Supplement

Reductive genome evolutionin chemoautotrophic intracellular symbionts ofdeep-sea Calyptogena clams

Hirokazu Kuwahara1, Yoshihiro Takaki1, Takao Yoshida1, Shigeru Shimamura1, Kiyotaka Takishita1, James D Reimer1, 2, Chiaki Kato1, Tadashi Maruyama1,§

Figure S1. Small subunit rRNA gene based NJ (Neighbor-Joining) tree of the Calyptogena symbionts, Buchnera aphidicola strains and two closely related bacteria, Escherichia coli and Salmonella typhimurium. In the clade of the Calyptogena symbionts, Vok and Rma are distantly related and respectively belong to two distinct lineages. Genetic distances are shown on each branch.

Figure S2. Number of each symbiont specific genes categorized by functional COG categories. The symbiont specific genes are the genes remaining in one of the Calyptogena symbiont genome but lost in the other genome. The most significant difference was found in the cell wall/membrane/envelope biogenesis category;C. magnifica symbiont (Ruthia magnifica: Rma)contains a significantly higher number of genes than C. okutanii symbiont (Vesicomyosocius okutanii: Vok)in this category. The difference in number of symbiont specific genes isalso prominent in the category of function unknown.

Table S1. List of Calyptogena okutanii symbiont (Vok) specific genes that are absent from the Calyptogena magnifica symbiont (Rma) genome.

Gene number / Product / Function
COSY_0147 / S-adenosylmethionine:tRNA ribosyltransferase-isomerase / Translation, ribosomal structure and biogenesis
COSY_0298 / RNA methyltransferase, TrmA family / Translation, ribosomal structure and biogenesis
COSY_0724 / queuine tRNA-ribosyltransferase / Translation, ribosomal structure and biogenesis
COSY_0807 / translation factor, Sua5/YciO/YrdC/YwlC family / Translation, ribosomal structure and biogenesis
COSY_0067 / nuclease / Replication, recombination and repair
COSY_0348 / holliday junction DNA helicase RuvA / Replication, recombination and repair
COSY_0674 / holliday junction DNA helicase RuvB / Replication, recombination and repair
COSY_0870 / ATP-dependent RNA helicase DbpA / Replication, recombination and repair
COSY_0624 / conserved hypothetical protein / Cell wall/membrane/envelope biogenesis
COSY_0687 / hypothetical protein / Cell wall/membrane/envelope biogenesis
COSY_0815 / glycosyltransferase, group 1 family / Cell wall/membrane/envelope biogenesis
COSY_0042 / cbb3-type cytochrome c oxidase subunit IV / Posttranslational modification, protein turnover, chaperones
COSY_0128 / cbb3-type cytochrome oxidase maturation protein / Posttranslational modification, protein turnover, chaperones
COSY_0605 / thiol:disulfide interchange protein DsbE / Posttranslational modification, protein turnover, chaperones
COSY_0782 / intracellular sulfur oxidation protein DsrR / Posttranslational modification, protein turnover, chaperones
COSY_0907 / thioredoxin / Posttranslational modification, protein turnover, chaperones
COSY_0925 / FKBP-type peptidyl-prolyl cis-trans isomerase 2 / Posttranslational modification, protein turnover, chaperones
COSY_0010 / ubiquinol-cytochrome c reductase cytochrome c1 subunit / Energy production and conversion
COSY_0102 / rubredoxin / Energy production and conversion
COSY_0646 / respiratory nitrate reductase gamma subunit / Energy production and conversion
COSY_0647 / respiratory nitrate reductase delta subunit / Energy production and conversion
COSY_0648 / respiratory nitrate reductase beta subunit / Energy production and conversion
COSY_0649 / respiratory nitrate reductase alpha subunit / Energy production and conversion
