Genome sequence of the small brown planthopper, Laodelphax striatellus

Chromosomal-level genomes of three rice planthoppers provide new insights into sex chromosome evolution

The brown planthopper Nilaparvata lugens, white-backed planthopper Sogatella furcifera, and small brown planthopper Laodelphax striatellus are three major insect pests of rice. They are genetically close; however, they differ in several ecological traits such as host range, migration capacity, and in their sex chromosomes. Though the draft genome of these three planthoppers have been previously released, the quality of genome assemblies need to be improved. The absence of chromosome-level genome resources has hindered in-depth research of these three species. Here, we performed a de novo genome assembly for N. lugens to increase its genome assembly quality with PacBio and Illumina platforms, increasing the contig N50 to 589.46 Kb. Then, with the new N. lugens genome and previously reported S. furcifera and L. striatellus genome assemblies, we generated chromosome-level scaffold assemblies of these three planthopper species using HiC scaffolding technique. The scaffold N50s significantly increased to 77.63 Mb, 43.36 Mb and 29.24 Mb for N. lugens, S. furcifera and L. striatellus, respectively. To identify sex chromosomes of these three planthopper species, we carried out genome re-sequencing of males and females and successfully determined the X and Y chromosomes for N. lugens, and X chromosome for S. furcifera and L. striatellus. The gene content of the sex chromosomes showed high diversity among these three planthoppers suggesting the rapid evolution of sex-linked genes, and all chromosomes showed high synteny. The chromosome-level genome assemblies of three planthoppers would provide a valuable resource for a broad range of future research in molecular ecology, and subsequently benefits development of modern pest control strategies.

Transcriptome and gene expression analysis of Rhynchophorus ferrugineus (Coleoptera: Curculionidae) during developmental stages

Background

Red palm weevil, Rhynchophorus ferrugineus Olivier, is one of the most destructive pests harming palm trees. However, genomic resources for R. ferrugineus are still lacking, limiting the ability to discover molecular and genetic means of pest control.

Methods

In this study, PacBio Iso-Seq and Illumina RNA-seq were used to generate transcriptome from three developmental stages of R. ferrugineus (pupa, 7th-instar larva, adult) to increase the understanding of the life cycle and molecular characteristics of the pest.

Results

Sequencing generated 625,983,256 clean reads, from which 63,801 full-length transcripts were assembled with N50 of 3,547 bp. Expression analyses revealed 8,583 differentially expressed genes (DEGs). Moreover, gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis revealed that these DEGs were mainly related to the peroxisome pathway which associated with metabolic pathways, material transportation and organ tissue formation. In summary, this work provides a valuable basis for further research on the growth and development, gene expression and gene prediction, and pest control of R. ferrugineus.

Apolygus lucorum genome provides insights into omnivorousness and mesophyll feeding

Apolygus lucorum (Miridae) is an omnivorous pest that occurs worldwide and is notorious for the serious damage it causes to various crops and substantial economic losses. Although some studies have examined the biological characteristics of the mirid bug, no reference genome is available in Miridae, limiting in-depth studies of this pest. Here, we present a chromosome-scale reference genome of A. lucorum, the first sequenced Miridae species. The assembled genome size was 1.02 Gb with a contig N50 of 785 kb. With Hi-C scaffolding, 1,016 Mb contig sequences were clustered, ordered and assembled into 17 large scaffolds with scaffold N50 length 68 Mb, each corresponding to a natural chromosome. Numerous transposable elements occur in this genome and contribute to the large genome size. Expansions of genes associated with omnivorousness and mesophyll feeding such as those related to digestion, chemosensory perception, and detoxification were observed in A. lucorum, suggesting that gene expansion contributed to its strong environmental adaptability and severe harm to crops. We clarified that a salivary enzyme polygalacturonase is unique in mirid bugs and has significantly expanded in A. lucorum, which may contribute to leaf damage from this pest. The reference genome of A. lucorum not only facilitates biological studies of Hemiptera as well as an understanding of the damage mechanism of mesophyll feeding, but also provides a basis on which to develop efficient control technologies for mirid bugs.

Genome-wide characterization and developmental expression profiling of long non-coding RNAs in Sogatella furcifera

The genome-wide characterization of long non-coding RNA (lncRNA) in insects demonstrates their importance in fundamental biological processes. Essentially, an in-depth understanding of the functional repertoire of lncRNA in insects is pivotal to insect resources utilization and sustainable pest control. Using a custom bioinformatics pipeline, we identified 1861 lncRNAs encoded by 1852 loci in the Sogatella furcifera genome. We profiled lncRNA expression in different developmental stages and observed that the expression of lncRNAs is more highly temporally restricted compared to protein-coding genes. More up-regulated Sogatella furcifera lncRNA expressed in the embryo, 4th and 5th instars, suggesting that increased lncRNA levels may play a role in these developmental stages. We compared the relationship between the expression of Sogatella furcifera lncRNA and its nearest protein gene and found that lncRNAs were more correlated to their downstream coding neighbors on the opposite strand. Our genome-wide profiling of lncRNAs in Sogatella furcifera identifies exciting candidates for characterization of lncRNAs, and also provides information on lncRNA regulation during insect development.

Ubiquitin-Conjugating Enzyme E2 E Inhibits the Accumulation of Rice Stripe Virus in Laodelphax striatellus (Fallén)

The ubiquitin-proteasome system (UPS) is an essential protagonist in host-pathogen interactions. Among the three classes of enzymes in the UPS, ubiquitin-conjugating enzyme E2 plays a dual role in viral pathogenesis; however, the role of insect E2s in interactions with plant viruses is unclear. Twenty E2-encoding genes in Laodelphax striatellus, the small brown planthopper, were identified and classified into 17 groups by transcriptomic and phylogenetic analysis. Full-length cDNAs of four LstrE2s (LstrE2 A/E/G2/H) were obtained by rapid-amplification of cDNA ends (RACE-PCR) analysis. Expression of the four LstrE2s showed tissue- and development-specific patterns. RT-qPCR analyses revealed that Rice stripe viruse (RSV) infection increased the level of LstrE2 A/E/G2/H. Further study indicated that repression of LstrE2 E via RNAi caused significant increases in the expression of RSV coat protein mRNA and protein levels. These findings suggest that LstrE2 E inhibits RSV accumulation in the planthopper body. Understanding the function of LstrE2 E in RSV accumulation may ultimately result in the development of novel antiviral strategies.

