Evidence for inter-specific recombination among the mitochondrial genomes of Fusarium
species in the Gibberella fujikuroi complex.
Gerda Fourie1, Nicolaas A. van der Merwe2, Brenda D.Wingfield2, Mesfin Bogale2, Bettina
Tudzynski3, Michael J Wingfield1, Emma T Steenkamp1.
Departments of Microbiology and Plant Pathology1 and Genetics2, Forestry and Agricultural
Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa. University of
Munster, Germany3.
*gerda1.fourie@fabi.up.ac.za.
SUPPLEMENTARY MATERIAL
Table S1. Mitochondrial amino acid codon usage and tRNA anti-codon sequences for Fusarium
circinatum, F. verticillioides and F. fujikuroi.
Table S2. Inverted, direct and dispersed repeats identified in the mitochondrial genomes of
Fusarium circinatum, F. verticillioides and F. fujikuroi.
Table S3. Intron distribution, type, size, and endonuclease of F. circinatum, F. verticillioides, F.
fujikuroi, F. oxysporum, F. graminearum and F. solani.
Table S4. Comparison of the alternative trees using the SH test.
Figure S1. Physical map and BLAST comparison of the mt genomes of F. circinatum against F.
oxysporum, F. verticillioides and F. fujikuroi.
Figure S2. Midpoint rooted maximum likelihood phylogenetic tree of the amino acid
LAGLIDADG endonuclease domains identified within intron regions of F. circinatum, F.
verticillioides, F. fujikuroi, F. oxysporum, F. graminearum and F. solani.
Figure S3. Midpoint rooted maximum likelihood phylogenetic tree of the amino acid GIY-YIG
endonuclease domains identified within intron regions of F. circinatum, F. verticillioides, F.
fujikuroi, F. oxysporum, F. graminearum and F. solani.
Figure S4. Maximum likelihood phylogenies for Fusarium based on mitochondrial proteincoding nucleotide sequences.
Figure S5. Maximum likelihood phylogenies for Saccharomyces species based on mitochondrial
protein-coding nucleotide sequences.
Table S1. Mitochondrial amino acid codon usage and tRNA anti-codon sequences for Fusarium
circinatum, F. verticillioidesa and F. fujikuroi b.
Amino acid
Codon
Codon usage c
Anti-codon d
(F. circinatum / F. verticillioides /
F. fujikuroi)
TGC / TGC / TGC
Alanine
GCG
GCA
GCT
GCC
(F. circinatum / F. verticillioides /
F. fujikuroi)
14 / 15 / 12
81 / 81 / 72
127 / 122 / 111
29 / 34 / 33
Arginine
AGG
AGA
CGG
CGA
CGT
CGC
0 / 0 / 15
75 / 75 / 72
0/0/0
1/1/5
6 / 8 / 12
2/0/1
ACG, TCG, TCT / ACG, TCG, TCT / ACG,
TCG, TCT, CCT
Asparagine
AAT
AAC
178 / 180 / 169
39 / 36 / 40
GTC / GTC /GTC
Aspartic acid
GAT
GAC
87 / 86 / 79
16 / 19 / 19
GTC / GTC / GTC
Cysteine
TGT
TGC
21 / 22 / 31
6 / 6 / 15
GCA / GCA / GCA
Glutamic acid
GAG
GAA
14 / 15 / 14
106 / 105 / 107
TTC / TTC / TTC
Glutamine
CAG
CAA
5/7/8
81 / 80 / 79
TTG / TTG / TTG
Glycine
GGG
GGA
GGT
GGC
24 / 25 / 23
121 / 123 / 123
144 / 144 / 135
2/1/1
TCC / TCC / -
Histidine
CAT
CAC
54 / 54 / 48
30 / 31 / 30
GTG / GTG / GTG
Isoleucine
ATA
ATT
ATC
365 / 365 / 360
135 / 133 / 154
32 / 33 / 35
GAT / GAT / GAT
Leucine
TTG
TTA
CTG
20 / 20 / 24
499 / 496 / 480
11 / 11 / 11
TAA, TAG / TAA, TAG / TAG
CTA
CTT
CTC
AAG
AAA
53 / 54 / 62
52 / 50 / 55
0/1/2
7 / 7 / 17
112 / 111 / 107
Methionine
ATG
129 / 129 / 117
CAT / CAT, GTT / CAT, GTT
Phenylalanine
TTT
TTC
236 / 236 / 239
124 / 124 / 113
GAA / GAA / GAA
Proline
CCG
CCA
CCT
CCC
10 / 8 / 9
40 / 40 / 34
86 / 91 / 83
12 / 9 / 12
TGG / TGG / TGG
Serine
AGT
AGC
TCG
TCA
TCT
TCC
131 / 130 / 126
24 / 25 / 29
6/6/4
91 / 91 / 89
110 / 111 / 112
10 / 8 / 11
GCT, CGA, TGA / GCT, TGA / GCT, TGA
Threonine
ACG
ACA
ACT
ACC
2/4/0
111 / 114 / 108
105 / 101 / 106
5 / 4 / 10
TGT / TGT / TGT
Tryptophan
TGG
TGA
2/2/9
59 / 59 / 51
TCA / TCA / TCA
Tyrosine
TAT
TAC
170 / 172 / 172
49 / 47 / 55
GTA / GTA / GTA
Valine
GTG
GTA
GTT
GTC
37 / 36 / 31
160 / 161 / 160
102 / 102 / 102
8 / 7 / 14
TAC / TAC / TAC
End
End
TAG
TAA
4/3/4
10 / 11 / 10
Lysine
a
TTT / TTT / TTT
In order to compare codon usage between species within GFC, the mitochondrial genome of F.
verticillioides described by Al-Reedy et al. were also included.
b
Codon usage was calculated with the online tool at http://www.protocol-online.org. Missing or
under-represented codons and corresponding third position G or C are indicated in italics.
c
Codon usage are indicated in the order F. circinatum, F. verticillioides and F. fujikuroi.
c
The tRNA anti-codon for each codon are indicated in the order F. circinatum, F. verticillioides
and F. fujikuroi.
