Comprehensive isoform-level analysis reveals the contribution of alternative isoforms to venom evolution and repertoire diversity.

Animal venom systems have emerged as valuable models for investigating how novel polygenic phenotypes may arise from gene evolution by varying molecular mechanisms. However, a significant portion of venom genes produce alternative mRNA isoforms that have not been extensively characterized, hindering a comprehensive understanding of venom biology. In this study, we present a full-length isoform-level profiling workflow integrating multiple RNA sequencing technologies, allowing us to reconstruct a high-resolution transcriptome landscape of venom genes in the parasitoid wasp Pteromalus puparum Our findings demonstrate that more than half of the venom genes generate multiple isoforms within the venom gland. Through mass spectrometry analysis, we confirm that alternative splicing contributes to the diversity of venom proteins, acting as a mechanism for expanding the venom repertoire. Notably, we identified seven venom genes that exhibit distinct isoform usages between the venom gland and other tissues. Furthermore, evolutionary analyses of venom serpin3 and orcokinin further reveal that the co-option of an ancient isoform and a newly evolved isoform, respectively, contributes to venom recruitment, providing valuable insights into the genetic mechanisms driving venom evolution in parasitoid wasps. Overall, our study presents a comprehensive investigation of venom genes at the isoform level, significantly advancing our understanding of alternative isoforms in venom diversity and evolution and setting the stage for further in-depth research on venoms.

DeepAlgPro: an interpretable deep neural network model for predicting allergenic proteins.

Allergies have become an emerging public health problem worldwide. The most effective way to prevent allergies is to find the causative allergen at the source and avoid re-exposure. However, most of the current computational methods used to identify allergens were based on homology or conventional machine learning methods, which were inefficient and still had room to be improved for the detection of allergens with low homology. In addition, few methods based on deep learning were reported, although deep learning has been successfully applied to several tasks in protein sequence analysis. In the present work, a deep neural network-based model, called DeepAlgPro, was proposed to identify allergens. We showed its great accuracy and applicability to large-scale forecasts by comparing it to other available tools. Additionally, we used ablation experiments to demonstrate the critical importance of the convolutional module in our model. Moreover, further analyses showed that epitope features contributed to model decision-making, thus improving the model's interpretability. Finally, we found that DeepAlgPro was capable of detecting potential new allergens. Overall, DeepAlgPro can serve as powerful software for identifying allergens.

InsectBase 2.0: a comprehensive gene resource for insects.

Insects are the largest group of animals on the planet and have a huge impact on human life by providing resources, transmitting diseases, and damaging agricultural crop production. Recently, a large amount of insect genome and gene data has been generated. A comprehensive database is highly desirable for managing, sharing, and mining these resources. Here, we present an updated database, InsectBase 2.0 (http://v2.insect-genome.com/), covering 815 insect genomes, 25 805 transcriptomes and >16 million genes, including 15 045 111 coding sequences, 3 436 022 3'UTRs, 4 345 664 5'UTRs, 112 162 miRNAs and 1 293 430 lncRNAs. In addition, we used an in-house standard pipeline to annotate 1 434 653 genes belonging to 164 gene families; 215 986 potential horizontally transferred genes; and 419 KEGG pathways. Web services such as BLAST, JBrowse2 and Synteny Viewer are provided for searching and visualization. InsectBase 2.0 serves as a valuable platform for entomologists and researchers in the related communities of animal evolution and invertebrate comparative genomics.

Genome of the parasitoid wasp Cotesia chilonis sheds light on amino acid resource exploitation.