A Plant Virus Ensures Viral Stability in the Hemolymph of Vector Insects through Suppressing Prophenoloxidase Activation

Large ratios of vector-borne plant viruses circulate in the hemolymph of their vector insects before entering the salivary glands to be transmitted to plants. The stability of virions in the hemolymph is vital in this process. Activation of the proteolytic prophenoloxidase (PPO) to produce active phenoloxidase (PO) is one of the major innate immune pathways in insect hemolymph. How a plant virus copes with the PPO immune reaction in its vector insect remains unclear. Here, we report that the PPO affects the stability of rice stripe virus (RSV), a notorious rice virus, in the hemolymph of a vector insect, the small brown planthopper. RSV suppresses PPO activation using viral nonstructural protein. Once the level of PO activity is elevated, RSV is melanized and eliminated from the hemolymph. Our work gives valuable clues for developing novel strategies for controlling the transmission of vector-borne plant viruses.

Most plant viruses require vector insects for transmission. Viral stability in the hemolymph of vector insects is a prerequisite for successful transmission of persistent plant viruses. However, knowledge of whether the proteolytic activation of prophenoloxidase (PPO) affects the stability of persistent plant viruses remains elusive. Here, we explored the interplay between rice stripe virus (RSV) and the PPO cascade of the vector small brown planthopper. Phenoloxidase (PO) activity was suppressed by RSV by approximately 60%. When the PPO cascade was activated, we found distinct melanization around RSV particles and serious damage to viral stability in the hemolymph. Viral suppression of PO activity was derived from obstruction of proteolytic cleavage of PPOs by binding of the viral nonstructural protein NS3. These results indicate that RSV attenuates the PPO response to ensure viral stability in the hemolymph of vector insects. Our research provides enlightening cues for controlling the transmission of vector-borne viruses.

Comparative analysis of diet-associated responses in two rice planthopper species

Background

Host adaptation is the primary determinant of insect diversification. However, knowledge of different host ranges in closely related species remains scarce. The brown planthopper (Nilaparvata lugens, BPH) and the small brown planthopper (Laodelphax striatellus, SBPH) are the most destructive insect pests within the family Delphacidae. These two species differ in their host range (SBPH can well colonize rice and wheat plants, whereas BPH survives on only rice plants), but the underlying mechanism of this difference remains unknown. High-throughput sequencing provides a powerful approach for analyzing the association between changes in gene expression and the physiological responses of insects. Therefore, gut transcriptomes were performed to elucidate the genes associated with host adaptation in planthoppers. The comparative analysis of planthopper responses to different diets will improve our knowledge of host adaptation regarding herbivorous insects.

Results

In the present study, we analyzed the change in gene expression of SBPHs that were transferred from rice plants to wheat plants over the short term (rSBPH vs tSBPH) or were colonized on wheat plants over the long term (rSBPH vs wSBPH). The results showed that the majority of differentially expressed genes in SBPH showed similar changes in expression for short-term transfer and long-term colonization. Based on a comparative analysis of BPH and SBPH after transfer, the genes associated with sugar transporters and heat-shock proteins showed similar variation. However, most of the genes were differentially regulated between the two species. The detoxification-related genes were upregulated in SBPH after transfer from the rice plants to the wheat plants, but these genes were downregulated in BPH under the same conditions. In contrast, ribosomal-related genes were downregulated in SBPH after transfer, but these genes were upregulated in BPH under the same conditions.

Conclusions

The results of this study provide evidence that host plants played a dominant role in shaping gene expression and that the low fitness of BPH on wheat plants might be determined within 24 h after transfer. This study deepens our understanding of different host ranges for the two planthopper species, which may provide a potential strategy for pest management.

Ento(o)mics: the intersection of 'omic' approaches to decipher plant defense against sap-sucking insect pests

Plants are constantly challenged by insect pests that can dramatically decrease yields. Insects with piercing-sucking mouthparts, for example, aphids, whiteflies, and leaf hoppers, seemingly cause less physical damage to tissues, however, they feed on the plant's sap by piercing plant tissue and extracting plant fluids, thereby transmitting several plant-pathogenic viruses as well. As a counter-defense, plants activate an array of dynamic defense machineries against insect pests including the rapid reprogramming of the host cell processes. For a holistic understanding of plant-sap-sucking insect interactions, there is a need to call for techniques with the capacity to concomitantly capture these dynamic changes. Recent progress with various 'omic' technologies possess this capacity. In this review, we will provide a concise summary of application of 'omic' technologies and their utilization in plant and sap-sucking insect interaction studies. Finally, we will provide a perspective on the integration of 'omics' data in uncovering novel plant defense mechanisms against sap-sucking insect pests.

Recent infection by Wolbachia alters microbial communities in wild Laodelphax striatellus populations

BACKGROUND

Host-associated microbial communities play an important role in the fitness of insect hosts. However, the factors shaping microbial communities in wild populations, including genetic background, ecological factors, and interactions among microbial species, remain largely unknown.

