Recent progress and prospects for advancing arachnid genomics

A robust genome assembly with transcriptomic data from the striped bark scorpion, Centruroides vittatus

Scorpions, a seemingly primitive, stinging arthropod taxa, are known to exhibit marked diversity in their venom components. These venoms are known for their human pathology, but they are also important as models for therapeutic and drug development applications. In this study, we report a high-quality genome assembly and annotation of the striped bark scorpion, Centruroides vittatus, created with several shotgun libraries. The final assembly is 760 Mb in size, with a BUSCO score of 97.8%, a 30.85% GC, and an N50 of 2.35 Mb. We estimated 36,189 proteins with 37.32% assigned to Gene Ontology (GO) terms in our GO annotation analysis. We mapped venom toxin genes to 18 contigs and 2 scaffolds. We were also able to identify expression differences between venom gland (telson) and body tissue (carapace) with 19 sodium toxin and 14 potassium toxin genes to 18 contigs and 2 scaffolds. This assembly, along with our transcriptomic data, provides further data to investigate scorpion venom genomics.

The Development and Expansion of in vivo Germline Editing Technologies in Arthropods: Receptor-Mediated Ovary Transduction of Cargo (ReMOT Control) and Beyond

In the past 20 years, sequencing technologies have led to easy access to genomic data from nonmodel organisms in all biological realms. Insect genetic manipulation, however, continues to be a challenge due to various factors, including technical and cost-related issues. Traditional techniques such as microinjection of gene-editing vectors into early stage embryos have been used for arthropod transgenesis and the discovery of Clustered regularly interspaced short palindromic repeats and CRISPR-associated protein (CRISPR-Cas) technologies allowed for targeted mutagenesis and the creation of knockouts or knock-ins in arthropods. Receptor-Mediated Ovary Transduction of Cargo (ReMOT Control) acts as an alternative to embryonic microinjections, which require expensive equipment and extensive hands-on training. ReMOT Control's main advantage is its ease of use coupled with the ability to hypothetically target any vitellogenic species, as injections are administered to the egg-laying adult rather than embryos. After its initial application in the mosquito Aedes aegypti, ReMOT Control has successfully produced mutants not only for mosquitoes but for multiple arthropod species from diverse orders, such as ticks, mites, wasps, beetles, and true bugs, and is being extended to crustaceans, demonstrating the versatility of the technique. In this review, we discuss the current state of ReMOT Control from its proof-of-concept to the advances and challenges in the application across species after 5 years since its development, including novel extensions of the technique such as direct parental (DIPA)-CRISPR.

A comprehensive review of recent advances in silk sericin: Extraction approaches, structure, biochemical characterization, and biomedical applications

Silks are natural polymers that have been widely used for centuries. Silk consists of a filament core protein, termed fibroin, and a glue-like coating substance formed of sericin (SER) proteins. This protein is extracted from the silkworm cocoons (particularly Bombyx mori) and is mainly composed of amino acids like glycine, serine, aspartic acid, and threonine. Silk SER can be obtained using numerous methods, including enzymatic extraction, high-temperature, autoclaving, ethanol precipitation, cross-linking, and utilizing acidic, alkali, or neutral aqueous solutions. Given the versatility and outstanding properties of SER, it is widely fabricated to produce sponges, films, and hydrogels for further use in diverse biomedical applications. Hence, many authors reported that SER benefits cell proliferation, tissue engineering, and skin tissue restoration thanks to its moisturizing features, antioxidant and anti-inflammatory properties, and mitogenic effect on mammalian cells. Remarkably, SER is used in drug delivery depending on its chemical reactivity and pH-responsiveness. These unique features of SER enhance the bioactivity of drugs, facilitating the fabrication of biomedical materials at nano- and microscales, hydrogels, and conjugated molecules. This review thoroughly outlines the extraction techniques, biological properties, and respective biomedical applications of SER.

