(A) Genome size and composition in terms of coding exonic, intronic and intergenic sequences of unicellular holozoan and selected metazoans. Percentage of repetitive sequences shown as black bars. Genome size of the Metazoa LCA (gray bar) from (Simakov and Kawashima, 2017) (exonic, intronic and intergenic composition not known). (B) Profile of TE composition for selected organisms. Density plots indicate the sequence similarity profile of the TE complement in each organism. Embedded pie-charts denote the relative abundance, in nucleotides, of the main TE superclasses in each genome: retrotransposons (SINE, LINE and LTR), DNA transposons (DNA) and unknown. Nc: total number TE copies in the genome; Nf: number of families to which these belong; P25f and P75f: percentage of most-frequent TE families that account for 25% and 75% of the total number of TE copies, respectively. (C) Heatmap of pairwise microsynteny conservation between 10 unicellular holozoan genomes. Species ordered according the number of shared syntenic genes (Euclidean distances, Ward clustering). At the right: selected pairwise comparisons of syntenic single-copy orthologs between unicellular holozoan genomes. Numbers denote number of syntenic genes, total number of single-copy orthologs, and proportions (%) of syntenic genes per the compared orthologs. Circle segments are scaffolds sharing ortholog pairs, connected by gray lines. (D) Phylogenetic distances between unicellular holozoans and four selected animals: Homo sapiens, Nematostella vectensis, Trichoplax adhaerens and Amphimedon queenslandica. Red asterisks denote organisms that have lower phylogenetic distances to metazoans than one (single asterisk) or both choanoflagellates (double asterisks) (p value < 0.05 in Wilcoxon rank sum test). † indicates significantly higher distances between Corallochytrium and metazoans. Figure 1—source data 1, Figure 3—source data 1, 2 and 3.
DOI:
http://dx.doi.org/10.7554/eLife.26036.010
Figure 3—source data 1. Annotated repetitive sequences from 10 unicellular Holozoa genomes.Includes transposable elements, simple repeats, low complexity regions and small RNAs. Used in
Figure 3.
Figure 3—source data 2. List of annotated transposable element families in 10 unicellular Holozoa genomes, with copy counts.
Figure 3—source data 3. List of annotated transposable element families shared between the genomes of 10 unicellular holozoans and 11 animals, including the number of species where the TE family is present.Three lists are included: all TE families present in any holozoan, a list restricted to the most abundant TE families accounting for 75% of all copies in each holozoan (P
75f statistic; see
Figure 3B), and
id. for 25% copies (P
25f statistic). Used in
Figure 3.