BACKGROUND: A fundamental feature of parasitism is the nutritional exploitation of host organisms by their parasites. Parasitoid wasps lay eggs on arthropod hosts, exploiting them for nutrition to support larval development by using diverse effectors aimed at regulating host metabolism. However, the genetic components and molecular mechanisms at the basis of such exploitation, especially the utilization of host amino acid resources, remain largely unknown. To address this question, here, we present a chromosome-level genome assembly of the parasitoid wasp Cotesia chilonis and reconstruct its amino acid biosynthetic pathway. RESULTS: Analyses of the amino acid synthetic pathway indicate that C. chilonis lost the ability to synthesize ten amino acids, which was confirmed by feeding experiments with amino acid-depleted media. Of the ten pathways, nine are known to have been lost in the common ancestor of animals. We find that the ability to synthesize arginine was also lost in C. chilonis because of the absence of two key genes in the arginine synthesis pathway. Further analyses of the genomes of 72 arthropods species show that the loss of arginine synthesis is common in arthropods. Metabolomic analyses by UPLC-MS/MS reveal that the temporal concentrations of arginine, serine, tyrosine, and alanine are significantly higher in host (Chilo suppressalis) hemolymph at 3 days after parasitism, whereas the temporal levels of 5-hydroxylysine, glutamic acid, methionine, and lysine are significantly lower. We sequence the transcriptomes of a parasitized host and non-parasitized control. Differential gene expression analyses using these transcriptomes indicate that parasitoid wasps inhibit amino acid utilization and activate protein degradation in the host, likely resulting in the increase of amino acid content in host hemolymph. CONCLUSIONS: We sequenced the genome of a parasitoid wasp, C. chilonis, and revealed the features of trait loss in amino acid biosynthesis. Our work provides new insights into amino acid exploitation by parasitoid wasps, and this knowledge can specifically be used to design parasitoid artificial diets that potentially benefit mass rearing of parasitoids for pest control.

Correction of Cicatricial Lower Eyelid Retraction and Entropion With Combined Scar Release, Hard Palate Graft, and Lateral Canthal Suspension.

OBJECTIVE: This study aimed to evaluate the outcome of a technique-combined scar release, hard palate spacer graft with the recession of the lower eyelid retractors, lateral canthal suspension in the repair of cicatricial lower eyelid retraction, and entropion. METHODS: Records of 12 patients with cicatricial lower eyelid retraction and entropion who underwent the surgery from January 2019 to August 2021 were reviewed. Surgical techniques include the following procedures: release of scar, hard palate graft with recession of the lower eyelid retractors, and lateral canthal tightening to strengthen the support of the lower eyelid. The follow-up period was at least 12 months. Postoperative outcomes were evaluated by the improvement of lower eyelid retraction, resolution of eyelid entropion, and complications. RESULTS: All patients showed resolution in lower lid entropion, and lower eyelid retraction was significantly improved with a mean elevation of 2.93±0.82 mm. None of the patients had severe complications postoperatively, and both ocular surface symptoms and cosmetic appearance were significantly improved. CONCLUSIONS: The technique achieves long-term stable outcomes in cicatricial lower lid retraction and entropion repair with a low morbidity rate.

Comparative Genomics Sheds Light on the Convergent Evolution of Miniaturized Wasps.

Miniaturization has occurred in many animal lineages, including insects and vertebrates, as a widespread trend during animal evolution. Among Hymenoptera, miniaturization has taken place in some parasitoid wasp lineages independently, and may have contributed to the diversity of species. However, the genomic basis of miniaturization is little understood. Diverged approximately 200 Ma, Telenomus wasps (Platygastroidea) and Trichogramma wasps (Chalcidoidea) have both evolved to a highly reduced body size independently, representing a paradigmatic example of convergent evolution. Here, we report a high-quality chromosomal genome of Telenomus remus, a promising candidate for controlling Spodoptera frugiperda, a notorious pest that has recently caused severe crop damage. The T. remus genome (129 Mb) is characterized by a low density of repetitive sequence and a reduction of intron length, resulting in the shrinkage of genome size. We show that hundreds of genes evolved faster in two miniaturized parasitoids Trichogramma pretiosum and T. remus. Among them, 38 genes exhibit extremely accelerated evolutionary rates in these miniaturized wasps, possessing diverse functions in eye and wing development as well as cell size control. These genes also highlight potential roles in body size regulation. In sum, our analyses uncover a set of genes with accelerated evolutionary rates in Tri. pretiosum and T. remus, which might be responsible for their convergent adaptations to miniaturization, and thus expand our understanding on the evolutionary basis of miniaturization. Additionally, the genome of T. remus represents the first genome resource of superfamily Platygastroidea, and will facilitate future studies of Hymenoptera evolution and pest control.

miR-34 modulates wing polyphenism in planthopper.