RESULTS

Here, we surveyed microbial communities of the small brown planthopper (SBPH, Laodelphax striatellus) across 17 geographical populations in China and Japan by using 16S rRNA amplicon sequencing. Using structural equation models (SEM) and Mantel analyses, we show that variation in microbial community structure is likely associated with longitude, annual mean precipitation (Bio12), and mitochondrial DNA variation. However, a Wolbachia infection, which is spreading to northern populations of SBPH, seems to have a relatively greater role than abiotic factors in shaping microbial community structure, leading to sharp decreases in bacterial taxon diversity and abundance in host-associated microbial communities. Comparative RNA-Seq analyses between Wolbachia-infected and -uninfected strains indicate that the Wolbachia do not seem to alter the immune reaction of SBPH, although Wolbachia affected expression of metabolism genes.

CONCLUSION

Together, our results identify potential factors and interactions among different microbial species in the microbial communities of SBPH, which can have effects on insect physiology, ecology, and evolution. Video Abstract.

SMRT sequencing of the full-length transcriptome of the Rhynchophorus ferrugineus (Coleoptera: Curculionidae)

Background

Red palm weevil Rhynchophorus ferrugineus (Coleoptera: Curculionidae) is one of the most destructive insects for palm trees in the world. However, its genome resources are still in the blank stage, which limits the study of molecular and growth development analysis.

Methods

In this study, we used PacBio Iso-Seq and Illumina RNA-seq to first generate transcriptome from three developmental stages of R. ferrugineus (pupa, 7th larva, female and male) to increase our understanding of the life cycle and molecular characteristics of R. ferrugineus.

Results

A total of 63,801 nonredundant full-length transcripts were generated with an average length of 2,964 bp from three developmental stages, including the 7th instar larva, pupa, female adult and male adult. These transcripts showed a high annotation rate in seven public databases, with 54,999 (86.20%) successfully annotated. Meanwhile, 2,184 alternative splicing (AS) events, 2,084 transcription factors (TFs), 66,230 simple sequence repeats (SSR) and 9,618 Long noncoding RNAs (lncRNAs) were identified. In summary, our results provide a new source of full-length transcriptional data and information for the further study of gene expression and genetics in R. ferrugineus.

A structural variation reference for medical and population genetics

Structural variants (SVs) rearrange large segments of DNA¹ and can have profound consequences in evolution and human disease^2,3. As national biobanks, disease-association studies, and clinical genetic testing have grown increasingly reliant on genome sequencing, population references such as the Genome Aggregation Database (gnomAD)⁴ have become integral in the interpretation of single-nucleotide variants (SNVs)⁵. However, there are no reference maps of SVs from high-coverage genome sequencing comparable to those for SNVs. Here we present a reference of sequence-resolved SVs constructed from 14,891 genomes across diverse global populations (54% non-European) in gnomAD. We discovered a rich and complex landscape of 433,371 SVs, from which we estimate that SVs are responsible for 25–29% of all rare protein-truncating events per genome. We found strong correlations between natural selection against damaging SNVs and rare SVs that disrupt or duplicate protein-coding sequence, which suggests that genes that are highly intolerant to loss-of-function are also sensitive to increased dosage⁶. We also uncovered modest selection against noncoding SVs in cis-regulatory elements, although selection against protein-truncating SVs was stronger than all noncoding effects. Finally, we identified very large (over one megabase), rare SVs in 3.9% of samples, and estimate that 0.13% of individuals may carry an SV that meets the existing criteria for clinically important incidental findings⁷. This SV resource is freely distributed via the gnomAD browser⁸ and will have broad utility in population genetics, disease-association studies, and diagnostic screening.

A large empirical assessment of sequence-resolved structural variants from 14,891 genomes across diverse global populations in the Genome Aggregation Database (gnomAD) provides a reference map for disease-association studies, population genetics, and diagnostic screening.

Triazophos-induced vertical transmission of rice stripe virus is associated with host vitellogenin in the small brown planthopper Laodelphax striatellus

BACKGROUND

Rice stripe virus (RSV) is one of the most serious rice diseases in East Asia. The small brown planthopper (SBPH), Laodelphax striatellus, is an economically important rice pest. SBPH transmits RSV horizontally and vertically, resulting in serious rice economic losses. Exposure to sublethal doses of insecticides can induce many physiological and cellular changes in insects. However, the mechanism underlying triazophos-induced RSV vertical transmission remains unclear. Here, we investigated the role of vitellogenin (Vg) in triazophos-induced RSV vertical transmission.

RESULTS

RSV vertical transmission rates were significantly induced by sublethal exposure to triazophos. The transcript abundance of viral RNA3 segment (RNA3) and capsid protein (CP) in the ovaries of SBPH were also significantly increased. Triazophos induced the expression level of Vg in L. striatellus (LsVg) and increased the contents of ovarian protein and fat body protein. Knockdown of Vg significantly reduced the expression levels of LsVg and Vg receptor (LsVgR), and decreased RSV accumulations in the ovaries. Double-stranded Vg (dsVg)-mediated down-regulation could be rescued by exposure to triazophos. Vertical transmission rate of the dsVg-injected group was significantly decreased compared with the dsGFP-injected group, and triazophos significantly rescued the RSV vertical transmission rate of the dsVg-injected group.

CONCLUSION

Our results indicate that triazophos-induced RSV vertical transmission is associated with Vg. This work will help us to further elucidate sublethal doses of insecticides-mediated effects and develop new strategies for pest control. © 2019 Society of Chemical Industry.

Rice stripe virus hitchhikes the vector insect vitellogenin ligand-receptor pathway for ovary entry

It is known that plant arboviruses infect insect vector cells by endocytosis; however, the cellular receptors that mediate endocytosis have not been well defined. In our recently published work and this study, by clarifying the vertical transmission mechanism of Rice stripe virus (RSV) in Laodelphax striatellus, we provide a novel paradigm for how arboviruses enter insect germ-line cells. Instead of direct interaction with a viral receptor, the virus binds to a secreted ligand protein, hitchhiking the ligand-receptor pathway to achieve cell entry. Vitellogenin (Vg) is an indispensable protein for embryo development that is synthesized extra-ovarially and taken up by germ-line cells through Vg receptor (VgR)-mediated endocytosis. After revealing that RSV invades L. striatellus ovary by a specific molecular interaction with the insect Vg in haemolymph, this study addressed VgR's function in mediating the RSV invasion of the germarium nurse cells, further confirming the ligand's receptor-mediated viral cell-invasion mechanism. Understanding the viral ovary-entry pathways in vectors will help to find suitable measures to block the trans-generation transmission of the viruses. This article is part of the theme issue 'Biotic signalling sheds light on smart pest management'.

