Desulfuromonas acetoxidans 4
Geobacter metallireducens 2
Geobacter sulfurreducens 2
Nitrosospira multiformis
Nitrosomonas europaea Rh50
Geobacter sp. M21
Strongylocentrotus purpuratus Rh50
Homo sapiens RHD
Naegleria gruberi 3
Dictyostelium discoideum rhgB
Dictyostelium discoideum rhgA
Rh (Outgroup)
Homo sapiens RHAG
Homo sapiens RHAG
Homo sapiens RHBG
Homo sapiens RHCG
Drosophila melanogaster Rh50
Chlamydomonas reinhardtii RHP1
Chlamydomonas reinhardtii RHP2
Methanocaldococcus jannaschii
AMT-Euk
MEP
0.1 substitutions/site