Gall Wasp Transcriptomes Unravel Potential Effectors Involved in Molecular Dialogues With Oak and Rose

Comparative transcriptome reprogramming in oak galls containing asexual or sexual generations of gall wasps

Oak gall wasps have evolved strategies to manipulate the developmental pathways of their host to induce gall formation. This provides shelter and nutrients for the developing larva. Galls are entirely host tissue; however, the initiation, development, and physical appearance are controlled by the inducer. The underlying molecular mechanisms of gall formation, by which one or a small number of cells are reprogrammed and commit to a novel developmental path, are poorly understood. In this study, we sought a deeper insight into the molecular underpinnings of this process. Oak gall wasps have two generations each year, one sexual, and one asexual. Galls formed by these two generations exhibit a markedly different appearance. We sequenced transcriptomes of both the asexual and sexual generations of Neuroterus quercusbaccarum and Neuroterus numismalis. We then deployed Nanopore sequencing to generate long-read sequences to test the hypothesis that gall wasps introduce DNA insertions to determine gall development. We detected potential genome rearrangements but did not uncover any non-host DNA insertions. Transcriptome analysis revealed that transcriptomes of the sexual generations of distinct species of wasp are more similar than inter-generational comparisons from the same species of wasp. Our results highlight the intricate interplay between the host leaves and gall development, suggesting that season and requirements of the gall structure play a larger role than species in controlling gall development and structure.

Two chromosome-level genome assemblies of galling aphids Slavum lentiscoides and Chaetogeoica ovagalla

Slavum lentiscoides and Chaetogeoica ovagalla are two aphid species from the subtribe Fordina of Fordini within the subfamily Eriosomatinae, and they produce galls on their primary host plants Pistacia. We assembled chromosome-level genomes of these two species using Nanopore long-read sequencing and Hi-C technology. A 332 Mb genome assembly of S. lentiscoides with a scaffold N50 of 19.77 Mb, including 11,747 genes, and a 289 Mb genome assembly of C. ovagalla with a scaffold N50 of 11.85 Mb, containing 14,492 genes, were obtained. The Benchmarking Universal Single-Copy Orthologs (BUSCO) benchmark of the two genome assemblies reached 93.7% (91.9% single-copy) and 97.0% (95.3% single-copy), respectively. The high-quality genome assemblies in our study provide valuable resources for future genomic research of galling aphids.

Anatomical Changes during Chestnut (Castanea mollissima BL.) Gall Development Stages Induced by the Gall Wasp Dryocosmus kuriphilus (Hymenoptera: Cynipidae)

This study delved into the larval development and the morphological and anatomical transformations that occur in the galls of chestnut trees (Castanea mollissima BL.) and are induced by the chestnut gall wasp Dryocosmus kuriphilus Yasumatsu (GWDK) across various stages: initial, growth, differentiation, maturity, and lignification. Chestnut galls in the five development stages were collected. Gall structural characteristics were observed with an anatomical stereomicroscope, and anatomical changes in galls were analyzed with staining and scanning electron microscope techniques. The chestnut gall wasp laid its eggs on young leaves and buds. Chestnut gall wasp parasitism caused plant tissues to form a gall chamber, with parenchyma, protective, and epidermal layers. The development of the gall structure caused by the infestation of the GWDK gall led to the weakening of the reactive oxygen species (ROS) elimination ability of the host. The accumulation of ROS led to cell wall peroxidation, resulting in structural damage and diminished host resistance, and the parenchyma layer exhibited significant nutrient supply and thickening. The thickness of the protective and epidermal layers varied notably across different growth stages. The oviposition of the chestnut gall wasp induced modifications in the original plant tissues, with gall formation being most favorable in young tissues, correlating with the maturity level of the host plant tissues. Variances in the internal structures of the galls primarily stemmed from nutrient supplementation, while those in the external structure were attributed to defensive characteristics. This research contributes a foundational understanding of gall development induced by the chestnut gall wasp in Chinese chestnut, offering valuable insights into the intricate interplay between insect infestation and plant physiology.

