Hox genes require homothorax and extradenticle for body wall identity specification but not for appendage identity specification during metamorphosis of Tribolium castaneum

The gnathosoma is a bad character rather than evidence for mite monophyly

In recent years, the case for the monophyly of mites or Acari (Parasitiformes + Acariformes) has looked increasingly weak. Much of the remaining doubt about the artificiality of this taxon stems from the importance long attributed to the gnathosoma, widely considered the most convincing morphological character supporting monophyly. The gnathosoma has long been interpreted as originating via the fusion together of the palpal coxae, which is thought to have contributed to the consolidation of the mouthparts into a compact feeding apparatus that articulates as a single unit. However, an investigation of the mouthparts of Acariformes, reported herein, revealed that fusion together of the palpal coxae is an uncommon state that convergently evolved in multiple acariform taxa rather than evolving only once, as a synapomorphy uniting Acariformes and Parasitiformes. Moreover, other defining features of the gnathosoma involve either very different modifications or structures that are not homologous between both main lineages of mites. Therefore, the gnathosoma is a bad character-poorly defined and based on a series of misinterpretations-that should not be treated as evidence for mite monophyly.

The role of Hox genes in shaping embryonic external morphology of the primitive insect Thermobia domestica (Zygentoma)

Insects represent one of the most evolutionarily successful groups, with their diversity hypothesized to be related to the regulatory roles of Hox genes, a set of related genes encoding homeodomain transcription factors determining the identity of segments along the anterior-posterior axis of the embryo. However, functional insights into the roles of Hox genes in primitive ametabolous insects, which represent the critical transition from aquatic crustaceans to winged insects, have been limited. In this study, we identified complete protein-coding sequences of 10 Hox genes in the Zygentoma Thermobia domestica, and applied clustered regularly interspaced short palindromic repeats (CRISPR) / CRISPR-associated nuclease 9 (Cas 9) mediated gene knockout (KO) to decipher their functions. We found that the roles of pb, Dfd, and Scr are vital in specifying the appendages of the head in T. domestica, and these roles are relatively conserved in crustaceans and winged insects. Antp is essential for the development of the prothorax segment and the first pair of legs in T. domestica. Ubx and abd-A fully repress appendage development in the abdomen of T. domestica, which implies a functional switch from crustaceans to insects. Additionally, the role of ftz in segmenting the abdomen of T. domestica suggests it has acquired new functions in primitive insects, beyond its traditional Hox-like roles. Although KOs of lab, Hox3, and Abd-B did not result in obvious external phenotypic changes, they led to a significant decrease in hatching rates and substantial deviations in daily survival numbers compared to the negative control. These findings underscore the indispensable roles of all Hox genes during the embryonic development of T. domestica. Our study sheds new light on the functional evolution of Hox genes in ametabolous insects and enhances our understanding of the genetic underpinnings of insect development and diversification.

A Novel Expression Domain of extradenticle Underlies the Evolutionary Developmental Origin of the Chelicerate Patella

Neofunctionalization of duplicated gene copies is thought to be an important process underlying the origin of evolutionary novelty and provides an elegant mechanism for the origin of new phenotypic traits. One putative case where a new gene copy has been linked to a novel morphological trait is the origin of the arachnid patella, a taxonomically restricted leg segment. In spiders, the origin of this segment has been linked to the origin of the paralog dachshund-2, suggesting that a new gene facilitated the expression of a new trait. However, various arachnid groups that possess patellae do not have a copy of dachshund-2, disfavoring the direct link between gene origin and trait origin. We investigated the developmental genetic basis for patellar patterning in the harvestman Phalangium opilio, which lacks dachshund-2. Here, we show that the harvestman patella is established by a novel expression domain of the transcription factor extradenticle. Leveraging this definition of patellar identity, we surveyed targeted groups across chelicerate phylogeny to assess when this trait evolved. We show that a patellar homolog is present in Pycnogonida (sea spiders) and various arachnid orders, suggesting a single origin of the patella in the ancestor of Chelicerata. A potential loss of the patella is observed in Ixodida. Our results suggest that the modification of an ancient gene, rather than the neofunctionalization of a new gene copy, underlies the origin of the patella. Broadly, this work underscores the value of comparative data and broad taxonomic sampling when testing hypotheses in evolutionary developmental biology.