Table S2. Inverted, direct and dispersed repeats identified in the mitochondrial genomes of Fusarium circinatum, F. verticillioides
and F. fujikuroi.
Sequence motif F. circinatum
GAGCTTTAGCTTGCG
ACGAAGTATGCTTGCGCCGGAATCGC
GCAAGCTAGAAAAAAATGT
TCGCGCAAGCTAGAA
TCTCTAAAAAAAATATATTTTTTTTT
ATA
GGGCTGCGCAAGCTAAAGCTC
GCTGCGCAAGCTAAAGCT
GCGCAAGCTAAAGCT
GAGGGCTGCGCAAGCTAAAGCTCC
AGAGCTTTAGCTTGCGC
GAGCTTCTATTTCATA
CGCGCAAGCTAAAGC
GCAAGCTAAAGCTCT
AGCTTCTGATTCCCTACGGG
CGCAAGCTAAAGCTAT
GCTCTTAGCTTTTAGGAGAC
CACAGTAAGGCGCTAGCTAT
AAAAAAAATGTATTTTTT
CCTACGAGTGACGCTGTGTGCACGTA
TTATAAT
Nucleotide position
Position relative to other genes
Typea
3084, 4500, 4538
3111, 6407
between nad2 and nad3
between nad2 and nad3 + atp9 and cox2
direct
dispersed
3133, 6429, 10695
between nad2 and nad3 + atp9 and cox2 +
nad5 and cob
between nad2 and nad3
dispersed
dispersed
4322, 4396, 6536, 8179,
8247, 11979
4389, 8172
4499, 4537
6158, 11611
6536, 8246
6539, 7819
7636, 7657
8247, 8269, 11979
between nad2 and nad3 + cox2 and nad4L
+ cox1 and nad1 + nad4 and atp8
between nad2 and nad3 + cox2 and nad4L
+ nad5 and cob
between nad2 and nad3 + atp9 and cox2 +
cox2 and nad4L + nad5 and cob
between nad2and nad3 + cox2 and nad4L
between nad2 and nad3
between atp9 and cox2 + nad5 and cob
between atp9 and cox2 + cox2 and nad4L
between atp9 and cox2 + cox2 and nad4L
between cox2 and nad4L
between cox2 and nad4L + nad5and cob
10 872, 10895
12557, 12582
19807, 20049
34754, 39038
between nad5 and cob
between nad5 and cob
between cob and cox1
between cox1 and nad1 + nad4 and atp8
4167, 4346
4317, 4391, 8174, 33982,
38967
4319, 4393, 8176, 11976
inverted
direct and
dispersed
direct and
dispersed
dispersed
direct
dispersed
dispersed
dispersed
direct
direct and
dispersed
inverted
inverted
inverted
dispersed
GGCTGCGCAAGCTAAAGCTC
CTTTAGCTTGCTAAATTATAGCTCGC
TATAGCT
GCGATTTTCTCCGAAAATAC
CTCTAACAAAGTGTACGCCTAT
GGAGCTTTAGCTTGCGC
CTAACAACGTGTATTCATAG
CTTGCGCATCGTTCT
TTTGCTTTTAGCTTTTACCT
AAGCTCTGTATTTTTTTTATAAA
TCGTTCTGGCTAGCCAGCC
TATATTTTTTTATATAGC
ATAAGGAATTACAGAAAT
CGCAAGCTAAAGCTCTCGGAGAAAAT
CGCGCAAGCT
ATCGTTCTGGCTAGCCAGCC
TATAAAAAAAGATATTTTTTTTATAG
CCCTCCTC
Sequence motif F. verticillioides
AGCTTTAGCATGCTG
TGCGCAAGCTAAAGCT
CGAAGCCGAAAAATATG
AGCTAGAAAAAAATGTATTTTTTTCT
AGCTT
38968, 40668
39420, 41139
between nad4 and atp8
between atp8 and atp6
inverted
inverted
43338, 43504
43426, 46901
dispersed
dispersed
48448, 55323
48984, 55097
48394, 53639
tRNA cluster upstream of rns
tRNA cluster upstream of rns + between
cox3 and nad6
tRNA cluster upstream of rns + nad6
tRNA cluster upstream of rns + nad6
tRNA cluster upstream of rns + rnnl
between cox3 and nad6
between cox3 and nad6
between cox3 and nad6 + tRNA cluster
upstream of rnnl
tRNA cluster upstream of nad6 + rnnl
tRNA cluster upstream of nad6 + rnnl
between nad6 and rnnl
dispersed
dispersed
dispersed
inverted
inverted
direct and
dispersed
direct
dispersed
dispersed
54169, 55346
65164, 66479
tRNA cluster upstream of rnnl
between ORF2 and nad2
direct
inverted
Nucleotide position
Position relative to other genes
Typea
1753, 1795
1997, 4363, 6863, 6894,
7679, 30276, 32013,
38724, 40439
1867, 13493
2009, 5530
between nad2 and nad3
between nad2 and nad3 + nad3 and atp9 +
cox2 and nad4L + tRNA cluster upstream
of rnnl
between nad2 and nad3 + cob and cox1
between nad2 and nad3 + atp9 and cox2
direct
direct and
dispersed
43405, 48361
44064, 48479
43480, 54162
46235, 46416
46439, 48225
46981, 54170, 55347
dispersed
dispersed
GCTAAAGCTCGCTCTC
GAGGGCTAACGAAGTA
TTCGGAGAAAATCGC
TCGGAGAAAATCGCGCA
AAATCGCTGCGCAAGCTAAAGCT
