The genomic history and global migration of a windborne pest.

Many insect pests, including the brown planthopper (BPH), undergo windborne migration that is challenging to observe and track. It remains controversial about their migration patterns and largely unknown regarding the underlying genetic basis. By analyzing 360 whole genomes from around the globe, we clarify the genetic sources of worldwide BPHs and illuminate a landscape of BPH migration showing that East Asian populations perform closed-circuit journeys between Indochina and the Far East, while populations of Malay Archipelago and South Asia undergo one-way migration to Indochina. We further find round-trip migration accelerates population differentiation, with highly diverged regions enriching in a gene desert chromosome that is simultaneously the speciation hotspot between BPH and related species. This study not only shows the power of applying genomic approaches to demystify the migration in windborne migrants but also enhances our understanding of how seasonal movements affect speciation and evolution in insects.

Molecular and biological characterization of a bunyavirus infecting the brown planthopper (Nilaparvata lugens).

A negative-strand symbiotic RNA virus, tentatively named Nilaparvata lugens Bunyavirus (NLBV), was identified in the brown planthopper (BPH, Nilaparvata lugens). Phylogenetic analysis indicated that NLBV is a member of the genus Mobuvirus (family Phenuiviridae, order Bunyavirales). Analysis of virus-derived small interfering RNA suggested that antiviral immunity of BPH was successfully activated by NLBV infection. Tissue-specific investigation showed that NLBV was mainly accumulated in the fat-body of BPH adults. Moreover, NLBV was detected in eggs of viruliferous female BPHs, suggesting the possibility of vertical transmission of NLBV in BPH. Additionally, no significant differences were observed for the biological properties between NLBV-infected and NLBV-free BPHs. Finally, analysis of geographic distribution indicated that NLBV may be prevalent in Southeast Asia. This study provided a comprehensive characterization on the molecular and biological properties of a symbiotic virus in BPH, which will contribute to our understanding of the increasingly discovered RNA viruses in insects.

Co-option of a non-retroviral endogenous viral element in planthoppers.

Non-retroviral endogenous viral elements (nrEVEs) are widely dispersed throughout the genomes of eukaryotes. Although nrEVEs are known to be involved in host antiviral immunity, it remains an open question whether they can be domesticated as functional proteins to serve cellular innovations in arthropods. In this study, we found that endogenous toti-like viral elements (ToEVEs) are ubiquitously integrated into the genomes of three planthopper species, with highly variable distributions and polymorphism levels in planthopper populations. Three ToEVEs display exon‒intron structures and active transcription, suggesting that they might have been domesticated by planthoppers. CRISPR/Cas9 experiments revealed that one ToEVE in Nilaparvata lugens, NlToEVE14, has been co-opted by its host and plays essential roles in planthopper development and fecundity. Large-scale analysis of ToEVEs in arthropod genomes indicated that the number of arthropod nrEVEs is currently underestimated and that they may contribute to the functional diversity of arthropod genes.

A chromosome-level genome assembly of Stenchaetothrips biformis and comparative genomic analysis highlights distinct host adaptations among thrips.

Insects have a limited host range due to genomic adaptation. Thysanoptera, commonly known as thrips, occupies distinct feeding habitats, but there is a lack of comparative genomic analyses and limited genomic resources available. In this study, the chromosome-level genome of Stenchaetothrips biformis, an oligophagous pest of rice, is assembled using multiple sequencing technologies, including PacBio, Illumina short-reads, and Hi-C technology. A 338.86 Mb genome is obtained, consisting of 1269 contigs with a contig N50 size of 381 kb and a scaffold N50 size of 18.21 Mb. Thereafter, 17,167 protein-coding genes and 36.25% repetitive elements are annotated. Comparative genomic analyses with two other polyphagous thrips, revealing contracted chemosensory-related and expanded stress response and detoxification gene families in S. biformis, potentially facilitating rice adaptation. In the polyphagous thrips species Frankliniella occidentalis and Thrips palmi, expanded gene families are enriched in metabolism of aromatic and anthocyanin-containing compounds, immunity against viruses, and detoxification enzymes. These expansion gene families play crucial roles not only in adapting to hosts but also in development of pesticide resistance, as evidenced by transcriptome results after insecticides treatment. This study provides a chromosome-level genome assembly and lays the foundation for further studies on thrips evolution and pest management.