Developmental and genomic insight into the origin of the tardigrade body plan

Tardigrada is an ancient lineage of miniaturized animals. As an outgroup of the well-studied Arthropoda and Onychophora, studies of tardigrades hold the potential to reveal important insights into body plan evolution in Panarthropoda. Previous studies have revealed interesting facets of tardigrade development and genomics that suggest that a highly compact body plan is a derived condition of this lineage, rather than it representing an ancestral state of Panarthropoda. This conclusion was based on studies of several species from Eutardigrada. We review these studies and expand on them by analyzing the publicly available genome and transcriptome assemblies of Echiniscus testudo, a representative of Heterotardigrada. These new analyses allow us to phylogenetically reconstruct important features of genome evolution in Tardigrada. We use available data from tardigrades to interrogate several recent models of body plan evolution in Panarthropoda. Although anterior segments of panarthropods are highly diverse in terms of anatomy and development, both within individuals and between species, we conclude that a simple one-to-one alignment of anterior segments across Panarthropoda is the best available model of segmental homology. In addition to providing important insight into body plan diversification within Panarthropoda, we speculate that studies of tardigrades may reveal generalizable pathways to miniaturization.

A novel expression domain of extradenticle underlies the evolutionary developmental origin of the chelicerate patella

Neofunctionalization of duplicated gene copies is thought to be an important process underlying the origin of evolutionary novelty and provides an elegant mechanism for the origin of new phenotypic traits. One putative case where a new gene copy has been linked to a novel morphological trait is the origin of the arachnid patella, a taxonomically restricted leg segment. In spiders, the origin of this segment has been linked to the origin of the paralog dachshund-2 , suggesting that a new gene facilitated the expression of a new trait. However, various arachnid groups that possess patellae do not have a copy of dachshund-2 , disfavoring the direct link between gene origin and trait origin. We investigated the developmental genetic basis for patellar patterning in the harvestman Phalangium opilio , which lacks dachshund-2 . Here, we show that the harvestman patella is established by a novel expression domain of the transcription factor extradenticle . Leveraging this definition of patellar identity, we surveyed targeted groups across chelicerate phylogeny to assess when this trait evolved. We show that a patellar homolog is present in Pycnogonida (sea spiders) and various arachnid orders, suggesting a single origin of the patella in the ancestor of Chelicerata. A potential loss of the patella is observed in Ixodida. Our results suggest that the modification of an ancient gene, rather than the neofunctionalization of a new gene copy, underlies the origin of the patella. Broadly, this work underscores the value of comparative data and broad taxonomic sampling when testing hypotheses in evolutionary developmental biology.

Upregulation of Hox genes leading to caste-specific morphogenesis in a termite

BACKGROUND

In social insects, interactions among colony members trigger caste differentiation with morphological modifications. In termite caste differentiation, caste-specific morphologies (such as mandibles in soldiers, genital organs in reproductives or wings in alates) are well developed during post-embryonic development under endocrine controls (e.g., juvenile hormone and ecdysone). Since body part-specific morphogenesis in caste differentiation is hormonally regulated by global factors circulated throughout the body, positional information should be required for the caste-specific and also body part-specific morphogenesis. To identify factors providing the positional information, expression and functional analyses of eight Hox genes were carried out during the three types of caste differentiation (i.e., soldier, neotenic and alate differentiation) in a termite, Hodotermopsis sjostedti.