High Diversity and Functional Complementation of Alimentary Canal Microbiota Ensure Small Brown Planthopper to Adapt Different Biogeographic Environments

Almost all insects harbor commensal bacteria in the alimentary canal lumen or within cells and often play a pivotal role in their host’s development, evolution, and environmental adaptation. However, little is known about the alimentary canal microbiota and their functions in sap-sucking insect pests of crops, which can damage plants by removing plant sap and by transmitting various plant viruses, especially in the small brown planthopper, Laodelphax striatellus. In this study, we characterized the alimentary canal microbiota of L. striatellus collected from seven regions in China by sequencing 16S rDNA. The insects harbored a rich diversity of microbes, mainly consisted of bacteria from phyla Proteobacteria, Actinobacteria, Firmicutes, Bacteroidetes, and Tenericutes. The composition and abundance of microbiota were more similar as the geographic distance decreased between the populations and clustered by geographic location into three groups: temperate, subtropical, and tropical populations. Although the abundance and species of microbes differed among the populations, the various major microbes for each population performed similar functions based on a clusters of orthologous group analysis. Greater diversity in ecological factors in different regions might lead to higher microbial diversity, thus enabling L. striatellus to adapt or tolerate various extreme environments to avoid the cost of long-distance migration. Moreover, the abundance of various metabolic functions in the Kaifeng populations might contribute to higher fecundity in L. striatellus.

Identification and comparative expression profiles of chemosensory genes in major chemoreception organs of a notorious pests, Laodelphax striatellus

The small brown planthopper, Laodelphax striatellus (Stål) (SBPH), is a notorious rice pest in East Asia and damages the host by feeding on the phloem and transmitting virus particles. Although SBPH relies on chemosensory perception for seeking the host, courtship, selecting oviposition sites and spreading virus particles, a systematic study of chemosensory genes in SBPH is lacking. In this study, we identified multi-gene chemosensory families from the transcriptome of SBPH olfactory organs and analyzed their expression patterns in male and female tissues. Among the chemosensory genes, 14 odorant-binding proteins (OBPs), 12 chemosensory proteins (CSPs), 7 sensory neuron membrane proteins (SNMPs) and 95 odorant receptors (ORs) were identified and annotated in SBPH olfactory organs. Based on expression profile and phylogenetic analysis, LstrOBP1, 2, 5, 6, 7, 10, LstrSNMP1, and most LstrORs showed an antennae-enriched expression pattern, which suggests an olfactory role for these genes. Relative expression of LstrOBPs was validated by quantitative real-time PCR. Our findings provide the genetic information for disrupting the feeding behavior of SBPH, which is essential for developing eco-friendly pest management technologies.

Genome-wide identification of chemosensory receptor genes in the small brown planthopper, Laodelphax striatellus

The small brown planthopper (SBPH), Laodelphax striatellus is one of the major insect pests of rice, but little is known about the molecular-level means by which it locates its hosts. SBPH host-seeking behavior heavily relies on chemosensory receptors (CRs). In this study, we utilized genome analysis of the SBPH to identify 169 CRs, including: 133 odorant receptors (ORs), 13 gustatory receptors (GRs) and 23 ionotropic receptors (IRs). The phylogenetic relationships of OR genes from three rice planthoppers and other insect species revealed that the odorant co-receptor (Orco) clade is the most conserved group. Among the candidate GRs, two sugar receptors and five fructose receptors have been identified but no carbon dioxide receptors investigated. Furthermore, we identified homologs of the three highly conserved IR co-receptors. The obtained results will provide us with precious information needed to better understand the interaction between insect pests and crop plants required for effective crop protection.

Salivary DNase II from Laodelphax striatellus acts as an effector that suppresses plant defence

Extracellular DNA, released by damaged plant cells, acts as a damage-associated molecular pattern (DAMP). We demonstrated previously that the small brown planthopper (Laodelphax striatellus, SBPH) secreted DNase II when feeding on artificial diets. However, the function of DNase II in insect feeding remained elusive. The influences of DNase II on SBPHs and rice plants were investigated by suppressing expression of DNase II or by application of heterogeneously expressed DNase II. We demonstrated that DNase II is mainly expressed in the salivary gland and is responsible for DNA-degrading activity of saliva. Knocking down the expression of DNase II resulted in decreased performance of SBPH reared on rice plants. The dsDNase II-treated SBPH did not influenced jasmonic acid (JA), salicylic acid (SA), ethylene (ET) pathways, but elicited a higher level of H2 O2 and callose accumulation. Application of heterogeneously expressed DNase II in DNase II-deficient saliva slightly reduced the wound-induced defence response. We propose a DNase II-based invading model for SBPH feeding on host plants, and provide a potential target for pest management.

