Structural and functional genome annotation
Structural annotation of the soft-masked genome was accomplished with BRAKER2 (Brůna, Hoff, Lomsadze, Stanke, & Borodovsky, 2021; Hoff, Lomsadze, Borodovsky, & Stanke, 2019; Stanke, Diekhans, Baertsch, & Haussler, 2008; Stanke, Schöffmann, Morgenstern, & Waack, 2006), using both D. silvatica RNAseq data (Vizueta et al., 2017) and orthologous sequences from five species of this genus (includingD. silvatica ) (Vizueta et al., 2019) as evidence (–etpmode) (Hoff et al., 2019). To perform the functional annotation of the gene models, we used BLASTP v2.4 searches (E -value = 10−5) against NCBI-nr, Swiss-Prot, and an updated version of the ArthropodDB databases (see Vizueta et al., 2017, for a detailed description of ArthropodDB). Furthermore, we also searched the predicted peptides for specific protein domain signatures in InterProScan v5.31.70.0 (Jones et al., 2014) and integrated all functional evidence.
Gene ontology (GO) terms (Ashburner et al, 2000) were obtained inherited from the BLAST (using top five significant hits) and InterProScan results. We used Blast2GO to associate KEGG enzymes and pathways to the annotated genes (Kanehisa, & Goto, 2000). We detected the transfer RNA genes (tRNAs) encoded in the genomic sequence of D. silvaticausing the tRNAscan-SE v2.0.7 software (Chan, Lin, Mak, & Lowe, 2019).
Homology searches
We searched for homologs of D. silvatica in the genome data of representatives of a broad taxonomic range across the order Araneae, namely Acanthoscurria geniculata (C. L. Koch, 1841) (Theraphosidae), in the suborder Mygalomorphae, and the representatives of the suborder Araneomorphae Loxosceles reclusa Gertsch & Mulaik, 1940 (Sicariidae), together with D. silvatica member of the clade Synspermiata, Stegodyphus mimosarum Pavesi, 1883 andS. dumicola Pocock, 1898 (Eresidae), and the AraneoideaParasteatoda tepidariorum (C. L. Koch, 1841) andLatrodectus hesperus Chamberlin & Ivie, 1935, both in the family Theridiidae, and the Araneidae Trichonephila clavipes (Linnaeus, 1767) and Argiope bruennichi (Scopoli, 1772) (Figure 1; Table S1), as well as all other arachnids, arthropods and ecdysozoa species surveyed in Sánchez-Herrero et al., (2019). The search was conducted by a series of BLASTP searches (E -value cutoff < 10−3; we also applied a filter of >30% alignment length to consider a hit as a positive). Finally, we also searched for orthogroups and establish homology relationships amongD. silvatica and the arachnids included in the OrthoDB (v10) (Kriventseva et al., 2019) database, namely the tick Ixodes scapularis Say, 1821 (Ullmann, Lima, Guerrero, Piesman, & Black IV, 2005), the mite Tetranychus urticae C. L. Koch, 1836 (Grbić et al., 2011), and the spiders Stegodyphus mimosarum (Sanggaard et al., 2014) and Parasteatoda tepidariorum(Schwager et al., 2017).