RESULTS

Spatio-temporal patterns of Hox gene expression during caste differentiation were elucidated by real-time qPCR, showing the caste-specific upregulations of Hox genes during the differentiation processes. Among eight Hox genes, Deformed (Dfd) was upregulated specifically in mandibles in soldier differentiation, abdominal-A (abd-A) and Abdominal-B (Abd-B) were upregulated in the abdomen in neotenic differentiation, while Sex-comb reduced (Scr) and Antennapedia (Antp) were upregulated during alate differentiation. Furthermore, RNAi knockdown of Dfd in soldier differentiation and of abd-A and Abd-B in neotenic differentiation distorted the modifications of caste-specific morphologies.

CONCLUSIONS

Gene expression and functional analyses in this study revealed that, in the caste differentiation in termites, upregulation of Hox genes provide positional identities of body segments, resulting in the caste-specific morphogenesis. The acquisition of such developmental modifications would have enabled the evolution of sophisticated caste systems in termites.

Toxicity effect of the edible pigment carmoisine on Polyrhachis vicina Roger (Hymenoptera: Formicidae)

Carmoisine belongs to a water-soluble synthetic dye and is often used as a food additive. Previous research has shown that carmoisine is toxic to rats and zebrafish, but there have been few reports on the effect of carmoisine on soil-dwelling social insects. The present study evaluated carmoisine toxicity in Polyrhachis vicina Roger. We found that the effects of different concentrations of carmoisine on the mortality of workers were dose-dependent. The 10% lethal dose (LD₁₀), 50% lethal dose (LD₅₀) and 90% lethal dose (LD₉₀) of carmoisine to workers at 96 h was calculated to be 0.504, 5.491 and 10.478 g/L, respectivily. LD₁₀ of workers were selected to treat the fourth instar larvae, pupae and adults for 10 days. The results showed that the survival rate of all ants, except for females, was significantly reduced, especially larvae and workers. The body weight of larvae, pupae and males decreased significantly, while weight gain was observed in the females and workers. The appearance of larvae, pupae and workers changed after carmoisine treatment, such as body darkening and epidermis shrinking of larvae and pupae, as well as body segment expansion of workers. Furthermore, carmoisine altered the expression of the estrogen-related receptor, tailless and homothorax of P. vicina (Pv-ERR, Pv-tll and Pv-hth) to varying degrees in larvae and adults. We believe that variations in body weight can lead to a decrease in survival rate and appearance changes in the ants, which may be related to abnormal gene expressions caused by carmoisine treatment. Therefore, we confirm that carmoisine has negative effects on the growth and development of P. vicina.

Effect of aspartame on survival, morphological and molecular levels of Polyrhachis vicina Roger (Hymenoptera, Formicidae)

Aspartame is a food additive that is widely used in the food industry. Previous data have shown that aspartame is toxic to humans and animals. However, there are few reports on the effect of aspartame on social insects living in the soil. The present study was designed to evaluate aspartame toxicity for Polyrhachis vicina Roger. Five dosages of aspartame were fed to the workers and 40 mg/kg (acceptable daily intake, ADI) aspartame was chosen to feed the 4th instar larvae, pupae, females and males in P. vicina. The results showed that the effect of aspartame on the survival rate of workers was in a time and dose dependent manner. The survival rate of 4th instar larvae, pupae and males decreased at 40 mg/kg aspartame. Meanwhile, we found that aspartame toxicity can cause weight and morphological changes. These changes may be related to the abnormal gene expression of Ecdysone receptor, Tailless and Extradenticle of P. vicina (PvEcR, PvTll and PvExd) resulting from aspartame treatment. The present study confirms the effect of aspartame toxicity on P. vicina even at the ADI dosage.

Tribolium castaneum: A Model Insect for Fundamental and Applied Research

Tribolium castaneum has a long history as a model species in many distinct subject areas, but improved connections among the genetics, genomics, behavioral, ecological, and pest management fields are needed to fully realize this species' potential as a model. Tribolium castaneum was the first beetle whose genome was sequenced, and a new genome assembly and enhanced annotation, combined with readily available genomic research tools, have facilitated its increased use in a wide range of functional genomics research. Research into T. castaneum's sensory systems, response to pheromones and kairomones, and patterns of movement and landscape utilization has improved our understanding of behavioral and ecological processes. Tribolium castaneum has also been a model in the development of pest monitoring and management tactics, including evaluation of insecticide resistance mechanisms. Application of functional genomics approaches to behavioral, ecological, and pest management research is in its infancy but offers a powerful tool that can link mechanism with function and facilitate exploitation of these relationships to better manage this important food pest.

