Deschamps-etal Supplementary Information

Table S1. Chi-square tests for distributions of gene classes in Thaumarchaeota as compared to GII/III-

Euryarchaeota. HT-genes, horizontally transferred genes. *, only case for which the two distribution

patterns were not significantly similar.

COG KEGG

Thaumarchaeota vs. GII/III Euryarchaeota archaeal core 0.301596376 0.123338621

Thaumarchaeota vs. GII/III Euryarchaeota-specific core non HT-genes 0.097462121 0.196948972

Thaumarchaeota vs. GII/III Euryarchaeota-specific HT-genes (early transfers) 0.544409189 0.050684926

Thaumarchaeota vs. GII/III Euryarchaeota shell HT-genes (late transfers) 0.324156576 4.03236E-07*

Fig. S1. Number of 40 genes usually found in single copy in prokaryotic genomes (Creevey et al, 2011) present in genomes of deep-Mediterranean Thaumarchaeota an GII-Euryarchaeota.

Thaumarchaeota

Euryarchaeota

0.2

Thaumarchaeotal fosmid KM3-84-F03

Methanocella paludicola SANAE [YP_003356279]

Euryarchaeotal fosmid KM3-98-B01

Archaeoglobus fulgidus DSM 4304 [NP_070719]


Haloferax volcanii DS2 [YP_003534431]

Candidatus Nitrososphaera gargensis Ga9.2 [YP_006863290]

Thaumarchaeotal fosmid SAT1000-40-A08

Uncultured marine archaeon SAT1000-21-C11 [ACF10069]

Aeropyrum pernix K1 [NP_147939]

Thaumarchaeotal fosmid KM3-47-C08

Candidatus Caldiarchaeum subterraneum [BAJ48749]

Thaumarchaeotal fosmid KM3-193-A03

Euryarchaeotal fosmid AD1000-53-H05

Candidatus Nitrosoarchaeum limnia SFB1 [ZP_08256590]

Thermoplasma acidophilum DSM 1728 [NP_393924]

Cenarchaeum symbiosum A [YP_875851]

Thaumarchaeotal fosmid KM3-67-E08


Uncultured marine group II euryarchaeote [EHR76655]

Methanocaldococcus jannaschii DSM 2661 [NP_248042]

Picrophilus torridus DSM 9790 [YP_023195]

Thaumarchaeotal fosmid AD1000-71-A04

Euryarchaeotal fosmid SAT1000-18-B12

Uncultured Nitrosocaldus sp. [BAE95243]

Euryarchaeotal fosmid KM3-88-D11Euryarchaeotal fosmid AD1000-28-D03

Thermococcus gammatolerans EJ3 [YP_002959763]

Methanosarcina barkeri str. Fusaro [YP_307129]



Euryarchaeotal fosmid KM3-85-C06

Uncultured marine archaeon SAT1000-23-F7 [ACF09510]

Sulfolobus solfataricus P2 [NP_342235]

Methanothermus fervidus [YP_004004206]

Thermoproteus tenax Kra 1 [YP_004892221]

Uncultured marine archaeon KM3-34-D9 [ACF09590]

Natrialba magadii ATCC 43099 [YP_003480297]

Euryarchaeotal fosmid KM3-54-D07

Pyrococcus abyssi GE5 [NP_125969]

Uncultured marine archaeon AD1000-202-A2 [ACF09691]

Nitrosopumilus maritimus SCM1 [YP_001582082]

Uncultured marine archaeon AD1000-207-H3 [ACF09842]

Methanospirillum hungatei JF 1 [YP_504239]


Euryarchaeotal fosmid KM3-51-E06

Thaumarchaeotal fosmid SAT1000-31-A02Thaumarchaeotal fosmid KM3-86-E11

Thaumarchaeotal fosmid SAT1000-12-D12

Thaumarchaeotal fosmid SAT1000-12-D12

Aciduliprofundum boonei T469 [YP_002577182]

100

99

100

100

92

100

100

99

81

56

100

100

73

100

89

100

100

100

58

70

87

100

100

100

95

81

100

97

100

52

9876

92

97

59

90

99

85

61

100

67

100

74

0.09

Thaumarchaeotal fosmid AD1000-41-B03Thaumarchaeotal fosmid KM3-199-D03

Methanospirillum hungatei JF 1 [YP_504303]