The Impact of Whole Genome Duplication on the Evolution of the Arachnids

The proliferation of genomic resources for Chelicerata in the past 10 years has revealed that the evolution of chelicerate genomes is more dynamic than previously thought, with multiple waves of ancient whole genome duplications affecting separate lineages. Such duplication events are fascinating from the perspective of evolutionary history because the burst of new gene copies associated with genome duplications facilitates the acquisition of new gene functions (neofunctionalization), which may in turn lead to morphological novelties and spur net diversification. While neofunctionalization has been invoked in several contexts with respect to the success and diversity of spiders, the overall impact of whole genome duplications on chelicerate evolution and development remains imperfectly understood. The purpose of this review is to examine critically the role of whole genome duplication on the diversification of the extant arachnid orders, as well as assess functional datasets for evidence of subfunctionalization or neofunctionalization in chelicerates. This examination focuses on functional data from two focal model taxa: the spider Parasteatoda tepidariorum, which exhibits evidence for an ancient duplication, and the harvestman Phalangium opilio, which exhibits an unduplicated genome. I show that there is no evidence that taxa with genome duplications are more successful than taxa with unduplicated genomes. I contend that evidence for sub- or neofunctionalization of duplicated developmental patterning genes in spiders is indirect or fragmentary at present, despite the appeal of this postulate for explaining the success of groups like spiders. Available expression data suggest that the condition of duplicated Hox modules may have played a role in promoting body plan disparity in the posterior tagma of some orders, such as spiders and scorpions, but functional data substantiating this postulate are critically missing. Spatiotemporal dynamics of duplicated transcription factors in spiders may represent cases of developmental system drift, rather than neofunctionalization. Developmental system drift may represent an important, but overlooked, null hypothesis for studies of paralogs in chelicerate developmental biology. To distinguish between subfunctionalization, neofunctionalization, and developmental system drift, concomitant establishment of comparative functional datasets from taxa exhibiting the genome duplication, as well as those that lack the paralogy, is sorely needed.

A molecular atlas reveals the tri-sectional spinning mechanism of spider dragline silk

The process of natural silk production in the spider major ampullate (Ma) gland endows dragline silk with extraordinary mechanical properties and the potential for biomimetic applications. However, the precise genetic roles of the Ma gland during this process remain unknown. Here, we performed a systematic molecular atlas of dragline silk production through a high-quality genome assembly for the golden orb-weaving spider Trichonephila clavata and a multiomics approach to defining the Ma gland tri-sectional architecture: Tail, Sac, and Duct. We uncovered a hierarchical biosynthesis of spidroins, organic acids, lipids, and chitin in the sectionalized Ma gland dedicated to fine silk constitution. The ordered secretion of spidroins was achieved by the synergetic regulation of epigenetic and ceRNA signatures for genomic group-distributed spidroin genes. Single-cellular and spatial RNA profiling identified ten cell types with partitioned functional division determining the tri-sectional organization of the Ma gland. Convergence analysis and genetic manipulation further validated that this tri-sectional architecture of the silk gland was analogous across Arthropoda and inextricably linked with silk formation. Collectively, our study provides multidimensional data that significantly expand the knowledge of spider dragline silk generation and ultimately benefit innovation in spider-inspired fibers.

Chromosome-level genome and the identification of sex chromosomes in Uloborus diversus

The orb web is a remarkable example of animal architecture that is observed in families of spiders that diverged over 200 million years ago. While several genomes exist for araneid orb-weavers, none exist for other orb-weaving families, hampering efforts to investigate the genetic basis of this complex behavior. Here we present a chromosome-level genome assembly for the cribellate orb-weaving spider Uloborus diversus. The assembly reinforces evidence of an ancient arachnid genome duplication and identifies complete open reading frames for every class of spidroin gene, which encode the proteins that are the key structural components of spider silks. We identified the 2 X chromosomes for U. diversus and identify candidate sex-determining loci. This chromosome-level assembly will be a valuable resource for evolutionary research into the origins of orb-weaving, spidroin evolution, chromosomal rearrangement, and chromosomal sex determination in spiders.