Out from under the wing: reconceptualizing the insect wing gene regulatory network as a versatile, general module for body-wall lobes in arthropods

Body plan evolution often occurs through the differentiation of serially homologous body parts, particularly in the evolution of arthropod body plans. Recently, homeotic transformations resulting from experimental manipulation of gene expression, along with comparative data on the expression and function of genes in the wing regulatory network, have provided a new perspective on an old question in insect evolution: how did the insect wing evolve? We investigated the metamorphic roles of a suite of 10 wing- and body-wall-related genes in a hemimetabolous insect, Oncopeltus fasciatus. Our results indicate that genes involved in wing development in O. fasciatus play similar roles in the development of adult body-wall flattened cuticular evaginations. We found extensive functional similarity between the development of wings and other bilayered evaginations of the body wall. Overall, our results support the existence of a versatile development module for building bilayered cuticular epithelial structures that pre-dates the evolutionary origin of wings. We explore the consequences of reconceptualizing the canonical wing-patterning network as a bilayered body-wall patterning network, including consequences for long-standing debates about wing homology, the origin of wings and the origin of novel bilayered body-wall structures. We conclude by presenting three testable predictions that result from this reconceptualization.

High-throughput profiling of diapause regulated genes from Trichogramma dendrolimi (Hymenoptera: Trichogrammatidae)

Background

The parasitoid wasp, Trichogramma dendrolimi, can enter diapause at the prepupal stage. Thus, diapause is an efficient preservation method during the mass production of T. dendrolimi. Previous studies on diapause have mainly focused on ecological characteristics, so the molecular basis of diapause in T. dendrolimi is unknown. We compared transcriptomes of diapause and non-diapause T. dendrolimi to identify key genes and pathways involved in diapause development.

Results

Transcriptome sequencing was performed on diapause prepupae, pupae after diapause, non-diapause prepupae, and pupae. Analysis yielded a total of 87,022 transcripts with an average length of 1604 bp. By removing redundant sequences and those without significant BLAST hits, a non-redundant dataset was generated, containing 7593 sequences with an average length of 3351 bp. Among them, 5702 genes were differentially expressed. The result of Gene Ontology (GO) enrichment analysis revealed that regulation of transcription, DNA-templated, oxidation-reduction process, and signal transduction were significantly affected. Ten genes were selected for validation using quantitative real-time PCR (qPCR). The changes showed the same trend as between the qPCR and RNA-Seq results. Several genes were identified as involved in diapause, including ribosomal proteins, zinc finger proteins, homeobox proteins, forkhead box proteins, UDP-glucuronosyltransferase, Glutathione-S-transferase, p53, and DNA damage-regulated gene 1 (pdrg1). Genes related to lipid metabolism were also included.

Conclusions

We generated a large amount of transcriptome data from T. dendrolimi, providing a resource for future gene function research. The diapause-related genes identified help reveal the molecular mechanisms of diapause, in T. dendrolimi, and other insect species.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-020-07285-4.

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.

Roles of Polycomb group proteins Enhancer of zeste (E(z)) and Polycomb (Pc) during metamorphosis and larval leg regeneration in the flour beetle Tribolium castaneum

