Posterior Hox gene reduction in an arthropod: Ultrabithorax and Abdominal-B are expressed in a single segment in the mite Archegozetes longisetosus

Dual Functions of labial Resolve the Hox Logic of Chelicerate Head Segments

Despite an abundance of gene expression surveys, comparatively little is known about Hox gene function in Chelicerata. Previous investigations of paralogs of labial (lab) and Deformed (Dfd) in a spider have shown that these play a role in tissue maintenance of the pedipalp segment (lab-1) and in patterning the first walking leg identity (Dfd-1), respectively. However, extrapolations of these data across chelicerates are hindered by the existence of duplicated Hox genes in arachnopulmonates (e.g., spiders and scorpions), which have resulted from an ancient whole genome duplication (WGD) event. Here, we investigated the function of the single-copy ortholog of lab in the harvestman Phalangium opilio, an exemplar of a lineage that was not subject to this WGD. Embryonic RNA interference against lab resulted in two classes of phenotypes: homeotic transformations of pedipalps to chelicerae, as well as reduction and fusion of the pedipalp and leg 1 segments. To test for combinatorial function, we performed a double knockdown of lab and Dfd, which resulted in a homeotic transformation of both pedipalps and the first walking legs into cheliceral identity, whereas the second walking leg is transformed into a pedipalpal identity. Taken together, these results elucidate a model for the Hox logic of head segments in Chelicerata. To substantiate the validity of this model, we performed expression surveys for lab and Dfd paralogs in scorpions and horseshoe crabs. We show that repetition of morphologically similar appendages is correlated with uniform expression levels of the Hox genes lab and Dfd, irrespective of the number of gene copies.

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.

The Chinese mitten crab genome provides insights into adaptive plasticity and developmental regulation

The infraorder Brachyura (true or short-tailed crabs) represents a successful group of marine invertebrates yet with limited genomic resources. Here we report a chromosome-anchored reference genome and transcriptomes of the Chinese mitten crab Eriocheir sinensis, a catadromous crab and invasive species with wide environmental tolerance, strong osmoregulatory capacity and high fertility. We show the expansion of specific gene families in the crab, including F-ATPase, which enhances our knowledge on the adaptive plasticity of this successful invasive species. Our analysis of spatio-temporal transcriptomes and the genome of E. sinensis and other decapods shows that brachyurization development is associated with down-regulation of Hox genes at the megalopa stage when tail shortening occurs. A better understanding of the molecular mechanism regulating sexual development is achieved by integrated analysis of multiple omics. These genomic resources significantly expand the gene repertoire of Brachyura, and provide insights into the biology of this group, and Crustacea in general.

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.

Genome streamlining in a minute herbivore that manipulates its host plant

The tomato russet mite, Aculops lycopersici, is among the smallest animals on earth. It is a worldwide pest on tomato and can potently suppress the host's natural resistance. We sequenced its genome, the first of an eriophyoid, and explored whether there are genomic features associated with the mite's minute size and lifestyle. At only 32.5 Mb, the genome is the smallest yet reported for any arthropod and, reminiscent of microbial eukaryotes, exceptionally streamlined. It has few transposable elements, tiny intergenic regions, and is remarkably intron-poor, as more than 80% of coding genes are intronless. Furthermore, in accordance with ecological specialization theory, this defense-suppressing herbivore has extremely reduced environmental response gene families such as those involved in chemoreception and detoxification. Other losses associate with this species' highly derived body plan. Our findings accelerate the understanding of evolutionary forces underpinning metazoan life at the limits of small physical and genome size.

Genomic resources and toolkits for developmental study of whip spiders (Amblypygi) provide insights into arachnid genome evolution and antenniform leg patterning

BACKGROUND

The resurgence of interest in the comparative developmental study of chelicerates has led to important insights, such as the discovery of a genome duplication shared by spiders and scorpions, inferred to have occurred in the most recent common ancestor of Arachnopulmonata (a clade comprising the five arachnid orders that bear book lungs). Nonetheless, several arachnid groups remain understudied in the context of development and genomics, such as the order Amblypygi (whip spiders). The phylogenetic position of Amblypygi in Arachnopulmonata posits them as an interesting group to test the incidence of the proposed genome duplication in the common ancestor of Arachnopulmonata, as well as the degree of retention of duplicates over 450 Myr. Moreover, whip spiders have their first pair of walking legs elongated and modified into sensory appendages (a convergence with the antennae of mandibulates), but the genetic patterning of these antenniform legs has never been investigated.

