A chromosome-level genome assembly of the woolly apple aphid, Eriosoma lanigerum Hausmann (Hemiptera: Aphididae)

A-to-I RNA editing of CYP18A1 mediates transgenerational wing dimorphism in aphids

Wing dimorphism is a common phenomenon that plays key roles in the environmental adaptation of aphid; however, the signal transduction in response to environmental cues and the regulation mechanism related to this event remain unknown. Adenosine (A) to inosine (I) RNA editing is a post-transcriptional modification that extends transcriptome variety without altering the genome, playing essential roles in numerous biological and physiological processes. Here, we present a chromosome-level genome assembly of the rose-grain aphid Metopolophium dirhodum by using PacBio long HiFi reads and Hi-C technology. The final genome assembly for M. dirhodum is 447.8 Mb, with 98.50% of the assembled sequences anchored to nine chromosomes. The contig and scaffold N50 values are 7.82 and 37.54 Mb, respectively. A total of 18,003 protein-coding genes were predicted, of which 92.05% were functionally annotated. In addition, 11,678 A-to-I RNA-editing sites were systematically identified based on this assembled M. dirhodum genome, and two synonymous A-to-I RNA-editing sites on CYP18A1 were closely associated with transgenerational wing dimorphism induced by crowding. One of these A-to-I RNA-editing sites may prevent the binding of miR-3036-5p to CYP18A1, thus elevating CYP18A1 expression, decreasing 20E titer, and finally regulating the wing dimorphism of offspring. Meanwhile, crowding can also inhibit miR-3036-5p expression and further increase CYP18A1 abundance, resulting in winged offspring. These findings support that A-to-I RNA editing is a dynamic mechanism in the regulation of transgenerational wing dimorphism in aphids and would advance our understanding of the roles of RNA editing in environmental adaptability and phenotypic plasticity.

Cytogenetics of insects in the era of chromosome-level genome assemblies

Over the past few years, a revolution has occurred in cytogenetics, driven by the emergence and spread of methods for obtaining high-quality chromosome-level genome assemblies. In fact, this has led to a new tool for studying chromosomes and chromosomal rearrangements, and this tool is thousands of times more powerful than light microscopy. This tool has revolutionized the cytogenetics of many groups of insects for which previously karyotype information, if available at all, was limited to the chromosome number. Even more impressive are the achievements of the genomic approach for studying the general patterns of chromosome organization and evolution in insects. Thus, it has been shown that rapid transformations of chromosomal numbers, which are often found in the order Lepidoptera, are most often carried out in the most parsimonious way, as a result of simple fusions and fissions of chromosomes. It has been established that these fusions and fissions are not random and occur independently in different phylogenetic lineages due to the reuse of the same ancestral chromosomal breakpoints. It has been shown that the tendency for chromosome fissions is correlated with the presence in chromosomes of the so-called interstitial telomeres, i. e. telomere-like structures located not at the ends of chromosomes, but inside them. It has been revealed that, in most insects, telomeric DNA is not just a set of short repeats, but a very long sequence consisting of (TTAGG)n (or other telomeric motifs), regularly and specifically interrupted by retrotransposons, and the telomeric motifs are diverse in terms of their length and nucleotide composition. The number of high-quality chromosome-level genome assemblies available for insects in the GenBank database is growing exponentially and now exceeds a thousand species. Therefore, the exceptional prospects for using genomic data for karyotype analysis are beyond doubt.

A comparative genomic analysis at the chromosomal-level reveals evolutionary patterns of aphid chromosomes

Genomic rearrangements are primary drivers of evolution, promoting biodiversity. Aphids, an agricultural pest with high species diversity, exhibit rapid chromosomal evolution and diverse karyotypes. These variations have been attributed to their unique holocentric chromosomes and parthenogenesis, though this hypothesis has faced scrutiny. In this study, we generated a chromosomal-level reference genome assembly of the celery aphid (Semiaphis heraclei) and conducted comparative genomic analysis, revealing varying chromosomal evolution rates among aphid lineages, positively correlating with species diversity. Aphid X chromosomes have undergone frequent intra-chromosomal recombination, while autosomes show accelerated inter-chromosomal recombination. Moreover, considering both inter- and intra-chromosomal rearrangements, the increased autosomal rearrangement rates may be common across the Aphidomorpha. We identified that the expansion of DNA transposable elements and short interspersed nuclear elements (SINEs), coupled with gene loss and duplication associated with karyotypic instability (such as RIF1, BRD8, DMC1, and TERT), may play crucial roles in aphid chromosomal evolution. Additionally, our analysis revealed that the mutation and expansion of detoxification gene families in S. heraclei may be a key factor in adapting to host plant chemical defenses. Our results provide new insights into chromosomal evolutionary patterns and detoxification gene families evolution in aphids, aiding the understanding of species diversity and adaptive evolution.