Many organisms both undergo dramatic morphological changes during post-embryonic development and also regenerate lost structures, but the roles of epigenetic regulators in such processes are only beginning to be understood. In the present study, the functions of two histone modifiers were examined during metamorphosis and larval limb regeneration in the red flour beetle Tribolium castaneum. Polycomb (Pc), a member of Polycomb repressive complex 1 (PRC1), and Enhancer of zeste (E(z)), a member of Polycomb repressive complex 2 (PRC2), were silenced in larvae using RNA interference. In the absence of Pc, the head appendages of adults transformed into a leg-like morphology, and the legs and wings assumed a metathoracic identity, indicating that Pc acts to specify proper segmental identity. Similarly, silencing of E(z) led to homeotic transformation of legs and wings. Additional defects were also observed in limb patterning as well as eye morphogenesis, indicating that PcG proteins play critical roles in imaginal precursor cells. In addition, larval legs and antennae failed to re-differentiate when either Pc or E(z) was knocked down, indicating that histone modification is necessary for proper blastema growth and differentiation. These findings indicate that PcG proteins play extensive roles in postembryonic plasticity of imaginal precursor cells.

Identification and characterization of a new long noncoding RNA iab-1 in the Hox cluster of silkworm, Bombyx mori identification of iab-1

Long noncoding RNAs (lncRNAs) areinvolvedin a variety of biological processes. In silkworm, numerous lncRNAs have been predicted through deep transcriptome sequencing, but no functional role has been experimentally validated yet. Here, we characterized a new lncRNA iab-1 that was mainly encoded by the intergenic region between Bmabd-A and Bmabd-B in the Homeobox (Hox) cluster of the silkworm, Bombyx mori. More than seven alternative splicing isoforms of lncRNA iab-1 were cloned, which were subgrouped into types 1 and 2 based on the location of the 3'-ends. The iab-1 was expressed at a low level, but the expression of iab-1 peaked at several specific development stages, including 3 to 4 days during the embryonic stage, stages before fourth molting, and the sixth hour after the fourth molting, and early stages during metamorphosis. It was highly expressed in the nervus and epidermis, especially the epidermis of the posterior abdomen at the fourth instar premolting stage. The relationship between iab-1 and nearby Hox genes was analyzed at different developmental stages. Iab-1 expression was highly associated with Bmabd-A as well as Bmabd-B in the embryonic and larval stages, while this association was decreased at the metamorphic stage; iab-1 expression was highly associated with BmUbx only in the embryonic stage. Downregulation of iab-1 expression by small interfering RNA led to the death of most of the treated individuals at the larval stage, suggesting that iab-1 transcript expression might be involved in certain relevant physiological processes. The expression of Bmabd-A and Bmabd-B did not change in iab-1 downregulated individuals, indicating that the relevance between the two genes and iab-1 was not induced by iab-1 transcript. Collectively, the results showed that the newly identified iab-1 may be involved in some physiological processes, and the interaction between iab-1 and Hox genes was also preliminarily analyzed.

Dual evolutionary origin of insect wings supported by an investigation of the abdominal wing serial homologs in Tribolium

The origin of insect wings is still a highly debated mystery in biology, despite the importance of this evolutionary innovation. There are currently two prominent, but contrasting wing origin hypotheses (the tergal origin hypothesis and the pleural origin hypothesis). Through studies in the Tribolium beetle, we have previously obtained functional evidence supporting a third hypothesis, the dual origin hypothesis. Although this hypothesis can potentially unify the two competing hypotheses, it requires further testing from various fields. Here, we investigated the genetic regulation of the tissues serially homologous to wings in the abdomen, outside of the appendage-bearing segments, in Tribolium We found that the formation of ectopic wings in the abdomen upon homeotic transformation relies not only on the previously identified abdominal wing serial homolog (gin-trap), but also on a secondary tissue in the pleural location. Using an enhancer trap line of nubbin (a wing lineage marker), we were able to visualize both of these two tissues (of tergal and pleural nature) contributing to form a complete wing. These results support the idea that the presence of two distinct sets of wing serial homologs per segment represents an ancestral state of the wing serial homologs, and can therefore further support a dual evolutionary origin of insect wings. Our analyses also uncovered detailed Hox regulation of abdominal wing serial homologs, which can be used as a foundation to elucidate the molecular mechanisms that have facilitated the evolution of bona fide insect wings, as well as the diversification of other wing serial homologs.

