Embryonic development and staging of the cobweb spider Parasteatoda tepidariorum C. L. Koch, 1841 (syn.: Achaearanea tepidariorum; Araneomorphae; Theridiidae)

Venom gland organogenesis in the common house spider

Venom is a remarkable innovation found across the animal kingdom, yet the evolutionary origins of venom systems in various groups, including spiders, remain enigmatic. Here, we investigated the organogenesis of the venom apparatus in the common house spider, Parasteatoda tepidariorum. The venom apparatus consists of a pair of secretory glands, each connected to an opening at the fang tip by a duct that runs through the chelicerae. We performed bulk RNA-seq to identify venom gland-specific markers and assayed their expression using RNA in situ hybridisation experiments on whole-mount time-series. These revealed that the gland primordium emerges during embryonic stage 13 at the chelicera tip, progresses proximally by the end of embryonic development and extends into the prosoma post-eclosion. The initiation of expression of an important toxin component in late postembryos marks the activation of venom-secreting cells. Our selected markers also exhibited distinct expression patterns in adult venom glands: sage and the toxin marker were expressed in the secretory epithelium, forkhead and sum-1 in the surrounding muscle layer, while Distal-less was predominantly expressed at the gland extremities. Our study provides the first comprehensive analysis of venom gland morphogenesis in spiders, offering key insights into their evolution and development.

An atlas of spider development at single-cell resolution provides new insights into arthropod embryogenesis

Spiders are a diverse order of chelicerates that diverged from other arthropods over 500 million years ago. Research on spider embryogenesis, particularly studies using the common house spider Parasteatoda tepidariorum, has made important contributions to understanding the evolution of animal development, including axis formation, segmentation, and patterning. However, we lack knowledge about the cells that build spider embryos, their gene expression profiles and fate. Single-cell transcriptomic analyses have been revolutionary in describing these complex landscapes of cellular genetics in a range of animals. Therefore, we carried out single-cell RNA sequencing of P. tepidariorum embryos at stages 7, 8 and 9, which encompass the establishment and patterning of the body plan, and initial differentiation of many tissues and organs. We identified 20 cell clusters, from 18.5 k cells, which were marked by many developmental toolkit genes, as well as a plethora of genes not previously investigated. We found differences in the cell cycle transcriptional signatures, suggestive of different proliferation dynamics, which related to distinctions between endodermal and some mesodermal clusters, compared with ectodermal clusters. We identified many Hox genes as markers of cell clusters, and Hox gene ohnologs were often present in different clusters. This provided additional evidence of sub- and/or neo-functionalisation of these important developmental genes after the whole genome duplication in an arachnopulmonate ancestor (spiders, scorpions, and related orders). We also examined the spatial expression of marker genes for each cluster to generate a comprehensive cell atlas of these embryonic stages. This revealed new insights into the cellular basis and genetic regulation of head patterning, hematopoiesis, limb development, gut development, and posterior segmentation. This atlas will serve as a platform for future analysis of spider cell specification and fate, and studying the evolution of these processes among animals at cellular resolution.

Single-cell RNA sequencing of mid-to-late stage spider embryos: new insights into spider development

BACKGROUND

The common house spider Parasteatoda tepidariorum represents an emerging new model organism of arthropod evolutionary and developmental (EvoDevo) studies. Recent technical advances have resulted in the first single-cell sequencing (SCS) data on this species allowing deeper insights to be gained into its early development, but mid-to-late stage embryos were not included in these pioneering studies.

RESULTS

Therefore, we performed SCS on mid-to-late stage embryos of Parasteatoda and characterized resulting cell clusters by means of in-silico analysis (comparison of key markers of each cluster with previously published information on these genes). In-silico prediction of the nature of each cluster was then tested/verified by means of additional in-situ hybridization experiments with additional markers of each cluster.

CONCLUSIONS

Our data show that SCS data reliably group cells with similar genetic fingerprints into more or less distinct clusters, and thus allows identification of developing cell types on a broader level, such as the distinction of ectodermal, mesodermal and endodermal cell lineages, as well as the identification of distinct developing tissues such as subtypes of nervous tissue cells, the developing heart, or the ventral sulcus (VS). In comparison with recent other SCS studies on the same species, our data represent later developmental stages, and thus provide insights into different stages of developing cell types and tissues such as differentiating neurons and the VS that are only present at these later stages.

Evolution of the Spider Homeobox Gene Repertoire by Tandem and Whole Genome Duplication

Gene duplication generates new genetic material that can contribute to the evolution of gene regulatory networks and phenotypes. Duplicated genes can undergo subfunctionalization to partition ancestral functions and/or neofunctionalization to assume a new function. We previously found there had been a whole genome duplication (WGD) in an ancestor of arachnopulmonates, the lineage including spiders and scorpions but excluding other arachnids like mites, ticks, and harvestmen. This WGD was evidenced by many duplicated homeobox genes, including two Hox clusters, in spiders. However, it was unclear which homeobox paralogues originated by WGD versus smaller-scale events such as tandem duplications. Understanding this is a key to determining the contribution of the WGD to arachnopulmonate genome evolution. Here we characterized the distribution of duplicated homeobox genes across eight chromosome-level spider genomes. We found that most duplicated homeobox genes in spiders are consistent with an origin by WGD. We also found two copies of conserved homeobox gene clusters, including the Hox, NK, HRO, Irx, and SINE clusters, in all eight species. Consistently, we observed one copy of each cluster was degenerated in terms of gene content and organization while the other remained more intact. Focussing on the NK cluster, we found evidence for regulatory subfunctionalization between the duplicated NK genes in the spider Parasteatoda tepidariorum compared to their single-copy orthologues in the harvestman Phalangium opilio. Our study provides new insights into the relative contributions of multiple modes of duplication to the homeobox gene repertoire during the evolution of spiders and the function of NK genes.

Appendage abnormalities in spiders induced by an alternating temperature protocol in the context of recent advances in molecular spider embryology

In the literature there are numerous reports of developmental deformities in arthropods collected in their natural habitat. Since such teratogenically affected individuals are found purely by chance, the causes of their defects are unknown. Numerous potential physical, mechanical, chemical, and biological teratogens have been considered and tested in the laboratory. Thermal shocks, frequently used in teratological research on the spider Eratigena atrica, have led to deformities on both the prosoma and the opisthosoma. In the 2020/2021 breeding season, by applying alternating temperatures (14 °C and 32 °C, changed every 12 h) for the first 10 days of embryonic development, we obtained 212 postembryos (out of 3,007) with the following anomalies: oligomely, heterosymely, bicephaly, schistomely, symely, polymely, complex anomalies, and others. From these we selected six spiders with defects on the prosoma and two with short appendages on the pedicel for further consideration. The latter cases seem particularly interesting because appendages do not normally develop on this body part, viewed as the first segment of the opisthosoma, and appear to represent examples of atavism. In view of the ongoing development of molecular techniques and recent research on developmental mechanisms in spiders, we believe the observed phenotypes may result, at least in part, from the erroneous suppression or expression of segmentation or appendage patterning genes. We consider "knockdown" experiments described in the literature as a means for generating hypotheses about the sources of temperature-induced body abnormalities in E. atrica.

