Journal: Open Research Europe

Article Title: Phylogeny-wide analysis of G-protein coupled receptors in social amoebas and implications for the evolution of multicellularity

doi: 10.12688/openreseurope.15250.2

Figure Lengend Snippet: Family 1 GPCRs were identified from InterproScan of the 8 Amoebozoan proteomes by the presence of InterproIDs IPR019336 or IPR009637 and further BLAST searches with rhodopsin-like receptors. Sequences were aligned and the phylogeny was inferred by Bayesian analysis. The scale bar indicates number of changes per site. Large trees have been split up and should be joined at the star signs. Locus tags are colour coded according to the species phylogenetic position (panel bottom right) and posterior probabilities of tree nodes (BIPP) are indicated by coloured dots. The locus tags are annotated with the SMART domain architecture of the protein shown next to it. Relative developmental stage and cell-type specific expression data for orthologous dictyostelid genes were presented as set of heatmaps for each clade, with transcriptional profiles for each gene identified by the first three and last two digits of the locus tag and ‘a’ and ‘b’ signifying replicate experiments. Legend for the heat maps (only alternative letters shown): (a-g) developmental stages, a: vegetative; b: lawn, starving cells, c: aggregates; d: tipped mounds; e: migrating slugs; f: early to mid-fruiting bodies; g: complete fruiting bodies; (h, i) precell types, h: prespore and i: prestalk cells; (j-m) mature cell types, j: vegetative, k: spore, l: stalk and m: cup cells; (n-p) and (q-t) encystation time courses of P.pal 0h to 48h into encystation, n: 0h, o: 24h, p: 48h, q: 0h, r: 8h, s: 16h, t: 24h. The colour legend beside the heat maps indicates the level of expression (yellow-red: (developmental expression): fraction of maximum value, white-green (pre-cell type expression) and white-red (cell-type specific expression): fraction of summed reads). For genes with summed maximal read counts <10, the heat map is shown at 30% opacity. The normalised transcript counts were obtained from published data ( Glöckner et al. , 2016 ; Kin et al. , 2018 ; Parikh et al. , 2010 ). Note that not all stage and cell-type data is available for all species. Genes with known functions are boxed red and assigned names for D.dis genes are shown in purple italic font. D.dis locus tags for genes that result from the strain AX4 specific chromosome 2 duplication are indicated by 50% opacity. contains a list of all abbreviations used including for domain names. Seven well-supported clades with either GpcrRhopsn4 or Lung_7-TM_R domains are recognised. In addition, two Phypo receptors forming an unresolved outgroup to the whole tree show bacteriorhodopsin domains.

Article Snippet: A total of 414 non-redundant GPCRs were identified , which were assigned to the GPCR class for which their Interpro domains showed the lowest E-value and for cases where this was equivocal according to their phylogenetic affinity.

Techniques: Expressing

Journal: Open Research Europe

Article Title: Phylogeny-wide analysis of G-protein coupled receptors in social amoebas and implications for the evolution of multicellularity

doi: 10.12688/openreseurope.15250.2

Figure Lengend Snippet: For each of the families we summarised and calculated the percentage of the different states of the following features: A . the total number of orthologs out of five species that were conserved for each gene. B . The host species of genes that were unique. C . The phylogenetic distribution of genes. D . The pre-cell (only for D.dis and D.pur ) and E . mature cell type specificity (not for D.fas ). The phylogenetic distribution of F . domain and G . expression profile conservation. H . The majority expression pattern during development. I . Expression tendency during encystation. (Data only available for P.pal. ) J . Number of solitary Amoebozoan orthologues in clades. The name of each family is shown at the X-axis and the last bar represents the averages across all families. The figure is based on the data shown in – that are compiled in supplemental file Compilation_GPCRs.xlsx and summarised in GPCR_traits.xlsx.

Article Snippet: A total of 414 non-redundant GPCRs were identified , which were assigned to the GPCR class for which their Interpro domains showed the lowest E-value and for cases where this was equivocal according to their phylogenetic affinity.