Aciduliprofundum boonei T469 [YP_002578452]


Natrialba magadii ATCC 43099 [YP_003478580]

Euryarchaeotal fosmid KM3-162-H08


Euryarchaeotal fosmid KM3-127-D04

Thaumarchaeotal fosmid SAT1000-18-G08

Picrophilus torridus DSM 9790 [YP_023295]

Thaumarchaeotal fosmid AD1000-60-A11

Methanosarcina barkeri str. Fusaro [YP_304962]

Haloferax volcanii DS2 [YP_003536788]

Methanocaldococcus jannaschii DSM 2661 [NP_247977]

Candidatus Caldiarchaeum subterraneum [BAJ47373]

Nitrosopumilus maritimus SCM1 [YP_001581650]Candidatus Nitrosoarchaeum limnia SFB1 [ZP_08257369]

Methanothermus fervidus [YP_004004453]

Thaumarchaeotal fosmid KM3-144-G01

Pyrococcus abyssi GE5 [NP_126228]

Candidatus Nitrososphaera gargensis Ga9.2 [YP_006861712]

Archaeoglobus fulgidus DSM 4304 [NP_069962]

Sulfolobus solfataricus P2 [NP_341638]

Uncultured marine group II euryarchaeote [EHR76040]

Euryarchaeotal fosmid KM3-69-F11

Euryarchaeotal fosmid KM3-13-C08

Euryarchaeotal fosmid AD1000-79-C02

Euryarchaeotal fosmid KM3-72-H01

Euryarchaeotal fosmid AD1000-53-H05Euryarchaeotal fosmid SAT1000-24-G08

Aeropyrum pernix K1 [NP_148143]

Methanocella paludicola SANAE [YP_003356696]


Thaumarchaeotal fosmid KM3-160-B06

Thermoproteus tenax Kra 1 [YP_004893593]

Thermoplasma acidophilum DSM 1728 [NP_394646]

Thermococcus gammatolerans EJ3 [YP_002960325]

Thaumarchaeotal fosmid KM3-201-G04

Cenarchaeum symbiosum A [YP_876535]


79

73

54

5178

100

6255

75

72

75

100

100

100

88

60

59

62

88

7983

80

76

100

100

78

83

53

93

53

80

57

95

100

EF2

rpS2

Fig. S2. Phylogenetic trees of elongation factor 2 (EF2) and ribosomal protein S2 genes present indeep-Mediterranean archaeal fosmids.

Thaum Eury

2331 1265

919 392

88 115

152 76

7 18

898 487

997 520

729 477

1 0

483 510

98 91

479 186

1595 1046

1107 624

13 0

1298 792

157 111

3 8

1242 470

17 5

541 231

54 45

78 102

636 349

1752 831

Translation, ribosomal structure and biogenesis

Transcription

Signal transduction mechanisms

Secondary metabolites biosynthesis, transport and catabolism

RNA processing and modification

Replication, recombination and repair

Posttranslational modification, protein turnover, chaperones

Nucleotide transport and metabolism

Nuclear structure

Lipid transport and metabolism

Intracellular trafficking, secretion, and vesicular transport

Inorganic ion transport and metabolism

General function prediction only

Function unknown

Extracellular structures

Energy production and conversion

Defense mechanisms

Cytoskeleton

Coenzyme transport and metabolism

Chromatin structure and dynamics

Cell wall/membrane/envelope biogenesis

Cell motility

Cell cycle control, cell division, chromosome partitioning

Carbohydrate transport and metabolism

Amino acid transport and metabolism

Fig. S3. Comparative distribution of genes in COG categories for the Thaumarchaeota (blue) and the Group II/III Euryarchaeota (red) in deep-Mediterranean archaeal fosmid metagenome sequence. Total gene counts are given on the right.

Thaumarchaeota

Euryarchaeota

Number of genes

Fig. S4. Comparative distribution of genes in KEGG classes for the Thaumarchaeota (blue) and the Group II/III Euryarchaeota (red) in deep-Mediterranean archaeal fosmid metagenome sequence. Total gene numbers are given on the right.