New Gall-Forming Insect Model, Smicronyx madaranus: Critical Stages for Gall Formation, Phylogeny, and Effectiveness of Gene Functional Analysis

The molecular mechanisms underlying insect gall formation remain unclear. A major reason for the inability to identify the responsible genes is that only a few systems can be experimentally validated in the laboratory. To overcome these problems, we established a new galling insect model, Smicronyx madaranus. Our manipulation experiments using nail polish sealing and insecticide treatment revealed an age-dependent change in gall formation by S. madaranus; adult females and larvae are responsible for gall induction and enlargement, respectively. Furthermore, it has been suggested that substances released during oviposition and larval feeding are involved in each process. Phylogenetic analysis showed that gall-forming weevils, including S. madaranus, belong to two distinct lineages that utilize different host plants. This may indicate that gall-forming traits evolved independently in these Smicronyx lineages. The efficacy of RNA interference (RNAi) in S. madaranus was confirmed by targeting the multicopper oxidase 2 gene. It is expected that the mechanisms of gall formation will be elucidated by a comprehensive functional analysis of candidate genes using RNAi and the S. madaranus galling system in the near future.

Microbiome and plant cell transformation trigger insect gall induction in cassava

Several specialised insects can manipulate normal plant development to induce a highly organised structure known as a gall, which represents one of the most complex interactions between insects and plants. Thus far, the mechanism for insect-induced plant galls has remained elusive. To study the induction mechanism of insect galls, we selected the gall induced by Iatrophobia brasiliensis (Diptera: Cecidomyiidae) in cassava (Euphorbiaceae: Manihot esculenta Crantz) as our model. PCR-based molecular markers and deep metagenomic sequencing data were employed to analyse the gall microbiome and to test the hypothesis that gall cells are genetically transformed by insect vectored bacteria. A shotgun sequencing discrimination approach was implemented to selectively discriminate between foreign DNA and the reference host plant genome. Several known candidate insertion sequences were identified, the most significant being DNA sequences found in bacterial genes related to the transcription regulatory factor CadR, cadmium-transporting ATPase encoded by the cadA gene, nitrate transport permease protein (nrtB gene), and arsenical pump ATPase (arsA gene). In addition, a DNA fragment associated with ubiquitin-like gene E2 was identified as a potential accessory genetic element involved in gall induction mechanism. Furthermore, our results suggest that the increased quality and rapid development of gall tissue are mostly driven by microbiome enrichment and the acquisition of critical endophytes. An initial gall-like structure was experimentally obtained in M. esculenta cultured tissues through inoculation assays using a Rhodococcus bacterial strain that originated from the inducing insect, which we related to the gall induction process. We provide evidence that the modification of the endophytic microbiome and the genetic transformation of plant cells in M. esculenta are two essential requirements for insect-induced gall formation. Based on these findings and having observed the same potential DNA marker in galls from other plant species (ubiquitin-like gene E2), we speculate that bacterially mediated genetic transformation of plant cells may represent a more widespread gall induction mechanism found in nature.

Discovery of the bicycle gene family provides new insights into insect manipulation of plant development during gall induction

Galls are complex structures that develop from plant tissue, providing protection and food for gall-forming organisms, such as insects or mites. However, the molecules used by insects or mites to manipulate plant development have proved elusive. A landmark study has tracked down a gene in a gall-forming aphid that controls whether galls on witch hazel are green or red. The 'green allele' is strongly expressed in aphid salivary glands and represses plant genes used for red color formation. Excitingly, the gene product is part of a large suite of proteins that aphids may use to interact with plant biology.

Molecular Aspects of Gall Formation Induced by Mites and Insects

Recent publications on gall formation induced on the leaves of dicotyledonous flowering plants by eriophyoid mites (Eriophyoidea) and representatives of four insect orders (Diptera, Hemiptera, Hymenoptera, Lepidoptera) are analyzed. Cellular and molecular level data on the stimuli that induce and sustain the development of both mite and insect galls, the expression of host plant genes during gallogenesis, and the effects of these galling arthropods on photosynthesis are considered. A hypothesis is proposed for the relationship between the size of galls and the volume of secretions injected by a parasite. Multistep, varying patterns of plant gene expression and accompanying histo-morphological changes in the transformed gall tissues are apparent. The main obstacle to better elucidating the nature of the induction of gallogenesis is the impossibility of collecting a sufficient amount of saliva for analysis, which is especially important in the case of microscopic eriophyoids. The use of modern omics technologies at the organismal level has revealed a spectrum of genetic mechanisms of gall formation at the molecular level but has not yet answered the questions regarding the nature of gall-inducing agents and the features of events occurring in plant cells at the very beginning of gall growth.

