Supplymentary Figure 1. Neighbor-joining phylogenetic trees illustrating HGT events. (a) large subunit of 3-isopropylmalate
dehydratase (ORF2 of W5-61a); (b) small subunit of 3-isopropylmalate dehydratase (ORF3 of W5-61a); (c) pyrroloquinoline quinone
biosynthesis protein C (ORF6 and ORF11 of W5-61a); (d) hypothetical protein (ORF25 of W4-93a); (e) small subunit of glutamate
synthase (ORF7 of W4-39b); (f) transposase (ORF22 of W4-39b); (g) cyclic nucleotide-binding protein (ORF24 of W4-39b); (h)
hypothetical protein (ORF25 of W4-39b); (i) cytochrome c family protein (ORF26 of W4-39b); (j) urease accessory protein UreD
(ORF4 of W4-87b); (k) thymidine kinase (ORF6 of W5-102b); (l) MIP family channel protein (ORF10 of W5-102b); (m) alcohol
dehydrogenase (ORF18 of W5-102b); (n) TonB-dependent receptor (ORF17 of W5-51b); (o) hypothetical protein (ORF18 of W5-51b);
(p) peptidase (ORF19 of W5-51b); (q) glutathione S-transferase (ORF22 of W5-15b). Amino acid sequences obtained in this study is
shown in bold. Numbers at nodes correspond to bootstrap values based on 500 replicates, and the values less than 50% were omitted.
(a)
Hydrogenobacter thermophilus TK-6
Firmicutes
Thermocrinis albus DSM 14484
97
0.1
Aquifex aeolicus VF5
Sulfurihydrogenibium azorense Az-Fu1
98
Thermaerobacter marianensis DSM 12885 Aquificae
81
Moorella
thermoacetica ATCC 39073
98
100
Acetohalobium arabaticum DSM 5501
69
Desulfotomaculum acetoxidans DSM 771
96
Pelotomaculum thermopropionicum SI
82
W5-61a ORF2
clone HF4000 APKG8O8
100
Thaumarchaeota
Candidatus Cenarchaeum symbiosum A
91
Nitrosopumilus maritimus SCM1
Methanosarcina mazei Go1
Euryarchaeota
54
Methanoculleus marisnigri JR1
100
Methanoplanus petrolearius DSM 11571
99
Methanocorpusculum labreanum Z
Pyrobaculum aerophilum IM2
Crenarchaeota
98
Ignisphaera aggregans DSM 17230
Ignicoccus hospitalis KIN4/I
87
Pyrolobus fumarii 1A
51
100
71
64
98
98 87
77
99
99
99
84
99
57
92
0.1
(c)
0.2
99
88
98
90
87
100
99
100
(d)
0.1
99
79
(e)
0.1
76
100
95
100
100
72
97
(j)
61
0.2
79
97
99
58
100
100
92
0.2
53
50
100
68
(m)
(n)
0.2
Flavobacterium johnsoniae UW101
Bacteroidetes
Chryseobacterium gleum ATCC 35910
W4-87b ORF4
Bizionia argentinensis JUB59
Mucilaginibacter paludis DSM 18603
Niastella koreensis GR20-10
Haemophilus haemolyticus M21621 Gammaroteobacteria
100
Pasteurella dagmatis ATCC 43325
83
Actinobacillus pleuropneumoniae Femo
Syntrophobotulus glycolicus DSM 8271
Firmicutes
Ethanoligenens harbinense YUAN-3
Nitrosospira multiformis ATCC 25196Betaroteobacteria
Burkholderia pseudomallei MSHR346
Geobacillus thermodenitrificans NG80-2 Firmicutes
Geobacillus sp. WCH70
Anoxybacillus flavithermus WK1
50
0.2
100 Bacillus sp. 2 A 57 CT2
68
Bacillus sp. NRRL B-14911
Sporosarcina newyorkensis 2681
