Download A genomic survey of the fish parasite Spironucleus

A genomic survey of the fish parasite Spironucleus salmonicida indicates genomic plasticity
among diplomonads and significant lateral gene transfer in eukaryote genome evolution
Jan O. Andersson, Åsa M. Sjögren, David S. Horner, Colleen A. Murphy, Patricia L. Dyal, Staffan G. Svärd, John M. Logsdon, Jr., Mark A. Ragan, Robert
P. Hirt, and Andrew J. Roger
Additional file 3
Candidate LGT genes in the Spironucleus salmonicida genome survey.
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Protein
Classification
SpESTZap1389
drug:H+ antiporter-2, DHA2 family
Environmental information processing; membrane transport; major
facilitator superfamily (MFS)
Genetic information processing; folding, sorting and degradation; protein
folding and associated processing
Genetic information processing; folding, sorting and degradation; protein
folding and associated processing
Genetic information processing; replication and repair; other replication,
recombination and repair factors
Genetic information processing; unclassified
SpESTC18
1
gZar958bT7
membrane protease subunit HflK
1
membrane protease subunit HflK
SpESTC43
DNA glycosylase
SpESTZap1340
tRNA (5-methylaminomethyl-2thiouridylate)-methyltransferase
alanyl-tRNA synthetase
aminoacylhistidine dipeptidase
aminoacylhistidine dipeptidase
aminoacylhistidine dipeptidase
5'-methylthioadenosine nucleosidase
arginine deiminase
ornithine carbamoyltransferase
prolyl-tRNA synthetase
sarcosine oxidase
27982008
1
SpESTC149
1
SpESTDH287
1
SpESTZap149
SpESTC31
SpESTC83
SpESTC221
27981826
1
gZar602gT3
gZap30gT3
1
sarcosine oxidase
27982357
threonine dehydratase
SpESTZap946
1
gZap84gT3
1
SpESTZap588
27983189
27983404
SpESTDH325
histidinol-phosphatase (PHP family)
alcohol dehydrogenase
alcohol dehydrogenase
alcohol dehydrogenase
alcohol dehydrogenase
alcohol dehydrogenase
Tree#
Metabolism; amino acid metabolism; alanine and aspartate metabolism
Metabolism; amino acid metabolism; alanine and aspartate metabolism
Metabolism; amino acid metabolism; alanine and aspartate metabolism
Metabolism; amino acid metabolism; alanine and aspartate metabolism
Metabolism; amino acid metabolism; arginine and proline metabolism
Metabolism; amino acid metabolism; arginine and proline metabolism
Metabolism; amino acid metabolism; arginine and proline metabolism
Metabolism; amino acid metabolism; arginine and proline metabolism
Metabolism; amino acid metabolism; glycine, serine and threonine
metabolism
Metabolism; amino acid metabolism; glycine, serine and threonine
metabolism
Metabolism; amino acid metabolism; glycine, serine and threonine
metabolism
Metabolism; amino acid metabolism; histidine metabolism
Metabolism; carbohydrate metabolism; glycolysis / gluconeogenesis
Metabolism; carbohydrate metabolism; glycolysis / gluconeogenesis
Metabolism; carbohydrate metabolism; glycolysis / gluconeogenesis
Metabolism; carbohydrate metabolism; glycolysis / gluconeogenesis
Metabolism; carbohydrate metabolism; glycolysis / gluconeogenesis
1 (3)
3
#aa
positions
Monophyletic
diplomonads
1
170
+
2
160
-
DD
3
125
-
DD
4
165
+
DD
5
107
-
6
7
7
7
8
9
10
11
12
451
247
247
247
168
356
303
175
218
+
+
+
+
+
+
+
+
-
12
218
-
13
269
+
14
15
16
16
16
17
113
121
147
147
147
223
+
+
+
+
+
-
4
4
Monophyletic
diplomonads
and
parabasalids
5
Eukaryotetoeukaryote
6
LGT event
5
+
+
+
+
EH
+
+
+
DD
EH
EH
+
EH
EH
23266714
SpESTZap404
18030018
gTol047bMF
SpESTC275
gTor983gT3
