Fig. 3. Phylogenetic relationship of the replicons of the family Burkholderiaceae. An unrooted RAxML maximum ... Fig. 3. Phylogenetic relationship of the.

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Fig. 3. Phylogenetic relationship of the replicons of the family Burkholderiaceae. An unrooted RAxML maximum ... Fig. 3. Phylogenetic relationship of the replicons of the family Burkholderiaceae. An unrooted RAxML maximum likelihood phylogeny of the replicons of the family Burkholderiaceae, based on the amino acid sequence of the ParB partitioning protein. Bootstrap values are based on 504 replicates. The scale represents the mean number of amino acid substitutions per site. The size of the triangles is proportional to the number of strains in the collapsed branch. The original expanded figure, the Newick formatted phylogeny, and the annotation file are available at github.com/diCenzo-GC/Burkholderiaceae_analyses. Unless provided in the caption above, the following copyright applies to the content of this slide: © The Author(s) 2019. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. All rights reserved. For permissions, please e-mail: journals.permissions@oup.comThis article is published and distributed under the terms of the Oxford University Press, Standard Journals Publication Model (https://academic.oup.com/journals/pages/open_access/funder_policies/chorus/standard_publication_model) Mol Biol Evol, Volume 36, Issue 3, 04 January 2019, Pages 562–574, https://doi.org/10.1093/molbev/msy248 The content of this slide may be subject to copyright: please see the slide notes for details.

Fig. 2. Genome organization within the family Burkholderiaceae Fig. 2. Genome organization within the family Burkholderiaceae. An unrooted RAxML maximum likelihood phylogeny of 293 ... Fig. 2. Genome organization within the family Burkholderiaceae. An unrooted RAxML maximum likelihood phylogeny of 293 Burkholderiaceae strains based on 28 highly conserved proteins (see supplementary information, Supplementary Material online). Bcc strains marked with an asterisks (*) contain genomic regions homologous to the chromosome, chromid, and megaplasmid, but with all or part of at least two of the replicons present as a cointegrant based on the assembly available through NCBI. Bootstrap values are based on 360 replicates. The scale represents the mean number of amino acid substitutions per site. The original figure, the Newick formatted phylogeny, and the annotation file are available at github.com/diCenzo-GC/Burkholderiaceae_analyses. Unless provided in the caption above, the following copyright applies to the content of this slide: © The Author(s) 2019. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. All rights reserved. For permissions, please e-mail: journals.permissions@oup.comThis article is published and distributed under the terms of the Oxford University Press, Standard Journals Publication Model (https://academic.oup.com/journals/pages/open_access/funder_policies/chorus/standard_publication_model) Mol Biol Evol, Volume 36, Issue 3, 04 January 2019, Pages 562–574, https://doi.org/10.1093/molbev/msy248 The content of this slide may be subject to copyright: please see the slide notes for details.

Fig. 1. Distribution of multipartite genomes in the β-proteobacteria Fig. 1. Distribution of multipartite genomes in the β-proteobacteria. An unrooted RAxML maximum likelihood phylogeny ... Fig. 1. Distribution of multipartite genomes in the β-proteobacteria. An unrooted RAxML maximum likelihood phylogeny of 176 representative β-proteobacteria based on 26 highly conserved proteins (see supplementary information, Supplementary Material online). Species with a putative chromid may also contain a megaplasmid. The clade consisting of Candidatus Zinderia insecticola, Candidatus Nasuia deltocephalinicola, Candidatus Tremblaya princeps, and Candidatus Tremblaya phenacola was collapsed due to extremely long branch lengths. Bootstrap values are based on 108 replicates. The scale represents the mean number of amino acid substitutions per site. The original figure, the Newick formatted phylogeny, and the annotation file are available at github.com/diCenzo-GC/Burkholderiaceae_analyses. A phylogeny of all 960 β-proteobacteria is provided as supplementary figure S11, Supplementary Material online. Unless provided in the caption above, the following copyright applies to the content of this slide: © The Author(s) 2019. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. All rights reserved. For permissions, please e-mail: journals.permissions@oup.comThis article is published and distributed under the terms of the Oxford University Press, Standard Journals Publication Model (https://academic.oup.com/journals/pages/open_access/funder_policies/chorus/standard_publication_model) Mol Biol Evol, Volume 36, Issue 3, 04 January 2019, Pages 562–574, https://doi.org/10.1093/molbev/msy248 The content of this slide may be subject to copyright: please see the slide notes for details.