Polyphenism is a successful strategy adopted by organisms to adapt to environmental changes. Brown planthoppers (BPH, Nilaparvata lugens) develop two wing phenotypes, including long-winged (LW) and short-winged (SW) morphs. Though insulin receptor (InR) and juvenile hormone (JH) have been known to regulate wing polyphenism in BPH, the interaction between these regulators remains largely elusive. Here, we discovered that a conserved microRNA, miR-34, modulates a positive autoregulatory feedback loop of JH and insulin/IGF signaling (IIS) pathway to control wing polyphenism in BPH. Nlu-miR-34 is abundant in SW BPHs and suppresses NlInR1 by targeting at two binding sites in the 3'UTR of NlInR1. Overexpressing miR-34 in LW BPHs by injecting agomir-34 induces the development towards SW BPHs, whereas knocking down miR-34 in SW BPHs by injecting antagomir-34 induces more LW BPHs when another NlInR1 suppressor, NlInR2, is also suppressed simultaneously. A cis-response element of Broad Complex (Br-C) is found in the promoter region of Nlu-miR-34, suggesting that 20-hydroxyecdysone (20E) might be involved in wing polyphenism regulation. Topic application of 20E downregulates miR-34 expression but does not change wing morphs. On the other hand, JH application upregulates miR-34 expression and induces more SW BPHs. Moreover, knocking down genes in IIS pathway changes JH titers and miR-34 abundance. In all, we showed that miRNA mediates the cross talk between JH, 20E and IIS pathway by forming a positive feedback loop, uncovering a comprehensive regulation mechanism which integrates almost all known regulators controlling wing polyphenism in insects.

Genome of the pincer wasp Gonatopus flavifemur reveals unique venom evolution and a dual adaptation to parasitism and predation.

BACKGROUND: Hymenoptera comprise extremely diverse insect species with extensive variation in their life histories. The Dryinidae, a family of solitary wasps of Hymenoptera, have evolved innovations that allow them to hunt using venom and a pair of chelae developed from the fore legs that can grasp prey. Dryinidae larvae are also parasitoids of Auchenorrhyncha, a group including common pests such as planthoppers and leafhoppers. Both of these traits make them effective and valuable for pest control, but little is yet known about the genetic basis of its dual adaptation to parasitism and predation. RESULTS: We sequenced and assembled a high-quality genome of the dryinid wasp Gonatopus flavifemur, which at 636.5 Mb is larger than most hymenopterans. The expansion of transposable elements, especially DNA transposons, is a major contributor to the genome size enlargement. Our genome-wide screens reveal a number of positively selected genes and rapidly evolving proteins involved in energy production and motor activity, which may contribute to the predatory adaptation of dryinid wasp. We further show that three female-biased, reproductive-associated yellow genes, in response to the prey feeding behavior, are significantly elevated in adult females, which may facilitate the egg production. Venom is a powerful weapon for dryinid wasp during parasitism and predation. We therefore analyze the transcriptomes of venom glands and describe specific expansions in venom Idgf-like genes and neprilysin-like genes. Furthermore, we find the LWS2-opsin gene is exclusively expressed in male G. flavifemur, which may contribute to partner searching and mating. CONCLUSIONS: Our results provide new insights into the genome evolution, predatory adaptation, venom evolution, and sex-biased genes in G. flavifemur, and present genomic resources for future in-depth comparative analyses of hymenopterans that may benefit pest control.

Reconstruction of Distal Nasal Defects With a Large Postauricular Skin-Fat-Fascia Composite Graft.

