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.