Introduction
Arthropoda is the most species-rich phylum on Earth, virtually found in all ecosystems, and includes about 80% of known animal species (Zhang, 2011, 2013). It encompasses four extant subphyla, namely Chelicerata, Myriapoda, Crustacea (paraphyletic) and Hexapoda, and the extinct Trilobita. Among them, Chelicerata accounts for about 10% of arthropod species, most of which belong to the class Arachnida (about 130,000 species; (Coddington, Jonathan A., Giribet, G., Harvey, M. S., Prendini, L., and Walter, 2004; Garb, Sharma, & Ayoub, 2018; Sharma et al., 2014). Despite this great representation and special interest in many basic and translational research areas, such as material sciences (silk from spiders), bioactive natural compounds (venom toxins from spiders and scorpions), or pest control (mites, Acari), there are currently very few available genome sequences of species from this group (Garb et al., 2018; Thomas et al., 2020; Vizueta, Rozas, & Sánchez-Gracia, 2018), being most of them highly fragmented and incomplete. In fact, only two chromosome-level spider genomes have been reported to date (Fan et al., 2021; Sheffer et al., 2021).
Spiders (order Araneae), the largest group within Arachnida, with at least ~49,000 known species (World Spider Catalog, 2021), is a highly diverse group of predators that can be found in nearly all terrestrial ecosystems (Figure 1). Recent studies have greatly helped to elucidate their phylogeny and delimitate its main evolutionary lineages (Wheeler et al., 2017; Kallal et al., 2020). The nocturnal ground-dwelling genus Dysdera Latreille 1804, which contains 286 species (World Spider Catalog, 2021), mostly with a circum-Mediterranean distribution, represents nearly half of the diversity of the Dysderidae family. Approximately 50 species of this genus are endemic from the Canary Islands archipelago, representing one of the most spectacular examples of diversification on islands within spiders (Arnedo, Oromí, Múrria, Macías-Hernández, & Ribera, 2007; Arnedo, Oromí, & Ribera, 2001; Macías-Hernández, López, Roca-Cusachs, Oromí, & Arnedo, 2016; Vizueta, Macías-Hernández, Arnedo, Rozas, & Sánchez-Gracia, 2019). Shifts in dietary preferences have been identified as one of the main drivers of island diversification in this group (Řezáč, Pekár, Arnedo, Macías-Hernández, & Řezáčová, 2021). Indeed, Dysdera includes some of the few reported cases of stenophagy (i.e. prey specialization) across the mostly generalists spiders (Pekár, Líznarová, & Řezáč, 2016), with some species (both continental and island species) facultatively or even obligatorily specialized in feeding on terrestrial woodlice (Crustacea: Isopoda). This trophic specialization was accompanied by morphological (modifications of mouthparts), behavioral (unique hunting strategies) and physiological adaptations to capture woodlice and to assimilate the toxic substances and heavy metals accumulated in these usually rejected prey (Hopkin & Martin, 1985; Řezáč, Pekár, & Lubin, 2008; Řezáč & Pekár, 2007; Toft & Macías-Hernández, 2017). In the Canary Islands, as in continental species, these diet shifts have occurred recurrently in different geographic areas.
The high rates of species proliferation coupled with multiple independent eco-phenotypic shifts make Dysdera an excellent model for understanding the genomic basis of adaptive radiations (Vizueta et al., 2019). With the aim of obtaining a reference genome for this genus, we sequenced the genome of Dysdera silvatica Schmidt, 1981 (~1.37 Gb) and generated the first de novo genome assembly of this species using a hybrid strategy (Sánchez-Herrero et al., 2019). Nevertheless, most of the assembly was based on short reads, which, added to the high repetitive nature of the genome sequences of this species (53.8%), resulted in a very fragmented genome draft (N50 of 38 kb). While this first draft has been a fruitful research resource, it prevented the study of genomic aspects requiring greater continuity, such as gene mapping across the chromosomes, the comprehensive annotation of very long genes and gene clusters, or the identification of structural variation. These features are fundamental for understanding the biological and evolutionary meaning of the genome structure and gene organization. Some clear examples of the benefits of having a highly continuous chromosome-level assembly are the study of the genome structure and evolution of gene families, the impact of a number genome features (e.g., recombination, base content, distribution of genes and repetitive regions, etc..) on adaptive processes, the analysis of impact of hybridization and divergence between populations, or the role of chromosomal evolution in speciation (Bleidorn, 2016; Pollard, Gurdasani, Mentzer, Porter, & Sandhu, 2018; Saha, 2019).
We present the first high-quality chromosome-level assembly of the species D. silvatica (D. silvatica genome draft, version 2.0) . Using the first version of the genome assembly of this species (Sánchez-Herrero et al., 2019) as a starting point, we used proximity ligation libraries (Chicago and Hi-C libraries; Dovetail genomics), and the HiRise pipeline (Putnam et al., 2016) to obtain an improved, highly continuous assembly of this genome. As an example of the enhanced utility of the version 2.0, we have identified and annotated the members of the two major arthropod chemoreceptor gene families in this genome and performed a comprehensive analysis of the physical clustering of all family members at chromosome-level scale. This new genomic resource will foster further studies of the molecular basis underlying rapid diversification in islands and ecological shifts by allowing comparative genomic analyses based on variation data that is inaccessible in currently available fragmented genomes, such as structural variants, repetitive elements, and large gene families. Additionally, this high-quality genomic data will contribute to improve our understanding of the structure, organization, and genome evolution in chelicerates.