SUPPLEMENTARY FIGURES AND TABLES Figure S1. Ancestral
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SUPPLEMENTARY FIGURES AND TABLES Figure S1. Ancestral State Reconstruction of Chitin Degradation. Phylogenetic tree was constructed with maximum likelihood in PAUP* using SSU and LSU ribosomal RNA genes. Branch lengths (inferred ages) were calculated using penalized likelihood in r8s. Age constraints for nodes are indicated by colored circles around nodes where the root (orange), Euryarchaeota (yellow), oxygen age constraints (pink), chitin age constraints (blue), and lignin age constraints (lime). Ages (in Ma) of nodes indicated on the horizontal scale, with ages shown by geologic time scale at the bottom. Ancestral character states were calculated using maximum likelihood in Mesquite where (a) white nodes indicate the absence of chitinase in the genome and black nodes indicate presence, (b, inset of Thermococcales) presence/absence of exo-D-glucosaminidase, (c, inset of Thermococcales) presence/absence of glucosamine-6-phosphate deaminase, and (d, inset of Thermococcales) presence/absence of diacetylchitobiose deacetylase. Gray nodes are equivocal. Figure S2. Ancestral State Reconstruction of Phenolic Compound Degradation. See legend for Figure S1. Ancestral character states were calculated where (a) white nodes indicate the absence of catechol dioxygenase in the genome and black nodes indicate presence, (b, inset of Sulfolobales) presence/absence of phenol hydroxylase, (c, inset of Sulfolobales) presence/absence of dihydroxyphenylacetic acid dioxygenase, and (d, inset of Sulfolobales) presence/absence of hydroxyphenylacetic acid hydroxylase. Figure S1. Ancestral State Reconstruction of Chitin Degradation. Figure S2. Ancestral State Reconstruction of Phenolic Compound Degradation. Table S1. List of genes in 72 x 100 dataset and their COG functional category. # Gene Gene ID COG Functional Category Class* 1 Gcp metal-dependent protease/peptidase Chaperons CP 2 GimC Prefoldin, chaperonin cofactor Chaperones CP 3 Ffh SRP GTPase Motility and Secretion CP 4 FtsY SRP GTPase Motility and Secretion CP 5 SecY Pre-protein Translocase Motility and Secretion CP 6 DnaG DNA primase (bacterial type) Replication recombination and repair IP 7 DnaN Dna Polymerase III beta subunit Replication recombination and repair IP 8 Exo 5'->3' exonuclease/flap-specific endo/exonuclease Replication recombination and repair IP 9 RnhB Ribonuclease HII Replication recombination and repair IP 10 Top6A DNA Topoisomerases VI subunit A Replication recombination and repair IP 11 HypProt Conserved hypothetical protein/histone acetyltransferases Transcription IP 12 NusG Transcription Antiterminator Transcription IP 13 PredTxReg Predicted transcriptional regulator Transcription IP 14 PTR2 Predicted transcriptional regulator Transcription IP 15 Rpb10 DNA-directed RNA polymerase subunit N Transcription IP 16 Rpb5 DNA-directed RNA polymerase, subunit H Transcription IP 17 RPB7 DNA-directed RNA polymerase subunit E' Transcription IP 18 RpoA DNA-directed RNA polymerase alpha Transcription IP 