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.