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. 2019 Aug 1;8(8):giz099.
doi: 10.1093/gigascience/giz099.

The draft genome sequence of the spider Dysdera silvatica (Araneae, Dysderidae): A valuable resource for functional and evolutionary genomic studies in chelicerates

Jose Francisco Sánchez-Herrero  1 , Cristina Frías-López  1 , Paula Escuer  1 , Silvia Hinojosa-Alvarez  1   2 , Miquel A Arnedo  3 , Alejandro Sánchez-Gracia  1 , Julio Rozas  1
Affiliations

The draft genome sequence of the spider Dysdera silvatica (Araneae, Dysderidae): A valuable resource for functional and evolutionary genomic studies in chelicerates

Jose Francisco Sánchez-Herrero et al. Gigascience. .

Abstract

Background: We present the draft genome sequence of Dysdera silvatica, a nocturnal ground-dwelling spider from a genus that has undergone a remarkable adaptive radiation in the Canary Islands.

Results: The draft assembly was obtained using short (Illumina) and long (PaciBio and Nanopore) sequencing reads. Our de novo assembly (1.36 Gb), which represents 80% of the genome size estimated by flow cytometry (1.7 Gb), is constituted by a high fraction of interspersed repetitive elements (53.8%). The assembly completeness, using BUSCO and core eukaryotic genes, ranges from 90% to 96%. Functional annotations based on both ab initio and evidence-based information (including D. silvatica RNA sequencing) yielded a total of 48,619 protein-coding sequences, of which 36,398 (74.9%) have the molecular hallmark of known protein domains, or sequence similarity with Swiss-Prot sequences. The D. silvatica assembly is the first representative of the superfamily Dysderoidea, and just the second available genome of Synspermiata, one of the major evolutionary lineages of the "true spiders" (Araneomorphae).

Conclusions: Dysderoids, which are known for their numerous instances of adaptation to underground environments, include some of the few examples of trophic specialization within spiders and are excellent models for the study of cryptic female choice. This resource will be therefore useful as a starting point to study fundamental evolutionary and functional questions, including the molecular bases of the adaptation to extreme environments and ecological shifts, as well of the origin and evolution of relevant spider traits, such as the venom and silk.

Keywords: Araneomorphae; Canary Islands; genome annotation; hybrid genome assembly.

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Figures

Figure 1
Figure 1
Male of Dysdera silvatica from Teselinde (La Gomera, Canary Islands). Photo credit: Miquel Arnedo.
Figure 2
Figure 2
Phylogenetic relationships of the species used for the D. silvatica genome annotation (see Supplementary Table S1-11 for further details) and completeness analysis. Because the chelicerata phylogeny is controversial (e.g., [20], [21]), we set the most conflictive clades as polytomies. Divergence times were obtained from Carlson et al. (2017) [22] and the TimeTree web server (http://www.timetree.org/). Cz, cretaceous period.
Figure 3
Figure 3
Bar plot of the annotation of the repetitive elements within the HCRs (2.5× threshold) at different intra-HCR length cutoffs (150, 500, 1,000, and 5,000 bp) (Supplementary Table S2-2a). Colors represent the type of repeat element identified by RepeatMasker. "Other types" class includes the LTR elements, small RNA, and satellite information that represent a small fraction.
Figure 4
Figure 4
(a) Pie chart illustrating the taxonomic distribution of positive BLAST hits of the D. silvatica protein-coding genes against the sequence data of species included in Fig. 2. (b) Homology relationships among D. silvatica (Dsil) and different chelicerates genomes available in OrthoDB v10 [56], Parasteatoda tepidariorum (Ptep), Stegodyphus mimosarum (Smim), Ixodes scapularis (Isca), and Tetranychus urticae (Turt). Red and orange bars indicate the fraction of single-copy genes (1:1 orthologs) identified in all species, and in all but 1 (e.g., missing in 1 species), respectively. The dark and light green bar indicate the fraction of orthologs present in all species and in all but 1, respectively, that are not included in previous categories. The blue bar (other orthology/homology) shows other more complex homologous relationships. The results were generated by uploading D. silvatica proteins to the OrthoDB web server.
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