Chromosome-level genome assembly of soybean aphid

Soybean aphid (Aphis glycines) is one of the main pests on soybeans, which causes serious damage to the soybean worldwide. The current genome of the soybean aphid is quite fragmented, which has impeded scientific research to some extent. In this study, we assembled a chromosome-level genome of the soybean aphid using MGI short reads, PacBio HiFi long reads and Hi-C reads. The genome sequence was anchored to four pseudo-chromosomes, with a total genome length of 324 Mb and a scaffold N50 length of 88.85 Mb. We evaluated the genome based on insecta_odb10 and the results show it has a completeness of 97.2%. A total of 20,781 protein-coding genes were predicted in the genome, of which 17,183 genes were annotated in at least one protein database. Our work provides a new genomic resource for the soybean aphid study.

Genome sequence of the sugarcane aphid, Melanaphis sacchari (Hemiptera: Aphididae)

The sugarcane aphid, Melanaphis sacchari, is an agricultural pest that causes damage to plants in the Poaceae (the grasses) family, such as sorghum and sugarcane. In this study, we used nanopore long reads and a high-throughput chromosome conformation capture chromatin interaction maps to generate a chromosome-level assembly with a total length of 356.1 Mb, of which 85.5% (304.6 Mb) is contained within the 3 autosomes and the X chromosome. Repetitive sequences accounted for 16.29% of the chromosomes, and a total of 12,530 protein-coding genes were annotated, achieving 95.8% Benchmarking Universal Single-Copy Ortholog gene completeness. This offered a substantial improvement compared with previous low-quality genomic resources. A phylogenomic analysis by comparing M. sacchari with 24 published aphid genomes representing 3 aphid tribes revealed that M. sacchari belonged to the tribe Aphidini and maintained a conserved chromosome structure with other Aphidini species. The high-quality genomic resources reported in this study are useful for understanding the evolution of aphid genomes and studying pest management of M. sacchari.

Implications of cell wall immunocytochemical profiles on the structural and functional traits of root and stem galls induced by Eriosoma lanigerum on Malus domestica

Alterations in cell wall composition imply in new structural and functional traits in gall developmental sites, even when the inducer is a sucking exophytophagous insect with strict feeding sites as the aphid associated to Malus domestica Borkh. This host plant is an economically important, fruit-bearing species, susceptible to gall induction by the sucking aphid Eriosoma lanigerum Hausmann, 1802. Herein, the immunocytochemical detection of arabinogalactan-proteins (AGPs), pectins, and hemicelluloses using monoclonal antibodies was performed in samples of non-galled roots and stems, and of root and stem galls on M. domestica. The dynamics of these cell wall components was discussed under the structural and functional traits of the galls proximal, median, and distal regions, according to the proximity of E. lanigerum colony feeding site. In the proximal region, the epitopes of AGPs and homogalacturonans (HGs) are related to cell growth and divisions, which result in the overproduction of parenchyma cells both in root and stem galls. In the proximal and median regions, the co-occurrence of HGs and arabinans in the cell walls of parenchyma and secondary tissues favors the nutrient flow and water-holding capacity, while the xylogalacturonans and hemicelluloses may function as additional carbohydrate resources to E. lanigerum. The immunocytochemical profile of the cell walls support the feeding activity of E. lanigerum mainly in the gall proximal region. The similarity of the cell wall components of the gall distal region and the non-galled portions, both in roots and stems, relates to the decrease of the cecidogenetic field the more distant the E. lanigerum colony is.

Major changes in domain arrangements are associated with the evolution of termites

