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

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.

Chromosome-level reference genome of the European wasp spiderArgiope bruennichi: a resource for studies on range expansion and evolutionary adaptation

“…(Table 3). [25] classification of these genes is poorly understood. With these three gene sets (Hox, spidroin, and venom), we performed a TBLASTN search against our genome assembly (v. 2.10.0+) (TBLASTN, RRID:SCR_011822) [62,63].…”

A Giant Genome for a Giant Crayfish (Cherax quadricarinatus) With Insights Into cox1 Pseudogenes in Decapod Genomes

“…The genetics of C. quadricarinatus has been well studied using PCR-based approaches and recently, next generation sequencing has been used for mitogenomic and transcriptomic studies (Baker et al, 2008;Gan et al, 2016;Tan et al, 2016). In this paper, we present the first genome assembly for a southern hemisphere crayfish using a hybrid assembly approach utilizing long Nanopore reads and short Illumina reads, which has proven to be an efficient and effective approach for the assembly and annotation of species with large and repetitive genomes (Austin et al, 2017;Tan et al, 2018;Gan et al, 2019;Sánchez-Herrero et al, 2019), but has only been minimally explored to support decapod assemblies (Van Quyen et al, 2020).…”

Gene sequence analysis of toxins from the spider Phoneutria nigriventer revealed an intronless feature

“…To the best of our knowledge, only seven spider genomes have been published to date: Acanthoscurria geniculata (Mygalomorphae) and Stegodyphus mimosarum (Araneomorphae) [43]; Trichonephila clavipes (Araneomorphae) [44]; Parasteatoda tepidariorum (Araneomorphae) [45]; Pardosa pseudoannulata (Araneomorpha) [46]; Araneus ventricosus (Araneomorphae) [47] and Dysdera silvatica (Araneomorphae) [48]. In addition, the 5000 arthropod genome initiative (i5K), which is committed to sequencing and analyzing 5000 highpriority arthropods [49], made available a draft of Loxosceles reclusa genome.…”