CTATAAAAAAATATATTTTTTTTTTA
ACATAGCGAGCTCGCTATGAAATACC
GCA
GCTTCTATTTCGGCG
GCTAGAGCTTGCGCCT
GGTGAGCTGGCGCCT
CGGAGAAAATCGCTGCGCAAGCTAAA
GCT
GGAGAAAATCGCTGCGCAAGCTAAAG
CT
GCAAGCTAAAGCTCT
GTAGCGCGAGCTCCCCTCCTAT
GATAATTTTGTTTATC
TTATATATAGCTTGC
GAGCTTGCGCCTTTCTA
AATTCTTATCCTTATCC
CACAGTAAGGCGCTAGCTAT
TAAAAAAAAAAAGAAAATTTTTTTTT
ATAGC
GCGCTAGAGCTTGCGCCT
GCTTGCTATGAAGGCT
TGCTTTAGCTTTTACAGCT
3041, 7728
3262, 5748
4216, 6848
4217, 6911
4356, 6856, 6887, 7672
4382, 5572
between nad2 and nad3 + cox2 and nad4L
between nad2 and nad3 + atp9 and cox2
between nad3 and atp9 + cox2 and nad4L
between nad3 and atp9 + cox2 and nad4L
between nad3 and atp9 + cox2 and nad4L
between nad3 + atp9
dispersed
dispersed
dispersed
dispersed
dispersed
inverted
4182, 5298
5349, 11217, 13412,
30228, 30409, 32084,
33310
6834, 7650
6850, 7666
between atp9 and cox2
between atp9 and cox2 + nad5 and cob +
cox1 and tRNA cluster upstream of nad6
direct
dispersed
between atp9 and cox2
between cox2 and nad4L
direct
direct
6851, 6882, 7667
between cox2 and nad4L
direct
6866, 6897, 7121
6965, 6990
7257, 7273
7318, 7455
7557, 13416
direct
inverted
direct
direct
dispersed
11329, 11350
11872, 11897
10235, 11175
between cox2 and nad4L
between cox2 and nad4L
between cox2 and nad4L
between cox2 and nad4L
between cox2 and nad4L + between cob
and cox1
between nad5 and cob
between nad5 and cob
between cob and cox1
14797, 19608, 30226,
33308
13964, 20315
20011, 20031
between cob and cox1 + cox1 and nad1 +
tRNA cluster upstream of rns + nad6
between cob and cox1 + within nad4
between cox1 and nad1
dispersed
inverted
inverted
inverted
dispersed
inverted
ACCTACGAGTGACGCTGTGTGCACGT
ATTATAATTA
TAGCTTTAGCTTGCTAT
TTTAGCTTGCCTTTAGCTTTTAGCT
AGGTGAGCTGGCGCCTTCGG
TAGCTTTAGCTTGCG
CTTTAGCTTGCGGAT
AGGGCTGCGCTAGAGCTT
ACATTCCTGCACTAGCTAG
AAGGCGCAAGCTCGTG
GCTATAAAAAAAAAATATATTTTTTT
TTTATA
TATGCTTTATAAAAAAAAATATATTT
TTTATAGCC
TTTATAAAAAAAAATAATTTGTTTAT
AGG
GAGCTATATAAAAAAATATATTTTTC
TTATAGC
Sequence motif F. fujikuroi
AAGGCTTTAGCTTAC
TATATTTAGGCGCAAGCTCTAGC
TTTAGCTTACGCAAGC
AGCTTGCACGGGACGGGTAAAAATGT
A
GAAAAATCAGCCAAAG
TTAGTAGTAGCGCGAGC
GATAATTTTGTTTATC
20595, 25748
between nad1 and nad4 + rns and cox3
dispersed
27540, 27559
29820, 31588
30246, 38694
30087, 37541, 40623
30090, 32043
inverted
inverted
dispersed
dispersed
dispersed
33302, 41409
33965, 40194
32106, 33337
39258, 40596
between atp6 and rns
between rns and cox3
tRNA cluster upstream of rns + rnnl
tRNA cluster upstream of rns + rnnl
tRNA cluster upstream rns + cox3 and
nad6
tRNA cluster upstream of rns + rnnl
tRNA cluster upstream of rns and rnnl
tRNA cluster upstream of nad6
tRNA cluster upstream of rnnl
41068, 41922
between rnnl and ORF2
inverted
50593, 51280
between ORF2 and nad2
inverted
52069, 52717
between ORF2 and nad2
inverted
Nucleotide position
Position relative to other genes
Typea
2650, 5636
2357, 5490
2765, 5641
3227, 3442
between nad3 and atp9 + cox2 and nad4L
between nad3 and atp9 + cox2 and nad4L
between nad3 and atp9 + cox2 and nad4L
between atp9 and cox2
dispersed
dispersed
dispersed
direct
3982, 13454
5457, 5532
5791, 5807
between atp9 and cox2 + cob and cox1
between cox2 and nad4L
between cox2 and nad4L
dispersed
inverted
direct
dispersed
dispersed
direct
inverted
TCAGCATGCTAAAGCT
TAGAGCTTGCGTAGAGCTTGCGTAGA
GCTTG
GTAGAGCTTGCGTAGAGCTTGC
GCTTGCGGCTAAAAAA
CACAGTAAGGCGCTAGCTAT
AAAAAAAAATACATTTTTTTTT
TGCTTTAGCTTTTACAGCT
AATTTTAAACGTATTAGATTATTCTA
TGAA
CTATGAAGGCGCAAGCTC
CGAGCTTTAGCTAGCTAGCCGCCGAA
AAA
AGGCTGGCGCAAGCTATGC
AAAAAAAAGTATTTTTTTTT
AAAAAAAATGTTAATTTTTTT
AAGCATACTTCGTTAGCCCTAAAAGA
AAGATATTT