Domains as functional protein units and their rearrangements along the phylogeny can shed light on the functional changes of proteomes associated with the evolution of complex traits like eusociality. This complex trait is associated with sterile soldiers and workers, and long-lived, highly fecund reproductives. Unlike in Hymenoptera (ants, bees, and wasps), the evolution of eusociality within Blattodea, where termites evolved from within cockroaches, was accompanied by a reduction in proteome size, raising the question of whether functional novelty was achieved with existing rather than novel proteins. To address this, we investigated the role of domain rearrangements during the evolution of termite eusociality. Analysing domain rearrangements in the proteomes of three solitary cockroaches and five eusocial termites, we inferred more than 5,000 rearrangements over the phylogeny of Blattodea. The 90 novel domain arrangements that emerged at the origin of termites were enriched for several functions related to longevity, such as protein homeostasis, DNA repair, mitochondrial activity, and nutrient sensing. Many domain rearrangements were related to changes in developmental pathways, important for the emergence of novel castes. Along with the elaboration of social complexity, including permanently sterile workers and larger, foraging colonies, we found 110 further domain arrangements with functions related to protein glycosylation and ion transport. We found an enrichment of caste-biased expression and splicing within rearranged genes, highlighting their importance for the evolution of castes. Furthermore, we found increased levels of DNA methylation among rearranged compared to non-rearranged genes suggesting fundamental differences in their regulation. Our findings indicate the importance of domain rearrangements in the generation of functional novelty necessary for termite eusociality to evolve.

Genome assembly and transcriptomic analysis to elucidate the ability of Nasonovia ribisnigri to break host plant resistance

Aphid genomic resources enable the study of complex life history traits and provide information on vector biology, host adaption and speciation. The currant-lettuce aphid (Nasonovia ribisnigri (Hemiptera: Aphididae) (Mosley)) is a cosmopolitan pest of outdoor lettuce (Lactuca sativa (Asterales: Asteraceae) (Linnaeus)). Until recently, the use of resistant cultivars was an effective method for managing N. ribisnigri. A resistant cultivar containing a single gene (Nr-locus), introduced in the 1980s, conferred complete resistance to feeding. Overreliance of this Nr-locus in lettuce resulted in N. ribisnigri's ability to break resistance mechanism, with first reports during 2003. Our work attempts to understand which candidate gene(s) are associated with this resistance-breaking mechanism. We present two de novo draft assembles for N. ribisnigri genomes, corresponding to both avirulent (Nr-locus susceptible) and virulent (Nr-locus resistant) biotypes. Changes in gene expression of the two N. ribisnigri biotypes were investigated using transcriptomic analyses of RNA-sequencing (RNA-seq) data to understand the potential mechanisms of resistance to the Nr-locus in lettuce. The draft genome assemblies were 94.2% and 91.4% complete for the avirulent and virulent biotypes, respectively. Out of the 18,872 differentially expressed genes, a single gene/locus was identified in N. ribisnigri that was shared between two resistant-breaking biotypes. This locus was further explored and validated in Real-Time Quantitative Reverse Transcription PCR (qRT-PCR) experiments and has predicted localisations in both the cytoplasm and nucleus. This is the first study to provide evidence that a single gene/locus is likely responsible for the ability of N. ribisnigri to overcome the Nr-locus resistance in the lettuce host.

Construction and Single-Crystal Structures of N-Isoxazolin-5-ylcarbonylindole Derivatives, and Their Pesticidal Activities and Toxicology Study

To explore natural product-based pesticide candidates, a series of indole derivatives containing the isoxazoline skeleton at the N-1 position were synthesized by 1,3-dipolar [2 + 3] cycloaddition reaction. Their structures were characterized by melting points (mp), infrared (IR) spectra, proton nuclear magnetic resonance spectra (1H NMR), carbon-13 nuclear magnetic resonance spectra (13C NMR), and high resolution mass spectrometry (HRMS). The single-crystal structures of five compounds were presented. Against Tetranychus cinnabarinus Boisduval, compound 3b showed greater than 3.8-fold acaricidal activity of indole and good control effects under glasshouse conditions. Against Aphis citricola Van der Goot, compounds 3b and 3q exhibited 48.3- and 36.8-fold aphicidal activity of indole and 6-methylindole, respectively. Particularly, compound 3b showed good bioactivities against T. cinnabarinus and A. citricola. Against Eriosoma lanigerum Hausmann, compound 3h and 3i showed 2.1 and 1.9 times higher aphicidal activity compared to indole. Furthermore, the construction of the epidermal cuticle layer of 3b-treated carmine spider mites was distinctly damaged, which ultimately led to their death.