19 RpoB RNA Polymerase beta and beta prime subunits Transcription IP 20 aIF2a Translation Initiation Factor IF-2, alpha subunit Translation IP 21 AlaS Alanyl-tRNA Synthetase Translation IP 22 ArgS Arginyl-tRNA synthetase Translation IP 23 Efp Translation elongation factor P Translation IP 24 eIF6 Translation Initiation Factor 6 Translation IP 25 eRf1 Peptide chain release factor Translation IP 26 FusA Translation Factor EF-G Translation IP 27 GatB tRNA-Gln Amidotransferase Translation IP 28 Gcd7 Translation initiation factor eIF-2 subunit, beta subunit Translation IP 29 GlnS Glutamyl- and glutaminyl-tRNA Synthetase Translation IP 30 HisS Histidyl-tRNA synthetase Translation IP 31 IleS Isoleucyl-tRNA synthetase Translation IP 32 KsgA Dimethyladenosine transferase Translation IP 33 L1 Ribosomal protein L1 Translation IP 34 L11 Ribosomal protein L11 Translation IP 35 L13 Ribosomal protein L13 Translation IP 36 L14 Ribosomal protein L14 Translation IP 37 L15e Ribosomal protein L15e Translation IP 38 L16 Ribosomal protein L16 Translation IP 39 L18 Ribosomal protein L18 Translation IP 40 L18e Ribosomal protein L18e Translation IP 41 L19e Ribosomal protein L19e Translation IP 42 L2 Ribosomal Protein L2 Translation IP 43 L21e Ribosomal protein L21e Translation IP 44 L3 Ribosomal protein L3 Translation IP 45 L5 Ribosomal protein L5 Translation IP 46 L6 Ribosomal protein L6 Translation IP 47 LeuS Leucyl-tRNA synthetase Translation IP 48 LSU Large subunit ribosomal RNA Translation IP 49 Map Methionine aminopeptidase Translation IP 50 MetS Methionyl-tRNA Transferase Translation IP 51 NOP1 Fibrillarin-like RNA methylase Translation IP 52 PES Predicted exosome subunit Translation IP 53 PheT Phenylalanyl-tRNA synthesase, beta subunit Translation IP 54 PredRNABP Predicted RNA-binding protein Translation IP 55 S11 Ribosomal protein S11 Translation IP 56 S12 Ribosomal protein S12 Translation IP 57 S13 Ribosomal protein S13 Translation IP 58 S17 Ribosomal protein S17 Translation IP 59 S19 Ribosomal protein S19 Translation IP 60 S19e Ribosomal protein S19e Translation IP 61 S2 Ribosomal protein S2 Translation IP 62 S3 Ribosomal Protein S3 Translation IP 63 S3e Ribosomal protein S3e Translation IP 64 S4e Ribosomal protein S4e Translation IP 65 S5 Ribosomal protein S5 Translation IP 66 S7 Ribosomal protein S7 Translation IP 67 S8 Ribosomal protein S8 Translation IP 68 S8e Ribosomal protein S8e Translation IP 69 S9 Ribosomal protein S9 Translation IP 70 SSU Small subunit ribosomal RNA Translation IP 71 Sui1 Translation initiation factor (SUI1) Translation IP 72 TruB Pseudouridine synthase Translation IP 73 TyrS Tyrosyl-tRNA synthetase Translation IP 74 ArgF Ornithine carbamoyltransferase Amino acid transport and metabolism Met 75 AroC chorismate synthase Amino acid transport and metabolism Met 76 Eno Enolase Carbohydrate metabolism Met 77 GapA Glyceraldehyde-3-phosphate dehydrogenase Carbohydrate metabolism Met 78 Pgk Phosphoglycerate Kinase Carbohydrate metabolism Met 79 Tpi Triose Phosphate Isomerase Carbohydrate metabolism Met 80 HemB Delta-aminolevulinic acid dehydratase