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).