Parallel Losses of Blue Opsin Correlate with Compensatory Neofunctionalization of UV-Opsin Gene Duplicates in Aphids and Planthoppers

Expanding on previous efforts to survey the visual opsin repertoires of the Hemiptera, this study confirms that homologs of the UV- and LW-opsin subfamilies are conserved in all Hemiptera, while the B-opsin subfamily is missing from the Heteroptera and subgroups of the Sternorrhyncha and Auchenorrhyncha, i.e., aphids (Aphidoidea) and planthoppers (Fulgoroidea), respectively. Unlike in the Heteroptera, which are characterized by multiple independent expansions of the LW-opsin subfamily, the lack of B-opsin correlates with the presence of tandem-duplicated UV-opsins in aphids and planthoppers. Available data on organismal wavelength sensitivities and retinal gene expression patterns lead to the conclusion that, in both groups, one UV-opsin paralog shifted from ancestral UV peak sensitivity to derived blue sensitivity, likely compensating for the lost B-opsin. Two parallel bona fide tuning site substitutions compare to 18 non-corresponding amino acid replacements in the blue-shifted UV-opsin paralogs of aphids and planthoppers. Most notably, while the aphid blue-shifted UV-opsin clade is characterized by a replacement substitution at one of the best-documented UV/blue tuning sites (Rhodopsin site 90), the planthopper blue-shifted UV-opsin paralogs retained the ancestral lysine at this position. Combined, the new findings identify aphid and planthopper UV-opsins as a new valuable data sample for studying adaptive opsin evolution.

Hybridisation has shaped a recent radiation of grass-feeding aphids

BACKGROUND

Aphids are common crop pests. These insects reproduce by facultative parthenogenesis involving several rounds of clonal reproduction interspersed with an occasional sexual cycle. Furthermore, clonal aphids give birth to live young that are already pregnant. These qualities enable rapid population growth and have facilitated the colonisation of crops globally. In several cases, so-called "super clones" have come to dominate agricultural systems. However, the extent to which the sexual stage of the aphid life cycle has shaped global pest populations has remained unclear, as have the origins of successful lineages. Here, we used chromosome-scale genome assemblies to disentangle the evolution of two global pests of cereals-the English (Sitobion avenae) and Indian (Sitobion miscanthi) grain aphids.

RESULTS

Genome-wide divergence between S. avenae and S. miscanthi is low. Moreover, comparison of haplotype-resolved assemblies revealed that the S. miscanthi isolate used for genome sequencing is likely a hybrid, with one of its diploid genome copies closely related to S. avenae (~ 0.5% divergence) and the other substantially more divergent (> 1%). Population genomics analyses of UK and China grain aphids showed that S. avenae and S. miscanthi are part of a cryptic species complex with many highly differentiated lineages that predate the origins of agriculture. The complex consists of hybrid lineages that display a tangled history of hybridisation and genetic introgression.

CONCLUSIONS

Our analyses reveal that hybridisation has substantially contributed to grain aphid diversity, and hence, to the evolutionary potential of this important pest species. Furthermore, we propose that aphids are particularly well placed to exploit hybridisation events via the rapid propagation of live-born "frozen hybrids" via asexual reproduction, increasing the likelihood of hybrid lineage formation.

Chromosome-level genome assembly of the spotted alfalfa aphid Therioaphis trifolii

The spotted alfalfa aphid (SAA, Therioaphis trifolii) (Hemiptera: Aphididae) is a destructive pest of cultivated alfalfa (Medicago sativa L.) that leads to large financial losses in the livestock industry around the world. Here, we present a chromosome-scale genome assembly of T. trifolii, the first genome assembly for the aphid subfamily Calaphidinae. Using PacBio long-read sequencing, Illumina sequencing, and Hi-C scaffolding techniques, a 541.26 Mb genome was generated, with 90.01% of the assembly anchored into eight scaffolds, and the contig and scaffold N50 are 2.54 Mb and 44.77 Mb, respectively. BUSCO assessment showed a completeness score of 96.6%. A total of 13,684 protein-coding genes were predicted. The high-quality genome assembly of T. trifolii not only provides a genomic resource for the more complete analysis of aphid evolution, but also provides insights into the ecological adaptation and insecticide resistance of T. trifolii.

NLRs are highly relevant resistance genes for aphid pests

Since the 20th century, when plant resistance to aphids was available, it has been widely used by farmers and the inheritance of plant resistance has been understood for several crops. However, it is only when the plant-aphid relationship was compared with that of microbial pathogens, that aphid resistance has begun to be understood and integrated into the plant immune network. Three of the four genes identified for plant resistance to aphid encode nucleotide-binding site leucine-rich repeat receptor (NLR) proteins responsible for aphid-effector triggered immunity, and NLRs are serious candidates for aphid resistance in four other plant species. Aphids are vectors for plant viruses, and aphid-effectors triggering immunity when they pierce plant cells are expected to trigger resistance to the viruses transmitted to the plant with effectors, as has been shown for aphid resistance in melon. This dual phenotype increases the interest of NLRs in the control of aphids.