The JAK-STAT pathway promotes persistent viral infection by activating apoptosis in insect vectors.

The Janus kinase-signal transducer and activator of transcription (JAK-STAT) pathway is an evolutionarily conserved signaling pathway that can regulate various biological processes. However, the role of JAK-STAT pathway in the persistent viral infection in insect vectors has rarely been investigated. Here, using a system that comprised two different plant viruses, Rice stripe virus (RSV) and Rice black-streaked dwarf virus (RBSDV), as well as their insect vector small brown planthopper, we elucidated the regulatory mechanism of JAK-STAT pathway in persistent viral infection. Both RSV and RBSDV infection activated the JAK-STAT pathway and promoted the accumulation of suppressor of cytokine signaling 5 (SOCS5), an E3 ubiquitin ligase regulated by the transcription factor STAT5B. Interestingly, the virus-induced SOCS5 directly interacted with the anti-apoptotic B-cell lymphoma-2 (BCL2) to accelerate the BCL2 degradation through the 26S proteasome pathway. As a result, the activation of apoptosis facilitated persistent viral infection in their vector. Furthermore, STAT5B activation promoted virus amplification, whereas STAT5B suppression inhibited apoptosis and reduced virus accumulation. In summary, our results reveal that virus-induced JAK-STAT pathway regulates apoptosis to promote viral infection, and uncover a new regulatory mechanism of the JAK-STAT pathway in the persistent plant virus transmission by arthropod vectors.

Planthopper salivary sheath protein LsSP1 contributes to manipulation of rice plant defenses.

Salivary elicitors secreted by herbivorous insects can be perceived by host plants to trigger plant immunity. However, how insects secrete other salivary components to subsequently attenuate the elicitor-induced plant immunity remains poorly understood. Here, we study the small brown planthopper, Laodelphax striatellus salivary sheath protein LsSP1. Using Y2H, BiFC and LUC assays, we show that LsSP1 is secreted into host plants and binds to salivary sheath via mucin-like protein (LsMLP). Rice plants pre-infested with dsLsSP1-treated L. striatellus are less attractive to L. striatellus nymphs than those pre-infected with dsGFP-treated controls. Transgenic rice plants with LsSP1 overexpression rescue the insect feeding defects caused by a deficiency of LsSP1 secretion, consistent with the potential role of LsSP1 in manipulating plant defenses. Our results illustrate the importance of salivary sheath proteins in mediating the interactions between plants and herbivorous insects.

Chromosome-level Assembly, Dosage Compensation and Sex-biased Gene Expression in the Small Brown Planthopper, Laodelphax striatellus.

In insects, sex chromosome differentiation often results in unequal gene dosages between sexes. Dosage compensation mechanisms evolve to balance gene expression, but the degree and mechanism of regulation often vary by insect species. In hemipteran species, the small brown planthopper (SBPH), Laodelphax striatellus, is an injurious crop pest, with a sex chromosome type XX in females and XO in males. This species offers the opportunity to study dosage compensation and sex-biased gene expression. In this study, we generated a chromosome-level genome of SBPH using Oxford Nanopore Technologies and high-throughput chromatin conformation capture (Hi-C) technology. We also sequenced RNA-seq data from 16 tissue samples to annotate the genome and analyze gene dosage compensation. We finally obtained a 510.2 megabases (Mb) genome with 99.12% of the scaffolds anchored on 15 chromosomes (14 autosomes and 1 X chromosome) and annotated 16,160 protein-coding genes based on full-length cDNA sequencing data. Furthermore, we found complete dosage compensation in all L. striatellus somatic tissues, but lack of dosage compensation in gonad tissue testis. We also found that female-biased genes were significantly enriched on the X chromosome in all tissues, whereas male-biased genes in gonad tissues were enriched on autosomes. This study not only provides a high-quality genome assembly but also lays a foundation for a better understanding of the sexual regulatory network in hemipteran insects.

A feminizing switch in a hemimetabolous insect.

