S4 Fig. Frankia phylogeny using the four published genomes of strains ACN14a (Fa) and CcI3
(Fc, Cluster I), Dg1 (Fd, Cluster II) and EAN1pec (Fe, Cluster III). Acidothermus cellulolyticus 11B
(Acido), Stackebrandtia nassauensis DSM 44728 (Stack), Geodermatophilus obscurus DSM 43160
(Go), Nakamurella multipartita DSM 44233 (Naka), and Thermobifida fusca YX (Thermo) were
used as outgroups. Forty housekeeping genes were analyzed.
Each gene sequence was identified in Candidatus Frankia datiscae Dg1. After identification, the
gene was used in a Blast search as the query. The corresponding Blast was restricted to Frankia
alni ACN14a, Frankia sp. Ccl3, Frankia sp. EaN1pec, A. cellulolyticus 11B, G. obscurus DSM
43160, S. nassauensis DSM 44728, N. multipartita DSM 44233 and T. fusca YX. All alignments
were created using MUSCLE (multiple sequence comparison by log- expectation; Edgar 2004) at
the EMBL-EBI website. Maximum parsimony analyses were performed using the software
package PAUP version 4.0b10 (Swofford 1999). All characters were weighted equally and gaps
in the alignment were treated as missing. A heuristic search strategy with 10 random replicates,
TBR branch-swapping and the MULTREES optimization was used. MAXTREES parameter was set
to 10,000. Support for branches was evaluated using bootstrap analysis (Felsenstein 1985) and
random sequence addition for 100 replicates, using the same parameters.
All 50 gene
Analysis
MP
100
100
100
100
100
100
Fc
Fa
Fe
All 50 gene
Analysis
NJ
100
100
99
Fd
100
Acido
Thermo
100
100
Fc
Fa
Fe
Fd
Acido
Thermo
Stack
Stack
Geo
Geo
Naka
Naka
16S 23S
100
97
aroK
100
63
88
97
77
100
Fe
Fd
Fd
Go
Go
Thermo
Thermo
Stack
Stack
Naka
Naka
Acido
Acido
Fc
Fe
bioA
80
55
100
Fe
Fd
Go
Naka
Stack
Thermo
Acido
Fc
Fa
62
Fd
79
Fa
Fe
Fa
97
Fc
81
Fa
100
atpA
Fc
73
100
Go
Thermo
Naka
Stack
Acido
bioB
83
Fc
dapA
97
99
Fa
62
75
Fa
99
Fe
Fe
Fd
100
Fd
Naka
70
Thermo
100
Fc
64
Naka
Stack
Stack
Go
Acido
Thermo
Acido
dnaA
99
folC
100
Fa
100
81
97
5
3
Fc
5
7
Fe
Fc
Fa
100
Fe
Fd
Fd
Go
Thermo
Stack
Stack
Naka
Go
Thermo
Naka
Acido
Acido
ftsZ
79
Fc
fusA
75
Fa
97
100
Fc
89
Fa
100
Fe
Fe
Fd
62
99
Fd
Go
Go
67
Naka
Naka
100
Stack
Stack
Thermo
Thermo
Acido
94
glmU
59
Fc
Fa
93
54
Acido
Fc
glpX
Fa
100
Fe
Fe
Fd
Fd
Thermo
Thermo
Naka
