Visualization of multiple alignments, phylogenies and gene family evolution

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1 nature methods Visualization of multiple alignments, phylogenies and gene family evolution James B Procter, Julie Thompson, Ivica Letunic, Chris Creevey, Fabrice Jossinet & Geoffrey J Barton Supplementary figures and text: Supplementary Figure 1 Supplementary Figure 2 Supplementary Figure 3 Supplementary Figure 4 Supplementary Figure 5 BLAST results for the human aryl sulfatase sequence as viewed in VectorNTI and Geneious Annotated visualization of the Pfam alignment for the sulfatase family and linked view of PDB structure 1fsu Visualizing the NCBI taxonomy Tree-based alignment analysis Annotating phylogenetic trees with complex data

2 Supplementary Figure 1 Blast results for the human aryl sulfatase sequence as viewed in VectorNTI (a), and Geneious (b). See main text for details. a Hierarchical hit list for further details. Hit distribution and consensus profile on query positions Alignment Trace showing context of aligned segments. Birds-eye view of hits on query sequence. b Alignment of Query and Hit Slider sets threshold to grey out clades in hitlist distance tree for hits in clade Top Hit

3 Supplementary Figure 2 Annotated visualization of the Pfam alignment for the sulfatase family and linked view of PDB structure 1fsu. Sulfatases are a highly conserved enzyme family. They hydrolyze sulfate ester bonds in a variety of structurally diverse compounds but have similar overall folds, mechanisms of action, and bivalent metal ion-binding sites 1, 2. (a) Pfam family alignment rendered with Jalview. Knowledge of the substrate specificity for each sequence allows the alignment to be divided into 6 functional subfamilies (names on the left were added manually). Conserved sequence regions calculated by MACSIMS are indicated by colored shapes. Regions 1-4 (above the alignment) are shown to be shared by all the sub-families. Within these, highlighted single residues correspond to known functionally active sites. Secondary structure annotation from PDB structure 1fsu (ARSB_HUMAN) is shown below the alignment, above the Livingstone and Barton conservation score.conserved sequence regions (Regions 1 and 2 above the alignment) were detected by MACSIMS and shared by all sub-families. Disulphide bond annotation above the alignment was obtained from PDB sequence 1n2l (ARSA_HUMAN). Secondary structure annotation from PDB structure 1fsu (ARSB_HUMAN) is below the alignment, above the Livingstone and Barton conservation score. (b) Image taken from Jalview s linked Jmol view of 1fsu, showing the structural context of regions 1-4 in a. (c). Close up of region underscored in red in (a) with annotated regions of sequences colored according to type and origin, locating PROSITE motifs and known mutations in the alignment. Inset box shows close up of Jalview tooltip conveying additional annotation information. The sequence annotations that were obtained from public databases (Uniprot 2, PDB 3 or Interpro 4 ), are colored using a dark shade. The features shown in a lighter shade were inferred by MACSIMS, which propagates these known properties to the uncharacterized sequences.

4 Supplementary Figure 2 Annotated visualization of the Pfam alignment for the sulfatase family and linked view of PDB structure 1fsu. a Region 1 Region 2 Region 3 Region 4 ARSA ARSG ARS STS/ ARSE/F ARSB ARSI/J b c Region 1 Region 2 disulphide bond ARSA ARSG ARS STS/ ARSE/F ARSB ARSI/J PROSITE sulfatase1 sulfatase2 metal binding active site glycosylation NAG binding hydrophobic mutation

5 Supplementary Figure 3 Visualizing the NCBI taxonomy. Perhaps, the closest we can get to the visualisation of the entire tree of life. In this figure, taken from Hughes et. al., 5 Walrus and Phylo3D were used to visualize the complete NCBI taxonomy, containing close to species, in a hyperbolic 3D space. Bacteria are focused in the image, and shown in orange. Eukaryotes are shown in yellow, in the left hand side. Archaea are represented with the red colored nodes shown in the top and background of the image.

6 Supplementary Figure 4 Tree Based Alignment Analysis. (a) Tree based alignment analysis of the sulfatase family using JevTrace, applied to the Pfam family alignment and tree. The panel on the left shows the algorithm s automatically generated tree partition. The alignment, shown adjacent to the leaves, is annotated with regions found to exhibit sub-family conservation. A view of the associated PDB structure (1fsu) is shown on the right, colored according to sub-family specific mutations. (b) Snapshot from Jalview showing same region of sulfatase alignment as in Figure S2C, with Clustal conservation based shading and colouring applied to each subgroup. This rendering style reveals subfamily specific conservation patterns that generally contain the residues known to be involved in substrate binding (c.f. annotation in figure S2c). (c) Neighbor-joining tree for the alignment in S2A calculated with Jalview, with sub-trees corresponding to each sub-family highlighted with different colors.