Genomic Assessment of the Contribution of the Wolbachia Endosymbiont of Eurosta solidaginis to Gall Induction

We explored the genome of the Wolbachia strain, wEsol, symbiotic with the plant-gall-inducing fly Eurosta solidaginis with the goal of determining if wEsol contributes to gall induction by its insect host. Gall induction by insects has been hypothesized to involve the secretion of the phytohormones cytokinin and auxin and/or proteinaceous effectors to stimulate cell division and growth in the host plant. We sequenced the metagenome of E. solidaginis and wEsol and assembled and annotated the genome of wEsol. The wEsol genome has an assembled length of 1.66 Mbp and contains 1878 protein-coding genes. The wEsol genome is replete with proteins encoded by mobile genetic elements and shows evidence of seven different prophages. We also detected evidence of multiple small insertions of wEsol genes into the genome of the host insect. Our characterization of the genome of wEsol indicates that it is compromised in the synthesis of dimethylallyl pyrophosphate (DMAPP) and S-adenosyl L-methionine (SAM), which are precursors required for the synthesis of cytokinins and methylthiolated cytokinins. wEsol is also incapable of synthesizing tryptophan, and its genome contains no enzymes in any of the known pathways for the synthesis of indole-3-acetic acid (IAA) from tryptophan. wEsol must steal DMAPP and L-methionine from its host and therefore is unlikely to provide cytokinin and auxin to its insect host for use in gall induction. Furthermore, in spite of its large repertoire of predicted Type IV secreted effector proteins, these effectors are more likely to contribute to the acquisition of nutrients and the manipulation of the host's cellular environment to contribute to growth and reproduction of wEsol than to aid E. solidaginis in manipulating its host plant. Combined with earlier work that shows that wEsol is absent from the salivary glands of E. solidaginis, our results suggest that wEsol does not contribute to gall induction by its host.

Comparative transcriptome analysis of juniper branches infected by Gymnosporangium spp. highlights their different infection strategies associated with cytokinins

BACKGROUND

Gymnosporangium asiaticum and G. yamadae can share Juniperus chinensis as the telial host, but the symptoms are completely different. The infection of G. yamadae causes the enlargement of the phloem and cortex of young branches as a gall, but not for G. asiaticum, suggesting that different molecular interaction mechanisms exist the two Gymnosporangium species with junipers.

RESULTS

Comparative transcriptome analysis was performed to investigate genes regulation of juniper in responses to the infections of G. asiaticum and G. yamadae at different stages. Functional enrichment analysis showed that genes related to transport, catabolism and transcription pathways were up-regulated, while genes related to energy metabolism and photosynthesis were down-regulated in juniper branch tissues after infection with G. asiaticum and G. yamadae. The transcript profiling of G. yamadae-induced gall tissues revealed that more genes involved in photosynthesis, sugar metabolism, plant hormones and defense-related pathways were up-regulated in the vigorous development stage of gall compared to the initial stage, and were eventually repressed overall. Furthermore, the concentration of cytokinins (CKs) in the galls tissue and the telia of G. yamadae was significantly higher than in healthy branch tissues of juniper. As well, tRNA-isopentenyltransferase (tRNA-IPT) was identified in G. yamadae with highly expression levels during the gall development stages.

CONCLUSIONS

In general, our study provided new insights into the host-specific mechanisms by which G. asiaticum and G. yamadae differentially utilize CKs and specific adaptations on juniper during their co-evolution.

A study on the effect of host plants on Chinese gallnut morphogenesis

Galls are products of the hyperplasia of host plant structures induced by gall-inducing organisms and have been considered as an extended phenotype of the inducers. There is little evidence regarding the effect of host plants on gall morphology. We hypothesised that the morphology and developmental pattern of galls are different because of the different location of their stimulation, even though two kinds of inducers are close relatives. We observed that horned galls and their leaflets of their host plant, Rhus chinensis required a longer rapid growth stage than fusiform galls and Rhus potaninii leaflets. The distribution of trichomes showed positional dependence. Molecular analysis showed that in the fusiform gall, the target genes that regulate the plastochron of leaflets and serration development were hardly expressed, and CUP-SHAPED COTYLEDON-2 may be a key gene that regulates the formation of the horns. In summary, horned and fusiform galls showed a developmental pattern similar to those of their host plant leaflets. We suggest that the inducing site is important in the morphology and development of galls.