fructose-bisphosphate aldolase, class II
glucokinase
glucose-6-phosphate isomerase
phosphoglycerate mutase
pyruvate kinase
phosphoglycolate phosphatase
SpESTC23
SpESTZap360
gZap797bT7
1
SpESTZap1028
1
gZap472bT7
SpESTC94
ribose 5-phosphate isomerase B
transketolase
acetyl-CoA synthetase (ADP-forming)
hydroxyacylglutathione hydrolase
hydroxyacylglutathione hydrolase
putative pyruvate-flavodoxin
oxidoreductase
glycogen(starch) synthase
carbamate kinase
cystathionine beta-lyase
cystathionine beta-lyase
cytochrome c biogenesis protein
CcmG, thiol:disulfide
interchangeprotein DsbE
glutamate synthase (NADPH) small
chain
hydroxylamine reductase
tryptophanase
tryptophanase
NADH dehydrogenase
NADH dehydrogenase
NADH dehydrogenase
NADH dehydrogenase
NADH dehydrogenase
cysteine synthase
cysteine synthase
fatty acid desaturase
NAD(P)H dehydrogenase (quinone)
long-chain fatty-acid-CoA ligase
glycerol-3-phosphate dehydrogenase
phosphatidylserine synthase
tripeptide aminopeptidase
adenine phosphoribosyltransferase
deoxyguanosine kinase
deoxyguanosine kinase
myosin ATPase
CTP synthase
A-type flavoprotein
A-type flavoprotein
carotenoid isomerase
carotenoid isomerase
rubrerythrin
rubrerythrin
conserved hypothetical protein
conserved hypothetical protein
conserved hypothetical protein
gZap510gT3
SpESTC239
2
gZap126bT7
2
gZap126gT3
1
SpESTC259
20530910
27983817
2
gTol313bMF
2
SpESTC204
gZal229bMF
SpESTC219
SpESTDH113
1
11127702
1
gTor1143gT3
1
SpESTC115
1
SpESTZap1933
gZap471gT3
SpESTZap110
27983595
SpESTZap2148
gTor927gT3
gZar919bT7
SpESTC154
SpESTC254
SpESTC251
gTor125bT7
27982526
1
27984028
1
SpESTZap2025
1
SpESTC196
1
gZap998gT3
1
SpESTC282
1
SpESTC267
gTor1213bT7
gTor541gT3
gTor565bT7
Metabolism; carbohydrate metabolism; glycolysis / gluconeogenesis
Metabolism; carbohydrate metabolism; glycolysis / gluconeogenesis
Metabolism; carbohydrate metabolism; glycolysis / gluconeogenesis
Metabolism; carbohydrate metabolism; glycolysis / gluconeogenesis
Metabolism; carbohydrate metabolism; glycolysis / gluconeogenesis
Metabolism; carbohydrate metabolism; glyoxylate and dicarboxylate
metabolism
Metabolism; carbohydrate metabolism; pentose phosphate pathway
Metabolism; carbohydrate metabolism; pentose phosphate pathway
Metabolism; carbohydrate metabolism; pyruvate metabolism
Metabolism; carbohydrate metabolism; pyruvate metabolism
Metabolism; carbohydrate metabolism; pyruvate metabolism
Metabolism; carbohydrate metabolism; pyruvate metabolism
18
19
20
21
22
23
300
192
412
184
205
116
+
+
+
+
4
+
-
24
25
26
27
27
28
136
196
121
164
164
167
+
+
+
+
+
+
Metabolism; carbohydrate metabolism; starch and sucrose metabolism
Metabolism; energy metabolism; nitrogen metabolism
Metabolism; energy metabolism; nitrogen metabolism
Metabolism; energy metabolism; nitrogen metabolism
Metabolism; energy metabolism; nitrogen metabolism
29
30
31
32
33
111
273
157
182
110
+
+
+
Metabolism; energy metabolism; nitrogen metabolism
34
243
+
Metabolism; energy metabolism; nitrogen metabolism
Metabolism; energy metabolism; nitrogen metabolism
Metabolism; energy metabolism; nitrogen metabolism
Metabolism; energy metabolism; oxidative phosphorylation
Metabolism; energy metabolism; oxidative phosphorylation
Metabolism; energy metabolism; oxidative phosphorylation
Metabolism; energy metabolism; oxidative phosphorylation
Metabolism; energy metabolism; oxidative phosphorylation
Metabolism; energy metabolism; sulfur metabolism
Metabolism; energy metabolism; sulfur metabolism
