Sampling, DNA Sequencing and Genome assembly
The new genome assembly of D. silvatica was obtained using the
previous genome assembly (denoted as version 1; Sánchez-Herrero et al.,
2019), which was further scaffolded using Chicago and Hi-C libraries.
Version 1 assembly was generated using a hybrid de novo genome
assembly by combining information from five individuals and four types
of sequencing libraries; see Table 1 in Sánchez-Herrero et al. 2019. We
generated the latest sequencing libraries using a single female of the
genus Dysdera , sampled in March 2012 in La Gomera (Canary
Islands), identified in the laboratory as D. silvatica , frozen in
nitrogen liquid and stored at -80°C until its use.
DNA extraction and sequencing were performed in Dovetail Genomics (Santa
Cruz; California). The newly generated sequence data was obtained as a
combination of Chicago (one library), Hi-C (one library) and Illumina
150-bp paired-end (HiSeq X ten platform; one lane) sequencing libraries.
The final assembly (D. silvatica reference genome version 2) was
generated using the HiRise scaffolding software (Putnam et al., 2016),
and further polished with NextPolish (Hu, Fan, Sun, & Liu, 2020) using
illumina short-read data from a single individual unequivocally
identified as D. silvatica (see results and discussion section).
We determined the completeness of the new assembly by applying the
pipeline of Benchmarking Universal Single Copy Orthologs (BUSCO; v.
5.0.0; Seppey, Manni, & Zdobnov, 2019), searching the arachnida (odb10;
2934 genes), arthropoda (odb10; 1013 genes) and eukaryota (odb10; 255
genes) datasets.