Florigen and its homologs of FT/CETS/PEBP/RKIP/YbhB family may be the enzymes of small molecule metabolism: review of the evidence

BACKGROUND

Flowering signals are sensed in plant leaves and transmitted to the shoot apical meristems, where the formation of flowers is initiated. Searches for a diffusible hormone-like signaling entity ("florigen") went on for many decades, until a product of plant gene FT was identified as the key component of florigen in the 1990s, based on the analysis of mutants, genetic complementation evidence, and protein and RNA localization studies. Sequence homologs of FT protein are found throughout prokaryotes and eukaryotes; some eukaryotic family members appear to bind phospholipids or interact with the components of the signal transduction cascades. Most FT homologs are known to share a constellation of five charged residues, three of which, i.e., two histidines and an aspartic acid, are located at the rim of a well-defined cavity on the protein surface.

RESULTS

We studied molecular features of the FT homologs in prokaryotes and analyzed their genome context, to find tentative evidence connecting the bacterial FT homologs with small molecule metabolism, often involving substrates that contain sugar or ribonucleoside moieties. We argue that the unifying feature of this protein family, i.e., a set of charged residues conserved at the sequence and structural levels, is more likely to be an enzymatic active center than a catalytically inert ligand-binding site.

CONCLUSIONS

We propose that most of FT-related proteins are enzymes operating on small diffusible molecules. Those metabolites may constitute an overlooked essential ingredient of the florigen signal.

Anatomy and Ultrastructure of Galls Induced by Neuroterus quercusbaccarum (Hymenoptera: Cynipidae) on Oak Leaves (Quercus robur)

Simple Summary

Galls induced by insects are commonly found on oak leaves in temperate climates. Their induction and development are, however, still only partially known. Our aim was to present a detailed description of their anatomy and fine structure. Using scanning electron microscopy (SEM), we observed the wax cover of a gall and two types of openings on its surface: one similar to degenerated stomata and the other one that we called “large openings on epidermal protuberance”. Nutritive tissue underwent marked changes with time: in a young gall, the cellular walls were not visible, and a distinct cellular structure appeared only later. In the mound of the gall, there was a distinct subepidermal layer of cells containing dense cytoplasm. Tannins occurred in vacuoles or in cell walls in granular form or in compact formations. The leaf subtending the gall showed additional cell divisions and strong lignification of cell walls in the tissue surrounding the peduncle of the gall.

Abstract

The structure and ultrastructure of two developmental stages of the spangle gall induced by Neuroterus quercusbaccarum (Hymenoptera, Cynipidae) were investigated using light microscopy (LM), fluorescence microscopy (FM), and transmission (TEM) and scanning (SEM) electron microscopy. The general design of the gall structure was typical of Cynipidae, but some structural features distinguished the spangle gall. Previously undescribed, characteristic multicellular epidermal protuberances with large openings were observed in autumn on the surface of galls. These may facilitate the gas exchange between the atmosphere and the inside of the gall, thus assisting larval respiration. The larval chamber is surrounded by both a sclerenchymatous capsule and numerous cells containing calcium oxalate crystals that may both serve as protective barriers. In young galls, the nutritive tissue is a wall-less protoplasmic mass, potentially easily accessible to young larvae with delicate mandibles. Cell walls only develop at a later stage. The nutritive tissue was found to be rich in proteins and lipids, but starch grains were not observed. Cellular topology suggests that spangle galls grow by anticlinal division of marginal epidermal cells and periclinal division of subepidermal cells. Cellular proliferation (hyperplasia) also occurs in the leaf tissue near the connection with the gall peduncle, which eventually lignifies.

Recent Progress Regarding the Molecular Aspects of Insect Gall Formation

Galls are characteristic plant structures formed by cell size enlargement and/or cell proliferation induced by parasitic or pathogenic organisms. Insects are a major inducer of galls, and insect galls can occur on plant leaves, stems, floral buds, flowers, fruits, or roots. Many of these exhibit unique shapes, providing shelter and nutrients to insects. To form unique gall structures, gall-inducing insects are believed to secrete certain effector molecules and hijack host developmental programs. However, the molecular mechanisms of insect gall induction and development remain largely unknown due to the difficulties associated with the study of non-model plants in the wild. Recent advances in next-generation sequencing have allowed us to determine the biological processes in non-model organisms, including gall-inducing insects and their host plants. In this review, we first summarize the adaptive significance of galls for insects and plants. Thereafter, we summarize recent progress regarding the molecular aspects of insect gall formation.