Assessing species coverage and assembly quality of rapidly accumulating sequenced genomes

BACKGROUND

Ambitious initiatives to coordinate genome sequencing of Earth's biodiversity mean that the accumulation of genomic data is growing rapidly. In addition to cataloguing biodiversity, these data provide the basis for understanding biological function and evolution. Accurate and complete genome assemblies offer a comprehensive and reliable foundation upon which to advance our understanding of organismal biology at genetic, species, and ecosystem levels. However, ever-changing sequencing technologies and analysis methods mean that available data are often heterogeneous in quality. To guide forthcoming genome generation efforts and promote efficient prioritization of resources, it is thus essential to define and monitor taxonomic coverage and quality of the data.

FINDINGS

Here we present an automated analysis workflow that surveys genome assemblies from the United States NCBI, assesses their completeness using the relevant BUSCO datasets, and collates the results into an interactively browsable resource. We apply our workflow to produce a community resource of available assemblies from the phylum Arthropoda, the Arthropoda Assembly Assessment Catalogue. Using this resource, we survey current taxonomic coverage and assembly quality at the NCBI, examine how key assembly metrics relate to gene content completeness, and compare results from using different BUSCO lineage datasets.

CONCLUSIONS

These results demonstrate how the workflow can be used to build a community resource that enables large-scale assessments to survey species coverage and data quality of available genome assemblies, and to guide prioritizations for ongoing and future sampling, sequencing, and genome generation initiatives.

Chromosomal-level genome of a sheet-web spider provides insight into the composition and evolution of venom

Spiders are the most abundant venomous predators in the world. Previous research related to spider venom has mostly relied on transcriptomes and proteomes, with only a few high-quality genomes available. This is far from consistent with the species diversity of spiders. In this study, we constructed a high-quality chromosome-level genome assembly of Hylyphantes graminicola, which contained 13 chromosomes, with a genome length of 931.68 Mb and scaffold N50 of 77.07 Mb. Integrating genome, transcriptome, and proteome profiling, we identified a total of 59 coding genes among nine toxin gene families. Among them, Group 7 allergen (ALL7) protein was reported in spider venom for the first time. Its coding genes had a predicted signal peptide and maintained high expression levels in the venom, suggesting that ALL7 plays an important role in venom and maybe is a type of newly discovered venom toxin in the spider. By implementing comparative genomics, we found a similar gene number of main toxin gene families in spiders and the scorpion genome with conservative evolutionary rates, indicating that these toxin genes could be an ancient (~400 million years) and a conserved "basic toolkit" for spiders and scorpions to perform primary defense functions. Obtaining high-quality chromosome-level genomes from spiders not only facilitates venom research and toxin resource application, but also can improve comparative genomic analysis in other important traits, like the evolution of silk or behavior.

The Tetragnatha kauaiensis Genome Sheds Light on the Origins of Genomic Novelty in Spiders

Spiders (Araneae) have a diverse spectrum of morphologies, behaviors, and physiologies. Attempts to understand the genomic-basis of this diversity are often hindered by their large, heterozygous, and AT-rich genomes with high repeat content resulting in highly fragmented, poor-quality assemblies. As a result, the key attributes of spider genomes, including gene family evolution, repeat content, and gene function, remain poorly understood. Here, we used Illumina and Dovetail Chicago technologies to sequence the genome of the long-jawed spider Tetragnatha kauaiensis, producing an assembly distributed along 3,925 scaffolds with an N50 of ∼2 Mb. Using comparative genomics tools, we explore genome evolution across available spider assemblies. Our findings suggest that the previously reported and vast genome size variation in spiders is linked to the different representation and number of transposable elements. Using statistical tools to uncover gene-family level evolution, we find expansions associated with the sensory perception of taste, immunity, and metabolism. In addition, we report strikingly different histories of chemosensory, venom, and silk gene families, with the first two evolving much earlier, affected by the ancestral whole genome duplication in Arachnopulmonata (∼450 Ma) and exhibiting higher numbers. Together, our findings reveal that spider genomes are highly variable and that genomic novelty may have been driven by the burst of an ancient whole genome duplication, followed by gene family and transposable element expansion.