The mechanism of sex determination remains poorly understood in hemimetabolous insects. Here, in the brown planthopper (BPH), Nilaparvata lugens, a hemipteran rice pest, we identified a feminizing switch or a female determiner (Nlfmd) that encodes a serine/arginine-rich protein. Knockdown of Nlfmd in female nymphs resulted in masculinization of both the somatic morphology and doublesex splicing. The female-specific isoform of Nlfmd, Nlfmd-F, is maternally deposited and zygotically transcribed. Depletion of Nlfmd by maternal RNAi or CRISPR-Cas9 resulted in female-specific embryonic lethality. Knockdown of an hnRNP40 family gene named female determiner 2 (Nlfmd2) also conferred masculinization. In vitro experiments showed that an Nlfmd2 isoform, NlFMD2340, bound the RAAGAA repeat motif in the Nldsx pre-mRNA and formed a protein complex with NlFMD-F to modulate Nldsx splicing, suggesting that NlFMD2 may function as an RNA binding partner of the feminizing switch NlFMD. Our results provide novel insights into the diverse mechanisms of insect sex determination.

Intersex Plays a Role in Microbial Homeostasis in the Brown Planthopper.

Insects harbor a wide variety of symbiotic microorganisms that are capable of regulating host health and promoting host adaptation to their environment and food sources. However, there is little knowledge concerning the mechanisms that maintain the microbial community homeostasis within insects. In this study, we found that the intersex (ix) gene played an essential role in maintaining microbial homeostasis in the brown planthopper (BPH), Nilaparvata lugens. Injection of the double-strand RNA targeting N. lugens ix (Nlix) into the newly emerged females resulted in abnormal expansion of the copulatory bursa of BPH after mating. Further observation by transmission electron microscopy (TEM) revealed that the abnormally enlarged copulatory bursa resulting from dsNlix treatment was full of microorganisms, while in contrast, the copulatory bursa of dsGFP-treated individuals stored a large number of sperm accompanied by a few bacteria. Moreover, RNA-seq analysis showed that the gene responses to bacteria were remarkably enriched in differentially expressed genes (DEGs). In addition, 16s rRNA sequencing indicated that, compared with control samples, changes in the composition of microbes presented in dsNlix-treated copulatory bursa. Together, our results revealed the immune functions of the Nlix gene in maintaining microbial homeostasis and combating infection in BPH.

Diversity and infectivity of the RNA virome among different cryptic species of an agriculturally important insect vector: whitefly Bemisia tabaci.

A large number of insect-specific viruses (ISVs) have recently been discovered, mostly from hematophagous insect vectors because of their medical importance, but little attention has been paid to important plant virus vectors such as the whitefly Bemisia tabaci, which exists as a complex of cryptic species. Public SRA datasets of B. tabaci and newly generated transcriptomes of three Chinese populations are here comprehensively investigated to characterize the whitefly viromes of different cryptic species. Twenty novel ISVs were confidently identified, mostly associated with a particular cryptic species while different cryptic species harbored one or more core ISVs. Microinjection experiments showed that some ISVs might cross-infect between the two invasive whitefly cryptic species, Middle East Asia Minor 1 (MEAM1) and Mediterranean (MED), but others appeared to have a more restricted host range, reflecting the possibility of distinct long-term coevolution of these ISVs and whitefly hosts. Moreover, analysis of the profiles of virus-derived small-interfering RNAs indicated that some of the ISVs can successfully replicate in whitefly and the antiviral RNAi pathway of B. tabaci is actively involved in response to ISV infections. Our study provides a comprehensive analysis of the RNA virome, the distinct relationships and cross-cryptic species infectivity of ISVs in an agriculturally important insect vector.

Pleiotropic Roles of the Orthologue of the Drosophila melanogaster Intersex Gene in the Brown Planthopper.

Intersex(ix), a gene involved in the sex-determining cascade of Drosophila melanogaster, works in concert with the female-specific product of doublesex (dsx) at the end of the hierarchy to implement the sex-specific differentiation of sexually dimorphic characters in female individuals. In this study, the ix homolog was identified in the brown planthopper (BPH), Nilaparvata lugens, which contained two splice variants expressed in both female and male insects. We found that Nlix played a vital role in the early nymphal development of BPH, showing an accumulated effect. RNAi-mediated knockdown of Nlix at 4th instar led to the external genital defects in both sexes, consequently resulting in the loss of reproductive ability in female and male individuals. After dsRNA injection, the males were normal on testes, while the females had defective ovarian development. Nlix was also required for early embryogenesis. Notably, when the dsNlix microinjection was performed in newly emerged females, the copulatory bursas were abnormally enlarged while the other tissues of the reproductive system developed normally. Our results demonstrated the pleiotropic roles of Nlix in embryogenesis and development of the reproductive system in a hemimetabolous insect species.