RESULTS

We established genomic resources and protocols for cultivation of embryos and gene expression assays by in situ hybridization to study the development of the whip spider Phrynus marginemaculatus. Using embryonic transcriptomes from three species of Amblypygi, we show that the ancestral whip spider exhibited duplications of all ten Hox genes. We deploy these resources to show that paralogs of the leg gap genes dachshund and homothorax retain arachnopulmonate-specific expression patterns in P. marginemaculatus. We characterize the expression of leg gap genes Distal-less, dachshund-1/2 and homothorax-1/2 in the embryonic antenniform leg and other appendages, and provide evidence that allometry, and by extension the antenniform leg fate, is specified early in embryogenesis.

CONCLUSION

This study is the first step in establishing P. marginemaculatus as a chelicerate model for modern evolutionary developmental study, and provides the first resources sampling whip spiders for comparative genomics. Our results suggest that Amblypygi share a genome duplication with spiders and scorpions, and set up a framework to study the genetic specification of antenniform legs. Future efforts to study whip spider development must emphasize the development of tools for functional experiments in P. marginemaculatus.

Loss of intermediate regions of perpendicular body axes contributed to miniaturization of tardigrades

Tardigrades have a miniaturized body plan. Miniaturization in tardigrades is associated with the loss of several organ systems and an intermediate region of their anteroposterior (AP) axis. However, how miniaturization has affected tardigrade legs is unclear. In arthropods and in onychophorans, the leg gap genes are expressed in regionalized proximodistal (PD) patterns in the legs. Functional studies indicate that these genes regulate growth in their respective expression domains and establish PD identities, partly through mutually antagonistic regulatory interactions. Here, we investigated the expression patterns of tardigrade orthologs of the leg gap genes. Rather than being restricted to a proximal leg region, as in arthropods and onychophorans, we detected coexpression of orthologues of homothorax and extradenticle broadly across the legs of the first three trunk segments in the tardigrade Hypsibius exemplaris. We could not identify a dachshund orthologue in tardigrade genomes, a gene that is expressed in an intermediate region of developing legs in arthropods and onychophorans, suggesting that this gene was lost in the tardigrade lineage. We detected Distal-less expression broadly across all developing leg buds in H. exemplaris embryos, unlike in arthropods and onychophorans, in which it exhibits a distally restricted expression domain. The broad expression patterns of the remaining leg gap genes in H. exemplaris legs may reflect the loss of dachshund and the accompanying loss of an intermediate region of the legs in the tardigrade lineage. We propose that the loss of intermediate regions of both the AP and PD body axes contributed to miniaturization of Tardigrada.

Genomic insights into mite phylogeny, fitness, development, and reproduction

BACKGROUND

Predatory mites (Acari: Phytoseiidae) are the most important beneficial arthropods used in augmentative biological pest control of protected crops around the world. However, the genomes of mites are far less well understood than those of insects and the evolutionary relationships among mite and other chelicerate orders are contested, with the enigmatic origin of mites at one of the centres in discussion of the evolution of Arachnida.

RESULTS

We here report the 173 Mb nuclear genome (from 51.75 Gb pairs of Illumina reads) of the predatory mite, Neoseiulus cucumeris, a biocontrol agent against pests such as mites and thrips worldwide. We identified nearly 20.6 Mb (~ 11.93% of this genome) of repetitive sequences and annotated 18,735 protein-coding genes (a typical gene 2888 bp in size); the total length of protein-coding genes was about 50.55 Mb (29.2% of this assembly). About 37% (6981) of the genes are unique to N. cucumeris based on comparison with other arachnid genomes. Our phylogenomic analysis supported the monophyly of Acari, therefore rejecting the biphyletic origin of mites advocated by other studies based on limited gene fragments or few taxa in recent years. Our transcriptomic analyses of different life stages of N. cucumeris provide new insights into genes involved in its development. Putative genes involved in vitellogenesis, regulation of oviposition, sex determination, development of legs, signal perception, detoxification and stress-resistance, and innate immune systems are identified.

CONCLUSIONS

Our genomics and developmental transcriptomics analyses of N. cucumeris provide invaluable resources for further research on the development, reproduction, and fitness of this economically important mite in particular and Arachnida in general.

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.