Interactions Between Figs and Gall-Inducing Fig Wasps: Adaptations, Constraints, and Unanswered Questions

The ancient interaction between figs (Ficus, Moraceae) and their pollinating fig wasps is an unusual example of a mutualism between plants and gall-inducing insects. This review intends to offer fresh perspectives into the relationship between figs and the diversity of gall-inducing sycophiles which inhabit their enclosed globular inflorescences that function as microcosms. Besides gall-inducing pollinators, fig inflorescences are also inhabited by other gall-inducing wasps. This review evaluates the state of current knowledge on gall-induction by fig wasps and exposes the many lacunae in this area. This review makes connections between fig and gall-inducing wasp traits, and suggests relatively unexplored research avenues. This manuscript calls for an integrated approach that incorporates such diverse fields as life-history theory, plant mate choice, wasp sexual selection and local mate competition, plant embryology as well as seed and fruit dispersal. It calls for collaboration between researchers such as plant developmental biologists, insect physiologists, chemical ecologists and sensory biologists to jointly solve the many valuable questions that can be addressed in community ecology, co-evolution and species interaction biology using the fig inflorescence microcosm, that is inhabited by gall-inducing mutualistic and parasitic wasps, as a model system.

The Localization of Phytohormones within the Gall-inducing Insect Eurosta solidaginis (Diptera: Tephritidae)

The phytohormone production hypothesis suggests that organisms, including insects, induce galls by producing and secreting plant growth hormones. Auxins and cytokinins are classes of phytohormones that induce cell growth and cell division, which could contribute to the plant tissue proliferation which constitutes the covering gall. Bacteria, symbiotic with insects, may also play a part in gall induction by insects through the synthesis of phytohormones or other effectors. Past studies have shown that concentrations of cytokinins and auxins in gall-inducing insects are higher than in their host plants. However, these analyses have involved whole-body extractions. Using immunolocalization of cytokinin and auxin, in the gall inducing stage of Eurosta solidaginis, we found both phytohormones to localize almost exclusively to the salivary glands. Co-localization of phytohormone label with a nucleic acid stain in the salivary glands revealed the absence of Wolbachia sp., the bacterial symbiont of E. solidaginis, which suggests that phytohormone production is symbiont independent. Our findings are consistent with the hypothesis that phytohormones are synthesized in and secreted from the salivary glands of E. solidaginis into host-plant tissues for the purpose of manipulating the host plant.

A novel family of secreted insect proteins linked to plant gall development

In an elaborate form of inter-species exploitation, many insects hijack plant development to induce novel plant organs called galls that provide the insect with a source of nutrition and a temporary home. Galls result from dramatic reprogramming of plant cell biology driven by insect molecules, but the roles of specific insect molecules in gall development have not yet been determined. Here, we study the aphid Hormaphis cornu, which makes distinctive "cone" galls on leaves of witch hazel Hamamelis virginiana. We found that derived genetic variants in the aphid gene determinant of gall color (dgc) are associated with strong downregulation of dgc transcription in aphid salivary glands, upregulation in galls of seven genes involved in anthocyanin synthesis, and deposition of two red anthocyanins in galls. We hypothesize that aphids inject DGC protein into galls and that this results in differential expression of a small number of plant genes. dgc is a member of a large, diverse family of novel predicted secreted proteins characterized by a pair of widely spaced cysteine-tyrosine-cysteine (CYC) residues, which we named BICYCLE proteins. bicycle genes are most strongly expressed in the salivary glands specifically of galling aphid generations, suggesting that they may regulate many aspects of gall development. bicycle genes have experienced unusually frequent diversifying selection, consistent with their potential role controlling gall development in a molecular arms race between aphids and their host plants.

A novel family of secreted insect proteins linked to plant gall development

In an elaborate form of inter-species exploitation, many insects hijack plant development to induce novel plant organs called galls that provide the insect with a source of nutrition and a temporary home. Galls result from dramatic reprogramming of plant cell biology driven by insect molecules, but the roles of specific insect molecules in gall development have not yet been determined. Here we study the aphidHormaphis cornu, which makes distinctive “cone” galls on leaves of witch hazelHamamelis virginiana. We found that derived genetic variants in the aphid genedeterminant of gall color(dgc) are associated with strong downregulation ofdgctranscription in aphid salivary glands, upregulation in galls of seven genes involved in anthocyanin synthesis, and deposition of two red anthocyanins in galls. We hypothesize that aphids inject DGC protein into galls, and that this results in differential expression of a small number of plant genes.Dgcis a member of a large, diverse family of novel predicted secreted proteins characterized by a pair of widely spaced cysteine-tyrosine-cysteine (CYC) residues, which we named BICYCLE proteins.Bicyclegenes are most strongly expressed in the salivary glands specifically of galling aphid generations, suggesting that they may regulate many aspects of gall development.Bicyclegenes have experienced unusually frequent diversifying selection, consistent with their potential role controlling gall development in a molecular arms race between aphids and their host plants.

