Figure Legends
Figure 1. Tree of life of the order Araneae. Relationships and divergence time estimates followed (Kallal et al., 2020). Main evolutionary lineages and taxonomic groups within spiders indicated as grey clades; the number in brackets indicates the estimated number of included families. Phylogenetic relationships of species with genomic information are highlighted (orange lines). Species used for the annotation and homology-based searches of D. silvatica genome are denoted with an asterisk.
Figure 2. Long-range contact heat-map of paired-end Hi-C reads. The x and y axes show the mapping positions of the first and second read in the read pair, respectively, grouped into bins; the color of each square gives the number of read pairs within that bin. The seven largest scaffolds, which likely correspond to the seven pseudochromosomes described in this species, represent the ~87% of total assembly. The large scaffold, which corresponds to the X chromosome, is 317.9 Mb long. In order of length, and after chromosome 6, the next scaffold is the ChrU1 (22.3 Mb long).
Figure 3. Homology-based search across different ecdysozoa species. A) Pie chart showing the taxonomic distribution of positive BLAST hits of the functional annotation set of D. silvatica(n = 28,904 genes) across the Araneae species illustrated in Figure 1 and the rest of the arachnida, arthropoda and ecdysozoa also analysed in Sánchez-Herrero et al. (2019). B) Homology relationships across D. silvatica (Dsil) and chelicerates genomes available in OrthoDB v10, P. tepidariorum (Ptep), S. mimosarum (Smim),Ixodes scapularis (Isca), and Tetranychus urticae (Turt). Red and orange bars indicate the fraction of single-copy genes identified in all species (1:1 orthologs), and those identified in four species (missing in one species), respectively. The dark and light green bars show orthologous relationships present in all, or in 4 species, respectively, that are not included in the two previous categories. The blue bar shows other more complex homologous relationships.
Figure 4. Distribution of the Gr (panel A) and Ir(panel B) family members across the seven pseudochromosomes and the scaffold ChrU1 of D. silvatica . Genes in clusters are shown to the left of pseudochromosomes.
Figure 5. Genome organization and relationships between physical and evolutionary distances of the members of the Gr andIr families on the D. silvatica pseudochromosome 1. A and C) Heatmaps illustrating the distribution of physical distances (in units of 100 kb) along the pseudochromosome. B and D) Plots comparing pairwise amino acid and physical (on a logarithmic scale) distances between Gr or Ir copies in the D. silvaticapseudochromosome. Colored and grey points show distances within and outside genomic clusters, respectively. Different clusters are depicted in different colors.
Figure 6. Phylogenetic relationships among the members of theGr family of D. silvatica and D. melanogaster . The tree only includes the copies of D. silvatica classified as complete genes. The outer ring indicates the chromosome (Chr; in different colors) in which the genes included in the tree are located. The inner ring shows information about genomic clusters (chromosome, in the same color scale that in outer ring, genomic cluster number: member number in the cluster). The scale bar refers to 1 amino acid substitution per site. The tree was rooted in its midpoint. Minor SC, minor scaffolds. Red and green terminal branches correspond to D. silvatica and D. melanogaster Gr , respectively. Given that the tree in this figure only includes complete copies, some genomic clusters in table 3 and figure 4A do not appear here.
Figure 7. Phylogenetic relationships among the members of theIr/IGluR family of D. silvatica and D. melanogaster . The tree only includes the copies classified as complete genes in this work. The light blue, dark blue and purpura shading of gene names designate the members of the iGluR , Ir25a/8aand Ir subfamilies, respectively. The tree was rooted considering NMDAR clade as the outgroup (Croset et al., 2010). The outer ring indicates the chromosome (Chr) in which the genes included in the tree are located. The inner ring shows information about genomic clusters (chromosome, in the same color scale that in outer ring, genomic cluster number: member number in the cluster). The scale bar refers to 1 amino acid substitution per site. Minor SC, minor scaffolds. Red and green terminal branches correspond to D. silvatica and D. melanogaster , respectively. The red triangles mark the D. silvatica genes with putative distant homologs in D. melanogaster . Given that the tree in this figure only includes complete copies, some genomic clusters in table 3 and figure 4B do not appear here.