The biology and evolution of spider venoms

Spiders are diverse, predatory arthropods that have inhabited Earth for around 400 million years. They are well known for their complex venom systems that are used to overpower their prey. Spider venoms contain many proteins and peptides with highly specific and potent activities suitable for biomedical or agrochemical applications, but the key role of venoms as an evolutionary innovation is often overlooked, even though this has enabled spiders to emerge as one of the most successful animal lineages. In this review, we discuss these neglected biological aspects of spider venoms. We focus on the morphology of spider venom systems, their major components, biochemical and chemical plasticity, as well as ecological and evolutionary trends. We argue that the effectiveness of spider venoms is due to their unprecedented complexity, with diverse components working synergistically to increase the overall potency. The analysis of spider venoms is difficult to standardize because they are dynamic systems, fine-tuned and modified by factors such as sex, life-history stage and biological role. Finally, we summarize the mechanisms that drive spider venom evolution and highlight the need for genome-based studies to reconstruct the evolutionary history and physiological networks of spider venom compounds with more certainty.

The chromosome-scale assembly of the Canary Islands endemic spider Dysdera silvatica (Arachnida, Araneae) sheds light on the origin and genome structure of chemoreceptor gene families in chelicerates

Here, we present the chromosome-level genome assembly of Dysdera silvatica Schmidt, 1981, a nocturnal ground-dwelling spider endemic from the Canary Islands. The genus Dysdera has undergone a remarkable diversification in this archipelago mostly associated with shifts in the level of trophic specialization, becoming an excellent model to study the genomic drivers of adaptive radiations. The new assembly (1.37 Gb; scaffold N50 of 174.2 Mb), was performed using the chromosome conformation capture scaffolding technique, represents a continuity improvement of more than 4500 times with respect to the previous version. The seven largest scaffolds or pseudochromosomes, which cover 87% of the total assembly size, probably correspond with the seven chromosomes of the karyotype of this species, including a characteristic large X chromosome. To illustrate the value of this new resource we performed a comprehensive analysis of the two major arthropod chemoreceptor gene families (i.e., gustatory and ionotropic receptors). We identified 545 chemoreceptor sequences distributed across all pseudochromosomes, with a notable underrepresentation in the X chromosome. At least 54% of them localize in 83 genomic clusters with a significantly lower evolutionary distances between them than the average of the family, suggesting a recent origin of many of them. This chromosome-level assembly is the first high-quality genome representative of the Synspermiata clade, and just the third among spiders, representing a new valuable resource to gain insights into the structure and organization of chelicerate genomes, including the role that structural variants, repetitive elements and large gene families played in the extraordinary biology of spiders.

The brain transcriptome of the wolf spider, Schizocosa ocreata

OBJECTIVES

Arachnids have fascinating and unique biology, particularly for questions on sex differences and behavior, creating the potential for development of powerful emerging models in this group. Recent advances in genomic techniques have paved the way for a significant increase in the breadth of genomic studies in non-model organisms. One growing area of research is comparative transcriptomics. When phylogenetic relationships to model organisms are known, comparative genomic studies provide context for analysis of homologous genes and pathways. The goal of this study was to lay the groundwork for comparative transcriptomics of sex differences in the brain of wolf spiders, a non-model organism of the pyhlum Euarthropoda, by generating transcriptomes and analyzing gene expression.