BACKGROUND: Composite grafts have previously been reported to achieve a good outcome for nasal defect repair, but composite grafts have greater metabolic needs than simple skin. Therefore, the traditionally recommended size of a composite graft for nasal reconstruction is less than 1.5 cm in diameter. However, the distal nose is generally well supplied with blood vessels, which might support the use of larger composite grafts in such a highly vascularized recipient site. The aim of the article is to investigate whether a large skin-fat-fascia composite graft (larger than 2.0 cm) is viable for the repair of partial-thickness nasal defects. METHODS: From October 2017 to December 2019, 13 patients with partial-thickness nasal defects underwent nasal reconstruction using a large postauricular skin-fat-fascia composite graft. Cases were followed up for 3 to 14 months postoperatively. The aesthetic outcome was evaluated in comparison with preoperative digital images. RESULTS: Skin-fat-fascia composite grafts survived without graft necrosis, dermal fibrosis, or skin contraction in all cases. Favorable aesthetic outcomes were obtained in all patients, and no further revision surgery was need. CONCLUSIONS: A postauricular composite graft larger than 2.0 cm is a safe and effective reconstruction approach for partial-thickness nasal defects. This technique offers significant advantages in terms of no additional facial scar, no visible asymmetry on the face, no additional surgery for revision, and with mild scar in the donor site of the postauricular region.

Genome-wide identification and analysis of genes encoding cuticular proteins in the endoparasitoid wasp Pteromalus puparum (Hymenoptera: Pteromalidae).

The multifunctional insect cuticle serves as the exoskeleton, determines body shape, restricts water loss, provides attachment sites for muscles and internal organs and is a formidable barrier to invaders. It is morphologically divided into three layers, including envelope, epicuticle, and procuticle and is composed of chitin and cuticular proteins (CPs). Annotation of CPs and their cognate genes may help understand the structure and functions of insect cuticles. In this paper, we interrogated the genome of Pteromalus puparum, an endoparasitoid wasp that parasitizes Pieris rapae and Papilio xuthus pupae, and identified 82 genes encoding CPs belonging to six CP families, including 62 in the CPR family, 8 in CPAP3, 5 in CPF/CPFL, 2 low complexity proteins, 2 in TWDL, and 3 in Apidermin. We used six RNA-seq libraries to determine CP gene expression profiles through development and compared the cuticle hydrophobicity between the P. puparum and the ectoparasitoid Nasonia vitripennis based on GRAVY values of CPR sequences. In the Nasonia-Pteromalus comparison, we found in both N. vitripennis and P. puparum, the peak of their CPR hydrophobicity displayed at their pupal stage, whereas their adult stage showed the lowest level. Except at the adult stage, the CPR hydrophobicity in N. vitripennis is always higher than P. puparum. Finally, we identified three novel Apidermin genes, a family found solely in Hymenoptera and revealed a new sequence feature of this family. This new information contributes to a broader understanding of insect CPs generally.

Genes acting in longevity-related pathways in the endoparasitoid, Pteromalus puparum.

Among insects, lifespans vary over a broad range, from the short-lived mayflies to the 17-year periodical cicadas. Generally, lifespans are determined by a phase in life, the reproductive lifespan, which varies among species. Numerous pathways, such as the insulin/insulin-like growth factor signaling pathway, the target of rapamycin pathway and the mitogen-activated protein kinase/extracellular signal-regulated kinases pathways, influence aging and lifespan. Components of these pathways were identified as lifespan-related genes, including genes mediating growth, metabolism, development, resistance, and other processes. Many age-related genes have been discovered in fruit flies, honeybees, and ants among other insect species. Studies of insect aging and longevity can help understand insect biology and develop new pest management technologies. In this paper, we interrogated the new Pteromalus puparum genome, from which we predicted 133 putative lifespan-related genes based on their homology with known lifespan-related genes of Drosophila melanogaster. These genes function in five signaling pathways and three physiological processes. The conserved domain structures of these genes were predicted and their expression patterns were analyzed. Amino acid sequence alignments and domain structure analysis indicate that most components remain conserved across at least six insect orders. The data in this paper will facilitate future work on parasitoid lifespans, which may have economic value in biocontrol programs.