Chromosome-level assembly of the brown planthopper genome with a characterized Y chromosome.

Hundreds of insect genome sequences have been reported; however, most sequencing projects have not determined the sex chromosomes, and no Y chromosomes from a heterometabolous insect have been identified and characterized to date. The brown planthopper (Nilaparvata lugens Stål) is the most economically damaging pest to rice and is also an ideal research subject for paddy ecology and functional genomics. We previously assembled a draft female genome mainly using second-generation sequencing technologies, with a contig N50 of only 24 kb, due to the large size and excessive repetitive regions in the N. lugens genome. Here, we utilize third-generation sequencing technologies and Hi-C data to generate a high-quality male N. lugens assembly with a contig N50 of 1.01 Mb, a scaffold N50 of 69.96 Mb and more than 95.6% of the assembled bases located on 16 chromosomes. Fourteen autosomes and two sex chromosomes (X + Y) were identified, filling in the gap related to the Y chromosome in heterometabolous insects. A total of 18,021 protein-coding genes and 6423 long-noncoding RNAs were predicted with full-length cDNA sequencing data. All 315 of the Y chromosome genes (Y-genes) were derived from autosomal and X-chromosome duplications. Large-scale RNA interference (RNAi) experiments were conducted against the N. lugens Y-genes, demonstrating that 7 Y-genes were essential for normal BPH development or male organ development, suggesting the importance of Y-genes. The first identified Y chromosome in heterometabolous insects will help gain more insight into sex determination, fertility and chromosome evolution.

Discovery of Two Novel Negeviruses in a Dungfly Collected from the Arctic.

Negeviruses are a proposed group of insect-specific viruses that can be separated into two distinct phylogenetic clades, Nelorpivirus and Sandewavirus. Negeviruses are well-known for their wide geographic distribution and broad host range among hematophagous insects. In this study, the full genomes of two novel negeviruses from each of these clades were identified by RNA extraction and sequencing from a single dungfly (Scathophaga furcata) collected from the Arctic Yellow River Station, where these genomes are the first negeviruses from cold zone regions to be discovered. Nelorpivirus dungfly1 (NVD1) and Sandewavirus dungfly1 (SVD1) have the typical negevirus genome organization and there was a very high coverage of viral transcripts. Small interfering RNAs derived from both viruses were readily detected in S. furcata, clearly showing that negeviruses are targeted by the host antiviral RNA interference (RNAi) pathway. These results and subsequent in silico analysis (studies) of public database and published virome data showed that the hosts of nege-like viruses include insects belonging to many orders as well as various non-insects in addition to the hematophagous insects previously reported. Phylogenetic analysis reveals at least three further groups of negeviruses, as well as several poorly resolved solitary branches, filling in the gaps within the two sub-groups of negeviruses and plant-associated viruses in the Kitaviridae. The results of this study will contribute to a better understanding of the geographic distribution, host range, evolution and host antiviral immune responses of negeviruses.

Activation of Toll Immune Pathway in an Insect Vector Induced by a Plant Virus.

The Toll pathway plays an important role in defense against infection of various pathogenic microorganisms, including viruses. However, current understanding of Toll pathway was mainly restricted in mammal and some model insects such as Drosophila and mosquitoes. Whether plant viruses can also activate the Toll signaling pathway in vector insects is still unknown. In this study, using rice stripe virus (RSV) and its insect vector (small brown planthopper, Laodelphax striatellus) as a model, we found that the Toll pathway was activated upon RSV infection. In comparison of viruliferous and non-viruliferous planthoppers, we found that four Toll pathway core genes (Toll, Tube, MyD88, and Dorsal) were upregulated in viruliferous planthoppers. When the planthoppers infected with RSV, the expressions of Toll and MyD88 were rapidly upregulated at the early stage (1 and 3 days post-infection), whereas Dorsal was upregulated at the late stage (9 days post-infection). Furthermore, induction of Toll pathway was initiated by interaction between a Toll receptor and RSV nucleocapsid protein (NP). Knockdown of Toll increased the proliferation of RSV in vector insect, and the dsToll-treated insects exhibited higher mortality than that of dsGFP-treated ones. Our results provide the first evidence that the Toll signaling pathway of an insect vector is potentially activated through the direct interaction between Toll receptor and a protein encoded by a plant virus, indicating that Toll immune pathway is an important strategy against plant virus infection in an insect vector.