DATA DESCRIPTION

To examine sex-differential gene expression, short read transcript sequencing and de novo transcriptome assembly were performed. Messenger RNA was isolated from brain tissue of male and female subadult and mature wolf spiders (Schizocosa ocreata). The raw data consist of sequences for the two different life stages in each sex. Computational analyses on these data include de novo transcriptome assembly and differential expression analyses. Sample-specific and combined transcriptomes, gene annotations, and differential expression results are described in this data note and are available from publicly-available databases.

Taxonomic Sampling and Rare Genomic Changes Overcome Long-Branch Attraction in the Phylogenetic Placement of Pseudoscorpions

Long-branch attraction is a systematic artifact that results in erroneous groupings of fast-evolving taxa. The combination of short, deep internodes in tandem with long-branch attraction artifacts has produced empirically intractable parts of the Tree of Life. One such group is the arthropod subphylum Chelicerata, whose backbone phylogeny has remained unstable despite improvements in phylogenetic methods and genome-scale data sets. Pseudoscorpion placement is particularly variable across data sets and analytical frameworks, with this group either clustering with other long-branch orders or with Arachnopulmonata (scorpions and tetrapulmonates). To surmount long-branch attraction, we investigated the effect of taxonomic sampling via sequential deletion of basally branching pseudoscorpion superfamilies, as well as varying gene occupancy thresholds in supermatrices. We show that concatenated supermatrices and coalescent-based summary species tree approaches support a sister group relationship of pseudoscorpions and scorpions, when more of the basally branching taxa are sampled. Matrix completeness had demonstrably less influence on tree topology. As an external arbiter of phylogenetic placement, we leveraged the recent discovery of an ancient genome duplication in the common ancestor of Arachnopulmonata as a litmus test for competing hypotheses of pseudoscorpion relationships. We generated a high-quality developmental transcriptome and the first genome for pseudoscorpions to assess the incidence of arachnopulmonate-specific duplications (e.g., homeobox genes and miRNAs). Our results support the inclusion of pseudoscorpions in Arachnopulmonata (new definition), as the sister group of scorpions. Panscorpiones (new name) is proposed for the clade uniting Scorpiones and Pseudoscorpiones.

Evolutionary pattern of karyotypes and meiosis in pholcid spiders (Araneae: Pholcidae): implications for reconstructing chromosome evolution of araneomorph spiders

BACKGROUND

Despite progress in genomic analysis of spiders, their chromosome evolution is not satisfactorily understood. Most information on spider chromosomes concerns the most diversified clade, entelegyne araneomorphs. Other clades are far less studied. Our study focused on haplogyne araneomorphs, which are remarkable for their unusual sex chromosome systems and for the co-evolution of sex chromosomes and nucleolus organizer regions (NORs); some haplogynes exhibit holokinetic chromosomes. To trace the karyotype evolution of haplogynes on the family level, we analysed the number and morphology of chromosomes, sex chromosomes, NORs, and meiosis in pholcids, which are among the most diverse haplogyne families. The evolution of spider NORs is largely unknown.

RESULTS

Our study is based on an extensive set of species representing all major pholcid clades. Pholcids exhibit a low 2n and predominance of biarmed chromosomes, which are typical haplogyne features. Sex chromosomes and NOR patterns of pholcids are diversified. We revealed six sex chromosome systems in pholcids (X0, XY, X1X20, X1X2X30, X1X2Y, and X1X2X3X4Y). The number of NOR loci ranges from one to nine. In some clades, NORs are also found on sex chromosomes.