97
61
Bacillus smithii 7 3 47FAA
75
Ornithinibacillus sp. TW25
100
Caloramator australicus RC3
W5-102b ORF6
Olsenella uli DSM 7084
Actinobacteria
Nocardiopsis
dassonvillei DSM 43111
96
Intrasporangium calvum DSM 43043
65
Arcanobacterium haemolyticum DSM 20595
(l)
Granulicella mallensis MP5ACTX8
Bacteria
Syntrophothermus lipocalidus DSM 12680
Pirellula staleyi DSM 6068
Thermocrinis albus DSM 14484
Phenylobacterium zucineum HLK1
89
Wolinella succinogenes DSM 1740
Thermodesulfobium narugense DSM 14796
Methanothermus fervidus DSM 2088
Euryarchaeota
Methanobrevibacter ruminantium M1
Methanothermobacter marburgensis Marburg
Methanosphaera stadtmanae DSM 3091
Methanothermobacter thermautotrophicus Delta H
Methanocaldococcus vulcanius M7
100
Methanocaldococcus infernus ME
Archaeoglobus fulgidus DSM 4304
W4-93a ORF25
Thermococcus barophilus MP
97
Thermococcus sibiricus MM 739
Nitrosopumilus maritimus SCM1
Thaumarchaeota
Candidatus Nitrosoarchaeum limnia SFB1
Candidatus Nitrosoarchaeum koreensis MY1
Meiothermus ruber DSM 1279
Deinococcus-Thermus
Meiothermus silvanus DSM 9946
Marinithermus hydrothermalis DSM 14884
Verrucomicrobia
bacterium Ellin514
Candidatus Protochlamydia amoebophila UWE25 Chlamydiae
W5-102b ORF10
99 Oryza sativa Indica Group
Eukarya
Triticum aestivum
100
99 Malus prunifolia
Gossypium hirsutum
Planctomycetes
Ktedonobacter racemifer DSM 44963
Candidatus Kuenenia stuttgartiensis
Chloroflexi
Intrasporangium calvum DSM 43043
Actinobacteria
Atopobium vaginae DSM 15829
Nesterenkonia sp. F
Nocardiopsis dassonvillei DSM 43111
Thermus thermophilus HB8
Deinococcus-Thermus
Thermus
sp. CCB US3 UF1
0.2
Marinithermus hydrothermalis DSM 14884
Meiothermus silvanus DSM 9946
99
Plesiocystis pacifica SIR-1
Deltaproteobacteria
Anaeromyxobacter dehalogenans 2CP-C
100
100
Anaeromyxobacter sp. Fw109-5
W5-102b ORF18
65
Natronomonas pharaonis DSM 2160 Euryarchaeota
100
Haladaptatus paucihalophilus DX253
57
99
Halorubrum lacusprofundi ATCC 49239
83
Haloferax volcanii DS2
83
Haloarcula marismortui ATCC 43049
Isoptericola variabilis 225
Actinobacteria
Frankia sp. EuI1c
Olsenella uli DSM 7084
100
59
100
100
100
84 100
100
10069
83
88
99
(o)
Sphingopyxis alaskensis RB2256
Alphaproteobacteria
Erythrobacter litoralis HTCC2594
Sphingobium chlorophenolicum L-1
Novosphingobium aromaticivorans DSM 12444
Rhodospirillum centenum SW
W5-51b ORF17
Sphingomonas wittichii RW1
Phenylobacterium zucineum HLK1
Azospirillum amazonense Y2
Desulfuromonas acetoxidans DSM 684 Deltaproteobacteria
Desulfobulbus propionicus DSM 2032
Anaeromyxobacter dehalogenans 2CP-C
Gemmatimonadetes
Gemmatimonas aurantiaca T-27
100
75
77
100
100
100
(f)
0.1
Sinorhizobium medicae WSM419 Alphaproteobacteria
Paracoccus sp. TRP
Rhodobacter sphaeroides ATCC 17025