70
Stack
66
55
Go
Stack
Go
Naka
Acido
Acido
72
gltA
92
100
Fc
gyrA
96
Fa
95
Fe
Fa
100
Fe
Fd
100
100
Go
Fd
97
56
Naka
100
82
Stack
Stack
Thermo
Acido
idi
Acido
Fe
Fd
Go
Go
Naka
Thermo
100
Fc
95
ispA
72
100
Fc
Fa
Fe
Fd
98
100
Fc
Thermo
Fa
Go
Naka
Stack
Acido
6
9
Stack
Naka
Acido
lipA
69
Stack
mraY
92
Thermo
78
Fa
100
Go
Fe
80
Naka
100
93
murA
99
93
100
Fd
Fc
Go
Fa
Naka
Fe
Thermo
Fd
Stack
Acido
Acido
Fc
murC
100
Fa
63
Fe
68
56
Fc
100
Fd
98
Fa
Fd
Fe
98
Thermo
Stack
Fc
52
Stack
Thermo
Naka
Naka
Go
Go
Acido
Acido
94
murG
65
Fc
Fa
100
99
recA
Fa
Fe
61
Fe
Fd
75
Fc
Fd
Stack
Stack
Thermo
Naka
Go
Go
Naka
Acido
Acido
100
ribA
69
Fc
ribE
91
99
Fa
98
94
Fe
9
2
Go
85
70
Fa
Fe
Fd
Fd
73
Fc
52
Naka
Go
Stack
Stack
Naka
Thermo
Acido
Thermo
Acido
93
rpoB
Fd
Fc
100
Fe
76
Go
61
Fa
100
Fe
shc
72
9
6
Fa
6
2
92
99
100
74
68
Naka
Thermo
Acido
trpE
Go
Stack
Fd
76
Fc
Acido
Fc
Fa
ribF
87
100
Fe
Fd
Naka
61
76
Fc
Fa
Fe
Fd
Naka
Go
Stack
Thermo
Go
Stack
Thermo
Acido
Acido
93
ribH
88
99
Fa
996
uppS
99
72
Fe
84
Fc
Fa
Fe
Fd
Fd
51
69
Fc
Thermo
Naka
Naka
Go
Stack
Stack
Go
Thermo
Acido
Acido
90
htpX
98
100
Fc
50
ksgA
Fa
Fc
Fa
100
Fe
Fe
Fd
70
Fd
Go
Stack
50
Stack
Thermo
Go
Thermo
Naka
Acido
Acido
62
lytB
Fc
Fa
76
99
99
Fe
Fd
99
dnaB
Fa
100
Fe
83
Fd
Go
Thermo
Naka
5
3
Stack
rplA
73
90
99
85
Naka
Go
Acido
Acido
Fc
Fa
54
rplB
69
100
Go
Fc
Fa
Fe
Fe
70
Stack
Thermo
Fd
76
Fc
Fd
70
Go
Naka
Naka
Stack
Stack
Thermo
Thermo
Acido
Acido
77
rplC
74
Fc
Fa
100
95
rplD
Fa
85
94
Fe
Fe
Fd
Fd
Stack
56
Go
60
Naka
rplE
Acido
rplF
100
Fa
89
Fe
Fd
Stack
Thermo
Stack
Naka
Acido
Fc
Go
Thermo
Thermo
53
Fc
Stack
Thermo
100
Fc
Fa
Fe
Fd
Go
Go
Naka
Acido
Naka
Acido
82
dapB
Fc
Fc
Fa
pgk
Fe
80
Fe
99
Fd
Acido
63
Fc
69
Fd
76
Thermo
90
Thermo
Acido
Naka
Stack
Stack
Geo
Go
Naka
79
tpiA
97
100
Fa
Fc
eno
Fd
81
Acido
Stack
Fc
Fe
Fa
Fd
Acido
72
Naka
88
95
Fe
Thermo
72
Thermo
Geo
Naka
Stack
Geo
82
metK
94
Fa
100
clpP
Fc
97
83
Fe
Fd
Fd
88
63
dxs
100
100
Acido
Thermo
63
Thermo
58
Stack
Stack
Naka
Naka
Geo
Geo
Fc
92
dxr
98
Fa
100
Fe
Thermo
Fc
Fe
Fa
Fd
Fd
76
Fe
Fa
Acido
8
8
94
87
Fc
59
Thermo
Acid
Geo
Stack
Stack
Geo
Naka
Acid
Naka
Fc
nth
100
Fe
100
mfd
Fa
100
Fd
62
Geo
68
Stack
73
100
aceE
94
100
59
100
Fc
Fa
Fe
Fd
Acid
68
Thermo
Thermo
Stack
Acid
Naka
Naka
Geo
Fa
Fc
Fe
Fd
Stack
Acido
Thermo
Geo
Naka