CONCLUSIONS

The evolution of cytogenetic characters was largely derived from character mapping on a recently published molecular phylogeny of the family. Based on an extensive set of species and mapping of their characters, numerous conclusions regarding the karyotype evolution of pholcids and spiders can be drawn. Our results suggest frequent autosome-autosome and autosome-sex chromosome rearrangements during pholcid evolution. Such events have previously been attributed to the reproductive isolation of species. The peculiar X1X2Y system is probably ancestral for haplogynes. Chromosomes of the X1X2Y system differ considerably in their pattern of evolution. In some pholcid clades, the X1X2Y system has transformed into the X1X20 or XY systems, and subsequently into the X0 system. The X1X2X30 system of Smeringopus pallidus probably arose from the X1X20 system by an X chromosome fission. The X1X2X3X4Y system of Kambiwa probably evolved from the X1X2Y system by integration of a chromosome pair. Nucleolus organizer regions have frequently expanded on sex chromosomes, most probably by ectopic recombination. Our data suggest the involvement of sex chromosome-linked NORs in achiasmatic pairing.

Targeted mutagenesis using CRISPR-Cas9 in the chelicerate herbivore Tetranychus urticae

The use of CRISPR-Cas9 has revolutionized functional genetic work in many organisms, including more and more insect species. However, successful gene editing or genetic transformation has not yet been reported for chelicerates, the second largest group of terrestrial animals. Within this group, some mite and tick species are economically very important for agriculture and human health, and the availability of a gene-editing tool would be a significant advancement for the field. Here, we report on the use of CRISPR-Cas9 in the spider mite Tetranychus urticae. The ovary of virgin adult females was injected with a mix of Cas9 and sgRNAs targeting the phytoene desaturase gene. Natural mutants of this laterally transferred gene have previously shown an easy-to-score albino phenotype. Albino sons of injected virgin females were mated with wild-type females, and two independent transformed lines where created and further characterized. Albinism inherited as a recessive monogenic trait. Sequencing of the complete target-gene of both lines revealed two different lesions at expected locations near the PAM site in the target-gene. Both lines did not genetically complement each other in dedicated crosses, nor when crossed to a reference albino strain with a known genetic defect in the same gene. In conclusion, two independent mutagenesis events were induced in the spider mite T. urticae using CRISPR-Cas9, hereby providing proof-of-concept that CRISPR-Cas9 can be used to create gene knockouts in mites.

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

BACKGROUND

Phoneutria nigriventer spider venom contains several cysteine-rich peptide toxins that act on different ion channels. Despite extensive studies on its venom and description of cDNA sequences of several of its toxin precursors, the gene structure of these toxins remains unknown.

METHODS

Genomic regions encoding the precursors of three previously characterized P. nigriventer toxins - PnTx1, PnTx2-5 and PnTx4(5-5) - were amplified by PCR using specific primers. PCR fragments were cloned and sequenced. Obtained sequences were compared with their corresponding cDNA sequences.

RESULTS

The size of PCR fragments obtained and sequences corresponding to genomic regions encoding for the toxin precursors matched their cDNA sequences.

CONCLUSIONS

Despite a few nucleotide substitutions in the genomic regions encoding for the toxin precursors when compared with cDNA sequences, the results of the present work indicate that P. nigriventer toxins do not contain introns in their genes sequences.

The common house spider Parasteatoda tepidariorum

The common house spider Parasteatoda tepidariorum, belonging to the Chelicerata in the phylum Arthropoda, has emerged as an experimental system for studying mechanisms of development from an evolutionary standpoint. In this article, we review the distinct characteristics of P. tepidariorum, the major research questions relevant to this organism, and the available key methods and resources. P. tepidariorum has a relatively short lifecycle and, once mated, periodically lays eggs. The morphogenetic field of the P. tepidariorum embryo is cellular from an early stage and exhibits stepwise symmetry-breaking events and stripe-forming processes that are associated with body axes formation and segmentation, respectively, before reaching the arthropod phylotypic stage. Self-regulatory capabilities of the embryonic field are a prominent feature in P. tepidariorum. The mechanisms and logic underlying the evolvability of heritable patterning systems at the phylum level could be one of the major avenues of research investigated using this animal. The sequenced genome reveals whole genome duplication (WGD) within chelicerates, which offers an invertebrate platform for investigating the potential roles of WGD in animal diversification and evolution. The development and evolution of lineage-specific organs, including the book lungs and the union of spinnerets and silk glands, are attractive subjects of study. Studies using P. tepidariorum can benefit from the use of parental RNA interference, microinjection applications (including cell labeling and embryonic RNA interference), multicolor fluorescence in situ hybridization, and laser ablation as well as rich genomic and transcriptomic resources. These techniques enable functional gene discoveries and the uncovering of cellular and molecular insights.