FGF signalling is involved in cumulus migration in the common house spider Parasteatoda tepidariorum

Cell migration is a fundamental component during the development of most multicellular organisms. In the early spider embryo, the collective migration of signalling cells, known as the cumulus, is required to set the dorsoventral body axis. Here, we show that FGF signalling plays an important role during cumulus migration in the spider Parasteatoda tepidariorum. Spider embryos with reduced FGF signalling show reduced or absent cumulus migration and display dorsoventral patterning defects. Our study reveals that the transcription factor Ets4 regulates the expression of several FGF signalling components in the cumulus. In conjunction with a previous study, we show that the expression of fgf8 in the germ-disc is regulated via the Hedgehog signalling pathway. We also demonstrate that FGF signalling influences the BMP signalling pathway activity in the region around cumulus cells. Finally, we show that FGFR signalling might also influence cumulus migration in basally branching spiders and we propose that fgf8 might act as a chemo-attractant to guide cumulus cells towards the future dorsal pole of the spider embryo.

Expression of netrin and its receptors uncoordinated-5 and frazzled in arthropods and onychophorans suggests conserved and diverged functions in neuronal pathfinding and synaptogenesis

BACKGROUND

Development of the nervous system and the correct connection of nerve cells require coordinated axonal pathfinding through an extracellular matrix. Outgrowing axons exhibit directional growth toward or away from external guidance cues such as Netrin. Guidance cues can be detected by growth cones that are located at the end of growing axons through membrane-bound receptors such as Uncoordianted-5 and Frazzled. Binding of Netrin causes reformation of the cytoskeleton and growth of the axon toward (or away from) the source of Netrin production.

RESULTS

Here, we investigate the embryonic mRNA expression patterns of netrin genes and their potential receptors, uncoordinated-5 and frazzled in arthropod species that cover all main branches of Arthropoda, that is, Pancrustacea, Myriapoda, and Chelicerata. We also studied the expression patterns in a closely related outgroup species, the onychophoran Euperipatoides kanangrensis, and provide data on expression profiles of these genes in larval tissues of the fly Drosophila melanogaster including the brain and the imaginal disks.

CONCLUSION

Our data reveal conserved and diverged aspects of neuronal guidance in Drosophila with respect to the other investigated species and suggest a conserved function in nervous system patterning of the developing appendages.

Female mating rates and their fitness consequences in the common house spider Parasteatoda tepidariorum

Mating systems, with varying female mating rates occurring with the same partner (monandry) or with multiple mates (polyandry), can have far reaching consequences for population viability and the rate of gene flow. Here, we investigate the mating rates of the common house spider Parasteatoda tepidariorum (Theridiidae), an emerging model for genetic studies, with yet undescribed reproductive behavior. It is hypothesized that spiders belonging to this family have low re-mating rates. We paired females twice with the same male (monandry) or with different males (polyandry), and recorded behaviors, mating success and fitness resulting from single- and double-matings, either monandrous or polyandrous. Despite the study being explorative in nature, we predict successful matings to be more frequent during first encounters, to reduce female risk of remaining unmated. For re-mating to be adaptive, we expect higher fitness of double-mated females, and polyandrous females to experience highest mating success and fitness if reproductive gains are achieved by mating with multiple partners. We show that the majority of the females did not mate, and those that did mated only once, not necessarily on their first encounter. The likelihood of re-mating did not differ between monandrous and polyandrous encounters and female mating experience (mated once, twice monandrous, twice polyandrous) did not affect fitness, indicated by similar offspring production. Female twanging of the web leads to successful matings suggesting female behavioral receptivity. Cannibalism rates were low and mostly occurred pre-copulatory. We discuss how the species ecology, with potentially high mating costs for males and limited female receptivity, may shape a mating system with low mating rates.

Extraembryonic tissue in chelicerates: a review and outlook

The formation of extraembryonic membranes (EEMs) contributes to the proper development of many animals. In arthropods, the formation and function of EEMs have been studied best in insects. Regarding the development of extraembryonic tissue in chelicerates (spiders and relatives), most information is available for spiders (Araneae). Especially two populations of cells have been considered to represent EEMs in spiders. The first of these potential EEMs develops shortly after egg deposition, opposite to a radially symmetrical germ disc that forms in one hemisphere of the egg and encloses the yolk. The second tissue, which has been described as being extraembryonic is the so-called dorsal field, which is required to cover the dorsal part of the developing spider germ rudiment before proper dorsal closure. In this review, we summarize the current knowledge regarding the formation of potential extraembryonic structures in the Chelicerata. We describe the early embryogenesis of spiders and other chelicerates, with a special focus on the formation of the potential extraembryonic tissues.

This article is part of the theme issue ‘Extraembryonic tissues: exploring concepts, definitions and functions across the animal kingdom’.

Hox genes in spiders: Their significance for development and evolution

Hox genes are known for their role in the specification of typical body plan features in animals. Evolutionary changes in Hox gene function are believed to be involved in the emergence of the diverse body plans we observe in animals today. Spiders share many body plan features with other arthropods, but also have numerous unique traits of their own. Studies of spider Hox genes have already provided insights into evolutionarily conserved and derived features of the spider body plan and their genetic basis. However, many aspects of Hox gene biology have been insufficiently studied in spiders so far. In this review, we highlight previous comparative studies of Hox genes in spiders and their significance for our understanding of the evolution of the spider body plan. We also identify aspects of Hox gene biology that need to be studied in greater detail. Many spider Hox genes have not been investigated beyond their mRNA expression patterns, and the role of Hox genes with apparently plesiomorphic or dual functions, like ftz and Hox3 is still unclear. Spiders have a duplicated Hox gene cluster, but possible sub- or neofunctionalisation of duplicates have not yet been studied systematically. Future research should therefore focus on these issues, in addition to the role of Polycomb and trithorax-mediated regulation, the identification of regulatory regions, cofactors or spider-specific target genes, and the significance of non-coding RNAs transcribed from within the Hox cluster and even from the antisense strand of particular Hox genes.

Lineage-specific, fast-evolving GATA-like gene regulates zygotic gene activation to promote endoderm specification and pattern formation in the Theridiidae spider

Background

The process of early development varies across the species-rich phylum Arthropoda. Owing to the limited research strategies for dissecting lineage-specific processes of development in arthropods, little is known about the variations in early arthropod development at molecular resolution. The Theridiidae spider, Parasteatoda tepidariorum, has its genome sequenced and could potentially contribute to dissecting early embryonic processes.

Results

We present genome-wide identification of candidate genes that exhibit locally restricted expression in germ disc forming stage embryos of P. tepidariorum, based on comparative transcriptomes of isolated cells from different regions of the embryo. A subsequent pilot screen by parental RNA interference identifies three genes required for body axis formation. One of them is a GATA-like gene that has been fast evolving after duplication and divergence from a canonical GATA family gene. This gene is designated fuchi nashi (fuchi) after its knockdown phenotypes, where the cell movement toward the formation of a germ disc was reversed. fuchi expression occurs in cells outside a forming germ disc and persists in the endoderm. Transcriptome and chromatin accessibility analyses of fuchi pRNAi embryos suggest that early fuchi activity regulates chromatin state and zygotic gene activation to promote endoderm specification and pattern formation. We also show that there are many uncharacterized genes regulated by fuchi.

Conclusions

Our genome-based research using an arthropod phylogenetically distant from Drosophila identifies a lineage-specific, fast-evolving gene with key developmental roles in one of the earliest, genome-wide regulatory events, and allows for molecular exploration of the developmental variations in early arthropod embryos.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12915-022-01421-0.