Metabolism; lipid metabolism; androgen and estrogen metabolism
Metabolism; lipid metabolism; biosynthesis of steroids
Metabolism; lipid metabolism; fatty acid metabolism
Metabolism; lipid metabolism; glycerophospholipid metabolism
Metabolism; lipid metabolism; glycerophospholipid metabolism
Metabolism; metabolism of other amino acids; glutathione metabolism
Metabolism; nucleotide metabolism; purine metabolism
Metabolism; nucleotide metabolism; purine metabolism
Metabolism; nucleotide metabolism; purine metabolism
Metabolism; nucleotide metabolism; purine metabolism
Metabolism; nucleotide metabolism; pyrimidine metabolism
Metabolism; unclassified
Metabolism; unclassified
Metabolism; unclassified
Metabolism; unclassified
Metabolism; unclassified
Metabolism; unclassified
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
52
53
54
55
56
57
57
58
58
59
60
61
471
160
164
105
315
155
303
155
200
214
143
127
682
185
168
214
154
182
182
135
511
383
168
211
211
173
173
144
199
160
+
4
+
4
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
2 (3)
+
+
+
MB
EH
EH
EH
EH
DD
DD
+
+
GZ
gTor916gT3
gTor930bT7
gZap260bT7
gZap950bT7
gZar587bT72
gZar847bT7
gZar96bT7
1
gZar978gT3
1
gZar789bT7
Sp11orf4
SpESTZap1004
SpESTZap1248
1
SpESTZap1299
1
SpESTZap1913
conserved hypothetical protein
conserved hypothetical protein
conserved hypothetical protein
conserved hypothetical protein
conserved hypothetical protein
conserved hypothetical protein
conserved hypothetical protein
conserved hypothetical protein
conserved hypothetical protein
conserved hypothetical protein
conserved hypothetical protein
conserved hypothetical protein
conserved hypothetical protein
conserved hypothetical protein
62
63
64
65
66
67
68
69
69
70
71
72
33
33
175
163
123
111
124
137
147
185
185
586
197
118
110
110
+
+
+
+
+
+
+
+
+
+
+
1
) The phylogenetic analyses of these genes indicate that they likely have undergone duplications after the putative LGT events.
) These pairs of sequences with identical annotations correspond to different parts of the protein and could represent the same gene in the genome.
3
) Phylogenetic trees for all candidate LGT genes are shown in Additional files 4-6.
4
) G. lamblia homologs for these proteins are present in the similarity searches and most likely are the closest relatives to the S. salmonicida sequences. However, the G.
lamblia homologs are absent from the phylogenetic trees listed since the automated generation of datasets [1] reached the maximum number of sequences to include
(200) and only selected a subset of the available homologous sequences in the databases.
5
) A previous phylogenetic study of alanyl tRNA synthetase has both shown diplomonads and parabasalids to be monophyletic, and gene transfers between eukaryotic
lineages [2]. These cases are not observed in the presented tree since the Trichomonas, Entamoeba, and ciliate homologs were excluded due to the reasons outlined
above.
6
) The putative recipient and/or donor eukaryotic lineages are indicted by DD (Dictyostelium discoideum), EH (Entamoeba histolytica), GZ (Gibberella zeae), and MB
(Mastigamoeba balamuthi).
2
References
1.
2.
Frickey T, Lupas AN: PhyloGenie: automated phylome generation and analysis. Nucleic Acids Res 2004, 32:5231-5238.
Andersson JO, Sarchfield SW, Roger AJ: Gene transfers from Nanoarchaeota to an ancestor of diplomonads and parabasalids. Mol Biol Evol 2005, 22:85-90.
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