Metabolic relay gene of aphid and primary symbiont as RNAi target loci for aphid control

INTRODUCTION

Aphids form a stable and mutually beneficial relationship with their primary symbiont Buchnera aphidicola, which play an important role in providing the missing nutrients to the host aphid. Based on the genome sequence of wheat aphid Siotobion miscanthi and its primary symbiont Buchnera that we obtained in our previously study, we identified a metabolic relay gene, ilvA, involved in the isoleucine synthesis pathway between aphids and Buchnera.

METHOD

In this study, we identified the location and sequence structure of ilvA gene in aphid genome, the expression level in different instars and tissues of aphids, and the effect of reducing ilvA expression on the growth and development of aphids by bioinformatics analysis, quantitative PCR, RNAi and bioassay experiments.

RESULT

Our study showed that ilvA was expressed at the highest level in the 2^nd instar of the aphid, while the expression of this gene was significantly higher in the aphid bacteriocytes than in other tissues. Notably, this gene is localized on the aphid sex chromosome and remains highly conserved and collinearity across different aphid genomes. Knocking down the expression of ilvA reduced the aphid body weight and production. However, the indices of mortality decreased slightly, but were not significantly different, compared to the control.

DISCUSSION

The results show that the relay genes between aphids and their symbionts in the metabolism of essential nutrients have potential roles in the growth and development of aphids, meanwhile, providing target loci and new ideas for RNAi-based aphid green control strategies.

Chromosome-scale assembly of the yellow mealworm genome

Background: The yellow mealworm beetle, Tenebrio molitor, is a promising alternative protein source for animal and human nutrition and its farming involves relatively low environmental costs. For these reasons, its industrial scale production started this century. However, to optimize and breed sustainable new T. molitor lines, the access to its genome remains essential. Methods: By combining Oxford Nanopore and Illumina Hi-C data, we constructed a high-quality chromosome-scale assembly of T. molitor. Then, we combined RNA-seq data and available coleoptera proteomes for gene prediction with GMOVE. Results: We produced a high-quality genome with a N50 = 21.9Mb with a completeness of 99.5% and predicted 21,435 genes with a median size of 1,780 bp. Gene orthology between T. molitor and Tribolium castaneum showed a highly conserved synteny between the two coleoptera and paralogs search revealed an expansion of histones in the T. molitor genome. Conclusions: The present genome will greatly help fundamental and applied research such as genetic breeding and will contribute to the sustainable production of the yellow mealworm.

Chromosome-scale assembly of the yellow mealworm genome

Background: The yellow mealworm beetle, Tenebrio molitor, is a promising alternative protein source for animal and human nutrition and its farming involves relatively low environmental costs. For these reasons, its industrial scale production started this century. However, to optimize and breed sustainable new T. molitor lines, the access to its genome remains essential. Methods: By combining Oxford Nanopore and Illumina Hi-C data, we constructed a high-quality chromosome-scale assembly of T. molitor. Then, we combined RNA-seq data and available coleoptera proteomes for gene prediction with GMOVE. Results: We produced a high-quality genome with a N50 = 21.9Mb with a completeness of 99.5% and predicted 21,435 genes with a median size of 1,780 bp. Gene orthology between T. molitor and Tribolium castaneum showed a highly conserved synteny between the two coleoptera and paralogs search revealed an expansion of histones in the T. molitor genome. Conclusions: The present genome will greatly help fundamental and applied research such as genetic breeding and will contribute to the sustainable production of the yellow mealworm.

The Adipokinetic Peptides of Hemiptera: Structure, Function, and Evolutionary Trends