Azospirillum sp. B510
W4-39b ORF22
Nitrobacter hamburgensis X14
100
95
Brevundimonas sp. BAL3
Thioalkalivibrio sp. K90mix
Gammaroteobacteria
100
Klebsiella pneumoniae 997
100
100
Edwardsiella ictaluri 93-146
77
Verminephrobacter
eiseniae EF01-2 Betaroteobacteria
86
Gallionella capsiferriformans ES-2
100
Nitrosomonas sp. Is79A3
Desulfatibacillum alkenivorans AK-01 Deltaproteobacteria
Desulfobacter postgatei 2ac9
Haliangium ochraceum DSM 14365
66
83
82
100
98
(g)
99
50
75 100
0.2
100
74
92
97
100
Sphingomonas sp. KC8
Alphaproteobacteria
Sphingomonas wittichii RW1
82
Novosphingobium aromaticivorans DSM 12444
Sphingobium
chlorophenolicum L-1
81
99
Sphingopyxis alaskensis RB2256
Novosphingobium pentaromativorans US6-1
78
Erythrobacter sp. NAP1
Methylotenera versatilis 301
Betaproteobacteria
100
99
Methylotenera mobilis JLW8
Gallionella capsiferriformans ES-2
W4-39b ORF25
Limnobacter sp. MED105
Isosphaera pallida ATCC 43644
Planctomycetes
Gemmata obscuriglobus UQM 2246
97
(h)
0.2
60
100
Sphingomonas sp. KC8
Alphaproteobacteria
Sphingomonas wittichii RW1
Sphingobium chlorophenolicum L-1
Sphingobium japonicum UT26S
Novosphingobium aromaticivorans DSM 12444
Sphingopyxis alaskensis RB2256
Novosphingobium pentaromativorans US6-1
Erythrobacter sp. NAP1
W4-39b ORF24
Limnobacter sp. MED105
Betaproteobacteria
Gallionella capsiferriformans ES-2
Methylotenera versatilis 301
Methylotenera mobilis JLW8
Sorangium cellulosum So ce 56 Deltaproteobacteria
75
0.1
(p)
(q)
Sphingobium chlorophenolicum L-1 Alphaproteobacteria
Sphingobium japonicum UT26S
Sphingopyxis alaskensis RB2256
Novosphingobium aromaticivorans DSM 12444
Sphingomonas sp. KC8
Sphingomonas wittichii RW1
Novosphingobium pentaromativorans US6-1
Erythrobacter sp. NAP1
W4-39b ORF26
Limnobacter sp. MED105
Betaproteobacteria
Gallionella capsiferriformans ES-2
Methylotenera mobilis JLW8
Methylotenera versatilis 301
76
93
(k)
Acinetobacter baumannii ACICU
Bacteria
Marinobacter adhaerens HP15
Cronobacter turicensis z3032
Acinetobacter sp. ADP1
100 Cupriavidus taiwanensis LMG 19424
Ralstonia eutropha H16
Mycobacterium smegmatis MC2 155
Saccharopolyspora erythraea NRRL 2338
Methylacidiphilum infernorum V4
Hydrogenobacter thermophilus TK-6
clone AD1000-325-A12
W5-61a ORF11
W5-61a ORF6
92 clone HF4000 APKG10F15
Thaumarchaeota
100 clone HF4000 APKG6D3
clone HF4000 ANIW141M18
Candidatus Cenarchaeum symbiosum A
clone eHwalsbyi 2B07
Euryarchaeota
Rhodococcus jostii RHA1
Actinobacteria
Nocardia farcinica IFM 10152
Gordonia alkanivorans NBRC 16433
100
100
0.1
Gordonia neofelifaecis NRRL B-59395
Mycobacterium smegmatis MC2 155
100
Mycobacterium abscessus ATCC 19977
Frankia sp. EuI1c
68
Saccharopolyspora spinosa NRRL 18395
100
Amycolatopsis mediterranei U32
78