One Sentence Summary

Aphidbicyclegenes, which encode diverse secreted proteins, contribute to plant gall development.

Phylogenetic analyses suggest centipede venom arsenals were repeatedly stocked by horizontal gene transfer

Venoms have evolved over a hundred times in animals. Venom toxins are thought to evolve mostly by recruitment of endogenous proteins with physiological functions. Here we report phylogenetic analyses of venom proteome-annotated venom gland transcriptome data, assisted by genomic analyses, to show that centipede venoms have recruited at least five gene families from bacterial and fungal donors, involving at least eight horizontal gene transfer events. These results establish centipedes as currently the only known animals with venoms used in predation and defence that contain multiple gene families derived from horizontal gene transfer. The results also provide the first evidence for the implication of horizontal gene transfer in the evolutionary origin of venom in an animal lineage. Three of the bacterial gene families encode virulence factors, suggesting that horizontal gene transfer can provide a fast track channel for the evolution of novelty by the exaptation of bacterial weapons into animal venoms.

Phytohormones Regulate Both "Fish Scale" Galls and Cones on Picea koraiensis

The larch adelgid Adelges laricis laricis Vallot is a specialist insect parasite of Picea koraiensis (Korean spruce) and forms fish scale-like galls that damage the growth of the host plants. Our investigation reveals that both these galls and the fruits (cones) of P. koraiensis display lower concentrations of phytosynthetic pigments and accumulate anthocyanin cyanidin-3-O-glucoside and soluble sugars in the mature stages. Interestingly, high concentrations of 6-benzylaminopurine (BAP) both in the cauline gall tissues and in the larch adelgids themselves (4064.61 ± 167.83 and 3655.42 ± 210.29 ng/g FW, respectively), suggested that this vital phytohormone may be synthesized by the insects to control the development of gall tissues. These results indicate that the galls and cones are sink organs, and the development of gall tissues is possibly regulated by phytohormones in a way similar to that of the growth of cones. The concentrations of phytohormones related to growth [indole-3-acetic acid (IAA), cytokinins (CTK), and gibberellins (GAs)] and defense [salicylic acid (SA)], as well as SA-related phenolics [benzoic acid (BA) and p-hydroxybenzoic acid (pHBA)] in gall tissues were positively correlated with those in cones during the development stage. The levels of 1-aminocyclopropane-1-carboxylic acid (ACC) in the developmental stage of the cones correlates negatively with their concentrations in the gall tissues (R = -0.92, p < 0.001), suggesting that downregulation of ACC might be the reason why galls are not abscised after a year. Our results provide a new perspective on the potential mechanism of the development of cauline galls on P. koraiensis, which are regulated by phytohormones.

Comprehensive phylogenomic analyses re-write the evolution of parasitism within cynipoid wasps

BACKGROUND

Parasitoidism, a specialized life strategy in which a parasite eventually kills its host, is frequently found within the insect order Hymenoptera (wasps, ants and bees). A parasitoid lifestyle is one of two dominant life strategies within the hymenopteran superfamily Cynipoidea, with the other being an unusual plant-feeding behavior known as galling. Less commonly, cynipoid wasps exhibit inquilinism, a strategy where some species have adapted to usurp other species' galls instead of inducing their own. Using a phylogenomic data set of ultraconserved elements from nearly all lineages of Cynipoidea, we here generate a robust phylogenetic framework and timescale to understand cynipoid systematics and the evolution of these life histories.