The Hemiptera comprise the most species-rich order of the hemimetabolous insects. Members of a number of superfamilies, most notably especially the more basal ones such as white flies, psyllids and aphids, belong to the most destructive agricultural insects known worldwide. At the other end of the phylogenetic tree are hemipterans that are notorious medical pests (e.g. kissing bugs). Most of the hemipteran species are good flyers, and lipid oxidation plays a pivotal role to power the contraction of flight muscles and, in aquatic water bugs, also deliver the ATP for the extensive swimming action of the leg muscles. Mobilization of stored lipids (mostly triacylglycerols in the fat body) to circulating diacylglycerols in the hemolymph is regulated by a set of small neuropeptides, the adipokinetic hormones (AKHs). We searched the literature and publicly available databases of transcriptomes and genomes to present here AKH sequences from 191 hemipteran species. Only few of these peptides were sequenced via Edman degradation or mass spectrometry, and even fewer were characterized with molecular biology methods; thus, the majority of the AKHs we have identified by bioinformatics are merely predicted sequences at this stage. Nonetheless, a total of 42 AKH primary sequences are assigned to Hemiptera. About 50% of these structures occur also in other insect orders, while the remaining 50% are currently unique for Hemiptera. We find 9 novel AKHs not shown to be synthesized before in any insect. Most of the hemipteran AKHs are octapeptides (28) but there is an impressive number of decapeptides (12) compared to other speciose orders such as Diptera and Lepidoptera. We attempt to construct a hypothetical molecular peptide evolution of hemipteran AKHs and find quite a bit of overlapping with current phylogenetic ideas of the Hemiptera. Lastly, we discuss the possibility to use the sequence of the aphid AKH as lead peptide for the research into a peptide mimetic fulfilling criteria of a green insecticide.

Gene Editing and Genetic Control of Hemipteran Pests: Progress, Challenges and Perspectives

The origin of the order Hemiptera can be traced to the late Permian Period more than 230 MYA, well before the origin of flowering plants 100 MY later in during the Cretaceous period. Hemipteran species consume their liquid diets using a sucking proboscis; for phytophagous hemipterans their mouthparts (stylets) are elegant structures that enable voracious feeding from plant xylem or phloem. This adaptation has resulted in some hemipteran species becoming globally significant pests of agriculture resulting in significant annual crop losses. Due to the reliance on chemical insecticides for the control of insect pests in agricultural settings, many hemipteran pests have evolved resistance to insecticides resulting in an urgent need to develop new, species-specific and environmentally friendly methods of pest control. The rapid advances in CRISPR/Cas9 technologies in model insects such as Drosophila melanogaster, Tribolium castaneum, Bombyx mori, and Aedes aegypti has spurred a new round of innovative genetic control strategies in the Diptera and Lepidoptera and an increased interest in assessing genetic control technologies for the Hemiptera. Genetic control approaches in the Hemiptera have, to date, been largely overlooked due to the problems of introducing genetic material into the germline of these insects. The high frequency of CRISPR-mediated mutagenesis in model insect species suggest that, if the delivery problem for Hemiptera could be solved, then gene editing in the Hemiptera might be quickly achieved. Significant advances in CRISPR/Cas9 editing have been realized in nine species of Hemiptera over the past 4 years. Here we review progress in the Hemiptera and discuss the challenges and opportunities for extending contemporary genetic control strategies into species in this agriculturally important insect orderr.

Efficacy of RNA interference using nanocarrier-based transdermal dsRNA delivery system in the woolly apple aphid, Eriosoma lanigerum

RNA interference (RNAi) is an essential approach for studying gene function and has been considered as a promising strategy for pest control. However, RNAi method has not been conducted in Woolly apple aphid (Eriosoma lanigerum Hausmann), one of the most damaging apple pests in the world. In the study, we investigated the efficacy of RNAi of V-ATPase subunit D (ATPD), an efficacious target for RNAi in other insects, in E. lanigerum by a transdermal double-stranded RNA (dsRNA) delivery system with nanocarriers. Our results showed although topical application of dsATPD in E. lanigerum for 24 h produced 40.5% gene silencing, the additional help of nanocarriers extremely improved the interference efficiency with 98.5% gene silencing. Moreover, a 55.75% mortality was observed 5 days after topical application of nanocarriers and dsATPD, relative to the control (topical application of nanocarriers and double-stranded green fluorescent protein [dsGFP]). The nanocarrier-based transdermal dsRNA delivery system will promote the development of functional analysis of vital genes and also provide a potential target for RNAi-based management of E. lanigerum.

Elucidation of host and symbiont contributions to peptidoglycan metabolism based on comparative genomics of eight aphid subfamilies and their Buchnera