W4-39b ORF7
Nitrosococcus halophilus Nc4
100
Gammaroteobacteria
Methylococcus capsulatus Bath
100
100
Burkholderia ambifaria MEX-5
Betaroteobacteria
98
Variovorax paradoxus S110
100
Polaromonas sp. JS666
Geobacter bemidjiensis Bem
Deltaproteobacteria
Desulfobulbus propionicus DSM 2032
Desulfovibrio vulgaris DP4
100
Desulfovibrio alaskensis G20
99
100
70
99
96
98
100
62
90
Eubacterium limosum KIST612
Firmicutes
Subdoligranulum variabile DSM 15176
W5-61a ORF3
Caldicellulosiruptor kristjanssonii 177R1B
Thermoanaerobacter tengcongensis MB4
Syntrophothermus lipocalidus DSM 12680
Heliobacterium modesticaldum Ice1
Sulfurihydrogenibium azorense Az-Fu1
Aquificae
Aquifex aeolicus VF5
Hydrogenobacter thermophilus TK-6
Nitrosopumilus maritimus SCM1
99
Thaumarchaeota
Candidatus Nitrosoarchaeum limnia SFB1
Candidatus Cenarchaeum symbiosum A
Methanoplanus petrolearius DSM 11571 Euryarchaeota
Methanoculleus marisnigri JR1
Methanothermus fervidus DSM 2088
Archaeoglobus profundus DSM 5631
Ignicoccus hospitalis KIN4/I
Crenarchaeota
Pyrobaculum aerophilum IM2
Sulfolobus acidocaldarius DSM 639
Vulcanisaeta distributa DSM 14429
83
59
(b)
(i)
Grimontia hollisae CIP 101886
Gammaproteobacteria
Shewanella frigidimarina NCIMB 400
Alteromonas macleodii Deep ecotype
Pseudoalteromonas sp. BSi20439
W5-51b ORF18
Thauera sp. MZ1T
Betaproteobacteria
Methylibium petroleiphilum PM1
Methylomicrobium alcaliphilum 20Z
Thiocystis violascens DSM 198
Thiorhodovibrio sp. 970
Mycobacterium smegmatis MC2 155
Actinobacteria
Mycobacterium colombiense CECT 3035
Thermomonospora curvata DSM 43183
Streptomyces avermitilis MA-4680
Streptomyces lividans TK24
Vibrio sp. EJY3
Gammaproteobacteria
Psychromonas ingrahamii 37
70
Alteromonas macleodii Deep ecotype
0.2
Arthrospira maxima CS-328
100
81
Oscillatoria sp. PCC 6506
Shewanella frigidimarina NCIMB 400
97
Shewanella violacea DSS12
W5-51b ORF19
75
Methylomicrobium alcaliphilum 20Z
Thiocapsa marina 5811
92
Thiorhodovibrio sp. 970
60
Thiorhodococcus drewsii AZ1
97
Thiocystis violascens DSM 198
Thauera sp. MZ1T
Betaproteobacteria
Leptothrix cholodnii SP-6
65
87
Drosophila virilis
Eukarya (animal)
Drosophila persimilis
Drosophila ananassae
100
100
Drosophila simulans
Helicoverpa armigera
100
Antheraea pernyi
Bordetella petrii DSM 12804
100
Bacteria
Myxococcus fulvus HW-1
97
Burkholderia multivorans CGD2M
100
Starkeya novella DSM 506
Pseudomonas syringae ES4326
98
100
Photorhabdus luminescens TTO1
Acinetobacter baumannii ATCC 19606
77
W5-15b ORF22
88
Oryza sativa Indica Group
Eukarya (plant)
100
Triticum aestivum
100
Zea mays
100
0.2
95
HGT from Bacteria to Bacteria
HGT from Bacteria to Thaumarchaeota
HGT from Euryarchaeota to Thaumarchaeota
HGT from Euryarchaeota to bacteria
HGT from Eukarya to Bacteria