Fig 1.
Overview of inspected taxonomic groups and distribution of FIB protein sequences through the three domains of life.
a) Depiction of the major taxonomic groups analyzed in this study. FIB sequences were sought across a total of 1002 genomes from the three domains of life (212 Bacteria, 148 Archaea, and 642 Eukarya). Graph dimensions are not to scale. b) The number of FIB sequences (purple bars) per analyzed genome are grouped according to major taxa in a species phylogenetic tree. Concentric circles indicate the number of FIB sequences. c) Unrooted phylogenetic tree of the total 1063 FIB proteins found in Archaea and Eukarya, colored by main taxonomic groups.
Fig 2.
Depiction of the number of FIB proteins detected in Eukarya.
a) FIB proteins detected in the protist group. b) FIB proteins detected in Fungi. c) FIBs detected in Plant genomes. d) FIBs detected in invertebrates. e) FIBs detected in vertebrates. Each circle represents the number of FIBs per species (y-axis). Each taxonomic group is presented in a unique color (dots and strips under the x-axis) consistently throughout the text and figures.
Fig 3.
Microsynteny networks of FIB genes of the three major Eukaryotic taxa.
a) Microsynteny networks of FIB genes in Fungi. Nine microsynteny communities from three different phyla (Mucoromycota, Basidiomycota, and Ascomycota). b) Microsynteny networks of FIB genes in plants formed six synteny clusters: a synteny supercluster for all angiosperms (purple nodes), and five small synteny clusters for specific clade such as Rosids (green nodes), Fabaceae (blue nodes), PACMAD (orange nodes), Oryza-specific cluster (red nodes), and a small Fabaceae group (pink nodes) that poorly linked to the Angiosperm supercluster (one link). c) Microsynteny networks of FIB genes in animals. Three major clusters include a specific Fish-Reptilia syntenic cluster (pink and blue nodes), and two mammalian-specific syntenic clusters (green and yellow nodes). Nodes represent FIB genes, and edges represent synteny relationships between them. Nodes sizes are proportional to the number of synteny connections they share. All depicted microsynteny networks were clustered by Clique percolation method (k-clique = 3) to find densely connected communities.
Fig 4.
Phylogenomic microsynteny analysis of the fungal FIB homologues.
a) Phylogeny of the 170 FIB proteins identified in fungi. Tree leaves are labelled by color according to main taxonomic groups, as indicated in the legend (left). The color of inner strips is by major groups: early-diverging fungi (red), Ascomycota (blue), and Basidiomycota (yellow). Internal pairwise connections between tree leaves represent pairwise synteny relationships and are colored to indicate the nine fungal microsynteny communities; gray connections represent synteny pairwise relationships not included in any community. b) Phylogenetic profiling of the microsynteny communities of FIB proteins found in fungi. The cladogram at the bottom represents analyzed fungal species; branches are colored by main taxonomic groups, as indicated in the left legend. The presence or absence of the synteny communities in each species shown in the matrix above the cladogram. Closed figures indicate the presence of a microsynteny community.
Fig 5.
Phylogenomic microsynteny analysis of plant FIB homologues.
Phylogeny of the total 327 FIB proteins detected from 153 plant genomes (13 algae and 140 plants). Names of genes are placed on the tree by taxonomic affiliation, as indicated on the right. Colors of inner strips are according to major taxonomic groups: algae (red) and angiosperms (green). Internal pairwise connections between tree leaves represent pairwise synteny relationships and are colored according to the detected microsynteny clusters, as shown in Fig 2B and S9 Fig. Gray connections represent synteny pairwise relationships not included in any community. Black filled circles on the tip of the leaves represent genes belonging to the only orthogroup detected in plants. Yellow filled circles represent tandem duplicated genes and part of the unique orthogroup.
Fig 6.
Phylogenomic microsynteny analysis of animal FIB proteins.
a) Phylogenetic tree of the total 319 FIB proteins detected across 257 inspected genomes (195 Vertebrata and 62 Invertebrata). Color-coded gene names are on the tree by taxonomic affiliation, as indicated on the left. The color of the first inner strips is by major taxonomic groups: Invertebrata (black) and Vertebrata (yellow). The second inner strips are colored by relevant taxonomic group, as indicated on the left. Internal pairwise connections between tree leaves represent pairwise synteny relationships and are colored by the four detected microsynteny clusters in Vertebrata, as shown in Fig 2B and S13 Fig. Internal pairwise connections in gray represent minor microsynteny relationships not included in any community. Black dots on the tip of the leaves represent genes belonging to the only orthogroup detected in animals. b) Representation of microsynteny blocks of FIB and FIB-like genes. The Xenarthra species D. novemcinctus is absent in the FIB syntenic block. In the FIB-like syntenic block, only sequences from eutherian mammals are present. Colored blocks represent syntenic genes.
Fig 7.
Evolutionary differences between the two microsynteny mammalian clusters.
a) Violin plot of the number of exons in each of the five major clades of Chordata animals and arthropods. Points on the plot represent specific data. The number of exons in Actinopterygii, amphibians, and reptiles ranges from 7–10 exons, while that in mammals ranges from 1–10. The curved arrow above the mammalian violin plot indicates the two microsynteny clusters in figure b. b) Two microsynteny clusters detected in mammals and belonging to FIB (cluster A) and FIB-like genes (cluster B) specifically. Arrows under clusters indicate specific boxplots in figure c. c) Boxplot of the number of exons of the genes from the specific microsynteny clusters of mammals. Genes from cluster A (FIB genes) have a mean of 9 exons, while those in microsynteny cluster B (FIB-like genes) have a mean of one exon per gene. d) Depiction of microsynteny communities on a phylogenetic gene tree of animals. The pairwise syntenic relationship of clusters A and B (FIB and FIB-like, respectively) are indicated with black arrows, and the links are colored following Fig 5 to show the absence of syntenic relationship in both clusters (evolving from different genomic context). Green and yellow lines on the tree represent syntenic pairwise connections. e) Ks values for each microsynteny cluster. For the analysis, we carried 1800 and 2664 comparisons of homologous proteins for clusters A and B, respectively. f) Genes chosen from each syntenic cluster were inspected for expression values from transcriptomic atlases (as described in materials and methods). Colored nodes within clusters represent the genes chosen for the analysis. We use genes from species that had two copies, one in each cluster (one FIB and one FIB-like gene), and that had expression information available in the Expression Atlas (EMBL-EBI). g) Heatmap from the expression values of chosen genes in f, clustered according to taxonomy. On the "x" axis (*)frontal lobe, and (**)lung are the tissues used in the analysis.