Chelicerates and the Conquest of Land: A View of Arachnid Origins Through an Evo-Devo Spyglass

The internal phylogeny of Chelicerata and the attendant evolutionary scenario of arachnid terrestrialization have a long and contentious history. Previous studies of developmental gene expression data have suggested that respiratory systems of spiders, crustaceans, and insects are all serially homologous structures derived from the epipods (outer appendage rami) of the arthropod ancestor, corresponding to an ancestral gill. A separate body of evidence has suggested that the respiratory systems of arachnids are modified, inverted telopods (inner rami, or legs). Here I review these dissonant homology statements and compare the developmental genetic basis for respiratory system development in insects and arachnids. I show that the respiratory primordia of arachnids are not positionally homologous to those of insects. I further demonstrate that candidate genes critical to tracheal fate specification in Drosophila melanogaster are expressed very differently in arachnid exemplars. Taken together, these data suggest that mechanisms of respiratory system development are not derived from homologous structures or mechanisms in insects and arachnids, and that different terrestrial arthropod lineages have solved the challenge of aerial respiration using different developmental mechanisms.

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.

Segmentation and tagmosis in Chelicerata

Patterns of segmentation and tagmosis are reviewed for Chelicerata. Depending on the outgroup, chelicerate origins are either among taxa with an anterior tagma of six somites, or taxa in which the appendages of somite I became increasingly raptorial. All Chelicerata have appendage I as a chelate or clasp-knife chelicera. The basic trend has obviously been to consolidate food-gathering and walking limbs as a prosoma and respiratory appendages on the opisthosoma. However, the boundary of the prosoma is debatable in that some taxa have functionally incorporated somite VII and/or its appendages into the prosoma. Euchelicerata can be defined on having plate-like opisthosomal appendages, further modified within Arachnida. Total somite counts for Chelicerata range from a maximum of nineteen in groups like Scorpiones and the extinct Eurypterida down to seven in modern Pycnogonida. Mites may also show reduced somite counts, but reconstructing segmentation in these animals remains challenging. Several innovations relating to tagmosis or the appendages borne on particular somites are summarised here as putative apomorphies of individual higher taxa. We also present our observations within the concept of pseudotagma, whereby the true tagmata - the prosoma and opisthosoma - can be defined on a fundamental change in the limb series while pseudotagmata, such as the cephalosoma/proterosoma, are expressed as divisions in sclerites covering the body without an accompanying change in the appendages.

Genome Sequencing of the Phytoseiid Predatory Mite Metaseiulus occidentalis Reveals Completely Atomized Hox Genes and Superdynamic Intron Evolution

Metaseiulus occidentalis is an eyeless phytoseiid predatory mite employed for the biological control of agricultural pests including spider mites. Despite appearances, these predator and prey mites are separated by some 400 Myr of evolution and radically different lifestyles. We present a 152-Mb draft assembly of the M. occidentalis genome: Larger than that of its favored prey, Tetranychus urticae, but considerably smaller than those of many other chelicerates, enabling an extremely contiguous and complete assembly to be built-the best arachnid to date. Aided by transcriptome data, genome annotation cataloged 18,338 protein-coding genes and identified large numbers of Helitron transposable elements. Comparisons with other arthropods revealed a particularly dynamic and turbulent genomic evolutionary history. Its genes exhibit elevated molecular evolution, with strikingly high numbers of intron gains and losses, in stark contrast to the deer tick Ixodes scapularis Uniquely among examined arthropods, this predatory mite's Hox genes are completely atomized, dispersed across the genome, and it encodes five copies of the normally single-copy RNA processing Dicer-2 gene. Examining gene families linked to characteristic biological traits of this tiny predator provides initial insights into processes of sex determination, development, immune defense, and how it detects, disables, and digests its prey. As the first reference genome for the Phytoseiidae, and for any species with the rare sex determination system of parahaploidy, the genome of the western orchard predatory mite improves genomic sampling of chelicerates and provides invaluable new resources for functional genomic analyses of this family of agriculturally important mites.

A survey of conservation of sea spider and Drosophila Hox protein activities

Hox proteins have well-established functions in development and evolution, controlling the final morphology of bilaterian animals. The common phylogenetic origin of Hox proteins and the associated evolutionary diversification of protein sequences provide a unique framework to explore the relationship between changes in protein sequence and function. In this study, we aimed at questioning how sequence variation within arthropod Hox proteins influences function. This was achieved by exploring the functional impact of sequence conservation/divergence of the Hox genes, labial, Sex comb reduced, Deformed, Ultrabithorax and abdominalA from two distant arthropods, the sea spider and the well-studied Drosophila. Results highlight a correlation between sequence conservation within the homeodomain and the degree of functional conservation, and identify a novel functional domain in the Labial protein.