Pea aphids (Acyrthosiphon pisum) are insects containing genes of bacterial origin with putative functions in peptidoglycan (PGN) metabolism. Of these, rlpA1-5, amiD, and ldcA are highly expressed in bacteriocytes, specialized aphid cells that harbor the obligate bacterial symbiont Buchnera aphidicola, required for amino acid supplementation of the host's nutrient-poor diet. Despite genome reduction associated with endosymbiosis, pea aphid Buchnera retains genes for the synthesis of PGN while Buchnera of many other aphid species partially or completely lack these genes. To explore the evolution of aphid horizontally-transferred genes (HTGs) and to elucidate how host and symbiont genes contribute to PGN production, we sequenced genomes from four deeply branching lineages, such that paired aphid and Buchnera genomes are now available for 17 species representing eight subfamilies. We identified all host and symbiont genes putatively involved in PGN metabolism. Phylogenetic analyses indicate that each HTG family was present in the aphid shared ancestor, but that each underwent a unique pattern of gene loss or duplication in descendant lineages. While four aphid rlpA gene subfamilies show no relation to symbiont PGN gene repertoire, the loss of aphid amiD and ldcA HTGs coincides with the loss of symbiont PGN metabolism genes. In particular, the coincident loss of host amiD and symbiont murCEF in tribe Aphidini, in contrast to tribe Macrosiphini, suggests either 1) functional linkage between these host and symbiont genes, or 2) Aphidini has lost functional PGN synthesis and other retained PGN pathway genes are non-functional. To test these hypotheses experimentally, we used cell-wall labeling methods involving a d-alanine probe and found that both Macrosiphini and Aphidini retain Buchnera PGN synthesis. Our results imply that compensatory adaptations can preserve PGN synthesis despite the loss of some genes considered essential for this pathway, highlighting the importance of the cell wall in these symbioses.

Chromosome‐level genome assembly for the horned‐gall aphid provides insights into interactions between gall‐making insect and its host plant

The aphid Schlechtendalia chinensis is an economically important insect that can induce horned galls, which are valuable for the medicinal and chemical industries. Up to now, more than twenty aphid genomes have been reported. Most of the sequenced genomes are derived from free‐living aphids. Here, we generated a high‐quality genome assembly from a galling aphid. The final genome assembly is 271.52 Mb, representing one of the smallest sequenced genomes of aphids. The genome assembly is based on contig and scaffold N50 values of the genome sequence are 3.77 Mb and 20.41 Mb, respectively. Nine‐seven percent of the assembled sequences was anchored onto 13 chromosomes. Based on BUSCO analysis, the assembly involved 96.9% of conserved arthropod and 98.5% of the conserved Hemiptera single‐copy orthologous genes. A total of 14,089 protein‐coding genes were predicted. Phylogenetic analysis revealed that S. chinensis diverged from the common ancestor of Eriosoma lanigerum approximately 57 million years ago (MYA). In addition, 35 genes encoding salivary gland proteins showed differentially when S. chinensis forms a gall, suggesting they have potential roles in gall formation and plant defense suppression. Taken together, this high‐quality S. chinensis genome assembly and annotation provide a solid genetic foundation for future research to reveal the mechanism of gall formation and to explore the interaction between aphids and their host plants.

Aphid hologenomics: current status and future challenges

Aphids are important model organisms in ecological, developmental, and evolutionary studies of, for example, symbiosis, insect-plant interactions, pest management, and developmental polyphenism. Here, we review the recent progress made in the genomics of aphids and their symbionts: hologenomics. The reference genome of Acyrthosiphon pisum has been greatly improved, and chromosome-level assembly is now available. The genomes of over 20 aphid species have been sequenced, and comparative genomic analyses have revealed pervasive gene duplication and dynamic chromosomal rearrangements. Over 120 symbiont genomes (both obligate and facultative) have been sequenced, and modern deep-sequencing technologies have identified novel symbionts. The advances in hologenomics have helped to elucidate the dynamic evolution of facultative and co-obligate symbionts with the ancient obligate symbiont Buchnera.

A Review on Transcriptional Responses of Interactions between Insect Vectors and Plant Viruses

This review provides a synopsis of transcriptional responses pertaining to interactions between plant viruses and the insect vectors that transmit them in diverse modes. In the process, it attempts to catalog differential gene expression pertinent to virus–vector interactions in vectors such as virus reception, virus cell entry, virus tissue tropism, virus multiplication, and vector immune responses. Whiteflies, leafhoppers, planthoppers, and thrips are the main insect groups reviewed, along with aphids and leaf beetles. Much of the focus on gene expression pertinent to vector–virus interactions has centered around whole-body RNA extraction, whereas data on virus-induced tissue-specific gene expression in vectors is limited. This review compares transcriptional responses in different insect groups following the acquisition of non-persistent, semi-persistent, and persistent (non-propagative and propagative) plant viruses and identifies parallels and divergences in gene expression patterns. Understanding virus-induced changes in vectors at a transcriptional level can aid in the identification of candidate genes for targeting with RNAi and/or CRISPR editing in insect vectors for management approaches.