A comprehensive study of arthropod and onychophoran Fox gene expression patterns

Fox genes represent an evolutionary old class of transcription factor encoding genes that evolved in the last common ancestor of fungi and animals. They represent key-components of multiple gene regulatory networks (GRNs) that are essential for embryonic development. Most of our knowledge about the function of Fox genes comes from vertebrate research, and for arthropods the only comprehensive gene expression analysis is that of the fly Drosophila melanogaster. For other arthropods, only selected Fox genes have been investigated. In this study, we provide the first comprehensive gene expression analysis of arthropod Fox genes including representative species of all main groups of arthropods, Pancrustacea, Myriapoda and Chelicerata. We also provide the first comprehensive analysis of Fox gene expression in an onychophoran species. Our data show that many of the Fox genes likely retained their function during panarthropod evolution highlighting their importance in development. Comparison with published data from other groups of animals shows that this high degree of evolutionary conservation often dates back beyond the last common ancestor of Panarthropoda.

Eggs to long-legs: embryonic staging of the harvestman Phalangium opilio (Opiliones), an emerging model arachnid

Background

The comparative embryology of Chelicerata has greatly advanced in recent years with the integration of classical studies and genetics, prominently spearheaded by developmental genetic works in spiders. Nonetheless, the understanding of the evolution of development and polarization of embryological characters in Chelicerata is presently limited, as few non-spider species have been well studied. A promising focal species for chelicerate evo-devo is the daddy-long-legs (harvestman) Phalangium opilio, a member of the order Opiliones. Phalangium opilio, breeds prolifically and is easily accessible in many parts of the world, as well as tractable in a laboratory setting. Resources for this species include developmental transcriptomes, a draft genome, and protocols for RNA interference, but a modern staging system is critically missing for this emerging model system.

Results

We present a staging system of P. opilio embryogenesis that spans the most important morphogenetic events with respect to segment formation, appendage elongation and head development. Using time-lapse imaging, confocal microscopy, colorimetric in situ hybridization, and immunohistochemistry, we tracked the development of synchronous clutches from egg laying to adulthood. We describe key events in segmentation, myogenesis, neurogenesis, and germ cell formation.

Conclusion

Considering the phylogenetic position of Opiliones and the unduplicated condition of its genome (in contrast to groups like spiders and scorpions), this species is poised to serve as a linchpin for comparative studies in arthropod development and genome evolution. The staging system presented herein provides a valuable reference for P. opilio that we anticipate being useful to the arthropod evo-devo community, with the goal of revitalizing research in the comparative development of non-spider arachnids.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12983-022-00454-z.

It takes Two: Discovery of Spider Pax2 Duplicates Indicates Prominent Role in Chelicerate Central Nervous System, Eye, as Well as External Sense Organ Precursor Formation and Diversification After Neo- and Subfunctionalization

Paired box genes are conserved across animals and encode transcription factors playing key roles in development, especially neurogenesis. Pax6 is a chief example for functional conservation required for eye development in most bilaterian lineages except chelicerates. Pax6 is ancestrally linked and was shown to have interchangeable functions with Pax2. Drosophila melanogaster Pax2 plays an important role in the development of sensory hairs across the whole body. In addition, it is required for the differentiation of compound eyes, making it a prime candidate to study the genetic basis of arthropod sense organ development and diversification, as well as the role of Pax genes in eye development. Interestingly, in previous studies identification of chelicerate Pax2 was either neglected or failed. Here we report the expression of two Pax2 orthologs in the common house spider Parasteatoda tepidariorum, a model organism for chelicerate development. The two Pax2 orthologs most likely arose as a consequence of a whole genome duplication in the last common ancestor of spiders and scorpions. Pax2.1 is expressed in the peripheral nervous system, including developing lateral eyes and external sensilla, as well as the ventral neuroectoderm of P. tepidariorum embryos. This not only hints at a conserved dual role of Pax2/5/8 orthologs in arthropod sense organ development but suggests that in chelicerates, Pax2 could have acquired the role usually played by Pax6. For the other paralog, Pt-Pax2.2, expression was detected in the brain, but not in the lateral eyes and the expression pattern associated with sensory hairs differs in timing, pattern, and strength. To achieve a broader phylogenetic sampling, we also studied the expression of both Pax2 genes in the haplogyne cellar spider Pholcus phalangioides. We found that the expression difference between paralogs is even more extreme in this species, since Pp-Pax2.2 shows an interesting expression pattern in the ventral neuroectoderm while the expression in the prosomal appendages is strictly mesodermal. This expression divergence indicates both sub- and neofunctionalization after Pax2 duplication in spiders and thus presents an opportunity to study the evolution of functional divergence after gene duplication and its impact on sense organ diversification.

Regulation of Eye Determination and Regionalization in the Spider Parasteatoda tepidariorum

Animal visual systems are enormously diverse, but their development appears to be controlled by a set of conserved retinal determination genes (RDGs). Spiders are particular masters of visual system innovation, and offer an excellent opportunity to study the evolution of animal eyes. Several RDGs have been identified in spider eye primordia, but their interactions and regulation remain unclear. From our knowledge of RDG network regulation in Drosophila melanogaster, we hypothesize that orthologs of Pax6, eyegone, Wnt genes, hh, dpp, and atonal could play important roles in controlling eye development in spiders. We analyzed the expression of these genes in developing embryos of the spider Parasteatodatepidariorum, both independently and in relation to the eye primordia, marked using probes for the RDG sine oculis. Our results support conserved roles for Wnt genes in restricting the size and position of the eye field, as well as for atonal initiating photoreceptor differentiation. However, we found no strong evidence for an upstream role of Pax6 in eye development, despite its label as a master regulator of animal eye development; nor do eyg, hh or dpp compensate for the absence of Pax6. Conversely, our results indicate that hh may work with Wnt signaling to restrict eye growth, a role similar to that of Sonichedgehog (Shh) in vertebrates.

The velvet worm brain unveils homologies and evolutionary novelties across panarthropods

Background

The evolution of the brain and its major neuropils in Panarthropoda (comprising Arthropoda, Tardigrada and Onychophora) remains enigmatic. As one of the closest relatives of arthropods, onychophorans are regarded as indispensable for a broad understanding of the evolution of panarthropod organ systems, including the brain, whose anatomical and functional organisation is often used to gain insights into evolutionary relations. However, while numerous recent studies have clarified the organisation of many arthropod nervous systems, a detailed investigation of the onychophoran brain with current state-of-the-art approaches is lacking, and further inconsistencies in nomenclature and interpretation hamper its understanding. To clarify the origins and homology of cerebral structures across panarthropods, we analysed the brain architecture in the onychophoran Euperipatoides rowelli by combining X-ray micro-computed tomography, histology, immunohistochemistry, confocal microscopy, and three-dimensional reconstruction.

Results

Here, we use this detailed information to generate a consistent glossary for neuroanatomical studies of Onychophora. In addition, we report novel cerebral structures, provide novel details on previously known brain areas, and characterise further structures and neuropils in order to improve the reproducibility of neuroanatomical observations. Our findings support homology of mushroom bodies and central bodies in onychophorans and arthropods. Their antennal nerve cords and olfactory lobes most likely evolved independently. In contrast to previous reports, we found no evidence for second-order visual neuropils, or a frontal ganglion in the velvet worm brain.

Conclusion

We imaged the velvet worm nervous system at an unprecedented level of detail and compiled a comprehensive glossary of known and previously uncharacterised neuroanatomical structures to provide an in-depth characterisation of the onychophoran brain architecture. We expect that our data will improve the reproducibility and comparability of future neuroanatomical studies.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12915-021-01196-w.