Proteomic analysis of Laodelphax striatellus gonads reveals proteins that may manipulate host reproduction by Wolbachia

Wolbachia are intracellular bacteria that manipulate host reproduction by several mechanisms including cytoplasmic incompatibility (CI). However, the underlying mechanisms of Wolbachia-induced CI are not entirely clear. Here, we monitored the Wolbachia distribution in the male gonads of the small brown planthopper (Laodelphax striatellus, SBPH) at different development stages, and investigated the influence of Wolbachia on male gonads by a quantitative proteomic analysis. A total of 276 differentially expressed proteins were identified, with the majority of them participating in metabolism, modification, and reproduction. Knocking down the expression of outer dense fiber protein (ODFP) and venom allergen 5-like (VA5L) showed decreased egg reproduction, and these two genes might be responsible for Wolbachia improved fecundity in infected L. striatellus; whereas knocking down the expression of cytosol amino-peptidase-like (CAL) significantly decreased the egg hatch rate in Wolbachia-uninfected L. striatellus, but not in the Wolbachia-infected one. Considering that the mRNA/protein level of CAL was downregulated by Wolbachia infection and dsCAL treatment closely mimicked Wolbachia-induced CI, we presumed that CAL might be one of the factors determining the CI phenotype.

A high-quality genome assembly from a single, field-collected spotted lanternfly (Lycorma delicatula) using the PacBio Sequel II system

BACKGROUND

A high-quality reference genome is an essential tool for applied and basic research on arthropods. Long-read sequencing technologies may be used to generate more complete and contiguous genome assemblies than alternate technologies; however, long-read methods have historically had greater input DNA requirements and higher costs than next-generation sequencing, which are barriers to their use on many samples. Here, we present a 2.3 Gb de novo genome assembly of a field-collected adult female spotted lanternfly (Lycorma delicatula) using a single Pacific Biosciences SMRT Cell. The spotted lanternfly is an invasive species recently discovered in the northeastern United States that threatens to damage economically important crop plants in the region.

RESULTS

The DNA from 1 individual was used to make 1 standard, size-selected library with an average DNA fragment size of ∼20 kb. The library was run on 1 Sequel II SMRT Cell 8M, generating a total of 132 Gb of long-read sequences, of which 82 Gb were from unique library molecules, representing ∼36× coverage of the genome. The assembly had high contiguity (contig N50 length = 1.5 Mb), completeness, and sequence level accuracy as estimated by conserved gene set analysis (96.8% of conserved genes both complete and without frame shift errors). Furthermore, it was possible to segregate more than half of the diploid genome into the 2 separate haplotypes. The assembly also recovered 2 microbial symbiont genomes known to be associated with L. delicatula, each microbial genome being assembled into a single contig.

CONCLUSIONS

We demonstrate that field-collected arthropods can be used for the rapid generation of high-quality genome assemblies, an attractive approach for projects on emerging invasive species, disease vectors, or conservation efforts of endangered species.

Genome-Wide Single Nucleotide Polymorphisms are Robust in Resolving Fine-Scale Population Genetic Structure of the Small Brown Planthopper, Laodelphax striatellus (Fallén) (Hemiptera: Delphacidae)

Deciphering genetic structure and inferring migration routes of insects with high migratory ability have been challenging, due to weak genetic differentiation and limited resolution offered by traditional genotyping methods. Here, we tested the ability of double digest restriction-site associated DNA sequencing (ddRADseq)-based single nucleotide polymorphisms (SNPs) in revealing the population structure relative to 13 microsatellite markers by using four small brown planthopper populations as subjects. Using ddRADseq, we identified 230,000 RAD loci and 5,535 SNP sites, which were present in at least 80% of individuals across the four populations with a minimum sequencing depth of 10. Our results show that this large SNP panel is more powerful than traditional microsatellite markers in revealing fine-scale population structure among the small brown planthopper populations. In contrast to the mixed population structure suggested by microsatellites, discriminant analysis of principal components (DAPC) of the SNP dataset clearly separated the individuals into four geographic populations. Our results also suggest the DAPC analysis is more powerful than the principal component analysis (PCA) in resolving population genetic structure of high migratory taxa, probably due to the advantages of DAPC in using more genetic variation and the discriminant analysis function. Together, these results point to ddRADseq being a promising approach for population genetic and migration studies of small brown planthopper.

Contribution to the mitogenome diversity in Delphacinae: Phylogenetic and ecological implications

We document the complete (or nearly complete) mitogenomes of 20 Delphacidae taxa, and together with 17 other delphacid mitogenomes currently in GenBank, to reconstruct the phylogeny of the Delphacinae and to investigate mitogenome differences among members of Delphacini, Tropidocephalini and Saccharosydnini. The mitogenomes of the 20 species encode the complete set of 37 genes usually found in animal mitogenomes. The length of complete mitogenomes in Delphacinae ranges from 15,531 to 16,231 bp. The gene order of all newly sequenced mitogenomes are identical, and the mitogenome gene order of Stenocranus matsumurai Metcalf in Stenocraninae has a transposition of tRNA^Thr. The two-clade system in Tropidocephalini was supported with high value (PP = 1, BS = 100), and the monophyly of Bambusiphaga was recovered in this study. Finally, we found that the host shift from plants with a C₃ to a C₄ photosynthetic pathway appears to have occurred independently in several clades.

The complete mitochondrial genome of Laodelphax striatellus (Fallén, 1826) (Hemiptera: Delphacidae) collected in a mid-Western part of Korean peninsula

Laodelphax striatellus (Fallén, 1826) is one of key rice pests in Northeast Asia. We have determined the mitochondrial genome of L. striatellus collected in a mid-western part of Korean peninsula. The circular mitogenome of L. striatellus is 16,359 bp long including 13 protein-coding genes, two ribosomal RNA genes, 22 transfer RNAs, and a single large non-coding region of 1,972 bp. The base composition was AT-biased (77.3%). In comparison of the two Chinese L. striatellus mitogenomes with Korean mitogenome, total 140 and 40 single nucleotide polymorphisms and 166 and 118 insertions and deletions were identified, presenting intra-species variations based on geographical distribution.