Techniques: Expressing

Journal: Open Research Europe

Article Title: Phylogeny-wide analysis of G-protein coupled receptors in social amoebas and implications for the evolution of multicellularity

doi: 10.12688/openreseurope.15250.2

Figure Lengend Snippet: The family 2 GPCRs were identified by the presence of Interpro domain IPR000832 and by BLAST search and phylogenetic inference. A phylogeny was inferred from the final set of aligned proteins with MrBayes, which was annotated with the protein domain architectures and heatmaps of gene expression profiles as outlined in the legend to . Note that clade 2 gene DDB_G0279599 was previously identified as a family 2 Car-like GPCR , but we found it showed stronger phylogenetic affinity to family 2 GPCRs. Legend and labels as in .

Article Snippet: A total of 414 non-redundant GPCRs were identified , which were assigned to the GPCR class for which their Interpro domains showed the lowest E-value and for cases where this was equivocal according to their phylogenetic affinity.

Techniques: Gene Expression

Journal: Open Research Europe

Article Title: Phylogeny-wide analysis of G-protein coupled receptors in social amoebas and implications for the evolution of multicellularity

doi: 10.12688/openreseurope.15250.2

Figure Lengend Snippet: The family 3 GPCRs were identified by the presence of Interpro domain IPR017978 and by BLASTp search as outlined in the methods. A phylogeny was inferred from the final set of aligned proteins with RAxML, which was annotated with the protein domain architectures and heatmaps of gene expression profiles as outlined in the legend to . Bootstrap support of nodes is shown colour coded according to the legend. Apart from clade 1, GrlE, all other family 3 GPCRs form a single cluster of almost exclusively dictyostelid members. Other receptors of this family are only found in Physarum polycephalum, but not in other Amoebozoa.

Article Snippet: A total of 414 non-redundant GPCRs were identified , which were assigned to the GPCR class for which their Interpro domains showed the lowest E-value and for cases where this was equivocal according to their phylogenetic affinity.

Techniques: Gene Expression

Journal: Open Research Europe

Article Title: Phylogeny-wide analysis of G-protein coupled receptors in social amoebas and implications for the evolution of multicellularity

doi: 10.12688/openreseurope.15250.2

Figure Lengend Snippet: The family 5 GPCRs were identified by the presence of Interpro domain IPR000539 and by BLASTp search as outlined in the methods. A phylogeny was inferred from the final set of aligned proteins with MrBayes, which was annotated with the protein domain architectures and heatmaps of gene expression profiles as outlined in the legend to . The family 5 experienced independent amplifications in different lines of Amoebozoa and especially within group4 dictyostelids. The dictyostelid members all originate at the base of Dictyostelia and have no Amoebozoan orthologues.

Article Snippet: A total of 414 non-redundant GPCRs were identified , which were assigned to the GPCR class for which their Interpro domains showed the lowest E-value and for cases where this was equivocal according to their phylogenetic affinity.

Techniques: Gene Expression

Journal: Open Research Europe

Article Title: Phylogeny-wide analysis of G-protein coupled receptors in social amoebas and implications for the evolution of multicellularity

doi: 10.12688/openreseurope.15250.2

Figure Lengend Snippet: The family 6 GPCRs were identified by the presence of Interpro domain IPR000848 and by BLASTp search as outlined in the methods. A phylogeny was inferred from the final set of aligned proteins with MrBayes. Even after 3 million generations analysis did not converge and the deeper nodes of the tree are unresolved. Orthologous clades are, however, well defined. The tree was annotated with the protein domain architectures and heatmaps of gene expression profiles as outlined in the legend to .

Article Snippet: A total of 414 non-redundant GPCRs were identified , which were assigned to the GPCR class for which their Interpro domains showed the lowest E-value and for cases where this was equivocal according to their phylogenetic affinity.

Techniques: Gene Expression