GCTTGCGCCTAAAAAATATATTTTTT
TTA
a
6227, 6269
8703, 8725, 8747, 8769
between cox2 and nad4L
between nad5 and cob
direct
direct
8735, 8757
8784, 13111
9952, 9977
12753, 13012
16227, 16247
16546, 20167
between nad5 and cob
between nad5 and cob + cob and cox1
between nad5 and cob
between cob and cox1
between cox1 and ORF1
between ORF1 and nad1
direct
dispersed
inverted
inverted
inverted
direct
24804, 26664
26665, 27967
between cox3 and nad6 + nad6 and rnnl
between cox3 and nad6
dispersed
inverted
33490, 34926
35640, 36606
43563, 43639
43874, 44224
between rnnl and ORF2
between rnnl and ORF2
between ORF2 and nad2
between ORF2 and nad2
inverted
inverted
inverted
inverted
44578, 46190
between ORF2 and nad2
inverted
Direct repeats are repeat units within the same intergenic region. Dispersed direct repeats are direct repeat units within
different intergenic regions. Inverted repeats are repeat units within the same intergenic region however the repeat sequence
is in a reverse sequence orientation. Inverted repeats for each genome were identified with Einverted EMBOSS and
intergenic exact repeat elements were identified using REPFIND (http://zlab.bu.edu/repfind). Repeats in blue are the single
repeat motif shared between F. circinatum and F. verticillioides and the repeat in red are the single repeat motif shared
between F. verticilllioides and F. fujikuroi.
Table S3. Intron distribution, type, size, and endonuclease of F. circinatum, F. verticillioides, F.
fujikuroi, F. oxysporum, F. graminearum and F. solani.
Typea
Insertion
position b
Size
Core
structurec
ORF Typed
Protein
length
Domainse
cox1
f.cir.cox1.intron1
f.cir.cox1.intron2
f.cir.cox1.intron3
f.cir.cox1.intron4f
group 1B
group 1B
group 1D
group 1B
395
622
716
871
1296
1182
1434
2287
44-1183
18-1078
1214-1332
1287-2238
53-1182
859-1039
989-1309
1058-1357
1116-1194
18-1069
1158-1276
18-956
26-196
34-1040
LAGLIDADGD
LAGLIDADGD
LAGLIDADGD
LAGLIDADGD
LAGLIDADGS
GIY-YIG
LAGLIDADGS
GIY-YIG
LAGLIDADGD
GIY-YIG
GIY-YIG
LAGLIDADGD
LAGLIDADGD
LAGLIDADGD
LAGLIDADGD
LAGLIDADGD
LAGLIDADGD
LAGLIDADGD
LAGLIDADGS
GIY-YIG
GIY-YIG
LAGLIDADGS
GIY-YIG
LAGLIDADGD
LAGLIDADGD
LAGLIDADGD
LAGLIDADGD
LAGLIDADGD
LAGLIDADGD
GIY-YIG
LAGLIDADGS
383
356
312
357
378
455
362
281
305
400
335
378
359
307
313
324
410
352
320
440
73
379
277
313
302
289
352
352
308
314
342
109-205; 260-350
82-173; 206-311
68-155; 187-283
96-191; 220-320
247-344
161-254
96-174
54-151
68-155; 187-283
135-228
82-163
108-204; 259-350
83-179; 204-315
62-152; 184-279
87-165; 193-280
84-165; 196-295
121-219; 278-380
92-187; 212-312
190-287
147-230
1-62
92-170
92-170
31-119; 150-271
33-126; 153-263
24-118; 173-262
82-178; 203-308
65-152;184-280
80-159; 189-285
127-210
95-170
f.cir.cox1.intron5
f.cir.cox1.intron6
f.cir.cox1.intron7
f.ver.cox1.intron1
f.ver.cox1.intron2
f.gram.cox1.intron1
f.gram.cox1.intron2
f.gram.cox1.intron3
f.gram.cox1.intron4
f.gram.cox1.intron5
f.gram.cox1.intron6
f.gram.cox1.intron7
f.gram.cox1.intron8
f.gram.cox1.intron9
f.gram.cox1.intron10f
group 1B
group 1B
group 1B
group 1D
group 1B
group1B
group1B
group 1B
group1D
group 1B
group 1B
group 1B
group 1B
group 1B
group 1B
1067
1134
1271
716
1067
219
395
622
716
728
738
828
871
908
1067
1383
2151
1048
1499
1307
1295
1313
1200
1364
985
1114
1286
1200
1019
2383
23-193
53-1116
857-1040
1279-1397
23-193
1185-1254
216-1203
26-1098
1157-1275
19-953
18-986
48-262
52-1111
23-99
35-205
f.gram.cox1.intron11
f.gram.cox1.intron12
f.solani.cox1.intron1
f.solani.cox1.intron2
f.solani.cox1.intron3
f.solani.cox1.intron4
f.solani.cox1.intron5
f.solani.cox1.intron6