Evaluation of Rice stripe virus transmission efficiency by quantification of viral load in the saliva of insect vector

BACKGROUND

Persistent plant viruses transfer from insect gut to the hemolymph, and finally to the salivary glands before inoculation into the plant hosts with saliva during insect feeding. Virus accumulation in saliva is an important indicator for the transmission ability of an insect vector. In order to evaluate the transmission ability of the small brown planthopper to rice stripe virus (RSV), we successfully measured accumulation of RSV in the saliva of planthoppers via the absolute real-time quantitative polymerase chain reaction method by quantifying the copy numbers of viral genes.

RESULTS

After feeding on an artificial diet for 24 h, the copy numbers of viral genes of capsid protein (CP) and disease-specific protein (SP) can be detected in the saliva collected from as few as ten viruliferous planthoppers and ten non-viruliferous planthoppers after infected with RSV for 7 days. When the expression of planthopper G protein pathway suppressor 2 or c-Jun N-terminal kinase was knocked down, the copy numbers of CP and SP in the saliva varied accordingly.

CONCLUSION

Our study provided an accurate and convenient detection system to evaluate the transmission efficiency of RSV by small brown planthoppers, and this method may also be suitable for other persistent plant viruses. © 2019 Society of Chemical Industry.

Evolution and functional analysis of odorant-binding proteins in three rice planthoppers: Nilaparvata lugens, Sogatella furcifera, and Laodelphax striatellus

BACKGROUND

The white-backed planthopper (WBPH) Sogatella furcifera, the brown planthopper (BPH) Nilaparvata lugens, and the small brown planthopper (SBPH) Laodelphax striatellus are three notorious rice pests that cause annual losses in rice yield through sap-sucking and virus transmission. Odorant-binding proteins (OBPs) are crucial olfactory genes involved in host-seeking behavior.

RESULTS

We discovered the presence of 12, 12, and 16 OBPs in WBPH, BPH, and SBPH, respectively, including two novel OBPs in BPH and seven novel OBPs in SBPH. Phylogenetic analysis indicated that most of these OBPs have homologous genes, and one group (SfurOBP11, NlugOBP8, and LstrOBP2) show a slower evolution rate and are more conserved. Further, in vitro binding studies demonstrated that the three OBPs have similar binding affinities for some rice plant volatiles. Finally, RNA interference (RNAi) successfully inhibited the mRNA expression of the three OBPs, and in vivo behavioral tests showed that the OBP-deficient rice planthoppers were partly anosmic and lost some of their ability to locate rice plants.

CONCLUSION

These results demonstrate the crucial role of the rice planthopper OBP genes in seeking rice plants. This information complements the current genetic resources for the development of RNAi-based transgenic rice and other pest management technologies. © 2018 Society of Chemical Industry.

Immune function of an angiotensin-converting enzyme against Rice stripe virus infection in a vector insect

Angiotensin-converting enzyme (ACE) plays diverse roles in the animal kingdom. However, whether ACE plays an immune function against viral infection in vector insects is unclear. In this study, an ACE gene (LsACE) from the small brown planthopper was found to respond to Rice stripe virus (RSV) infection. The enzymatic activities of LsACE were characterized at different pH and temperature. Twenty planthopper proteins were found to interact with LsACE. RSV infection significantly upregulated LsACE expression in the testicle and fat body. When the expression of LsACE in viruliferous planthoppers was inhibited, the RNA level of the RSV SP gene was upregulated 2-fold in planthoppers, and all RSV genes showed higher RNA levels in the rice plants consumed by these planthoppers, leading to a higher viral infection rate and disease rating index. These results indicate that LsACE plays a role in the immune response against RSV transmission by planthoppers.

The vitellogenin receptor has an essential role in vertical transmission of rice stripe virus during oogenesis in the small brown plant hopper

BACKGROUND

The small brown plant hopper (SBPH), Laodelphax striatellus Fallén, is one of the most destructive pests on rice. This pest transmits rice stripe virus (RSV) both horizontally and vertically, leading to major yield and economic losses in rice production. However, the way that RSV particles enter oocytes of SBPH remains largely unknown. Thus, identification of key factors involved in the interaction between SBPH and RSV in the ovary is crucial.

RESULTS

Transcriptome of non-viruliferous (NV) or high viruliferous (HV) SBPH ovaries at 24 and 48 h of emergence was sequenced. Differentially expressed genes analysis showed that vitellogenin receptor was significantly highly expressed in the ovary of the HV SBPH strains compared to NV strains. Quantitative real-time polymer chain reaction showed that the vitellogenin receptor in L. striatellus (LsVgR) was highly expressed in the ovaries of female adults and maintained a high level of expression at the early stage of ovary development. By using RNA interference, the expression of LsVgR in the ovaries of the HV strain was significantly decreased by 98.1%. RSV titer was reduced by 60.9% as quantified by viral RNA3 intergenic region and the transcripts of nucleocapsid protein gene (CP) reduced by 46.3%. The numbers of offspring hatched were significantly reduced in dsRNA-treated groups. The transcripts of CP were not affected by silencing LsVgR, whereas the abundance of RNA-dependent RNA polymerase increased by 15-fold in the member of surviving progenies.

CONCLUSION

Our results suggest that vitellogenin receptor participates in regulating RSV replication during oogenesis. © 2018 Society of Chemical Industry.

Distinct replication and gene expression strategies of the Rice Stripe virus in vector insects and host plants

Persistent propagative plant viruses are usually transmitted between a vector insect and a host plant. To adapt to the two different organisms, viruses may show distinct genomic replication or gene expression patterns. To verify this hypothesis, we applied an aboslute real-time quantitative PCR method to measure and compare the replication levels of four genomic RNA segments and the expression levels of seven genes of rice stripe virus (RSV) according to the infection time in the small brown planthopper and rice plant, respectively. In the vector insect, RNA3 began replicating later than the other segments, and RNA2 remained nearly constant during the infection process. RNA1 was the dominant segment, and a difference of over 300-fold appeared among the four segments. In rice plants, the size of the four segments increased with infection time, but decreased to a low level in the late infection period. The ratios of the four segments varied by no more than 15-fold. In planthoppers, three expression patterns were observed for the seven viral genes during viral infection, while in rice plants, the expression patterns of the seven viral genes were similar. These results reflect distinct genomic replication and gene expression patterns in a persistent propagative plant virus in adapting to vector insects and host plants.