A chelicerate Wnt gene expression atlas: novel insights into the complexity of arthropod Wnt-patterning

The Wnt genes represent a large family of secreted glycoprotein ligands that date back to early animal evolution. Multiple duplication events generated a set of 13 Wnt families of which 12 are preserved in protostomes. Embryonic Wnt expression patterns (Wnt-patterning) are complex, representing the plentitude of functions these genes play during development. Here, we comprehensively investigated the embryonic expression patterns of Wnt genes from three species of spiders covering both main groups of true spiders, Haplogynae and Entelegynae, a mygalomorph species (tarantula), as well as a distantly related chelicerate outgroup species, the harvestman Phalangium opilio. All spiders possess the same ten classes of Wnt genes, but retained partially different sets of duplicated Wnt genes after whole genome duplication, some of which representing impressive examples of sub- and neo-functionalization. The harvestman, however, possesses a more complete set of 11 Wnt genes but with no duplicates. Our comprehensive data-analysis suggests a high degree of complexity and evolutionary flexibility of Wnt-patterning likely providing a firm network of mutational protection. We discuss the new data on Wnt gene expression in terms of their potential function in segmentation, posterior elongation, and appendage development and critically review previous research on these topics. We conclude that earlier research may have suffered from the absence of comprehensive gene expression data leading to partial misconceptions about the roles of Wnt genes in development and evolution.

Panarthropod tiptop/teashirt and spalt orthologs and their potential role as "trunk"-selector genes

BACKGROUND

In the vinegar fly Drosophila melanogaster, the homeodomain containing transcription factor Teashirt (Tsh) appears to specify trunk identity in concert with the function of the Hox genes. While in Drosophila there is a second gene closely related to tsh, called tiptop (tio), in other arthropods species only one copy exists (called tio/tsh). The expression of tsh and tio/tsh, respectively, is surprisingly similar among arthropods suggesting that its function as trunk selector gene may be conserved. Other research, for example on the beetle Tribolium castaneum, questions even conservation of Tsh function among insects. The zinc-finger transcription factor Spalt (Sal) is involved in the regulation of Drosophila tsh, but this regulatory interaction does not appear to be conserved in Tribolium either. Whether the function and interaction of tsh and sal as potential trunk-specifiers, however, is conserved is still unclear because comparative studies on sal expression (except for Tribolium) are lacking, and functional data are (if at all existing) restricted to Insecta.

RESULTS

Here, we provide additional data on arthropod tsh expression, show the first data on onychophoran tio/tsh expression, and provide a comprehensive investigation on sal expression patterns in arthropods and an onychophoran.

CONCLUSIONS

Our data support the idea that tio/tsh genes are involved in the development of "trunk" segments by regulating limb development. Our data suggest further that the function of Sal is indeed unlikely to be conserved in trunk vs head development like in Drosophila, but early expression of sal is in line with a potential homeotic function, at least in Arthropoda.

Oscillating waves of Fox, Cyclin and CDK gene expression indicate unique spatiotemporal control of cell cycling during nervous system development in onychophorans

Forkhead box (Fox) genes code for a class of transcription factors with many different fundamental functions in animal development including cell cycle control. Other important factors of cell cycle control are Cyclins and Cyclin-dependent kinases (CDKs). Here we report on the oscillating expression of three Fox genes, FoxM, FoxN14 (jumeaux) and FoxN23 (Checkpoint suppressor like-1), Cyclins and CDKs in an onychophoran, a representative of a relatively small group of animals that are closely related to the arthropods. Expression of these genes is in the form of several waves that start as dot-like domains in the center of each segment and then transform into concentric rings that run towards the periphery of the segments. This oscillating gene expression, however, occurs exclusively along the anterior-posterior body axis in the tissue ventral to the base of the appendages, a region where the central nervous system and the enigmatic ventral and preventral organs of the onychophoran develop. We suggest that the oscillating gene expression and the resulting waves of expression we report are likely correlated with cell cycle control during the development of the onychophoran nervous system. This intriguing patterning appears to be unique for onychophorans as it is not found in any of the arthropods we also investigated in this study, and is likely correlated with the slow embryonic development of onychophorans compared to arthropods.

The Evolution of Sox Gene Repertoires and Regulation of Segmentation in Arachnids

The Sox family of transcription factors regulates many processes during metazoan development, including stem cell maintenance and nervous system specification. Characterizing the repertoires and roles of these genes can therefore provide important insights into animal evolution and development. We further characterized the Sox repertoires of several arachnid species with and without an ancestral whole-genome duplication and compared their expression between the spider Parasteatoda tepidariorum and the harvestman Phalangium opilio. We found that most Sox families have been retained as ohnologs after whole-genome duplication and evidence for potential subfunctionalization and/or neofunctionalization events. Our results also suggest that Sox21b-1 likely regulated segmentation ancestrally in arachnids, playing a similar role to the closely related SoxB gene, Dichaete, in insects. We previously showed that Sox21b-1 is required for the simultaneous formation of prosomal segments and sequential addition of opisthosomal segments in P. tepidariorum. We studied the expression and function of Sox21b-1 further in this spider and found that although this gene regulates the generation of both prosomal and opisthosomal segments, it plays different roles in the formation of these tagmata reflecting their contrasting modes of segmentation and deployment of gene regulatory networks with different architectures.

A conserved role for arrow in posterior axis patterning across Arthropoda

Segmentation is a key characteristic of Arthropoda that is linked to the evolutionary success of this lineage. It has previously been shown in both vertebrates and short germ insects that posterior segmentation requires canonical Wnt (cWnt) signaling, which maintains the expression of Caudal and the posterior growth zone; disruption of cWnt signaling incurs posterior truncations in these lineages due to the loss of the tail bud. However, comparable datasets for Wnt signaling are limited outside of holometabolous insects, due to incomparable phenotypic spectra and inefficacy of gene misexpression methods in certain model species. We applied RNA interference (RNAi) against the Wnt co-receptor arrow (arr), a key member of the cWnt signaling pathway in holometabolous insects and vertebrates, to examine posterior axis elongation of the cobweb spider Parasteatoda tepidariorum (short germ embryogenesis; one Wnt8 homolog), the cricket Gryllus bimaculatus (intermediate germ; one Wnt8 homolog), and the milkweed bug Oncopeltus fasciatus (short germ; two Wnt8 homologs). Knockdown of arr in insects resulted in posterior truncations affecting the gnathos through the abdomen in O. fasciatus, whereas posterior truncations only affected the T3 segment through the abdomen in G. bimaculatus. Spider embryos with disrupted arr expression exhibited defects along the entire axis, including segmentation defects throughout the germband. RNA-Seq-based differential gene expression analysis of severe Ptep-arr loss-of-function phenotypes at two developmental stages was used to confirm that knockdown of Ptep-arr results in systemic disruption of the Wnt pathway. Intriguingly, we found that knockdown of arr did not abrogate Wnt8 expression in any of the three species, with cad expression additionally retained in severe loss-of-function phenotypes in the cricket and the spider. Together with data from a holometabolous insect, our results suggest that cWnt signaling is not required for maintenance of Wnt8 expression across Arthropoda. These outcomes underscore the diagnostic power of differential gene expression analyses in characterizing catastrophic phenotypes in emerging model species.

Systemic paralogy and function of retinal determination network homologs in arachnids

BACKGROUND

Arachnids are important components of cave ecosystems and display many examples of troglomorphisms, such as blindness, depigmentation, and elongate appendages. Little is known about how the eyes of arachnids are specified genetically, let alone the mechanisms for eye reduction and loss in troglomorphic arachnids. Additionally, duplication of Retinal Determination Gene Network (RDGN) homologs in spiders has convoluted functional inferences extrapolated from single-copy homologs in pancrustacean models.