RESULTS

Our reconstructed evolutionary history for Cynipoidea differs considerably from previous hypotheses. Rooting our analyses with non-cynipoid outgroups, the Paraulacini, a group of inquilines, emerged as sister-group to the rest of Cynipoidea, rendering the gall wasp family Cynipidae paraphyletic. The families Ibaliidae and Liopteridae, long considered archaic and early-branching parasitoid lineages, were found nested well within the Cynipoidea as sister-group to the parasitoid Figitidae. Cynipoidea originated in the early Jurassic around 190 Ma. Either inquilinism or parasitoidism is suggested as the ancestral and dominant strategy throughout the early evolution of cynipoids, depending on whether a simple (three states: parasitoidism, inquilinism and galling) or more complex (seven states: parasitoidism, inquilinism and galling split by host use) model is employed.

CONCLUSIONS

Our study has significant impact on understanding cynipoid evolution and highlights the importance of adequate outgroup sampling. We discuss the evolutionary timescale of the superfamily in relation to their insect hosts and host plants, and outline how phytophagous galling behavior may have evolved from entomophagous, parasitoid cynipoids. Our study has established the framework for further physiological and comparative genomic work between gall-making, inquiline and parasitoid lineages, which could also have significant implications for the evolution of diverse life histories in other Hymenoptera.

From Inquilines to Gall Inducers: Genomic Signature of a Life-Style Transition in Synergus Gall Wasps

Gall wasps (Hymenoptera: Cynipidae) induce complex galls on oaks, roses, and other plants, but the mechanism of gall induction is still unknown. Here, we take a comparative genomic approach to revealing the genetic basis of gall induction. We focus on Synergus itoensis, a species that induces galls inside oak acorns. Previous studies suggested that this species evolved the ability to initiate gall formation recently, as it is deeply nested within the genus Synergus, whose members are mostly inquilines that develop inside the galls of other species. We compared the genome of S. itoensis with that of three related Synergus inquilines to identify genomic changes associated with the origin of gall induction. We used a novel Bayesian selection analysis, which accounts for branch-specific and gene-specific selection effects, to search for signatures of selection in 7,600 single-copy orthologous genes shared by the four Synergus species. We found that the terminal branch leading to S. itoensis had more genes with a significantly elevated dN/dS ratio (positive signature genes) than the other terminal branches in the tree; the S. itoensis branch also had more genes with a significantly decreased dN/dS ratio. Gene set enrichment analysis showed that the positive signature gene set of S. itoensis, unlike those of the inquiline species, is enriched in several biological process Gene Ontology terms, the most prominent of which is “Ovarian Follicle Cell Development.” Our results indicate that the origin of gall induction is associated with distinct genomic changes, and provide a good starting point for further characterization of the genes involved.

The Evolution of Endophagy in Herbivorous Insects

Herbivorous feeding inside plant tissues, or endophagy, is a common lifestyle across Insecta, and occurs in insect taxa that bore, roll, tie, mine, gall, or otherwise modify plant tissues so that the tissues surround the insects while they are feeding. Some researchers have developed hypotheses to explain the adaptive significance of certain endophytic lifestyles (e.g., miners or gallers), but we are unaware of previous efforts to broadly characterize the adaptive significance of endophagy more generally. To fill this knowledge gap, we characterized the limited set of evolutionary selection pressures that could have encouraged phytophagous insects to feed inside plants, and then consider how these factors align with evidence for endophagy in the evolutionary history of orders of herbivorous insects. Reviewing the occurrence of endophytic taxa of various feeding guilds reveals that the pattern of evolution of endophagy varies strongly among insect orders, in some cases being an ancestral trait (e.g., Coleoptera and Lepidoptera) while being more derived in others (e.g., Diptera). Despite the large diversity of endophagous lifestyles and evolutionary trajectories that have led to endophagy in insects, our consideration of selection pressures leads us to hypothesize that nutritionally based factors may have had a stronger influence on evolution of endophagy than other factors, but that competition, water conservation, and natural enemies may have played significant roles in the development of endophagy.

Gall-Inducing Parasites: Convergent and Conserved Strategies of Plant Manipulation by Insects and Nematodes

Gall-inducing insects and nematodes engage in sophisticated interactions with their host plants. These parasites can induce major morphological and physiological changes in host roots, leaves, and other tissues. Sedentary endoparasitic nematodes, root-knot and cyst nematodes in particular, as well as gall-inducing and leaf-mining insects, manipulate plant development to form unique organs that provide them with food from feeding cells. Sometimes, infected tissues may undergo a developmental switch resulting in the formation of aberrant and spectacular structures (clubs or galls). We describe here the complex interactions between these plant-reprogramming sedentary endoparasites and their infected hosts, focusing on similarities between strategies of plant manipulation. We highlight progress in our understanding of the host plant response to infection and focus on the nematode and insect molecules secreted in planta. We suggest thatlooking at similarities may identify convergent and conserved strategies and shed light on the promise they hold for the development of new management strategies in agriculture and forestry.