Identification and characterization of miRNAs in an endoparasitoid wasp, Pteromalus puparum.

MicroRNAs (miRNAs) are a form of endogenous small noncoding RNAs that regulate protein-coding gene expression at the posttranscriptional level. So far, knowledge of miRNAs in parasitoids remains rudimentary. We investigated miRNAs in Pteromalus puparum, a pupal endoparasitoid wasp with genome and transcriptome sequences completed. In this study, we constructed eight small RNA libraries from selected developmental stages and genders: male embryos, male larvae, male pupae, male adults, mixed-sex embryos, mixed-sex larvae, mixed-sex pupae, and female adults. We identified 254 mature miRNAs with 5p/3p arm features originated from 75 known and 119 novel miRNA genes in P. puparum, 88 of which reside in 26 clusters. The miRNAs in more than half of the clusters exhibit a consistent expression pattern, indicating they were co-transcribed from a long transcript. Comparing miRNA expression in the eight libraries, we found that 84 mature miRNAs were differentially expressed between embryos and larvae, 20 between larvae and pupae, and 26 between pupae and adults. We found some miRNAs were differentially expressed between sexes in embryos (10), larvae (29), pupae (8), and adults (14). Target predictions resulted in 211,571 miRNA-mRNA interactions for 254 different mature miRNAs. These miRNAs may be involved in sexual and developmental regulation of gene expression.

An Ovarian Protein Involved in Passive Avoidance of an Endoparasitoid To Evade Its Host Immune Response.

Through a combination of transcriptomic and proteomic analyses, we identified 817 secreted ovarian proteins from an endoparasitoid wasp, Cotesia chilonis, of which five proteins are probably involved in passive evasion. The results of an encapsulation assay revealed that one of these passive evasion-associated proteins (Crp32B), a homologue of a 32-kDa protein (Crp32) from C. rubecula, could protect resin beads from being encapsulated by host hemocytes in a dose-dependent manner. Crp32B is transcribed in ovarian cells, nurse cells, follicular cells, and oocytes, and the protein is located throughout the ovary and on the egg surface. Moreover, Crp32B has antigenic similarity to several host components. These results indicate that C. chilonis may use molecular mimicry as a mechanism to avoid host cellular immune response.

Adipose-derived stem cells alleviate osteoporosis by enhancing osteogenesis and inhibiting adipogenesis in a rabbit model.

BACKGROUND AIMS: Osteoporosis (OP) is characterized by a reduction in bone quality, which is associated with inadequacies in bone marrow mesenchymal stromal cells (BMSCs). As an alternative cell source to BMSCs, adipose-derived stem cells (ASCs) have been investigated for bone repair because of their osteogenic potential and self-renewal capability. Nevertheless, whether autologous ASCs can be used to promote bone regeneration under osteoporotic conditions has not been elucidated. METHODS: The OP rabbit model was established by means of bilateral ovariectomy (OVX). Both BMSCs and ASCs were harvested from OVX rabbits and expanded in vitro. The effects of osteogenic-induced ASCs on the in vitro adipogenic and osteogenic capabilities of BMSCs were evaluated. Autologous ASCs were then encapsulated by calcium alginate gel and transplanted into the distal femurs of OVX rabbits (n = 12). Hydrogel without loading cells was injected into the contralateral femurs as a control. Animals were killed for investigation at 12 weeks after transplantation. RESULTS: Osteogenic-induced ASCs were able to promote osteogenesis and inhibit adipogenesis of osteoporotic BMSCs through activation of the bone morphogenetic protein 2/bone morphogenetic protein receptor type IB signal pathway. Local bone mineral density began to increase at 8 weeks after ASC transplantation (P < 0.05). At 12 weeks, micro-computed tomography and histological evaluation revealed more new bone formation in the cell-treated femurs than in the control group (P < 0.05). CONCLUSIONS: This study demonstrated that ASCs could stimulate proliferation and osteogenic differentiation of BMSCs in vitro and enhance bone regeneration in vivo, which suggests that autologous osteogenic-induced ASCs might be useful to alleviate OP temporally.