f.solani.cox1.intron7
f.solani.cox1.intron8
group 1B
group 1B
group 1B
group 1B
group 1B
group 1B
group 1D
group 1B
group 1B
group 1B
1134
1271
246
287
395
622
716
738
1067
1134
1217
1053
1337
2196
1402
1173
1378
1030
1283
1082
cox2
f.gram.cox2.intron1
f.gram.cox2.intron2
f.gram.cox2.intron3
group1C2
group 1B
group1C1
112
230
653
1511
1183
1865
39-264
924-1148
44-274
LAGLIDADGD
GIY-YIG
GIY-YIG
298
294
185
17-115; 174-276
58-142
116-175
cox3
f.cir.cox3.intron1
f.gram.cox3.intron1
f.gram.cox3.intron2
f.gram.cox3.intron2
f.solani.cox3.intron1
f.solani.cox3.intron2
group 1B
group 1B
group1C2
group1C2
group 1B
group 1A
221
221
336
336
221
642
1159
1510
1433
1433
1540
1532
978-1127
1083-1472
27-255
27-255
803-991
1037-1499
LAGLIDADGD
LAGLIDADGD
LAGLIDADGS
LAGLIDADGS
304
340
352
352
68-155; 187-283
56-157; 182-318
160-259
160-259
LAGLIDADGD
426
55-153; 200-297
cob
f.cir.cob.intron1
group 1B
205
1626
20-177
f.cir.cob.intron2
f.cir.cob.intron3
f.cir.cob.intron4f
group 1D
group 1A
group 1B
396
491
507
1790
1232
973
494-647
967-1177
24-182
f.fuj.cob.intron1
f.gram.cob.intron1
f.gram.cob.intron2
group1A
group1C1
group1D
491
279
396
740
2236
2271
475-685
1778-2009
1049-1168
LAGLIDADGS
LAGLIDADGS
no ORF
LAGLIDADGD
LAGLIDADGS
LAGLIDADGS
LAGLIDADGS
LAGLIDADGD
GIY-YIG
320
157
no ORF
295
140
107
131
488
292
61-171
59-144
no ORF
51-138; 189-278
45-139
6-89
26-116
98-188; 236-349
76-164
Intron
f.gram.cob.intron3f
group1A
491
2427
2179-2373
38-986
56-343
LAGLIDADGS
LAGLIDADGS
LAGLIDADGD
no ORF
267
247
319
no ORF
73-162
60-229
74-170; 206-303
no ORF
f.gram.cob.intron4
f.gram.cob.intron5
group 1B
group1C1
507
780
1062
1960
nad1
f.cir.nad1.intron1
f.ver.nad1.intron1
f.gram.nad1.intron1
f.gram.nad1.intron2
group 1B
group 1B
group1A
group 1B
637
637
146
637
367
1105
319
1157
24-220
20-180
64-261
33-160
no ORF
GIY-YIG
no ORF
GIY-YIG
no ORF
305
no ORF
136
no ORF
87-175
no ORF
9-48
nad2
f.cir.nad2.intron1
f.gram.nad2.intron1
f.gram.nad2.intron2
f.gram.nad2.intron3
f.gram.nad2.intron4
f.solani.nad2.intron1
group 1C
group1C2
group1C2
group1C2
group1A
group II
763
379
763
1181
1624
421
1335
1434
1494
1614
1632
2362
44-275
59-302
49-292
32-269
1322-1553
LAGLIDADGD
no ORF
no ORF
LAGLIDADGD
LAGLIDADGD
421
no ORF
no ORF
418
349
131-231; 291-389
no ORF
no ORF
137-235; 298-398
61-157; 219-314
nad3
f.gram.nad3.intron1
group1C2
91
1450
42-285
LAGLIDADGD
423
139-238; 295-395
nad4L
f.gram.nad4L.intron1
group1C1
240
1822
1341-1770
LAGLIDADGD
351
58-157; 220-319
nad4
f.solani.nad4.intron1
group 1C2
505
1397
17-295
LAGLIDADGD
429
139-235; 295-396
nad5
f.oxy.nad5.intron1
f.gram.nad5.intron1
f.solani.nad5.intron1
group 1B
group 1B
group 1C2
718
718
324
1010
1019
1348
22-934
26-941
38-272
LAGLIDADGD
LAGLIDADGD
LAGLIDADGD
304
302
429
68-195; 182-280
65-156; 220-319
139-240; 299-399
atp6
f.gram.atp6.intron1
group 1B
367
1450
1127-1414
LAGLIDADGD
356
67-165; 228-323
atp9
f.gram.atp9.intron1
group1A
181
1088
32-206
GIY-YIG
276
55-138
a
Intron type determined by RNAweasal (http://megasun.bch.umontreal.ca/RNAweasel)[57].
b
Nucleotide insertion position with regards to the start of the coding sequence.
c
The region that contain the core structure of the introns (P3, P4, P6, P7, P8) identified with
RNAweasal.
d
ORF type identified with ORF finder (genetic code 4; Mold, Mitochondria) and BLASTp
comparison.
e
Protein domains characterized with InterProScan (http://www.ebi.ac.uk/Tools/pfa/iprscan).
LAGLIDADGD contained two domains whereas LAGLIDADGS only one.
f
Biorfic intron encodes two OFRs.
Table S4. Comparison of the alternative trees using the SH testa.