Horizontal Transfer of a Retrotransposon from the Rice Planthopper to the Genome of an Insect DNA Virus

This study provides an example of the horizontal transfer event from a rice planthopper genome to an IIV-6 genome. A small region of the IIV-6 genome (∼300 nt) is highly homologous to the sequences presented in high copy numbers of three rice planthopper genomes that are related to the SINEs, a class of retroposons. The expression of these planthopper SINE-like sequences was confirmed, and corresponding Piwi-interacting RNA-like small RNAs were identified and comprehensively characterized. Phylogenetic analysis suggests that the giant invertebrate iridovirus IIV-6 obtains this SINE-related sequence from Sogatella furcifera through a horizontal transfer event in the past. To the best of our knowledge, this is the first report of a horizontal transfer event between a planthopper and a giant DNA virus and also is the first evidence for the eukaryotic origin of genetic material in iridoviruses.

Horizontal transfer of genetic materials between virus and host has been frequently identified. Three rice planthoppers, Laodelphax striatellus, Nilaparvata lugens, and Sogatella furcifera, are agriculturally important insects because they are destructive rice pests and also the vector of a number of phytopathogenic viruses. In this study, we discovered that a small region (∼300 nucleotides [nt]) of the genome of invertebrate iridescent virus 6 (IIV-6; genus Iridovirus, family Iridoviridae), a giant DNA virus that infects invertebrates but is not known to infect planthoppers, is highly homologous to the sequences present in high copy numbers in these three planthopper genomes. These sequences are related to the short interspersed nuclear elements (SINEs), a class of non-long terminal repeat (LTR) retrotransposons (retroposons), suggesting a horizontal transfer event of a transposable element from the rice planthopper genome to the IIV-6 genome. In addition, a number of planthopper transcripts mapped to these rice planthopper SINE-like sequences (RPSlSs) were identified and appear to be transcriptionally regulated along the different developmental stages of planthoppers. Small RNAs derived from these RPSlSs are predominantly 26 to 28 nt long, which is a typical characteristic of PIWI-interacting RNAs. Phylogenetic analysis suggests that IIV-6 acquires a SINE-like retrotransposon from S. furcifera after the evolutionary divergence of the three rice planthoppers. This study provides further examples of the horizontal transfer of an insect transposon to virus and suggests the association of rice planthoppers with iridoviruses in the past or present.

IMPORTANCE This study provides an example of the horizontal transfer event from a rice planthopper genome to an IIV-6 genome. A small region of the IIV-6 genome (∼300 nt) is highly homologous to the sequences presented in high copy numbers of three rice planthopper genomes that are related to the SINEs, a class of retroposons. The expression of these planthopper SINE-like sequences was confirmed, and corresponding Piwi-interacting RNA-like small RNAs were identified and comprehensively characterized. Phylogenetic analysis suggests that the giant invertebrate iridovirus IIV-6 obtains this SINE-related sequence from Sogatella furcifera through a horizontal transfer event in the past. To the best of our knowledge, this is the first report of a horizontal transfer event between a planthopper and a giant DNA virus and also is the first evidence for the eukaryotic origin of genetic material in iridoviruses.

Transgenic microRNA-14 rice shows high resistance to rice stem borer

Rice stem borer (RSB, Chilo suppressalis) is an insect pest that causes huge economic losses every year. Control efforts rely heavily on chemical insecticides, which leads to serious problems such as insecticide resistance, environment pollution, and food safety issues. Therefore, developing alternative pest control methods is an important task. Here, we identified an insect-specific microRNA, miR-14, in RSB, which was predicted to target Spook (Spo) and Ecdysone receptor (EcR) in the ecdysone signalling network. In-vitro dual luciferase assays using HEK293T cells confirmed the interactions of Csu-miR-14 with CsSpo and with CsEcR. Csu-miR-14 exhibited high levels of expression at the end of each larval instar stage, and its expression was negatively correlated with the expression of its two target genes. Overexpression of Csu-miR-14 at the third day of the fifth instar stage led to high mortality and developmental defects in RSB individuals. We produced 35 rice transformants to express miR-14 and found that three lines had a single copy with highly abundant miR-14 mature transcripts. Feeding bioassays using both T0 and T1 generations of transgenic miR-14 rice indicated that at least one line (C#24) showed high resistance to RSB. These results indicated that the approach of miRNAs as targets has potential for improving pest control methods. Moreover, using insect-specific miRNAs rather than protein-encoding genes for pest control may prove benign to non-insect species, and thus is worthy of further exploration.

Immune responses induced by different genotypes of the disease-specific protein of Rice stripe virus in the vector insect

Persistent plant viruses circulate between host plants and vector insects, possibly leading to the genetic divergence in viral populations. We analyzed the single nucleotide polymorphisms (SNPs) of Rice stripe virus (RSV) when it incubated in the small brown planthopper and rice. Two SNPs, which lead to nonsynonymous substitutions in the disease-specific protein (SP) of RSV, produced three genotypes, i.e., GG, AA and GA. The GG type mainly existed in the early infection period of RSV in the planthoppers and was gradually substituted by the other two genotypes during viral transmission. The two SNPs did not affect the interactions of SP with rice PsbP or with RSV coat protein. The GG genotype of SP induced stronger immune responses than those of the other two genotypes in the pattern recognition molecule and immune-responsive effector pathways. These findings demonstrated the population variations of RSV during the circulation between the vector insect and host plant.