CRISPR/Cas9-mediated mutagenesis of the white gene in an ectoparasitic wasp, Habrobracon hebetor.

BACKGROUND: The ectoparasitic wasp Habrobracon hebetor (Hymenoptera, Braconidae) can parasitize various species of lepidopteran pests. To maximize its potential for biological control, it is necessary to investigate its gene function through genome engineering. RESULTS: To test the effectiveness of genome engineering system in H. hebetor, we injected the mixture of clustered regularly interspaced short palindromic repeats (CRISPR) -associated (Cas) 9 protein and single guide RNA(s) targeting gene white into embryos. The resulting mutants display a phenotype of eye pigment loss. The phenotype was caused by small indel and is heritable. Then, we compared some biological parameters between wildtype and mutant, and found there were no significant differences in other parameters except for the offspring female rate and adult longevity. In addition, cocoons could be used to extract genomic DNA for genotype during the gene editing process without causing unnecessary harm to H. hebetor. CONCLUSION: Our results demonstrate that the CRISPR/Cas9 system can be used for H. hebetor genome editing and it does not adversely affect biological parameters of the parasitoid wasps. We also provide a feasible non-invasive genotype detection method using genomic DNA extracted from cocoons. Our study introduces a novel tool and method for studying gene function in H. hebetor, and may contribute to better application of H. hebetor in biocontrol. © 2023 Society of Chemical Industry.

Regulatory network in heat stress response in parasitoid wasp focusing on Xap5 heat stress regulator.

Insects are susceptible to elevated temperatures, resulting in impaired fertility, and shortened lifespan. This study investigated the genetic mechanisms underlying heat stress effects. We conducted RNA sequencing on Pteromalus puparum exposed to 25°C and 35°C, revealing transcriptional signatures. Weighted Gene Co-expression Network Analysis uncovered heat stress-associated modules, forming a regulatory network of 113 genes. The network is naturally divided into two subgroups, one linked to acute heat stress, including heat shock proteins (HSPs), and the other to chronic heat stress, involving lipogenesis genes. We identified an Xap5 Heat Shock Regulator (XHSR) gene as a crucial network component, validated through RNA interference and quantitative PCR assays. XHSR knockdown reduced wasps' lifespan while directly inducing HSPs and mediating lipogenesis gene induction. CRISPR/Cas9-mediated knockout of the Drosophila XHSR homolog reduced mutants' survival, highlighting its conserved role. This research sheds light on thermal tolerance mechanisms, offering potential applications in pest control amid global warming.

Involvement of acid-sensing ion channel 1a in functions of cultured human retinal pigment epithelial cells.

In the retina, pH fluctuations may play an important role in adapting retinal responses to different light intensities and are involved in the fine tuning of visual perception. Acidosis occurs in the subretinal space (SRS) under pathological conditions such as age-related macular degeneration (AMD). Although it is well known that many transporters in the retinal pigment epithelium (RPE) cells can maintain pH homeostasis efficiently, other receptors in RPE may also be involved in sensing acidosis, such as acid-sensing ion channels (ASICs). In this study, we investigated whether ASIC1a was expressed in the RPE cells and whether it was involved in the function of these cells. Real-time RT-PCR and Western blotting were used to analyze the ASIC1a expression in ARPE-19 cells during oxidative stress induced by hydrogen peroxide (H(2)O(2)). Furthermore, inhibition or over-expression of ASIC1a in RPE cells was obtained using inhibitors (amiloride and PCTx1) or by the transfection of cDNA encoding hASIC1a. Cell viability was determined by using the MTT assay. The real-time RT-PCR and Western blotting results showed that both the mRNA and protein of ASIC1a were expressed in RPE cells. Inhibition of ASICs by amiloride in normal RPE cells resulted in cell death, indicating that ASICs play an important physiological role in RPE cells. Furthermore, over-expression of ASIC1a in RPE cells prolonged cell survival under oxidative stress induced by H(2)O(2). In conclusion, ASIC1a is functionally expressed in RPE cells and may play an important role in the physiological function of RPE cells by protecting them from oxidative stress.