COSY_0841 / alpha-ribazole phosphatase / Carbohydrate transport and metabolism
COSY_0226 / L-asparaginase / Amino acid transport and metabolism
COSY_0391 / threonine dehydratase / Amino acid transport and metabolism
COSY_0466 / 5-methyltetrahydrofolate--homocysteine methyltransferase / Amino acid transport and metabolism
COSY_0627 / conserved hypothetical protein / Amino acid transport and metabolism
COSY_0222 / oxygen-independent coproporphyrinogen III oxidase / Coenzyme transport and metabolism
COSY_0583 / cob(I)alamin adenosyltransferase / Coenzyme transport and metabolism
COSY_0660 / conserved hypothetical protein / Lipid transport and metabolism
COSY_0008 / stringent starvation protein B / General function prediction only
COSY_0099 / conserved hypothetical protein / General function prediction only
COSY_0104 / conserved hypothetical protein / General function prediction only
COSY_0317 / conserved hypothetical protein / General function prediction only
COSY_0495 / conserved hypothetical protein / General function prediction only
COSY_0808 / conserved hypothetical protein / General function prediction only
COSY_0859 / polyphosphate kinase / General function prediction only
COSY_0023 / hypothetical protein / Function unknown
COSY_0038 / conserved hypothetical protein / Function unknown
COSY_0045 / hypothetical protein / Function unknown
COSY_0051 / hypothetical protein / Function unknown
COSY_0068 / hypothetical protein / Function unknown
COSY_0069 / hypothetical protein / Function unknown
COSY_0119 / conserved hypothetical protein / Function unknown
COSY_0133 / hypothetical protein / Function unknown
COSY_0141 / conserved hypothetical protein / Function unknown
COSY_0206 / conserved hypothetical protein / Function unknown
COSY_0245 / hypothetical protein / Function unknown
COSY_0255 / conserved hypothetical protein / Function unknown
COSY_0268 / conserved hypothetical protein / Function unknown
COSY_0277 / conserved hypothetical protein / Function unknown
COSY_0283 / conserved hypothetical protein / Function unknown
COSY_0311 / hypothetical protein / Function unknown
COSY_0333 / hypothetical protein / Function unknown
COSY_0377 / hypothetical protein / Function unknown
COSY_0395 / conserved hypothetical protein / Function unknown
COSY_0417 / conserved hypothetical protein / Function unknown
COSY_0420 / hypothetical protein / Function unknown
COSY_0430 / conserved hypothetical protein / Function unknown
COSY_0494 / conserved hypothetical protein / Function unknown
COSY_0517 / hypothetical protein / Function unknown
COSY_0578 / hypothetical protein / Function unknown
COSY_0582 / hypothetical protein / Function unknown
COSY_0616 / conserved hypothetical protein / Function unknown
COSY_0623 / hypothetical protein / Function unknown
COSY_0625 / conserved hypothetical protein / Function unknown
COSY_0626 / hypothetical protein / Function unknown
COSY_0628 / conserved hypothetical protein / Function unknown
COSY_0645 / hypothetical protein / Function unknown
COSY_0694 / conserved hypothetical protein / Function unknown
COSY_0713 / hypothetical protein / Function unknown
COSY_0752 / hypothetical protein / Function unknown
COSY_0813 / conserved hypothetical protein / Function unknown
COSY_0850 / hypothetical protein / Function unknown
COSY_0860 / hypothetical protein / Function unknown
COSY_0964 / hypothetical protein / Function unknown
COSY_0973 / hypothetical protein / Function unknown
COSY_0974 / hypothetical protein / Function unknown
COSY_0978 / conserved hypothetical protein / Function unknown