Hox gene duplications correlate with posterior heteronomy in scorpions

The evolutionary success of the largest animal phylum, Arthropoda, has been attributed to tagmatization, the coordinated evolution of adjacent metameres to form morphologically and functionally distinct segmental regions called tagmata. Specification of regional identity is regulated by the Hox genes, of which 10 are inferred to be present in the ancestor of arthropods. With six different posterior segmental identities divided into two tagmata, the bauplan of scorpions is the most heteronomous within Chelicerata. Expression domains of the anterior eight Hox genes are conserved in previously surveyed chelicerates, but it is unknown how Hox genes regionalize the three tagmata of scorpions. Here, we show that the scorpion Centruroides sculpturatus has two paralogues of all Hox genes except Hox3, suggesting cluster and/or whole genome duplication in this arachnid order. Embryonic anterior expression domain boundaries of each of the last four pairs of Hox genes (two paralogues each of Antp, Ubx, abd-A and Abd-B) are unique and distinguish segmental groups, such as pectines, book lungs and the characteristic tail, while maintaining spatial collinearity. These distinct expression domains suggest neofunctionalization of Hox gene paralogues subsequent to duplication. Our data reconcile previous understanding of Hox gene function across arthropods with the extreme heteronomy of scorpions.

A review of Cunaxidae (Acariformes, Trombidiformes): Histories and diagnoses of subfamilies and genera, keys to world species, and some new locality records

Cunaxidae are predaceous mites found in a variety of habitats. This work provides comprehensive keys to world subfamilies, genera, and species. Diagnoses and historical reviews are provided for subfamilies and genera. Cunaxa boneti, C. denmarki, C. exoterica, C. floridanus, C. lehmanae, C. lukoschusi, C. metzi, C. myabunderensis, C newyorkensis, C. rackae, C. reevesi, and C. reticulatus are moved to Rubroscirus and C. otiosus, C. valentis, and C. rasile are returned to Rubroscirus. Cunaxoides neopectinatus is moved to Pulaeus. Neocunaxoides pradhani and N. gilbertoi are transferred to Scutopalus. Pulaeus minutus and P. subterraneus are moved to Lupaeus. Pseudobonzia bakari, P. malookensis, and P. shamshadi are transferred to Neobonzia. Dactyloscirus bifidus is transferred to Armascirus. Scirula papillata is reported from the Western Hemisphere for the first time. Armascirus ozarkensis, A. primigenius, and Dactyloscirus dolichosetosus are reported from new localities.

The Hox genes Ultrabithorax and abdominal-A specify three different types of abdominal appendage in the springtail Orchesella cincta (Collembola)

Background

In Drosophila and many other insects, the Hox genes Ultrabithorax (Ubx) and abdominal-A (abd-A) suppress limb formation on most or all segments of the abdomen. However, a number of basal hexapod lineages retain multiple appendages on the abdomen. In the collembolans or springtails, three abdominal segments develop specialized organs that originate from paired appendage primordia which fuse at the midline: the first abdominal segment bears the collophore (ventral tube), involved in osmoregulation; the fourth segment bears the furca, the leaping organ, and the third segment bears the retinaculum, which retains the furca at rest. Ubx and abd-A are known to be expressed in the springtail abdomen, but what role they play in specifying these distinct abdominal appendages is not known. This is largely because no genetic model has been established in collembolans or any other non-insect hexapod.

Results

We have developed a convenient method for laboratory culture of the collembolan Orchesella cincta on defined media, a method for in-situ hybridization to embryos and a procedure for gene knockdown by parental injection of double-stranded RNA (RNAi). We show that Orchesella Ubx transcripts are detectable in the first to third abdominal segments, and abd-A transcripts in the second to fourth segments. Knockdown of Oc-Ubx leads to the homeotic transformation of the collophore into a pair of walking legs (a more anterior identity) but the retinaculum into a furca (a more posterior identity). Knockdown of Oc-abd-A leads to the transformation of the retinaculum into a collophore and of the furca into legs (both anterior transformations). Simultaneous silencing of both Oc-Ubx and Oc-abd-A transformed all three of these appendages into paired legs, but did not cause appendages to develop on the second, or on the most posterior abdominal segments.

Conclusions

We conclude that, in Orchesella, Oc-Ubx alone specifies the collophore on the first and Oc-abd-A alone specifies the furca on the fourth abdominal segment. Oc-Ubx and Oc-abd-A function together, apparently combinatorially, to specify the retinaculum on the third segment. The efficiency of RNAi in Orchesella makes this an attractive model for further genetic studies of development and physiology in basal hexapods.

Electronic supplementary material

The online version of this article (doi:10.1186/2041-9139-5-2) contains supplementary material, which is available to authorized users.