RESULTS

We investigated a sister species pair of Israeli cave whip spiders, Charinus ioanniticus and C. israelensis (Arachnopulmonata, Amblypygi), of which one species has reduced eyes. We generated embryonic transcriptomes for both Amblypygi species, and discovered that several RDGN homologs exhibit duplications. We show that duplication of RDGN homologs is systemic across arachnopulmonates (arachnid orders that bear book lungs), rather than being a spider-specific phenomenon. A differential gene expression (DGE) analysis comparing the expression of RDGN genes in field-collected embryos of both species identified candidate RDGN genes involved in the formation and reduction of eyes in whip spiders. To ground bioinformatic inference of expression patterns with functional experiments, we interrogated the function of three candidate RDGN genes identified from DGE using RNAi in the spider Parasteatoda tepidariorum. We provide functional evidence that one of these paralogs, sine oculis/Six1 A (soA), is necessary for the development of all arachnid eye types.

CONCLUSIONS

Our work establishes a foundation to investigate the genetics of troglomorphic adaptations in cave arachnids, and links differential gene expression to an arthropod eye phenotype for the first time outside of Pancrustacea. Our results support the conservation of at least one RDGN component across Arthropoda and provide a framework for identifying the role of gene duplications in generating arachnid eye diversity.

Temperature fluctuations during embryonic development implicated in a naturally occurring instance of abnormal spinnerets in the spider Australomimetus maculosus (Araneae, Mimetidae)

We record developmental abnormalities of the spinnerets in a field-collected adult male specimen of Australomimetus maculosus. These include (1) a supernumerary right posterior lateral spinneret (PLS), (2) ectopic piriform silk gland spigots and tartipores on the left PLS that are normally restricted to anterior lateral spinnerets (ALSs), and (3) what appear to be ectopic ALS sensilla on the left posterior median spinneret (PMS). Published results of teratological experiments and climate data for the collection site indicate that fluctuating sub- and supra-optimal temperatures during embryogenesis may have been responsible for these anomalies. This specimen thus supports the view that spinneret abnormalities, among other aberrations, may be induced when embryos of entelegyne spiders are exposed to fluctuations between high and low temperatures, whether in the laboratory or, as here, in nature. To our knowledge, the ectopic structures seen on the left PLS and left PMS have not been observed previously. Their locations are consistent with a hypothesis by which only the lateral portion of the araneomorph ALS is serially homologous to the PLS, while the remainder of the ALS, along with the colulus/cribellum, is homologous to the PMS.

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.

six3 acts upstream of foxQ2 in labrum and neural development in the spider Parasteatoda tepidariorum

Anterior patterning in animals is based on a gene regulatory network, which comprises highly conserved transcription factors like six3, pax6 and otx. More recently, foxQ2 was found to be an ancestral component of this network but its regulatory interactions showed evolutionary differences. In most animals, foxQ2 is a downstream target of six3 and knockdown leads to mild or no epidermal phenotypes. In contrast, in the red flour beetle Tribolium castaneum, foxQ2 gained a more prominent role in patterning leading to strong epidermal and brain phenotypes and being required for six3 expression. However, it has remained unclear which of these novel aspects were insect or arthropod specific. Here, we study expression and RNAi phenotype of the single foxQ2 ortholog of the spider Parasteatoda tepidariorum. We find early anterior expression similar to the one of insects. Further, we show an epidermal phenotype in the labrum similar to the insect phenotype. However, our data indicate that foxQ2 is positioned downstream of six3 like in other animals but unlike insects. Hence, the epidermal and neural pattering function of foxQ2 is ancestral for arthropods while the upstream role of foxQ2 may have evolved in the lineage leading to the insects.

Homeobox Gene Duplication and Divergence in Arachnids

Homeobox genes are key toolkit genes that regulate the development of metazoans and changes in their regulation and copy number have contributed to the evolution of phenotypic diversity. We recently identified a whole genome duplication (WGD) event that occurred in an ancestor of spiders and scorpions (Arachnopulmonata), and that many homeobox genes, including two Hox clusters, appear to have been retained in arachnopulmonates. To better understand the consequences of this ancient WGD and the evolution of arachnid homeobox genes, we have characterized and compared the homeobox repertoires in a range of arachnids. We found that many families and clusters of these genes are duplicated in all studied arachnopulmonates (Parasteatoda tepidariorum, Pholcus phalangioides, Centruroides sculpturatus, and Mesobuthus martensii) compared with nonarachnopulmonate arachnids (Phalangium opilio, Neobisium carcinoides, Hesperochernes sp., and Ixodes scapularis). To assess divergence in the roles of homeobox ohnologs, we analyzed the expression of P. tepidariorum homeobox genes during embryogenesis and found pervasive changes in the level and timing of their expression. Furthermore, we compared the spatial expression of a subset of P. tepidariorum ohnologs with their single copy orthologs in P. opilio embryos. We found evidence for likely subfunctionlization and neofunctionalization of these genes in the spider. Overall our results show a high level of retention of homeobox genes in spiders and scorpions post-WGD, which is likely to have made a major contribution to their developmental evolution and diversification through pervasive subfunctionlization and neofunctionalization, and paralleling the outcomes of WGD in vertebrates.

Embryonic development and secondary axis induction in the Brazilian white knee tarantula Acanthoscurria geniculata, C. L. Koch, 1841 (Araneae; Mygalomorphae; Theraphosidae)

Tarantulas represent some of the heaviest and most famous spiders. However, there is little information about the embryonic development of these spiders or their relatives (infraorder Mygalomorphae) and time-lapse recording of the embryonic development is entirely missing. I here describe the complete development of the Brazilian white knee tarantula, Acanthoscurria geniculata, in fixed and live embryos. The establishment of the blastoderm, the formation, migration and signalling of the cumulus and the shape changes that occur in the segment addition zone are analysed in detail. In addition, I show that there might be differences in the contraction process of early embryos of different theraphosid spider species. A new embryonic reference transcriptome was generated for this study and was used to clone and analyse the expression of several important developmental genes. Finally, I show that embryos of A. geniculata are amenable to tissue transplantation and bead insertion experiments. Using these functional approaches, I induced axis duplication in embryos via cumulus transplantation and ectopic activation of BMP signalling. Overall, the mygalomorph spider A. geniculata is a useful laboratory system to analyse evolutionary developmental questions, and the availability of such a system will help understanding conserved and divergent aspects of spider/chelicerate development.

Distribution and development of the external sense organ pattern on the appendages of postembryonic and adult stages of the spider Parasteatoda tepidariorum

Spiders are equipped with a large number of innervated cuticular specializations, which respond to various sensory stimuli. The physiological function of mechanosensory organs has been analysed in great detail in some model spider species (e.g. Cupiennius salei); however, much less is known about the distribution and function of chemosensory organs. Furthermore, our knowledge on how the sense organ pattern develops on the spider appendages is limited. Here we analyse the development of the pattern and distribution of six different external mechano- and chemosensory organs in all postembryonic stages and in adult male and female spiders of the species Parasteatoda tepidariorum. We show that except for small mechanosensory setae, external sense organs appear in fixed positions on the pedipalps and first walking legs, arranged in longitudinal rows along the proximal-distal axis or in invariable positions relative to morphological landmarks (joints, distal tarsal tip). A comparison to other Entelegynae spiders shows that these features are conserved. We hope that this study lays the foundation for future molecular analysis to address the question how this conserved pattern is generated.