Table S2. List of Calyptogena magnifica symbiont specific genes that are absent from Calyptogena okutanii symbiont genome.

Gene number / Product / Function
Rmag_0209 / sun protein / Translation, ribosomal structure and biogenesis
Rmag_0442 / TIM-barrel protein, yjbN family / Translation, ribosomal structure and biogenesis
Rmag_0786 / tRNA/rRNA methyltransferase (SpoU) / Translation, ribosomal structure and biogenesis
Rmag_0631 / Ribonucleotide reductase regulator NrdR-like / Transcription
Rmag_0968 / helix-turn-helix, Fis-type / Transcription
Rmag_0986 / transcriptional regulator, LysR family / Transcription
Rmag_0426 / excinuclease ABC, B subunit / Replication, recombination and repair
Rmag_0598 / excinuclease ABC, C subunit / Replication, recombination and repair
Rmag_0637 / hypothetical protein / Replication, recombination and repair
Rmag_0768 / NUDIX hydrolase / Replication, recombination and repair
Rmag_0443 / cell division protein FtsA / Cell cycle control, cell division, chromosome partitioning
Rmag_0501 / cell cycle protein / Cell cycle control, cell division, chromosome partitioning
Rmag_0754 / Septum formation initiator / Cell cycle control, cell division, chromosome partitioning
Rmag_0255 / ABC transporter related / Defense mechanisms
Rmag_1042 / N-acetylmuramyl-L-alanine amidase, negative regulator of AmpC, AmpD / Defense mechanisms
Rmag_0159 / protein tyrosine phosphatase / Signal transduction mechanisms
Rmag_0069 / methyltransferase GidB / Cell wall/membrane/envelope biogenesis
Rmag_0129 / membrane bound O-acyl transferase, MBOAT family protein / Cell wall/membrane/envelope biogenesis
Rmag_0253 / outer membrane efflux protein / Cell wall/membrane/envelope biogenesis
Rmag_0256 / secretion protein HlyD family protein / Cell wall/membrane/envelope biogenesis
Rmag_0296 / Peptidoglycan glycosyltransferase / Cell wall/membrane/envelope biogenesis
Rmag_0467 / Nucleotidyl transferase / Cell wall/membrane/envelope biogenesis
Rmag_0644 / hypothetical protein / Cell wall/membrane/envelope biogenesis
Rmag_0663 / glycosyl transferase, family 51 / Cell wall/membrane/envelope biogenesis
Rmag_0742 / MscS Mechanosensitive ion channel / Cell wall/membrane/envelope biogenesis
Rmag_0751 / peptidase M23B / Cell wall/membrane/envelope biogenesis
Rmag_0760 / hypothetical protein / Cell wall/membrane/envelope biogenesis
Rmag_0762 / Lytic transglycosylase, catalytic / Cell wall/membrane/envelope biogenesis
Rmag_0886 / polysaccharide biosynthesis protein CapD / Cell wall/membrane/envelope biogenesis
Rmag_0887 / sugar transferase / Cell wall/membrane/envelope biogenesis
Rmag_0889 / glycosyl transferase, family 2 / Cell wall/membrane/envelope biogenesis
Rmag_0890 / glycosyl transferase, group 1 / Cell wall/membrane/envelope biogenesis
Rmag_0891 / glycosyl transferase, family 2 / Cell wall/membrane/envelope biogenesis
Rmag_0893 / cytidyltransferase-related domain / Cell wall/membrane/envelope biogenesis
Rmag_0897 / hypothetical protein / Cell wall/membrane/envelope biogenesis
Rmag_0902 / NAD-dependent epimerase/dehydratase / Cell wall/membrane/envelope biogenesis
Rmag_0903 / GDP-mannose 4,6-dehydratase / Cell wall/membrane/envelope biogenesis
Rmag_0904 / mannose-1-phosphate guanylyltransferase/mannose-6-phosphate isomerase / Cell wall/membrane/envelope biogenesis
Rmag_0908 / O-antigen polymerase / Cell wall/membrane/envelope biogenesis
Rmag_0983 / diacylglycerol kinase / Cell wall/membrane/envelope biogenesis
Rmag_0519 / multiple antibiotic resistance (MarC)-related proteins / Intracellular trafficking, secretion, and vesicular transport
Rmag_0014 / protein of unknown function UPF0075 / Posttranslational modification, protein turnover, chaperones
Rmag_0196 / methionine-R-sulfoxide reductase / Posttranslational modification, protein turnover, chaperones
Rmag_0210 / thiol-disulfide interchange protein DsbC / Posttranslational modification, protein turnover, chaperones
Rmag_0310 / Peptidylprolyl isomerase / Posttranslational modification, protein turnover, chaperones
Rmag_0912 / ATP-dependent Clp protease adaptor protein ClpS / Posttranslational modification, protein turnover, chaperones
Rmag_0939 / Redoxin domain protein / Posttranslational modification, protein turnover, chaperones
Rmag_0009 / ubiquinol-cytochrome c reductase
cytochrome c1 subunit / Energy production and conversion
Rmag_0202 / cytochrome c4 precursor / Energy production and conversion
Rmag_0538 / isocitrate lyase / Energy production and conversion
Rmag_0685 / molybdopterin oxidoreductase / Energy production and conversion