Treeb
1
2
3
4
5
6
1
2
3
4
5
6
1
2
3
4
5
6
1
2
3
4
5
6
1
2
3
4
5
6
1
2
3
4
5
6
1
2
ln L
Concatenated
23946.77288
24036.16059
24392.70239
23985.70301
23985.70301
24069.94940
cox2
1228.15556
1239.02323
1276.80028
1231.13107
1231.13107
1236.25901
cox3
1401.62495
1408.11666
1417.21305
1401.84707
1401.84707
1406.41134
nad2
3148.58325
3215.37298
3234.18315
3153.04252
3153.04252
3210.77348
nad5
3300.29017
3310.49859
3355.77261
3304.15995
3304.15995
3309.07299
atp6
1414.31761
1414.31761
1461.32707
1427.75361
1427.75361
1427.75361
cob
1950.24117
1950.24117
Δln L
(best)
89.3877
445.92951
38.93012
38.93012
123.17652
P Valuec
Significantly
worse?e
0.015
0.000
0.217
0.217
0.001
best
no
no
yes
yes
no
(best)
10.86767
48.64472
2.97551
2.97551
8.10345
0.298
0.003
0.697
0.697
0.403
best
yes
no
yes
yes
yes
(best)
6.49171
15.5881
0.22212
0.22212
4.78639
0.349
0.082
0.821
0.821
0.501
best
yes
yes
yes
yes
yes
0.000
0.000
0.564
0.564
0.000
best
no
no
yes
yes
no
0.373
0.005
0.689
0.689
0.419
best
yes
no
yes
yes
yes
(best)
66.78973
85.5999
4.45927
4.45927
62.19023
(best)
10.20842
55.48244
3.86978
3.86978
8.78282
0
(best)
47.00946
13.436
13.436
13.436
(best)
0
0.647
0.007
0.159
0.159
0.159
yes
best
no
yes
yes
yes
0.883
best
yes
3
4
5
6
1
2
3
4
5
6
1
2
3
4
5
6
1
2
3
4
5
6
1
2
3
4
5
6
1
2
3
4
5
6
1
2
3
4
5
6
1
2
1999.88279
1950.85218
1950.85218
1951.4114
nad4
2426.04132
2426.04132
2476.34155
2435.05980
2435.05980
2435.80133
nad1
1945.34168
1946.36185
2070.26604
1981.95746
1981.95746
1982.77271
atp8
190.34829
190.34829
190.34829
190.34829
190.34829
190.34829
atp9
401.32802
401.32802
401.32802
398.16849
398.16849
401.32802
nad4L
448.80268
448.80268
448.80268
448.80268
448.80268
448.80268
cox1
3224.81067
3232.70819
3279.47385
3214.10898
3214.10898
3240.97086
nad3
672.47475
676.02756
49.64162
0.61101
0.61101
1.17023
0.002
0.819
0.819
0.745
no
yes
yes
yes
0
(best)
50.30022
9.01848
9.01848
9.76001
0.66
0.008
0.336
0.336
0.302
yes
best
no
yes
yes
yes
(best)
1.02017
124.92435
36.61578
36.61578
37.43103
0.702
0.000
0.013
0.013
0.008
best
yes
no
no
no
no
0
(best)
0
0
0
0
0.000
3.15953
3.15953
3.15953
(best)
0
3.15953
0.164
0.164
0.164
0
0
(best)
0
0
0
0.000
0.000
10.70168
18.59921
65.36486
(best)
0
26.86188
0.38
0.18
0.000
0.78
0.032
yes
yes
no
best
yes
no
0.98611
4.53892
0.643
0.264
yes
yes
0.000
0.000
0.000
0.000
0.593
0.164
0.000
0.000
0.000
no
best
no
no
no
no
yes
yes
yes
best
yes
yes
no
no
yes
no
no
no
3
4
5
6
1
2
3
4
5
6
680.50691
671.48864
671.48864
673.52633
nad6
1147.84359
1152.62491
1161.45593
1146.60988
1146.60988
1144.14278
9.01827
(best)
0
2.03769
0.106
3.70081
8.48214
17.31315
2.4671
2.4671
(best)
0.6
0.219
0.068
0.705
0.705
0.792
0.643
yes
best
yes
yes
yes
yes
yes
yes
yes
best
a
The Shimodaira-Hasegawa tests were conducted in PAUP [89].
b
Tree topologies correspond to those presented in Figure 4. Newic format for the various trees
are as follows: Tree 1: (DQ364632,((F.fuj,(F.ver,Fsp34)),(AY945289,AY874423))); Tree 2:
(DQ364632,(fsp34,F.ver,f.fuj),(AY945289,AY874423)); Tree 3: (DQ364632,(fsp34,F.ver,f.fuj,
AY945289,AY874423)); Tree 4: (DQ364632,(((AY874423,AY945289),(f.ver,fsp34)),F.fuj));
Tree 5: (DQ364632,(f.fuj,((f.ver,fsp34),(AY945289,AY874423)))); Tree 6:(DQ364632,(Fsp34,
(F.ver,(F.fuj,(AY945289,AY874423))))). Species and isolates are designated as follows: Fsp34
= F. circinatum, F. ver = F. verticillioides, F. fuj = F. fujikuroi, DQ364632 = F. graminearum,
AY945289 = F. oxysporum isolate F11, AY874423 = F. oxysporum isolate VPRI 19292
c
d
P values for the SH tests.
For each dataset, the tree receiving the best likelihood score are indicated with “Best”; those
topologies that are significantly worse (P < 0.05) than the best tree are indicated with “Yes” and
those that are not (P > 0.05) with “No”.