The forkhead box containing transcription factor FoxB is a potential component of dorsal-ventral body axis formation in the spider Parasteatoda tepidariorum

In the spider, determination of the dorsal-ventral body (DV) axis depends on the interplay of the dorsal morphogen encoding gene decapentaplegic (Dpp) and its antagonist, short gastrulation (sog), a gene that is involved in the correct establishment of ventral tissues. Recent work demonstrated that the forkhead domain encoding gene FoxB is involved in dorsal-ventral axis formation in spider limbs. Here, Dpp likely acts as a dorsal morphogen, and FoxB is likely in control of ventral tissues as RNAi-mediated knockdown of FoxB causes dorsalization of the limbs. In this study, we present phenotypes of FoxB knockdown that demonstrate a function in the establishment of the DV body axis. Knockdown of FoxB function leads to embryos with partially duplicated median germ bands (Duplicitas media) that are possibly the result of ectopic activation of Dpp signalling. Another class of phenotypes is characterized by unnaturally slim (dorsal-ventrally compressed) germ bands in which ventral tissue is either not formed, or is specified incorrectly, likely a result of Dpp over-activity. These results suggest that FoxB functions as an antagonist of Dpp signalling during body axis patterning, similarly as it is the case in limb development. FoxB thus represents a general player in the establishment of dorsal-ventral structures during spider ontogeny.

Candidate gene screen for potential interaction partners and regulatory targets of the Hox gene labial in the spider Parasteatoda tepidariorum

The Hox gene labial (lab) governs the formation of the tritocerebral head segment in insects and spiders. However, the morphology that results from lab action is very different in the two groups. In insects, the tritocerebral segment (intercalary segment) is reduced and lacks appendages, whereas in spiders the corresponding segment (pedipalpal segment) is a proper segment including a pair of appendages (pedipalps). It is likely that this difference between lab action in insects and spiders is mediated by regulatory targets or interacting partners of lab. However, only a few such genes are known in insects and none in spiders. We have conducted a candidate gene screen in the spider Parasteatoda tepidariorum using as candidates Drosophila melanogaster genes known to (potentially) interact with lab or to be expressed in the intercalary segment. We have studied 75 P. tepidariorum genes (including previously published and duplicated genes). Only 3 of these (proboscipedia-A (pb-A) and two paralogs of extradenticle (exd)) showed differential expression between leg and pedipalp. The low success rate points to a weakness of the candidate gene approach when it is applied to lineage specific organs. The spider pedipalp has no counterpart in insects, and therefore relying on insect data apparently cannot identify larger numbers of factors implicated in its specification and formation. We argue that in these cases a de novo approach to gene discovery might be superior to the candidate gene approach.

FoxB, a new and highly conserved key factor in arthropod dorsal-ventral (DV) limb patterning

Forkhead box (Fox) transcription factors evolved early in animal evolution and represent important components of conserved gene regulatory networks (GRNs) during animal development. Most of the researches concerning Fox genes, however, are on vertebrates and only a relatively low number of studies investigate Fox gene function in invertebrates. In addition to this shortcoming, the focus of attention is often restricted to a few well-characterized Fox genes such as FoxA (forkhead), FoxC (crocodile) and FoxQ2. Although arthropods represent the largest and most diverse animal group, most other Fox genes have not been investigated in detail, not even in the arthropod model species Drosophila melanogaster. In a general gene expression pattern screen for panarthropod Fox genes including the red flour beetle Tribolium castaneum, the pill millipede Glomeris marginata, the common house spider Parasteatoda tepidariorum, and the velvet worm Euperipatoides kanangrensis, we identified a Fox gene with a highly conserved expression pattern along the ventral ectoderm of arthropod and onychophoran limbs. Functional investigation of FoxB in Parasteatoda reveals a hitherto unrecognized important function of FoxB upstream of wingless (wg) and decapentaplegic (dpp) in the GRN orchestrating dorsal–ventral limb patterning.

Developing an integrated understanding of the evolution of arthropod segmentation using fossils and evo-devo

Segmentation is fundamental to the arthropod body plan. Understanding the evolutionary steps by which arthropods became segmented is being transformed by the integration of data from evolutionary developmental biology (evo-devo), Cambrian fossils that allow the stepwise acquisition of segmental characters to be traced in the arthropod stem-group, and the incorporation of fossils into an increasingly well-supported phylogenetic framework for extant arthropods based on genomic-scale datasets. Both evo-devo and palaeontology make novel predictions about the evolution of segmentation that serve as testable hypotheses for the other, complementary data source. Fossils underpin such hypotheses as arthropodization originating in a frontal appendage and then being co-opted into other segments, and segmentation of the endodermal midgut in the arthropod stem-group. Insights from development, such as tagmatization being associated with different modes of segment generation in different body regions, and a distinct patterning of the anterior head segments, are complemented by palaeontological evidence for the pattern of tagmatization during ontogeny of exceptionally preserved fossils. Fossil and developmental data together provide evidence for a short head in stem-group arthropods and the mechanism of its formation and retention. Future breakthroughs are expected from identification of molecular signatures of developmental innovations within a phylogenetic framework, and from a focus on later developmental stages to identify the differentiation of repeated units of different systems within segmental precursors.

Phylogenetic analysis and embryonic expression of panarthropod Dmrt genes

Background

One set of the developmentally important Doublesex and Male-abnormal-3 Related Transcription factors (Dmrt) is subject of intense research, because of their role in sex-determination and sexual differentiation. This likely non-monophyletic group of Dmrt genes is represented by the Drosophila melanogaster gene Doublesex (Dsx), the Caenorhabditis elegans Male-abnormal-3 (Mab-3) gene, and vertebrate Dmrt1 genes. However, other members of the Dmrt family are much less well studied, and in arthropods, including the model organism Drosophila melanogaster, data on these genes are virtually absent with respect to their embryonic expression and function.

Results

Here we investigate the complete set of Dmrt genes in members of all main groups of Arthropoda and a member of Onychophora, extending our data to Panarthropoda as a whole. We confirm the presence of at least four families of Dmrt genes (including Dsx-like genes) in Panarthropoda and study their expression profiles during embryogenesis. Our work shows that the expression patterns of Dmrt11E, Dmrt93B, and Dmrt99B orthologs are highly conserved among panarthropods. Embryonic expression of Dsx-like genes, however, is more derived, likely as a result of neo-functionalization after duplication.

Conclusions

Our data suggest deep homology of most of the panarthropod Dmrt genes with respect to their function that likely dates back to their last common ancestor. The function of Dsx and Dsx-like genes which are critical for sexual differentiation in animals, however, appears to be much less conserved.

Electronic supplementary material

The online version of this article (10.1186/s12983-019-0322-0) contains supplementary material, which is available to authorized users.

Duplication and expression of Sox genes in spiders

BACKGROUND

The Sox family of transcription factors is an important part of the genetic 'toolbox' of all metazoans examined to date and is known to play important developmental roles in vertebrates and insects. However, outside the commonly studied Drosophila model little is known about the repertoire of Sox family transcription factors in other arthropod species. Here we characterise the Sox family in two chelicerate species, the spiders Parasteatoda tepidariorum and Stegodyphus mimosarum, which have experienced a whole genome duplication (WGD) in their evolutionary history.