Identification and functional analysis of the doublesex gene in the sexual development of a hemimetabolous insect, the brown planthopper.

In the sex determination cascade, the genes dsx (doublesex) in insects, mab-3 (male abnormal 3) in nematodes, and Dmrt1 (dsx/mab-3 related transcription factor-1) in vertebrates act as the base molecular switches and play important roles. Moreover, these genes share the same conserved feature domain-DNA-binding oligomerization domain (OD1), and female-specific dsx also has a conserved oligomerization domain 2 (OD2). Although sex determination and the functions of dsx in several holometabolous insects have been well documented, sex determination and the function of dsx in hemimetabolous insects remain a mystery. In this study, four dsx homologs were unexpectedly found in the Nilaparvata lugens (brown planthopper, BPH, order Hemiptera), which also showed a different evolutionary status. We found that only one of the four homologs, Nldsx, which has three alternative splicing variants (female-specific NldsxF, male-specific NldsxM, non-sex-specific NldsxC), was required in the sexual development of N. lugens. Compared with that of holometabolous species, the dsx of N. lugens contains a less conserved OD1, while the OD2 domain of BPH was not identifiable because the common region is poorly conserved, and the female-specific region is short. RNAi-mediated knockdown of Nldsx in female BPH resulted in a larger body size with a normal abdomen and reproductive system, while no changes in fertility were noted. However, adult males with RNA interference knockdown of NldsxM in nymphs became pseudofemales, were infertile, had abnormal copulatory organs, and had impassable deferent ducts with hyperplastic walls; additionally, the pseudofemales could not produce the normal courtship signals. Our results suggest that dsx plays a critical role in male BPH somatic development and mating behavior. This is the first study to show that dsx is essential for sexual development in a hemipteran species.

Characterization of NlHox3, an essential gene for embryonic development in Nilaparvata lugens.

Hox genes encode transcriptional regulatory proteins that control axial patterning in all bilaterians. The brown planthopper (BPH), Nilaparvata lugens (Hemiptera: Delphacidae), is a destructive insect pest of rice plants in Asian countries. During analysis of the N. lugens transcriptome, we identified a Hox3-like gene (NlHox3) that was highly and specifically expressed in the embryonic stage. We performed functional analysis on the gene to identify its roles in embryonic development and its potential use as a target in RNA interference (RNAi) based pest control. The sequence analysis showed that NlHox3 was homologous to the Hox3 gene and was most closely related with zen of Drosophila. There were no significant differences in oviposition between the treated and control females after injecting double-stranded RNA of NlHox3 (dsNlHox3) into newly emerged female adult BPHs; however, there was a significant difference in the hatchability of those eggs laid, which no egg from the treated group hatched normally. Injecting female adult BPHs with dsNlHox3 led to necrosis of these offspring embryos, with eye reversal and undeveloped organs, suggesting that NlHox3 was an essential gene for embryonic development and might be a potential target for RNAi-based control of this insect pest.

Tra-2 Mediates Cross-Talk Between Sex Determination and Wing Polyphenism in Female Nilaparvata lugens.

Sexual dimorphism and wing polyphenism are important and evolutionarily conserved features of many insect species. In this article, we found a cross-talk linking sexual differentiation with wing polyphenism in the brown planthopper (BPH) Nilaparvata lugens (order: Hemiptera). Knockdown of the sex determination gene Transformer-2 in N. lugens (NlTra-2) in nymph caused females to develop into infertile pseudomales containing undeveloped ovaries. Whereas males treated with dsNlTra-2 exhibited normal morphology, but lost fertility. Knockdown of NlTra-2 in adult females (maternal RNAi) resulted in long-winged female offspring, indicating that maternal RNAi changed the wing morphs in female offspring. In addition, silencing of NlTra-2 down-regulated the expression of the forkhead transcription factor FoxO (NlFoxO), and simultaneously up-regulated the expression of phosphatidylinositol-3-OH kinase (PI(3)K)-protein kinase B (NlAkt), the two critical genes in the insulin signaling pathway. Furthermore, the long-winged effect caused by maternal dsNlTra-2 RNAi could be reversed by silencing of NlInR1 and NlAkt, leading to short-winged morphs. We propose that there is a cross-talk between the sexual differentiation and wing polyphenism pathways mediated by NlTra-2 during embryonic stages.