Salivary proteins of Phloeomyzus passerinii, a plant-manipulating aphid, and their impact on early gene responses of susceptible and resistant poplar genotypes

Successful plant colonization by parasites requires the circumvention of host defenses, and sometimes a reprogramming of host metabolism, mediated by effector molecules delivered into the host. Using transcriptomic and enzymatic approaches, we characterized salivary glands and saliva of Phloeomyzus passerinii, an aphid exhibiting an atypical feeding strategy. Plant responses to salivary extracts of P. passerinii and Myzus persicae were assessed with poplar protoplasts of a susceptible and a resistant genotype, and in a heterologous Arabidopsis system. We predict that P. passerinii secretes a highly peculiar saliva containing effectors potentially interfering with host defenses, biotic stress signaling and plant metabolism, notably phosphatidylinositol phosphate kinases which seemed specific to P. passerinii. Gene expression profiles indicated that salivary extracts of M. persicae markedly affected host defenses and biotic stress signaling, while salivary extracts of P. passerinii induced only weak responses. The effector-triggered susceptibility was characterized by downregulations of genes involved in cytokinin signaling and auxin homeostasis. This suggests that P. passerinii induces an intracellular accumulation of auxin in susceptible host genotypes, which is supported by histochemical assays in Arabidopsis. This might in turn affect biotic stress signaling and contribute to host tissue manipulation by the aphid.

Genomic dissection of an extended phenotype: Oak galling by a cynipid gall wasp

Galls are plant tissues whose development is induced by another organism for the inducer's benefit. 30,000 arthropod species induce galls, and in most cases the inducing effectors and target plant systems are unknown. Cynipid gall wasps are a speciose monophyletic radiation that induce structurally complex galls on oaks and other plants. We used a model system comprising the gall wasp Biorhiza pallida and the oak Quercus robur to characterise inducer and host plant gene expression at defined stages through the development of galled and ungalled plant tissues, and tested alternative hypotheses for the origin and type of galling effectors and plant metabolic pathways involved. Oak gene expression patterns diverged markedly during development of galled and normal buds. Young galls showed elevated expression of oak genes similar to legume root nodule Nod factor-induced early nodulin (ENOD) genes and developmental parallels with oak buds. In contrast, mature galls showed substantially different patterns of gene expression to mature leaves. While most oak transcripts could be functionally annotated, many gall wasp transcripts of interest were novel. We found no evidence in the gall wasp for involvement of third-party symbionts in gall induction, for effector delivery using virus-like-particles, or for gallwasp expression of genes coding for plant hormones. Many differentially and highly expressed genes in young larvae encoded secretory peptides, which we hypothesise are effector proteins exported to plant tissues. Specifically, we propose that host arabinogalactan proteins and gall wasp chitinases interact in young galls to generate a somatic embryogenesis-like process in oak tissues surrounding the gall wasp larvae. Gall wasp larvae also expressed genes encoding multiple plant cell wall degrading enzymes (PCWDEs). These have functional orthologues in other gall inducing cynipids but not in figitid parasitoid sister groups, suggesting that they may be evolutionary innovations associated with cynipid gall induction.

Plant galls are induced by organisms that manipulate host plant development to produce novel structures. The organisms involved range from mutualistic (such as nitrogen fixing bacteria) to parasitic. In the case of parasites, the gall benefits only the gall-inducing partner. A wide range of organisms can induce galls, but the processes involved are understood only for some bacterial and fungal galls. Cynipid gall wasps induce diverse and structurally complex galls, particularly on oaks (Quercus). We used transcriptome and genome sequencing for one gall wasp and its host oak to identify genes active in gall development. On the plant side, when compared to normally developing bud tissues, young gall tissues showed elevated expression of loci similar to those found in nitrogen-fixing root nodules of leguminous plants. On the wasp side, we found no evidence for involvement of viruses or microorganisms carried by the insects in gall induction or delivery of inducing stimuli. We found that gall wasps express many genes whose products may be secreted to the host, including enzymes that degrade plant cell walls. Genome comparisons between galling and non-galling relatives showed cell wall-degrading enzymes are restricted to gall inducers, and hence potentially key components of a gall inducing lifestyle.