Genomic analyses provide insights into the genome evolution and environmental adaptation of the tobacco moth Ephestia elutella.

Ephestia elutella is a major pest responsible for significant damage to stored tobacco over many years. Here, we conduct a comparative genomic analysis on this pest, aiming to explore the genetic bases of environmental adaptation of this species. We find gene families associated with nutrient metabolism, detoxification, antioxidant defense and gustatory receptors are expanded in the E. elutella genome. Detailed phylogenetic analysis of P450 genes further reveals obvious duplications in the CYP3 clan in E. elutella compared to the closely related species, the Indianmeal moth Plodia interpunctella. We also identify 229 rapidly evolving genes and 207 positively selected genes in E. elutella, respectively, and highlight two positively selected heat shock protein 40 (Hsp40) genes. In addition, we find a number of species-specific genes related to diverse biological processes, such as mitochondria biology and development. These findings advance our understanding of the mechanisms underlying processes of environmental adaptation on E. elutella and will enable the development of novel pest management strategies.

Genome assembly of the ectoparasitoid wasp Theocolax elegans.

The ectoparasitoid wasp Theocolax elegans is a cosmopolitan and generalist pteromalid parasitoid of several major storage insect pests, and can effectively suppress a host population in warehouses. However, little molecular information about this wasp is currently available. In this study, we assembled the genome of T. elegans using PacBio long-read sequencing, Illumina sequencing, and Hi-C methods. The genome assembly is 662.73 Mb in length with contig and scaffold N50 values of 1.15 Mb and 88.8 Mb, respectively. The genome contains 56.4% repeat sequences and 23,212 protein-coding genes were annotated. Phylogenomic analyses revealed that T. elegans diverged from the lineage leading to subfamily Pteromalinae (Nasonia vitripennis and Pteromalus puparum) approximately 110.5 million years ago. We identified 130 significantly expanded gene families, 34 contracted families, 248 fast-evolving genes, and 365 positively selected genes in T. elegans. Additionally, 260 olfactory receptors and 285 venom proteins were identified. This genome assembly provides valuable genetic bases for future investigations on evolution, molecular biology and application of T. elegans.

Multi-Omic Identification of Venom Proteins Collected from Artificial Hosts of a Parasitoid Wasp.

Habrobracon hebetor is a parasitoid wasp capable of infesting many lepidopteran larvae. It uses venom proteins to immobilize host larvae and prevent host larval development, thus playing an important role in the biocontrol of lepidopteran pests. To identify and characterize its venom proteins, we developed a novel venom collection method using an artificial host (ACV), i.e., encapsulated amino acid solution in paraffin membrane, allowing parasitoid wasps to inject venom. We performed protein full mass spectrometry analysis of putative venom proteins collected from ACV and venom reservoirs (VRs) (control). To verify the accuracy of proteomic data, we also collected venom glands (VGs), Dufour's glands (DGs) and ovaries (OVs), and performed transcriptome analysis. In this paper, we identified 204 proteins in ACV via proteomic analysis; compared ACV putative venom proteins with those identified in VG, VR, and DG via proteome and transcriptome approaches; and verified a set of them using quantitative real-time polymerase chain reaction. Finally, 201 ACV proteins were identified as potential venom proteins. In addition, we screened 152 and 148 putative venom proteins identified in the VG transcriptome and the VR proteome against those in ACV, and found only 26 and 25 putative venom proteins, respectively, were overlapped with those in ACV. Altogether, our data suggest proteome analysis of ACV in combination with proteome-transcriptome analysis of other organs/tissues will provide the most comprehensive identification of true venom proteins in parasitoid wasps.