Comparative Genomics Identifies Putative Signatures of Sociality in Spiders

Comparative genomics has begun to elucidate the genomic basis of social life in insects, but insight into the genomic basis of spider sociality has lagged behind. To begin, to characterize genomic signatures associated with the evolution of social life in spiders, we performed one of the first spider comparative genomics studies including five solitary species and two social species, representing two independent origins of sociality in the genus Stegodyphus. We found that the two social spider species had a large expansion of gene families associated with transport and metabolic processes and an elevated genome-wide rate of molecular evolution compared with the five solitary spider species. Genes that were rapidly evolving in the two social species relative to the five solitary species were enriched for transport, behavior, and immune functions, whereas genes that were rapidly evolving in the solitary species were enriched for energy metabolism processes. Most rapidly evolving genes in the social species Stegodyphus dumicola were broadly expressed across four tissues and enriched for transport functions, but 12 rapidly evolving genes showed brain-specific expression and were enriched for social behavioral processes. Altogether, our study identifies putative genomic signatures and potential candidate genes associated with spider sociality. These results indicate that future spider comparative genomic studies, including broader sampling and additional independent origins of sociality, can further clarify the genomic causes and consequences of social life.

Sex differences in spiders: from phenotype to genomics

Sexual reproduction is pervasive in animals and has led to the evolution of sexual dimorphism. In most animals, males and females show marked differences in primary and secondary sexual traits. The formation of sex-specific organs and eventually sex-specific behaviors is defined during the development of an organism. Sex determination processes have been extensively studied in a few well-established model organisms. While some key molecular regulators are conserved across animals, the initiation of sex determination is highly diverse. To reveal the mechanisms underlying the development of sexual dimorphism and to identify the evolutionary forces driving the evolution of different sexes, sex determination mechanisms must thus be studied in detail in many different animal species beyond the typical model systems. In this perspective article, we argue that spiders represent an excellent group of animals in which to study sex determination mechanisms. We show that spiders are sexually dimorphic in various morphological, behavioral, and life history traits. The availability of an increasing number of genomic and transcriptomic resources and functional tools provides a great starting point to scrutinize the extensive sexual dimorphism present in spiders on a mechanistic level. We provide an overview of the current knowledge of sex determination in spiders and propose approaches to reveal the molecular and genetic underpinnings of sexual dimorphism in these exciting animals.

Spider Venom: Components, Modes of Action, and Novel Strategies in Transcriptomic and Proteomic Analyses

This review gives an overview on the development of research on spider venoms with a focus on structure and function of venom components and techniques of analysis. Major venom component groups are small molecular mass compounds, antimicrobial (also called cytolytic, or cationic) peptides (only in some spider families), cysteine-rich (neurotoxic) peptides, and enzymes and proteins. Cysteine-rich peptides are reviewed with respect to various structural motifs, their targets (ion channels, membrane receptors), nomenclature, and molecular binding. We further describe the latest findings concerning the maturation of antimicrobial, and cysteine-rich peptides that are in most known cases expressed as propeptide-containing precursors. Today, venom research, increasingly employs transcriptomic and mass spectrometric techniques. Pros and cons of venom gland transcriptome analysis with Sanger, 454, and Illumina sequencing are discussed and an overview on so far published transcriptome studies is given. In this respect, we also discuss the only recently described cross contamination arising from multiplexing in Illumina sequencing and its possible impacts on venom studies. High throughput mass spectrometric analysis of venom proteomes (bottom-up, top-down) are reviewed.