Chromosome-Level Genome Assembly Reveals Significant Gene Expansion in the Toll and IMD Signaling Pathways of Dendrolimus kikuchii

A high-quality genome is of significant value when seeking to control forest pests such as Dendrolimus kikuchii, a destructive member of the order Lepidoptera that is widespread in China. Herein, a high quality, chromosome-level reference genome for D. kikuchii based on Nanopore, Pacbio HiFi sequencing and the Hi-C capture system is presented. Overall, a final genome assembly of 705.51 Mb with contig and scaffold N50 values of 20.89 and 24.73 Mb, respectively, was obtained. Of these contigs, 95.89% had unique locations on 29 chromosomes. In silico analysis revealed that the genome contained 15,323 protein-coding genes and 63.44% repetitive sequences. Phylogenetic analyses indicated that D. kikuchii may diverged from the common ancestor of Thaumetopoea. Pityocampa, Thaumetopoea ni, Heliothis virescens, Hyphantria armigera, Spodoptera frugiperda, and Spodoptera litura approximately 122.05 million years ago. Many gene families were expanded in the D. kikuchii genome, particularly those of the Toll and IMD signaling pathway, which included 10 genes in peptidoglycan recognition protein, 19 genes in MODSP, and 11 genes in Toll. The findings from this study will help to elucidate the mechanisms involved in protection of D. kikuchii against foreign substances and pathogens, and may highlight a potential channel to control this pest.

Improved draft reference genome for the Glassy-winged Sharpshooter (Homalodisca vitripennis), a vector for Pierce's disease

Homalodisca vitripennis (Hemiptera: Cicadellidae), known as the glassy-winged sharpshooter, is a xylem feeding leafhopper and an important agricultural pest as a vector of Xylella fastidiosa, which causes Pierce’s disease in grapes and a variety of other scorch diseases. The current H. vitripennis reference genome from the Baylor College of Medicine's i5k pilot project is a 1.4-Gb assembly with 110,000 scaffolds, which still has significant gaps making identification of genes difficult. To improve on this effort, we used a combination of Oxford Nanopore long-read sequencing technology combined with Illumina sequencing reads to generate a better assembly and first-pass annotation of the whole genome sequence of a wild-caught Californian (Tulare County) individual of H. vitripennis. The improved reference genome assembly for H. vitripennis is 1.93-Gb in length (21,254 scaffolds, N50 = 650 Mb, BUSCO completeness = 94.3%), with 33.06% of the genome masked as repetitive. In total, 108,762 gene models were predicted including 98,296 protein-coding genes and 10,466 tRNA genes. As an additional community resource, we identified 27 orthologous candidate genes of interest for future experimental work including phenotypic marker genes like white. Furthermore, as part of the assembly process, we generated four endosymbiont metagenome-assembled genomes, including a high-quality near complete 1.7-Mb Wolbachia sp. genome (1 scaffold, CheckM completeness = 99.4%). The improved genome assembly and annotation for H. vitripennis, curated set of candidate genes, and endosymbiont MAGs will be invaluable resources for future research of H. vitripennis.

The Easter Egg Weevil (Pachyrhynchus) genome reveals syntenic patterns in Coleoptera across 200 million years of evolution

Patterns of genomic architecture across insects remain largely undocumented or decoupled from a broader phylogenetic context. For instance, it is unknown whether translocation rates differ between insect orders. We address broad scale patterns of genome architecture across Insecta by examining synteny in a phylogenetic framework from open-source insect genomes. To accomplish this, we add a chromosome level genome to a crucial lineage, Coleoptera. Our assembly of the Pachyrhynchus sulphureomaculatus genome is the first chromosome scale genome for the hyperdiverse Phytophaga lineage and currently the largest insect genome assembled to this scale. The genome is significantly larger than those of other weevils, and this increase in size is caused by repetitive elements. Our results also indicate that, among beetles, there are instances of long-lasting (>200 Ma) localization of genes to a particular chromosome with few translocation events. While some chromosomes have a paucity of translocations, intra-chromosomal synteny was almost absent, with gene order thoroughly shuffled along a chromosome. This large amount of reshuffling within chromosomes with few inter-chromosomal events contrasts with patterns seen in mammals in which the chromosomes tend to exchange larger blocks of material more readily. To place our findings in an evolutionary context, we compared syntenic patterns across Insecta in a phylogenetic framework. For the first time, we find that synteny decays at an exponential rate relative to phylogenetic distance. Additionally, there are significant differences in decay rates between insect orders, this pattern was not driven by Lepidoptera alone which has a substantially different rate.