Molecular Mechanisms of Wing Polymorphism in Insects

Many insects are capable of developing into either long-winged or short-winged (or wingless) morphs, which enables them to rapidly match heterogeneous environments. Thus, the wing polymorphism is an adaptation at the root of their ecological success. Wing polymorphism is orchestrated at various levels, starting with the insect's perception of environmental cues, then signal transduction and signal execution, and ultimately the transmitting of signals into physiological adaption in accordance with the particular morph produced. Juvenile hormone and ecdysteroid pathways have long been proposed to regulate wing polymorphism in insects, but rigorous experimental evidence is lacking. The breakthrough findings of ecdysone receptor regulation on transgenerational wing dimorphism in the aphid Acyrthosiphon pisum and of insulin signaling in the planthopper Nilaparvata lugens greatly broaden our understanding of wing polymorphism at the molecular level. Recently, the advent of high-throughput sequencing coupled with functional genomics provides powerful genetic tools for future insights into the molecular bases underlying wing polymorphism in insects.

Genome sequence of the small brown planthopper, Laodelphax striatellus

Background

Laodelphax striatellus Fallén (Hemiptera: Delphacidae) is one of the most destructive rice pests. L. striatellus is different from 2 other rice planthoppers with a released genome sequence, Sogatella furcifera and Nilaparvata lugens, in many biological characteristics, such as host range, dispersal capacity, and vectoring plant viruses. Deciphering the genome of L. striatellus will further the understanding of the genetic basis of the biological differences among the 3 rice planthoppers.

Findings

A total of 190 Gb of Illumina data and 32.4 Gb of Pacbio data were generated and used to assemble a high-quality L. striatellus genome sequence, which is 541 Mb in length and has a contig N50 of 118 Kb and a scaffold N50 of 1.08 Mb. Annotated repetitive elements account for 25.7% of the genome. A total of 17 736 protein-coding genes were annotated, capturing 97.6% and 98% of the BUSCO eukaryote and arthropoda genes, respectively. Compared with N. lugens and S. furcifera, L. striatellus has the smallest genome and the lowest gene number. Gene family expansion and transcriptomic analyses provided hints to the genomic basis of the differences in important traits such as host range, migratory habit, and plant virus transmission between L. striatellus and the other 2 planthoppers.

Conclusions

We report a high-quality genome assembly of L. striatellus, which is an important genomic resource not only for the study of the biology of L. striatellus and its interactions with plant hosts and plant viruses, but also for comparison with other planthoppers.

Rice stripe virus-derived siRNAs play different regulatory roles in rice and in the insect vector Laodelphax striatellus

BACKGROUND

Most plant viruses depend on vector insects for transmission. Upon viral infection, virus-derived small interfering RNAs (vsiRNAs) can target both viral and host transcripts. Rice stripe virus (RSV) is a persistent-propagative virus transmitted by the small brown planthopper (Laodelphax striatellus, Fallen) and can cause a severe disease on rice.

RESULTS

To investigate how vsiRNAs regulate gene expressions in the host plant and the insect vector, we analyzed the expression profiles of small RNAs (sRNAs) and mRNAs in RSV-infected rice and RSV-infected planthopper. We obtained 88,247 vsiRNAs in rice that were predominantly derived from the terminal regions of the RSV RNA segments, and 351,655 vsiRNAs in planthopper that displayed relatively even distributions on RSV RNA segments. 38,112 and 80,698 unique vsiRNAs were found only in rice and planthopper, respectively, while 14,006 unique vsiRNAs were found in both of them. Compared to mock-inoculated rice, 273 genes were significantly down-regulated genes (DRGs) in RSV-infected rice, among which 192 (70.3%) were potential targets of vsiRNAs based on sequence complementarity. Gene ontology (GO) analysis revealed that these 192 DRGs were enriched in genes involved in kinase activity, carbohydrate binding and protein binding. Similarly, 265 DRGs were identified in RSV-infected planthoppers, among which 126 (47.5%) were potential targets of vsiRNAs. These planthopper target genes were enriched in genes that are involved in structural constituent of cuticle, serine-type endopeptidase activity, and oxidoreductase activity.

CONCLUSIONS

Taken together, our results reveal that infection by the same virus can generate distinct vsiRNAs in different hosts to potentially regulate different biological processes, thus reflecting distinct virus-host interactions.

Characterization and comparative analysis of microRNAs in the rice pest Sogatella furcifera

MicroRNAs (miRNAs) are a class of endogenous regulatory RNA molecules 21-24 nucleotides in length that act as functional regulators of post-transcriptional repression of messenger RNA. We report the identification and characterization of a conserved miRNA and 171 novel miRNAs in the migratory rice pest Sogatella furcifera by deep sequencing, which were observed to be biased towards female adults of the insect, modulating the functionality and targets of the miRNAs in sex differentiation. A switch in arm usage was also observed in 9 miRNA when compared to the insect ancestor during insect evolution. The miRNA loci showed high 5’ fidelity in both miRNA and star species and about 93.4% of WBPH miRNAs conserved within non-planthopper species were homologous with planthopper species. The novel miRNAs identified in this study provide a better understanding of the sRNA and the regulatory role of miRNA in sexual dimorphism and alteration in the expression or function of miRNAs in the rice pest.

By land, air, and sea: hemipteran diversity through the genomic lens

Thanks to a recent spate of sequencing projects, the Hemiptera are the first hemimetabolous insect order to achieve a critical mass of species with sequenced genomes, establishing the basis for comparative genomics of the bugs. However, as the most speciose hemimetabolous order, there is still a vast swathe of the hemipteran phylogeny that awaits genomic representation across subterranean, terrestrial, and aquatic habitats, and with lineage-specific and developmentally plastic cases of both wing polyphenisms and flightlessness. In this review, we highlight opportunities for taxonomic sampling beyond obvious pest species candidates, motivated by intriguing biological features of certain groups as well as the rich research tradition of ecological, physiological, developmental, and particularly cytogenetic investigation that spans the diversity of the Hemiptera.