Coenzyme transport and metabolism Met 81 MoaC Molybdenum Cofactor Biosynthesis Enzyme Coenzyme Metabolism Met 82 NadR Nicotinamide mononucleotide adenylyltransferase Coenzyme Biosynthesis Met 83 PdxS Pyridoxine biosynthesis protein Coenzyme transport and metabolism Met 84 PdxT SNO Glutamine amidotransferase subunit Coenzyme transport and metabolism Met 85 Sam1 S-adenosylhomocysteine hydrolase Coenzyme Metabolism Met 86 SNZ1 Pyridoxine biosynthesis enzyme Coenzyme Biosynthesis Met 87 UbiX Phenylacrylic acid decarboxylase Coenzyme transport and metabolism Met 88 NtpB Archaeal/vacuolar-type H+-ATPase subunit B Energy production and conversion Met 89 RNaseLI RNase L Inhibitor General Function Prediction Unknown 90 PksG 3-hydroxy-3-methylglutaryl CoA synthase Lipid metabolism Met 91 UppS Undecaprenyl Pyrophosphate Synthase Lipid metabolism Met 92 Cmk Cytidylate kinase 2 Nucleotide transport and metabolism Met 93 GuaA GMP synthase - PP-ATPase domain Nucleotide transport and metabolism Met 94 Ndk Nucleoside Diphosphate Kinase Nucleotide transport and metabolism Met 95 PurL phosphoribosylformylglycinamidine synthase II Nucleotide transport and metabolism Met 96 PurM phosphoribosylformylglycinamidine cyclo-ligase Nucleotide transport and metabolism Met 97 PyrB aspartate carbamoyltransferase catalytic subunit Nucleotide transport and metabolism Met 98 PyrE orotate phosphoribosyl transferase Nucleotide transport and metabolism Met 99 PyrG CTP Synthase Nucleotide Metabolism Met 100 Xan Xanthosine triphosphate pyrophosphatase Nucleotide transport and metabolism Met *CP = Cellular Processes; IP = Information Processing; Met = Metabolism Table S2. Results of Approximately Unbiased Topology Tests*. Sequence p value L1 0.088 aIF2a 0.016 L11 0.002 Alas 7.00E-07 L13 0.237 ArgF 0.036 L14 2.00E-04 ArgS 0.014 L15e 0.001 AroC 3.00E-04 L16 0.008 Cmk 0.226 L18 0.02 DnaG 0.602 L18e 0.039 DnaN 0.335 L19e 0.01 Efp 0.002 L2 0.003 eIF6 0.011 L21e 0.076 Enolase 1.00E-55 L3 0.01 Erf1 0.043 L5 0.051 Exo 0.334 L6 0.071 Ffh 0.691 LeuS 2.00E-70 FtsY 0.009 LSU+SSU 0.605 FusA 0.429 Map 0.04 GapA 1.00E-04 Mets 2.00E-61 GatB 0.007 MoaC 0.003 Gcd7 3.00E-08 NadR 6.00E-10 Gcp 0.073 Ndk 0.088 GimC 0.117 NOP1 0.061 GlnS 2.00E-13 NtpB 0.012 GuaA 0.017 NusG 0.466 HemB 0.07 PdxS 4.00E-06 HisS 6.00E-05 PdxT 0.007 HypProt 6.00E-59 PES 0.253 IleS 2.00E-04 Pgk 1.00E-06 KsgA 0.12 PheT 4.00E-38 PksG 0.11 S8e 0.003 PredRNABP 0.143 S9 0.012 PredTxReg 0.25 Sam1 8.00E-06 PTR2 0.006 SecY 0.016 PurL 1.00E-68 SNZ1 1.00E-11 PurM 0.06 Sui1 4.00E-06 PyrB 0.002 Top6A 9.00E-05 PyrE 0.003 Tpi 5.00E-07 PyrG 0.024 TruB 0.012 RNaseLI 0.144 TyrS 7.00E-11 Sequence p value UbiX 0.075 RnhB 0.195 UppS 0.495 Rpb10 0.015 Xan 4.00E-04 Rpb5 0.003 RPB7 0.048 *evaluates whether the best single gene tree is significantly different from the consensus genome tree Text in red: datasets incongruent with the genome topology. RpoA 0.02 Text in black: datasets congruent with the genome topology Rpob 4.00E-36 S11 4.00E-04 S12 0.146 S13 0.052 S17 0.102 S19 3.00E-04 S19e 0.204 S2 0.14 S3 0.017 S3e 0.008 S4e 0.107 S5 0.003 S7 0.042 S8 0.001