RESULTS

We find that virtually all of the duplicate Sox genes have been retained in these spiders after the WGD. Analysis of the expression of Sox genes in P. tepidariorum embryos suggests that it is likely that some of these genes have neofunctionalised after duplication. Our expression analysis also strengthens the view that an orthologue of vertebrate Group B1 genes, SoxNeuro, is implicated in the earliest events of CNS specification in both vertebrates and invertebrates. In addition, a gene in the Dichaete/Sox21b class is dynamically expressed in the spider segment addition zone, suggestive of an ancient regulatory mechanism controlling arthropod segmentation as recently suggested for flies and beetles. Together with the recent analysis of Sox gene expression in the embryos of other arthropods, our findings support the idea of conserved functions for some of these genes, including a potential role for SoxC and SoxD genes in CNS development and SoxF in limb development.

CONCLUSIONS

Our study provides a new chelicerate perspective to understanding the evolution and function of Sox genes and how the retention of duplicates of such important tool-box genes after WGD has contributed to different aspects of spider embryogenesis. Future characterisation of the function of these genes in spiders will help us to better understand the evolution of the regulation of important developmental processes in arthropods and other metazoans including neurogenesis and segmentation.

Gene expression analysis of potential morphogen signalling modifying factors in Panarthropoda

Background

Morphogen signalling represents a key mechanism of developmental processes during animal development. Previously, several evolutionary conserved morphogen signalling pathways have been identified, and their players such as the morphogen receptors, morphogen modulating factors (MMFs) and the morphogens themselves have been studied. MMFs are factors that regulate morphogen distribution and activity. The interactions of MMFs with different morphogen signalling pathways such as Wnt signalling, Hedgehog (Hh) signalling and Decapentaplegic (Dpp) signalling are complex because some of the MMFs have been shown to interact with more than one signalling pathway, and depending on genetic context, to have different, biphasic or even opposing function. This complicates the interpretation of expression data and functional data of MMFs and may be one reason why data on MMFs in other arthropods than Drosophila are scarce or totally lacking.

Results

As a first step to a better understanding of the potential roles of MMFs in arthropod development, we investigate here the embryonic expression patterns of division abnormally delayed (dally), dally-like protein (dlp), shifted (shf) and secreted frizzled-related protein 125 (sFRP125) and sFRP34 in the beetle Tribolium castaneum, the spider Parasteatoda tepidariorum, the millipede Glomeris marginata and the onychophoran Euperipatoides kanangrensis. This pioneer study represents the first comprehensive comparative data set of these genes in panarthropods.

Conclusions

Expression profiles reveal a high degree of diversity, suggesting that MMFs may represent highly evolvable nodes in otherwise conserved gene regulatory networks. Conserved aspects of MMF expression, however, appear to concern function in segmentation and limb development, two of the key topics of evolutionary developmental research.

Electronic supplementary material

The online version of this article (10.1186/s13227-018-0109-y) contains supplementary material, which is available to authorized users.

A SoxB gene acts as an anterior gap gene and regulates posterior segment addition in a spider

Sox genes encode a set of highly conserved transcription factors that regulate many developmental processes. In insects, the SoxB gene Dichaete is the only Sox gene known to be involved in segmentation. To determine if similar mechanisms are used in other arthropods, we investigated the role of Sox genes during segmentation in the spider Parasteatoda tepidariorum. While Dichaete does not appear to be involved in spider segmentation, we found that the closely related Sox21b-1 gene acts as a gap gene during formation of anterior segments and is also part of the segmentation clock for development of the segment addition zone and sequential addition of opisthosomal segments. Thus, we have found that two different mechanisms of segmentation in a non-mandibulate arthropod are regulated by a SoxB gene. Our work provides new insights into the function of an important and conserved gene family, and the evolution of the regulation of segmentation in arthropods.

Early segmentation in the mite Archegozetes longisetosus reveals conserved and derived aspects of chelicerate development

The arthropod body plan is comprised of several repeating segments along the anteroposterior body axis. This high degree of conservation, however, obfuscates the wide degree of underlying developmental variation present across and within arthropod groups. In chelicerates, the arthropod clade containing mites, spiders, scorpions, and horseshoe crabs, development is the most similar at the stages following early germ band segmentation. Comparative studies of chelicerate segmentation prior to these events, however, remain scarce. In order to elucidate and identify possible shared and derived aspects of chelicerate segmentation, we followed the early prosomal (anterior) segmentation in the model mite Archegozetes longisetosus using the expression of the conserved segmental marker hedgehog (hh). Our data indicate that the ancestral chelicerate likely utilized the gene hedgehog in a group of cells surrounding the germ disc. We also provide evidence that chelicerate segmentation, albeit via the conserved "short/intermediate germ" mode, progresses differently in the prosoma between Archegozetes and spiders and thus early, anterior segmentation in chelicerates is heterochronic.

Genome-scale embryonic developmental profile of gene expression in the common house spider Parasteatoda tepidariorum

We performed RNA sequencing (RNA-Seq) at ten successive developmental stages in embryos of the common house spider Parasteatoda tepidariorum. Two independent datasets from two pairs of parents represent the normalized coverage of mapped RNA-Seq reads along scaffolds of the P. tepidariorum genome assembly. Transcript abundance was calculated against existing AUGUSTUS gene models. The datasets have been deposited in the Gene Expression Omnibus (GEO) Database at the National Center for Biotechnology Information (NCBI) under the accession number GSE112712.

Book lung development in juveniles and adults of the cobweb spider, Parasteatoda tepidariorum C. L. Koch, 1841 (Araneomorphae, Theridiidae)

Light and transmission electron microscopy were used to study the development of new book lung lamellae in juvenile and adult spiders (Parasteatoda tepidariorum). As hypothesized earlier in a study of embryos, mesenchyme cells dispersed throughout the opisthosoma (EMT) are a likely source of precursor epithelial cells (MET) for the new lamellae. The precursor cells in juveniles and adults continue many of the complex activities observed in embryos, e.g., migration, alignment, lumen formation, thinning, elongation, and secretion of the cuticle of air channel walls and trabeculae. The apicobasal polarity of precursor cells for new channels is apparently induced by the polarity pattern of precursor cells of channels produced earlier. Thus, new air and hemolymph channels extend and continue the alternating pattern of older channels. At sites more distant from the spiracle and atrium, new channels are usually produced by the mode II process (intracellular alignment and merging of vesicles). These air channels have bridging trabeculae and are quite stable in size throughout their length. At sites closer to the spiracle and atrium, new channels may be produced by mode I (coalescence of merocrine vesicle secretion). This raises the hypothesis that structural and functional differences in mode I and II channels and differing oxygen and fluid conditions with distance from the spiracle and atrium determine the mode of formation of new channels. Observations herein support an earlier hypothesis that there is some intercellular apical/apical and basal/basal affinity among the opposed surfaces of aligned precursor cells. This results in the alternating pattern of air channels at the apical and hemolymph channels at the basal cell surfaces.

Recent progress and prospects for advancing arachnid genomics

Arachnids exhibit tremendous species richness and adaptations of biomedical, industrial, and agricultural importance. Yet genomic resources for arachnids are limited, with the first few spider and scorpion genomes becoming accessible in the last four years. We review key insights from these genome projects, and recommend additional genomes for sequencing, emphasizing taxa of greatest value to the scientific community. We suggest greater sampling of spiders whose genomes are understudied but hold important protein recipes for silk and venom production. We further recommend arachnid genomes to address significant evolutionary topics, including the phenotypic impact of genome duplications. A barrier to high-quality arachnid genomes are assemblies based solely on short-read data, which may be overcome by long-range sequencing and other emerging methods.