F. circinatum CDS
F. circinatum tRNA genes
F. oxysporum
F. verticillioides
F. fujikuroi
Figure S1. Physical map and BLAST comparison of the mt genomes of F. circinatum against F.
oxysporum, F. verticillioides and F. fujikuroi. The coding sequences (CDSs) and tRNA genes
predicted in the F. circinatum genome are indicated in blue and red, respectively. The GC
content of the F. circinatum mt genome is indicated in black and was plotted (using a sliding
window) as the deviation from the average of 31.4% that was calculated over the entire
sequence. The map and BLAST comparison was constructed with CGView Server
(http://stothard.afns.ualberta.ca/cgview_server/).
100
F. gram nad3 intron1 LAGLIDADG1
F. sol nad5 intron 1 LAGLIDADG 1
F. gram cox3 intron 2 LAGLIDADG1
F. gram cox2 intron1 LAGLIDADG1
F. solani nad4 intron1 LAGLIDADG1
F. gram atp6.intron1 LADLIDADG1
F. gram nad2 intron4 LAGLIDADG1
F. gram nad2 intron3 LAGLIDADG1
F. cir nad2 intron1 LAGLIDADG1
F. gram nad4L intron1 LAGLIDADG1
F. gram cox1 intron7 LAGLIDADG1
F. gram cox1 intron7 LAGLIDADG2
F. sol nad5 intron2 LAGLIDADG2
F. gram atp6 intron1 LAGLIDADG2
F. gram nad3 intron1 LAGLIDADG2
F. sol nad4 intron1 LAGLIDADG2
F. gram cox2 intron1 LAGLIDADG2
F. gram nad2 intron4 LAGLIDADG2
F. gram nad2 intron3 LAGLIDADG2
F. cir nad2 intron1 LAGLIDADG2
F. gram nad4L intron 1 LAGLIDADG2
F. ver cox1 intron1 LAGLIDADG2
100
F. sol cox1 intron5 LAGLIDADG2
F. cir cox1 intron3 LAGLIDADG2
96
F. gram cox1 intron4 LAGLIDADG2
F. gram cox1 intron8 LAGLIDADG2
F. cir cox1 inton4 ORF1 LAGLIDADG2
100 F. gram cox1 intron9 LAGLIDADG1
F. cir cox1 intron4 LAGLIDADG2
F. gram cox1 intron6 LAGLIDADG2
100
F. sol cox1 intron8 LAGLIDADG2
100 F. sol cox1 intron6 LAGLIDADG2
F. gram nad5 intron1 LAGLIDADG2
F. cir cob intron3 LAGLIDADG2
F. gram cob intron4 LAGLIDADG2
F. sol cox3 intron1 LAGLIDADG1
F. cir cob intron1 ORF2 LAGLIDADG1
100 F .gram cox1 intron2 LAGLIDADG1
89
F. cir cox1 intron1 LAGLIDADG1
F. sol cox1intron3 LAGLIDADG1
F. gram cob intron4 LAGLIDADG1
F. oxy nad5 intron1 LAGLIDADG2
100 F. oxy nad5 intron1 LAGLIDADG1
F. gram nad5 intron1 LAGLIDADG1
94 F. gram cox1 intron4 LAGLIDADG1
F. ver cox1 intron1 LAGLIDADG1
100 F. sol cox1 intron5 LAGLIDADG1
F. cir cox1 intron3 LAGLIDADG1
F. gram cox1 intron2 LAGLIDADG2
F. cir cox1 intron1 LAGLIDADG2
F .sol cox1 intron3 LAGLIDADG2
F. cir cox3 intron1 LAGLIDADG2
F. gram cob intron1 LAGLIDADG1
F .gram cox1 intron5 LAGLIDADG2
F .gram cox1 intron8 LAGLIDADG1
100 F .cir cox1 intron4 ORF1 LAGLIDADG1
F. gram cox3 intron1 LAGLIDADG1
100 F. cir cox3 intron1 LAGLIDADG1
F. sol cox1 intron2 LAGLIDADG2
F. sol cox1 intron1 LAGLIDADG2
F. gram cox1 intron3 LAGLIDADG2
F. sol cox1 intron4 LAGLIDADG2
F. cir cox1 intron2 LAGLIDADG2
100 F .gram cox1 intron1 LAGLIDADG1.
F .cir cox1 intron6 LAGLIDADG1
F. gram cob intron3 ORF1 LAGLIDADG1
F. cir cob intron3 LAGLIDADG1
99
F. gram cox1 intron5 LAGLIDADG1
99
F. sol cox1 intron6 LAGLIDADG1
F. gram cox1 intron6 LAGLIDADG1
F. sol cox1 intron2 LAGLIDADG1
F .sol cox1 intron1 LAGLIDADG1
F. cir cox1 intron2 LAGLIDADG1
100 F. sol cox1 intron4 LAGLIDADG1
F .gram cox1 intron3 LAGLIDADG1
F. sol cox3 intron1 LAGLIDADG2
F. cir cob intron3 LAGLIDADG1
F. cir cob intron4 ORF1 LAGLIDADG1
0.5
Figure S2. Midpoint rooted maximum likelihood phylogenetic tree of the amino acid
LAGLIDADG endonuclease domains identified within intron regions of F. circinatum (F.cir), F.
verticillioides (F.ver), F.fujikuroi (F. fuj), F. oxysporum (F. oxy), F. solani (F. sol) as well as F.
graminearum (F. gram). Bootstrap values (>85%), based on 1000 replications are indicated at
the internodes. LAGLIDADG1 and 2 = the first and second conserved domain of the double
LAGLIDADG.