New data from the Middle Jurassic of China shed light on the phylogeny and origin of the proboscis in the Mesopsychidae (Insecta: Mecoptera)

BACKGROUND

The Mesopsychidae is an extinct family of Mecoptera, comprising eleven described genera from Upper Permian to Lower Cretaceous deposits. In 2009, several well-preserved mesopsychids with long proboscides were reported from the mid Mesozoic of Northeastern China, suggesting the presence of pollination mutualisms with gymnosperm plants and highlighting their elevated genus-level diversity. Since that time, additional mesopsychid taxa have been described. However, the phylogeny of genera within Mesopsychidae has not been studied formally, attributable to the limited number of well-preserved fossils.

RESULTS

Here, we describe two new species, Lichnomesopsyche prochorista sp. nov. and Vitimopsyche pristina sp. nov. and revise the diagnosis of Lichnomesopsyche daohugouensis Ren, Labandeira and Shih, 2010, based on ten specimens from the latest Middle Jurassic Jiulongshan Formation of Inner Mongolia, China. After compiling data from these new fossil species and previously reported representative taxa, we conducted phylogenetic analyses and geometric morphometric studies that now shed light on the taxonomy and phylogeny of Mesopsychidae. We also evaluate the recurring origin of the siphonate proboscis in the Mecoptera and propose an evolutionary developmental model for its multiple origins.

CONCLUSIONS

Phylogenetic and geometric morphometric results confirm the establishment of two new species, each to Lichnomesopsyche and Vitimopsyche. Vitimopsyche pristina sp. nov. extends the existence of the genus Vitimopsyche Novokshonov and Sukacheva, 2001, from the mid Lower Cretaceous to the latest Middle Jurassic. Two methods of analyses indicate an affiliation of Mesopsyche dobrokhotovae Novokshonov, 1997 with Permopsyche Bashkuev, 2011. A phylogenetic analysis of the Mesopsychidae supports: 1), Mesopsychidae as a monophyletic group; 2), Mesopsyche as a paraphyletic group, to be revised pending future examination of additional material; and 3), the independent origin of the proboscis in the Pseudopolycentropodidae, its subsequent loss in earliest Mesopsychidae such as Epicharmesopsyche, its re-origination in the common ancestor (or perhaps independently) in the Vitimopsyche and Lichnomesopsyche clades of the Mesopsychidae. The third conclusion indicates that the proboscis originated four or five times within early Mecoptera, whose origin is explained by an evolutionary developmental model.

CRISPR/Cas9 Mutagenesis Reveals Versatile Roles of Hox Genes in Crustacean Limb Specification and Evolution

Crustaceans possess a diverse array of specialized limbs. Although shifts in Hox gene expression domains have been postulated to play a role in generating this limb diversity, little functional data have been provided to understand the precise roles of Hox genes during crustacean development. We used a combination of CRISPR/Cas9-targeted mutagenesis and RNAi knockdown to decipher the function of the six Hox genes expressed in the developing mouth and trunk of the amphipod Parhyale hawaiensis. These experimentally manipulated animals display specific and striking homeotic transformations. We found that abdominal-A (abd-A) and Abdominal-B (Abd-B) are required for proper posterior patterning, with knockout of Abd-B resulting in an animal with thoracic type legs along what would have been an abdomen, and abd-A disruption generating a simplified body plan characterized by a loss of specialization in both abdominal and thoracic appendages. In the thorax, Ubx is necessary for gill development and for repression of gnathal fate, and Antp dictates claw morphology. In the mouth, Scr and Antp confer the part-gnathal, part-thoracic hybrid identity of the maxilliped, and Scr and Dfd prevent antennal identity in posterior head segments. Our results allow us to define the role Hox genes play in specifying each appendage type in Parhyale, including the modular nature by which some appendages are patterned by Hox gene inputs. In addition, we define how changes in Hox gene expression have generated morphological differences between crustacean species. Finally, we also highlight the utility of CRISPR/Cas9-based somatic mutagenesis in emerging model organisms.