Fig. 4. Relationship between COG category abundances in replicon-specific accessory pangenomes. Scatterplots ... Fig. 4. Relationship between COG category abundances in replicon-specific accessory pangenomes. Scatterplots displaying the percentage of proteins in the accessory pangenome of chromids compared with that of chromosomes are shown. In both plots, the X-axes show the percentage of proteins in the chromosomal accessory genome annotated with a specific COG, whereas the Y-axes show the percentage of proteins in the chromid accessory genome annotated with a specific COG category. The dashed line indicates the 1:1 line. Each point in the plots represents a single COG category, and a few COG categories showing the greatest biases are indicated. The data underlying these plots are provided in supplementary Data Set S4, Supplementary Material online. The figures are shown for (A) all Burkholderia strains and (B) all Cupriavidus strains. See supplementary figure S7, Supplementary Material online, for similar plots for chromids and megaplasmids of the Burkholderia cepacia complex, the Paraburkholderia strains, and the Ralstonia strains. Unless provided in the caption above, the following copyright applies to the content of this slide: © The Author(s) 2019. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. All rights reserved. For permissions, please e-mail: journals.permissions@oup.comThis article is published and distributed under the terms of the Oxford University Press, Standard Journals Publication Model (https://academic.oup.com/journals/pages/open_access/funder_policies/chorus/standard_publication_model) Mol Biol Evol, Volume 36, Issue 3, 04 January 2019, Pages 562–574, https://doi.org/10.1093/molbev/msy248 The content of this slide may be subject to copyright: please see the slide notes for details.

Fig. 5. Accessory pangenome COG category abundances Fig. 5. Accessory pangenome COG category abundances. Heatmaps displaying the relative abundance of proteins annotated ... Fig. 5. Accessory pangenome COG category abundances. Heatmaps displaying the relative abundance of proteins annotated with each COG category in the (A) chromosome pangenomes and (B) secondary replicon pangenomes are shown. Values shown are the percentage of proteins annotated with the COG category, divided by the average value for all samples shown in the heatmap. Only those COG categories with an unequal distribution between groups are shown, as determined with chi-square tests using 10 degrees of freedom and an unadjusted P value of 0.001 (supplementary table S2, Supplementary Material online). Additionally, COG Category S (general functional prediction only) was excluded. Both axes were clustered with hierarchical clustering using average linkage and a Pearson correlation distance. Unless provided in the caption above, the following copyright applies to the content of this slide: © The Author(s) 2019. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. All rights reserved. For permissions, please e-mail: journals.permissions@oup.comThis article is published and distributed under the terms of the Oxford University Press, Standard Journals Publication Model (https://academic.oup.com/journals/pages/open_access/funder_policies/chorus/standard_publication_model) Mol Biol Evol, Volume 36, Issue 3, 04 January 2019, Pages 562–574, https://doi.org/10.1093/molbev/msy248 The content of this slide may be subject to copyright: please see the slide notes for details.

Fig. 6. Correlation between replicon and lifestyle functional biases Fig. 6. Correlation between replicon and lifestyle functional biases. Plots display the chromosomal COG functional ... Fig. 6. Correlation between replicon and lifestyle functional biases. Plots display the chromosomal COG functional category abundance ratios for environmental genera versus pathogenic genera (X-axes), compared with the COG functional category abundance ratios for chromids versus chromosomes (Y-axes). The axes display the ratio of the percentage of proteins annotated with a COG category. Each point on the plots represents one COG category. COG abundance data are from the replicon-specific accessory genomes. Data points are limited to COG categories with an abundance of at least 0.5%. Lines represent the robust linear regression determined with the “rlm” command of the MASS package for R (Venables and Ripley 2002). (A) Data for Burkholderia and Paraburkholderia. (B) Data for Ralstonia and Cupriavidus. Unless provided in the caption above, the following copyright applies to the content of this slide: © The Author(s) 2019. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. All rights reserved. For permissions, please e-mail: journals.permissions@oup.comThis article is published and distributed under the terms of the Oxford University Press, Standard Journals Publication Model (https://academic.oup.com/journals/pages/open_access/funder_policies/chorus/standard_publication_model) Mol Biol Evol, Volume 36, Issue 3, 04 January 2019, Pages 562–574, https://doi.org/10.1093/molbev/msy248 The content of this slide may be subject to copyright: please see the slide notes for details.

Fig. 7. Ancestral state reconstruction of genome content Fig. 7. Ancestral state reconstruction of genome content. A subtree of the phylogeny provided in figure 2 is shown, ... Fig. 7. Ancestral state reconstruction of genome content. A subtree of the phylogeny provided in figure 2 is shown, displaying the genera Cupriavidus and Ralstonia. At each node (space permitting), the number of genes found belonging to the chromosomal pangenome (bottom numbers) and the chromid pangenome (top numbers) of the extant strains that are predicted to have been present in that ancestor are indicated. The scale represents the mean number of amino acid substitutions per site. See supplementary figure S8, Supplementary Material online, for a version with taxa names, and for the data for the genera Burkholderia and Ralstonia. Unless provided in the caption above, the following copyright applies to the content of this slide: © The Author(s) 2019. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. All rights reserved. For permissions, please e-mail: journals.permissions@oup.comThis article is published and distributed under the terms of the Oxford University Press, Standard Journals Publication Model (https://academic.oup.com/journals/pages/open_access/funder_policies/chorus/standard_publication_model) Mol Biol Evol, Volume 36, Issue 3, 04 January 2019, Pages 562–574, https://doi.org/10.1093/molbev/msy248 The content of this slide may be subject to copyright: please see the slide notes for details.