Rmag_0317 / major facilitator superfamily MFS_1 / Carbohydrate transport and metabolism
Rmag_0318 / Beta-N-acetylhexosaminidase / Carbohydrate transport and metabolism
Rmag_0898 / glucose-1-phosphate adenylyltransferase related protein / Carbohydrate transport and metabolism
Rmag_0948 / fructosamine kinase / Carbohydrate transport and metabolism
Rmag_0440 / aminopeptidase N / Amino acid transport and metabolism
Rmag_0625 / histidinol-phosphate aminotransferase / Amino acid transport and metabolism
Rmag_0821 / glycine dehydrogenase / Amino acid transport and metabolism
Rmag_0978 / Glyoxalase/bleomycin resistance protein/dioxygenase / Amino acid transport and metabolism
Rmag_0985 / 5-methyltetrahydropteroyltriglutamate-- homocysteine S-methyltransferase / Amino acid transport and metabolism
Rmag_0509 / histidine triad (HIT) protein / Nucleotide transport and metabolism
Rmag_0764 / oxidoreductase FAD/NAD(P)-binding domain protein / Coenzyme transport and metabolism
Rmag_0316 / Rhodanese domain protein / Inorganic ion transport and metabolism
Rmag_0251 / glycosyl hydrolase, BNR repeat-containing protein / Secondary metabolites biosynthesis, transport and catabolism
Rmag_0259 / methyltransferase, putative / Secondary metabolites biosynthesis, transport and catabolism
Rmag_0896 / hypothetical protein / Secondary metabolites biosynthesis, transport and catabolism
Rmag_0930 / putative methyltransferase / Secondary metabolites biosynthesis, transport and catabolism
Rmag_0084 / OstA family protein / General function prediction only
Rmag_0207 / small GTP-binding protein / General function prediction only
Rmag_0391 / protein of unknown function DUF45 / General function prediction only
Rmag_0441 / CinA domain protein / General function prediction only
Rmag_0468 / aminoglycoside phosphotransferase / General function prediction only
Rmag_0488 / HAD-superfamily hydrolase, subfamily IA, variant 1 / General function prediction only
Rmag_0752 / RDD domain containing protein / General function prediction only
Rmag_0777 / peptidase M16 domain protein / General function prediction only
Rmag_0778 / peptidase M16 domain protein / General function prediction only
Rmag_0849 / sodium pump decarboxylases, gamma subunit / General function prediction only
Rmag_0894 / methyltransferase FkbM / General function prediction only
Rmag_0900 / putative 3-deoxy-D-manno-octulosonate 8-phosphate phosphatase / General function prediction only
Rmag_0901 / polysaccharide biosynthesis protein / General function prediction only
Rmag_0937 / sulfatase / General function prediction only
Rmag_0095 / hypothetical protein / Function unknown
Rmag_0114 / hypothetical protein / Function unknown
Rmag_0128 / hypothetical protein / Function unknown
Rmag_0130 / hypothetical protein / Function unknown
Rmag_0157 / hypothetical protein / Function unknown
Rmag_0252 / hypothetical protein / Function unknown
Rmag_0254 / hypothetical protein / Function unknown
Rmag_0260 / hypothetical protein / Function unknown
Rmag_0264 / hypothetical protein / Function unknown
Rmag_0297 / hypothetical protein / Function unknown
Rmag_0299 / hypothetical protein / Function unknown
Rmag_0326 / iojap-like protein / Function unknown
Rmag_0346 / protein of unknown function UPF0061 / Function unknown
Rmag_0376 / hypothetical protein / Function unknown
Rmag_0408 / hypothetical protein / Function unknown
Rmag_0460 / hypothetical protein / Function unknown
Rmag_0489 / protein of unknown function DUF195 / Function unknown
Rmag_0521 / hypothetical protein / Function unknown
Rmag_0586 / hypothetical protein / Function unknown
Rmag_0638 / hypothetical protein / Function unknown
Rmag_0639 / protein of unknown function UPF0118 / Function unknown
Rmag_0655 / hypothetical protein / Function unknown
Rmag_0660 / hypothetical protein / Function unknown
Rmag_0729 / hypothetical protein / Function unknown
Rmag_0761 / hypothetical protein / Function unknown
Rmag_0771 / hypothetical protein / Function unknown
Rmag_0775 / hypothetical protein / Function unknown
Rmag_0776 / hypothetical protein / Function unknown
Rmag_0782 / hypothetical protein / Function unknown
Rmag_0802 / hypothetical protein / Function unknown
Rmag_0829 / hypothetical protein / Function unknown
Rmag_0892 / hypothetical protein / Function unknown
Rmag_0895 / hypothetical protein / Function unknown
Rmag_0899 / hypothetical protein / Function unknown
Rmag_0945 / hypothetical protein / Function unknown
Rmag_1056 / hypothetical protein / Function unknown
Rmag_1065 / hypothetical protein / Function unknown
Rmag_1074 / hypothetical protein / Function unknown