F. sol cox1 intron 7
F. gram cox1 intron10 ORF1
100
F. cir cox1 intron5
F. ver cox1 intron2
F. gram cox1 intron10 ORF2
F. gram cob intron2
F. ver nad1 intron1
F. gram cox2 intron2
F. gram cox1 intron1
97
F. gram atp9 intron1
F. gram cox1 intron12
F.cir cox1 intron7
F. gram cox2 intron3
F. gram nad1 intron2
1
Figure S3. Midpoint rooted maximum likelihood phylogenetic tree of the amino acid GIY-YIG
endonuclease domains identified within intron regions of F. circinatum (F.cir), F. verticillioides
(F.ver), F.fujikuroi (F. fuj), F. oxysporum (F. oxy), F. solani (F. sol) as well as F. graminearum
(F. gram). Bootstrap values (>85%), based on 1000 replications are indicated at the internodes.
atp6
F. circinatum
99
99
atp8
F. fujikuroi
F. verticillioides
F. circinatum
F. oxysporum
85
100
atp9
F. verticillioides
F. fujikuroi
96
F. oxysporum
F. oxysporum
F. oxysporum
F. verticillioides
F. oxysporum
81
F. graminearum
F. solani
F. graminearum
F.solani
F. solani
NC 003388
NC003388
NC003388
AY884128
AY884128
NC004514
NC004514
NC004514
0.02
0.02
0.05
cob
cox1
cox2
F. verticillioides
84
F. verticillioides
F. circinatum
F. circinatum
F. fujikuroi
91 F. verticillioides
F. oxysporum
100
F. oxysporum
100
F. graminearum
F. solani
NC 003388
AY884128
NC 004514
cox3
97
F. oxysporum
99
97
82
F. oxysporum
100
100
F. graminearum
95
NC 003388
AY884128
NC 004514
NC 004514
0.05
nad2
F. verticillioides
100
100
F. fujikuroi
98
F. circinatum
92
F. oxysporum
83
99
100
F. graminearum
F. solani
87
88
F. graminearum
AY945289
AY884128
AY884128
NC 004514
F. solani
AY874423
NC 003388
AY884128
NC 003388
NC 004514
0.02
NC 004514
0.05
nad3
0.05
nad4L
F. verticillioides
F. circinatum
nad4
F. circinatum
97
F. fujikuroi
F. oxysporum
F. oxysporum
F. graminearum
95
F. solani
F. verticillioides
F. solani
F. graminearum
NC 003388
AY884128
F. verticillioides
F. fujikuroi
100 F. circinatum
F.oxysporum
100
97
F.oxysporum
100
F. graminearum
F. solani
NC 003388
AY884128
NC 004514
F. oxysporum
F. oxysporum
F. fujikuroi
100
F. circinatum
F. fujikuroi
F. graminearum
F. oxysporum
F. solani
NC 003388
85
F. verticillioides
F. oxysporum
F. oxysporum
F. fujikuroi
85
F. graminearum
NC 003388
AY884128
F. circinatum
100
F. oxysporum
F. solani
nad1
95
F. fujikuroi
100 F. oxysporum
F. solani
F. verticillioides
88
85
NC 003388
AY884128
NC 004514
0.05
F. circinatum
F. fujikuroi
98
0.02
0.05
100
F. fujkuroi
100
F. graminearum
AY884128
96
F. circinatum
83
F. oxysporum
NC 004514
0.02
0.02
nad5
F. verticillioides
nad6
F. oxysporum
F. circinatum
100
100
88
F. fujikuroi
F. fujikuroi
93
F. oxysporum
91
94
F. oxysporum
100
100
F. graminearum
99
F. solani
NC 003388
AY884128
F. verticillioides
F. circinatum
F. graminearum
F. solani
NC003388
AY884128
NC004514
NC 004514
0.05
F. oxysporum
0.1
Figure S4. Maximum likelihood phylogenies for Fusarium based on mitochondrial proteincoding nucleotide sequences. Species and isolates designated as follows: F. circinatum
(JX910419), F. verticillioides (JN041210), F. fujikuroi (JX910420), F. graminearum
(DQ364632)F.oxysporum (AY945289, AY874423), F. solani (JN041209) Trichoderma reesi
(NC 003388), Metarhizium anisopliae (AY884128), Lecanicillium muscarium (NC004514).
concatenated dataset
atp6
S. cerevisiae NC 012145
97
S. castellii NC 003920
97
S. cerevisiae NC 012145
S. castellii NC 003920
81
C. glabrata NC 004691
0.02
0.05
cob
S. servazzii NC 004918
100
S. castellii NC 003920
S. castellii NC 004918
94
S. servazzii NC 003920
C. glabrata NC 004691
cox2
S. cerevisiae NC 012145
91
S. cerevisiae NC 012145
S. servazzii NC 004918
S. castellii NC 003920
S. castellii NC 003920
S. servazzii NC 004918
C. glabrata NC 004691
S. cerevisiae NC 012145
S. pastorianus NC 001224
S. pastorianus NC 001224
S. pastorianus NC 001224
0.02
S. pastorianus NC 001224
0.01
cox1
100
S.cerevisiae NC 012145
S. servazzii NC 004918
S. pastorianus NC 001224
C. glabrata NC 004691
93
97
S. pastorianus NC 001224
S. servazzii NC 004918
100
atp8
C. glabrata NC 004691
C. glabrata NC 004691
0.02
0.02
Figure S5. Maximum likelihood phylogenies for Saccharomyces species based on mitochondrial
protein-coding nucleotide sequences.