Transcriptome annotation and characterization of novel toxins in six scorpion species

Background

Venom has evolved in parallel in multiple animals for the purpose of self-defense, prey capture or both. These venoms typically consist of highly complex mixtures of toxins: diverse bioactive peptides and/or proteins each with a specific pharmacological activity. Because of their specificity, they can be used as experimental tools to study cell mechanisms and develop novel medicines and drugs. It is therefore potentially valuable to explore the venoms of various animals to characterize their toxins and identify novel toxin-families. This study focuses on the annotation and exploration of the transcriptomes of six scorpion species from three different families. The transcriptomes were annotated with a custom-built automated pipeline, primarily consisting of Basic Local Alignment Search Tool searches against UniProt databases and filter steps based on transcript coverage.

Results

We annotated the transcriptomes of four scorpions from the family Buthidae, one from Iuridae and one from Diplocentridae using our annotation pipeline. We found that the four buthid scorpions primarily produce disulfide-bridged ion-channel targeting toxins, while the non-buthid scorpions have a higher abundance of non-disulfide-bridged toxins. Furthermore, analysis of the “unidentified” transcripts resulted in the discovery of six novel putative toxin families containing a total of 37 novel putative toxins. Additionally, 33 novel toxins in existing toxin-families were found. Lastly, 19 novel putative secreted proteins without toxin-like disulfide bonds were found.

Conclusions

We were able to assign most transcripts to a toxin family and classify the venom composition for all six scorpions. In addition to advancing our fundamental knowledge of scorpion venomics, this study may serve as a starting point for future research by facilitating the identification of the venom composition of scorpions and identifying novel putative toxin families.

Electronic supplementary material

The online version of this article (10.1186/s12864-019-6013-6) contains supplementary material, which is available to authorized users.

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

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.

Transcriptome analysis of the spider Phoneutria pertyi venom glands reveals novel venom components for the genus Phoneutria

Phoneutria nigriventer spider venom has been studied for more than 40 years and several components with pharmacological potential have been described in it. However, studies on venoms from other species of the Phoneutria genus are scarce. In this work, a conventional cDNA library from the species Phoneutria pertyi venom glands was constructed, aiming to identify novel putative cysteine-rich peptide toxins for the genus Phoneutria. 296 unique sequences were identified and 51 sequences corresponded to putative cysteine-rich peptide toxins. Besides cysteine-rich peptide toxins, other putative venom components such as protease inhibitors, defensins and serine proteinases were identified. Furthermore, by manual curation of the sequences with no match at UniProt, we were able to identify glycine-rich proteins (GRP), a class of venom component never described in Phoneutria genus. This work describes the first complete sequences of toxins from the venom of P. pertyi and reveals that, despite most of the retrieved toxins show a high identity to toxins identified in Phoneutria genus, novel putative toxins remains to be described.

Transcriptomic Analysis of Pseudoscorpion Venom Reveals a Unique Cocktail Dominated by Enzymes and Protease Inhibitors

Transcriptomic and genomic analyses have illuminated the diversity of venoms in three of the four venomous arachnid orders (scorpions, spiders, and ticks). To date, no venom gland transcriptome analysis has been available for pseudoscorpions, the fourth venomous arachnid lineage. To redress this gap, we sequenced an mRNA library generated from the venom glands of the species Synsphyronus apimelus (Garypidae). High-throughput sequencing by the Illumina protocol, followed by de novo assembly, resulted in a total of 238,331 transcripts. From those, we annotated 131 transcripts, which code for putative peptides/proteins with similar sequences to previously reported venom components available from different arachnid species in protein databases. Transcripts putatively coding for enzymes showed the richest diversity, followed by other venom components such as peptidase inhibitors, cysteine-rich peptides, and thyroglobulin 1-like peptides. Only 11 transcripts were found that code for putatively low molecular mass spider toxins. This study constitutes the first report of the diversity of components within pseudoscorpion venom.