Thaumarchaeota

Euryarchaeota

Thaum Eury

33 40

18 9

1833 983

129 49

0 0

31 17

359 163

1053 655

1 2

0 0

170 75

94 39

1202 503

205 145

178 229

19 9

0 1

80 43

464 222

0 1

779 384

0 13

0 0

0 0

40 41

1114 485

1 4

67 18

1823 711

4515 2623

Number of genes

Fig. S5. Number of genes related to ammonium and urea metabolism in deep-Mediterranean Thaumarchaeotal genomes as compared to the number of typical single copy genes.

0

5

10

15

20

25

Gen

e co

un

t

Fig. S6. Synteny proxies per classes of gene origin in Thaumarchaeota (Thaum) and GII/III-Euryarchaeota (Eury) genomes. A, mean synteny block length per block origin. B, cluster of synteny blocks as a function of block bounds. A block is defined as an array of contiguous genes from same origin (class). 'Others' includes orphans plus non-HGT shell genes.

A

B

Mea

n b

lock

len

gth

Archaeal core in Thaum Archaeal core in Eury Eury_Shell_Late HTGs Thaum_Shell_Late HTGs Eury_Early HTGs Thaum_Early HTGs Thaum (others) Eury (others) Thaum-specific Eury-specific

Thaumarchaeota

Euryarchaeota O

the

r –

Oth

er

Oth

er –

Earl

y H

TGs

Oth

er –

Thau

m/E

yry-

spe

cifi

c

Oth

er –

Arc

hae

al c

ore

Oth

er –

She

ll /

late

HTG

s

Earl

y H

TGs –

Earl

y H

TGs

Earl

y H

TGs –

Thau

m/E

ury

-sp

eci

fic

Earl

y H

TGs –

Arc

hae

al C

ore

Earl

y H

TGs –

She

ll_La

te H

TGs

Thau

m/E

ury

-sp

eci

fic –

Thau

m/E

ury

-sp

eci

fic

Thau

m/E

ury

-sp

eci

fic –

Arc

hae

al c

ore

Thau

m/E

ury

-sp

eci

fic –

She

ll_LA

te H

TGs

Arc

hae

al c

ore

– A

rch

aeal

Co

re

Arc

hae

al c

ore

– S

he

ll_La

te H

TGs

She

ll_La

te H

TGs

- S

he

ll_la

te H

TGs

Archaeal core in Thaum Archaeal core in Eury Thaum-specific Eury-specific Eury_Shell_Late HTGs Thaum_Shell_Late HTGs Eury_Early HTGs Thaum_Early HTGs Thaum (others) Eury (others)

Fig. S7. Codon adaptation index (CAI) of different gene classes in deep-sea Thaumarchaeota and GII/III-Euryarchaeota as referred to the codon usage of thaumarchaeotal (Thaum) or GII/III-euryarchaeotal (Eury) ribosomal genes. Avg, average value; Std, standard deviation. HTG, horizontally transferred genes.

Reference: codon usage of Thaumarchaeotal ribosomal proteins

CA

I C

AI

Reference: codon usage of Euryarchaeotal ribosomal proteins

Fig. S8. Distribution of gene clusters of deep Mediterranean Thaumarchaeota in archaeal core, Thaumarchaeota-specific core, Thaumarchaeota early HTG and accessory (shell) HTG distributed in COG categories.

Thaum-specific core

Archaeal core

Thaum-specific core_early HTG

Thaum-shell_late HTG

Percentage of genes Number of genes

Fig. S9. Distribution of gene clusters of deep Mediterranean GII/III Euryarchaeota in archaeal core, Euryarchaeota-specific core, Euryarchaeota early HTG and accessory (shell) HTG distributed in COG categories.

Eury-specific core

Archaeal core

Eury-specific core_early HTG

Eury-shell_late HTG

Percentage of genes Number of genes

Fig. S10. Distribution of gene clusters (archaeal core, lineage-specific core, early HTG and accessory genes) distributed in KEGG pathways. Only pathways represented by more than 40 gene copies are included.

THAUMARCHAEOTA EURYARCHAEOTA

Eury-specific core

Archaeal core

Eury-specific core_early HTG

Eury-shell_late HTG

Thaum-specific core

Archaeal core

Thaum-specific core_early HTG

Thaum-shell_late HTG

Percentage of genes Number of genes Percentage of genes Number of genes

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Deschamps-etal Supplementary Information