The effect of temperature and light on embryogenesis and post-embryogenesis of the spider Eratigena atrica (Araneae, Agelenidae)

Embryogenesis and post-embryogenesis of spiders depend on several environmental factors including light and temperature. This study was aimed at evaluating the impact of different thermal and lighting conditions on embryonic and early post-embryonic development of Eratigena atrica. Embryos, larvae, nymphs I and II were incubated at constant temperatures of 12, 22, 25 and 32°C under three different light regimes: light, dark, light/dark. Extreme temperatures (12 and 32°C) significantly increased mortality of embryos (to 100%) and nymphs II, whereas larvae and nymphs I suffered reduced survival only at the lowest temperature. Moreover, the lowest temperature reduced the development rate of all stages. The impact of light conditions was less pronounced and more variable: constant light reduced the survival of nymphs I at lower temperatures, but increased that of larvae. Moreover, light increased the time of embryonic development and duration of nymphal stages, particularly at lower temperatures (12-22°C). Thus, the most optimal locations for spiders seem to be dark (though except larval stage) and warm (25°C) sites, where their development is fastest and mortality lowest.

Expression and function of the zinc finger transcription factor Sp6-9 in the spider Parasteatoda tepidariorum

Zinc finger transcription factors of the Sp6-9 group are evolutionarily conserved in all metazoans and have important functions in, e.g., limb formation and heart development. The function of Sp6-9-related genes has been studied in a number of vertebrates and invertebrates, but data from chelicerates (spiders and allies) was lacking so far. We have isolated the ortholog of Sp6-9 from the common house spider Parasteatoda tepidariorum and the cellar spider Pholcus phalangioides. We show that the Sp6-9 gene in these spider species is expressed in the developing appendages thus suggesting a conserved role in limb formation. Indeed, RNAi with Sp6-9 in P. tepidariorum leads not only to strong limb defects, but also to the loss of body segments and head defects in more strongly affected animals. Together with a new expression domain in the early embryo, these data suggest that Sp6-9 has a dual role P. tepidariorum. The early role in head and body segment formation is not known from other arthropods, but the role in limb formation is evolutionarily highly conserved.

A novel role for Ets4 in axis specification and cell migration in the spider Parasteatoda tepidariorum

Organizers play important roles during the embryonic development of many animals. The most famous example is the Spemann organizer that sets up embryonic axes in amphibian embryos. In spiders, a group of BMP secreting mesenchymal cells (the cumulus) functions as an organizer of the dorsoventral axis. Similar to experiments performed with the Spemann organizer, transplantation of the cumulus is able to induce a secondary axis in spiders. Despite the importance of this structure, it is unknown which factors are needed to activate cumulus specific gene expression. To address this question, we performed a transcriptomic analysis of early embryonic development in the spider Parasteatoda tepidariorum. Through this work, we found that the transcription factor Pt-Ets4 is needed for cumulus integrity, dorsoventral patterning and for the activation of Pt-hunchback and Pt-twist expression. Furthermore, ectopic expression of Pt-Ets4 is sufficient to induce cell delamination and migration by inducing a mesoderm-like cell fate.

The house spider genome reveals an ancient whole-genome duplication during arachnid evolution

BACKGROUND

The duplication of genes can occur through various mechanisms and is thought to make a major contribution to the evolutionary diversification of organisms. There is increasing evidence for a large-scale duplication of genes in some chelicerate lineages including two rounds of whole genome duplication (WGD) in horseshoe crabs. To investigate this further, we sequenced and analyzed the genome of the common house spider Parasteatoda tepidariorum.

RESULTS

We found pervasive duplication of both coding and non-coding genes in this spider, including two clusters of Hox genes. Analysis of synteny conservation across the P. tepidariorum genome suggests that there has been an ancient WGD in spiders. Comparison with the genomes of other chelicerates, including that of the newly sequenced bark scorpion Centruroides sculpturatus, suggests that this event occurred in the common ancestor of spiders and scorpions, and is probably independent of the WGDs in horseshoe crabs. Furthermore, characterization of the sequence and expression of the Hox paralogs in P. tepidariorum suggests that many have been subject to neo-functionalization and/or sub-functionalization since their duplication.

CONCLUSIONS

Our results reveal that spiders and scorpions are likely the descendants of a polyploid ancestor that lived more than 450 MYA. Given the extensive morphological diversity and ecological adaptations found among these animals, rivaling those of vertebrates, our study of the ancient WGD event in Arachnopulmonata provides a new comparative platform to explore common and divergent evolutionary outcomes of polyploidization events across eukaryotes.

The house spider genome reveals an ancient whole-genome duplication during arachnid evolution

Background

The duplication of genes can occur through various mechanisms and is thought to make a major contribution to the evolutionary diversification of organisms. There is increasing evidence for a large-scale duplication of genes in some chelicerate lineages including two rounds of whole genome duplication (WGD) in horseshoe crabs. To investigate this further, we sequenced and analyzed the genome of the common house spider Parasteatoda tepidariorum.

Results

We found pervasive duplication of both coding and non-coding genes in this spider, including two clusters of Hox genes. Analysis of synteny conservation across the P. tepidariorum genome suggests that there has been an ancient WGD in spiders. Comparison with the genomes of other chelicerates, including that of the newly sequenced bark scorpion Centruroides sculpturatus, suggests that this event occurred in the common ancestor of spiders and scorpions, and is probably independent of the WGDs in horseshoe crabs. Furthermore, characterization of the sequence and expression of the Hox paralogs in P. tepidariorum suggests that many have been subject to neo-functionalization and/or sub-functionalization since their duplication.

Conclusions

Our results reveal that spiders and scorpions are likely the descendants of a polyploid ancestor that lived more than 450 MYA. Given the extensive morphological diversity and ecological adaptations found among these animals, rivaling those of vertebrates, our study of the ancient WGD event in Arachnopulmonata provides a new comparative platform to explore common and divergent evolutionary outcomes of polyploidization events across eukaryotes.

Electronic supplementary material

The online version of this article (doi:10.1186/s12915-017-0399-x) contains supplementary material, which is available to authorized users.

Expression and function of spineless orthologs correlate with distal deutocerebral appendage morphology across Arthropoda

The deutocerebral (second) head segment is putatively homologous across Arthropoda, in spite of remarkable disparity of form and function of deutocerebral appendages. In Mandibulata this segment bears a pair of sensory antennae, whereas in Chelicerata the same segment bears a pair of feeding appendages called chelicerae. Part of the evidence for the homology of deutocerebral appendages is the conserved function of homothorax (hth), which has been shown to specify antennal or cheliceral fate in the absence of Hox signaling, in both mandibulate and chelicerate exemplars. However, the genetic basis for the morphological disparity of antenna and chelicera is not understood. To test whether downstream targets of hth have diverged in a lineage-specific manner, we examined the evolution of the function and expression of spineless (ss), which in two holometabolous insects is known to act as a hth target and distal antennal determinant. Toward expanding phylogenetic representation of gene expression data, here we show that strong expression of ss is observed in developing antennae of a hemimetabolous insect, a centipede, and an amphipod crustacean. By contrast, ss orthologs are not expressed throughout the cheliceral limb buds of spiders or harvestmen during developmental stages when appendage fate is specified. RNA interference-mediated knockdown of ss in Oncopeltus fasciatus, which bears a simple plesiomorphic antenna, resulted in homeotic distal antenna-to-leg transformation, comparable to data from holometabolous insect counterparts. Knockdown of hth in Oncopeltus fasciatus abrogated ss expression, suggesting conservation of upstream regulation. These data suggest that ss may be a flagellar (distal antennal) determinant more broadly, and that this function was acquired at the base of Mandibulata.