Comparative analysis of the transcriptional responses to low and high temperatures in three rice planthopper species.

The brown planthopper (Nilaparvata lugens, BPH), white-backed planthopper (Sogatella furcifera, WBPH) and small brown planthopper (Laodelphax striatellus, SBPH) are important rice pests in Asia. These three species differ in thermal tolerance and exhibit quite different migration and overwintering strategies. To understand the underlying mechanisms, we sequenced and compared the transcriptome of the three species under different temperature treatments. We found that metabolism-, exoskeleton- and chemosensory-related genes were modulated. In high temperature (37 °C), heat shock protein (HSP) genes were the most co-regulated; other genes related with fatty acid metabolism, amino acid metabolism and transportation were also differentially expressed. In low temperature (5 °C), the differences in gene expression of the genes for fatty acid synthesis, transport proteins and cytochrome P450 might explain why SBPH can overwinter in high latitudes, while BPH and WBPH cannot. In addition, other genes related with moulting, and membrane lipid composition might also play roles in resistance to low and high temperatures. Our study illustrates the common responses and different tolerance mechanisms of three rice planthoppers in coping with temperature change, and provides a potential strategy for pest management.

Effect of RNAi-mediated knockdown of NlTOR gene on fertility of male Nilaparvata lugens.

The target gene of rapamycin (TOR) is conserved from invertebrates to vertebrates, and plays critical roles in cell growth, nutrient sensing, lifespan and reproduction. In this paper, we employed RNA interference (RNAi) to study the function of TOR in male brown planthoppers (BPH), Nilaparvata lugens. Here we discovered that no offspring was produced when wildtype females BPH mated with NlTOR RNAi males. To understand the influence of NlTOR on male BPH infertility, we dissected the reproductive system of a NlTOR RNAi male, and found that the testes were normal and the seminal vesicles were full of sperm, while the accessory gland was poorly developed after knocking down NlTOR expression. Furthermore, transmission electron microscopy data showed defective structure of epithelial cells of the accessory gland, and the deferent duct was collapsed. Also, behavioral data revealed that wildtype virgin females refused to mate with NlTOR RNAi males, and the acoustic signals of dsNlTOR males differed from controls. Our results indicate that NlTOR plays an essential role in the development of the male BPH reproductive system and regulates mating behavior.

Screening and Functional Analyses of Nilaparvata lugens Salivary Proteome.

Most phloem-feeding insects secrete gelling and watery saliva during the feeding process. However, the functions of salivary proteins are poorly understood. In this study, our purpose was to reveal the components and functions of saliva in a rice sap-sucking insect pest, Nilaparvata lugens. The accomplishment of the whole genome and transcriptome sequencing in N. lugens would be helpful for elucidating the gene information and expression specificity of the salivary proteins. In this study, we have, for the first time, identified the abundant protein components from gelling and watery saliva in a monophagous sap-sucking insect species through shotgun proteomic detection combined with the genomic and transcriptomic analysis. Eight unknown secreted proteins were limited to N. lugens, indicating species-specific saliva components. A group of annexin-like proteins first identified in the secreted saliva displayed different domain structure and expression specificity with typical insect annexins. Nineteen genes encoding five annexin-like proteins, six salivaps (salivary glands-specific proteins with unknown function), seven putative enzymes, and a mucin-like protein showed salivary gland-specific expression pattern, suggesting their importance in the physiological mechanisms of salivary gland and saliva in this insect species. RNA interference revealed that salivap-3 is a key protein factor in forming the salivary sheath, while annexin-like5 and carbonic anhydrase are indispensable for N. lugens survival. These novel findings will greatly help to clarify the detailed functions of salivary proteins in the physiological process of N. lugens and elucidate the interaction mechanisms between N. lugens and the rice plant, which could provide important targets for the future management of rice pests.