7 Supplementary Figure 4 Tree Based Alignment Analysis. a b c ARSA ARSG ARS STS/ ARSE/F ARSB ARSI/J

8 Ureaplasma parvum Brucella melitensis Tropheryma whipplei str Twist Streptomyces coelicolor Streptomyces avermitilis Supplementary Figure 5 Annotating phylogenetic trees with complex data. itol 6 was used to annotate an automatically generated Tree of life. 7 Blue barcharts represent the genome sizes, defined as number of predicted protein coding genes. Piecharts show the distribution of preferred habitats for various taxa identified in several metagenomics sequencing projects. 8 Thalassiosira pseudonana CCMP1335 Cryptosporidium hominis Giardia lamblia ATCC Methanothermobacter thermautotrophicus str Delta H Thermoplasma volcanium Thermoplasma acidophilum Sulfolobus solfataricus Sulfolobus tokodaii Aeropyrum pernix Methanocaldococcus jannaschii Methanopyrus kandleri Pyrococcus horikoshii Pyrococcus abyssi Pyrococcus furiosus Methanosarcina mazei Methanosarcina acetivorans Halobacterium sp NRC 1 Archaeoglobus fulgidus Plasmodium falciparum 3D7 Leishmania major Methanococcus maripaludis Cyanidioschyzon merolae Schizosaccharomyces pombe Dictyostelium discoideum Arabidopsis thaliana Oryza sativa Eremothecium gossypii Caenorhabditis elegans Saccharomyces cerevisiae Anopheles gambiae str PEST Drosophila melanogaster Caenorhabditis briggsae Takifugu rubripes Danio rerio Gallus gallus Mus musculus Rattus norvegicus Homo sapiens Thermoanaerobacter tengcongensis Pan troglodytes Clostridium acetobutylicum Clostridium tetani Clostridium perfringens Onion yellows phytoplasma Mycoplasma mycoides subsp mycoides SC Mycoplasma mobile 163K Mycoplasma pulmonis Mycoplasma penetrans Mycoplasma gallisepticum Mycoplasma pneumoniae Mycoplasma genitalium Staphylococcus epidermidis Staphylococcus aureus subsp aureus MW2 Staphylococcus aureus subsp aureus N315 Staphylococcus aureus subsp aureus Mu50 Listeria innocua Listeria monocytogenes str 4b F2365 Listeria monocytogenes Bacillus halodurans Oceanobacillus iheyensis Bacillus subtilis Bacillus anthracis str Ames Bacillus cereus ATCC Bacillus cereus ATCC Lactobacillus plantarum Lactobacillus johnsonii Enterococcus faecalis Lactococcus lactis subsp lactis Streptococcus pneumoniae R6 Streptococcus pneumoniae Streptococcus mutans Streptococcus agalactiae serogroup III Streptococcus agalactiae serogroup V Streptococcus pyogenes Streptococcus pyogenes MGAS8232 Streptococcus pyogenes MGAS315 Streptococcus pyogenes SSI 1 Fibrobacter succinogenes subsp succinogenes S85 Chlorobaculum tepidum Porphyromonas gingivalis Bacteroides thetaiotaomicron Chlamydia muridarum Chlamydia trachomatis Chlamydophila caviae Chlamydophila pneumoniae TW 183 Chlamydophila pneumoniae J138 Chlamydophila pneumoniae CWL029 Chlamydophila pneumoniae AR39 Gemmata obscuriglobus UQM 2246 Pirellula sp Leptospira interrogans serovar Copenhageni Leptospira interrogans Borrelia burgdorferi Treponema denticola Pyrobaculum aerophilum Treponema pallidum Nanoarchaeum equitans Bifidobacterium longum Tropheryma whipplei TW0827 Corynebacterium diphtheriae Shigella flexneri Shigella flexneri 2a str 2457T Escherichia coli Escherichia coli O6 Escherichia coli O157:H7 Escherichia coli O157:H7 EDL Yersinia pestis Yersinia pestis KIM Salmonella enterica subsp enterica serovar Typhi str Ty2 Yersinia pestis biovar Microtus str Photorhabdus luminescens subsp laumondii Buchnera aphidicola (Schizaphis graminum) Buchnera aphidicola (Acyrthosiphon pisum) Buchnera aphidicola (Baizongia pistaciae) Haemophilus influenzae Pasteurella multocida Candidatus Blochmannia floridanus Wigglesworthia glossinidia endosymbiont of Glossina brevipalpis Vibrio vulnificus Haemophilus ducreyi Vibrio vulnificus YJ016 Vibrio parahaemolyticus Vibrio cholerae Shewanella oneidensis Photobacterium profundum Pseudomonas aeruginosa Pseudomonas putida KT2440 Pseudomonas syringae pv tomato Xylella fastidiosa Temecula1 Xylella fastidiosa Xanthomonas axonopodis pv citri Xanthomonas campestris pv campestris Coxiella burnetii Bordetella parapertussis Bordetella bronchiseptica Bordetella pertussis Ralstonia solanacearum Neisseria meningitidis serogroup A Neisseria meningitidis serogroup B Chromobacterium violaceum Nitrosomonas europaea Brucella suis Mesorhizobium loti Sinorhizobium meliloti Bradyrhizobium japonicum Rhodopseudomonas palustris Caulobacter vibrioides Rickettsia prowazekii Rickettsia conorii Wolbachia sp wmel Helicobacter pylori Helicobacter pylori J99 Corynebacterium efficiens Corynebacterium glutamicum Corynebacterium glutamicum ATCC Mycobacterium avium subsp paratuberculosis Mycobacterium leprae Mycobacterium bovis Mycobacterium tuberculosis CDC1551 Mycobacterium tuberculosis H37Rv Fusobacterium nucleatum subsp nucleatum Thermotoga maritima Aquifex aeolicus Dehalococcoides ethenogenes 195 Thermus thermophilus HB27 Deinococcus radiodurans Gloeobacter violaceus Synechococcus elongatus Nostoc sp PCC 7120 Synechocystis sp PCC 6803 Prochlorococcus marinus Prochlorococcus marinus str MIT 9313 Synechococcus sp WH 8102 Acidobacterium capsulatum ATCC Candidatus Solibacter usitatus Ellin6076 Desulfovibrio vulgaris str Hildenborough Geobacter sulfurreducens Bdellovibrio bacteriovorus Campylobacter jejuni Wolinella succinogenes Helicobacter hepaticus Prochlorococcus marinus subsp pastoris str CCMP1986

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