The genetic basis of population fecundity prediction across multiple field populations of Nilaparvata lugens

Population density modulates insect progenitive plasticity through the regulation of dopamine biosynthesis

Insect fecundity is a quantitative phenotype strongly affected by genotypes and the environment. However, interactions between genotypes and environmental factors in modulating insect fecundity remain largely unknown. This study investigated the impact of population density on the fecundity of Nilaparvata lugens (brown planthopper; BPH) carrying homozygous high- (HFG) or low- (LFG) fecundity homozygous genotypes. Under low population densities, the fecundity and population growth rate of both genotypes showed similar increasing trends across generations, while the trends between HFG and LFG under high population densities were opposite. Through a combination of temporal analysis and weighted gene co-expression network analyses on RNA-seq data of HFG and LFG under low and high population densities in the 1st, 3rd, and 5th generations, we identified 2 gene modules that were associated with these density-dependent progenitive phenotypes. Four pathways related to the neural system were simultaneously enriched by the 2 gene modules. Furthermore, Nlpale, which encodes a tyrosine hydroxylase, was identified as a key gene. The RNA interference of this gene and manipulation of its downstream product dopamine significantly affected the basic and density-dependent progenitive phenotypes of BPH. These findings indicated that dopamine biosynthesis is the key regulatory factor that determines fecundity in response to density changes in different BPH genotypes. Thus, this study provides insights into the interaction of a typical environmental factor and insect genotype during the process of population regulation.

Transcriptome and metabolome analyses reveal the responses of brown planthoppers to RH resistant rice cultivar

The brown planthopper (BPH) Nilaparvata lugens (Stål) (Hemiptera: Delphacidae) is one of the most destructive rice pests in Asia. The application of insect-resistant rice cultivars is currently one of the principal means of controlling BPH. Understanding the physiological response mechanisms of BPH feeding on insect-resistant rice is the key for maintaining rice yield. Here, we measured the ecological fitness and analyzed the whole-body transcriptome and metabolome of BPH reared on susceptible cultivar Taichung Native 1 (TN1) and resistant cultivar Rathu Heenati (RH). Our results showed that RH significantly decreased the survival rate, female adult weight, honeydew secretion, the number of eggs laid per female and fat content of BPH. We identified 333 upregulated and 486 downregulated genes in BPH feeding on RH. These genes were mainly involved in energy metabolism, amino acid metabolism, hormone synthesis and vitamin metabolism pathways. We also detected 145 differentially accumulated metabolites in BPH reared on RH plants compared to BPH reared on TN1 plants, including multiple carbohydrates, amino acids, lipids, and some nucleosides. Combined analyses of transcriptome and metabolome showed that five pathways, including starch, sucrose, and galactose metabolism, were altered. The network for these pathways was subsequently visualized. Our results provide insights into the mechanisms of metabolite accumulation in BPH feeding on the RH rice variety. The results could help us better understand how insect-resistant rice cultivars combat BPH infestation, which is important for the comprehensive management of BPH.

Genome-Wide Identification and Characterization of Amino Acid Polyamine Organocation Transporter Family Genes Reveal Their Role in Fecundity Regulation in a Brown Planthopper Species (Nilaparvata lugens)

The brown planthopper (BPH), Nilaparvata lugens Stål (Hemiptera:Delphacidae), is one of the most destructive pests of rice worldwide. As a sap-feeding insect, the BPH is incapable of synthesizing several amino acids which are essential for normal growth and development. Therefore, the insects have to acquire these amino acids from dietary sources or their endosymbionts, in which amino acid transporters (AATs) play a crucial role by enabling the movement of amino acids into and out of insect cells. In this study, a common amino acid transporter gene family of amino acid/polyamine/organocation (APC) was identified in BPHs and analyzed. Based on a homology search and conserved functional domain recognition, 20 putative APC transporters were identified in the BPH genome. Molecular trait analysis showed that the verified BPH APC family members were highly variable in protein features, conserved motif distribution patterns, and exon/intron organization. Phylogenetic analysis of five hemipteran species revealed an evolutionary pattern of interfamily conservation and lineage-specific expansion of this gene family. Moreover, stage- and tissue-specific expression analysis revealed diverse expression patterns in the 20 BPH APC transporter genes. Lastly, a potential BPH fecundity regulatory gene of NlAPC09 was identified and shown to participate in the fecundity regulation through the use of quantitative polymerase chain reaction (qPCR) and RNA inference experiments. Our results provide a basis for further functional investigations of APC transporters in BPH.

Disease swamps molecular signatures of genetic-environmental associations to abiotic factors in Tasmanian devil (Sarcophilus harrisii) populations

Landscape genomics studies focus on identifying candidate genes under selection via spatial variation in abiotic environmental variables, but rarely by biotic factors (i.e., disease). The Tasmanian devil (Sarcophilus harrisii) is found only on the environmentally heterogeneous island of Tasmania and is threatened with extinction by a transmissible cancer, devil facial tumor disease (DFTD). Devils persist in regions of long-term infection despite epidemiological model predictions of species' extinction, suggesting possible adaptation to DFTD. Here, we test the extent to which spatial variation and genetic diversity are associated with the abiotic environment (i.e., climatic variables, elevation, vegetation cover) and/or DFTD. We employ genetic-environment association analyses using 6886 SNPs from 3287 individuals sampled pre- and post-disease arrival across the devil's geographic range. Pre-disease, we find significant correlations of allele frequencies with environmental variables, including 365 unique loci linked to 71 genes, suggesting local adaptation to abiotic environment. The majority of candidate loci detected pre-DFTD are not detected post-DFTD arrival. Several post-DFTD candidate loci are associated with disease prevalence and were in linkage disequilibrium with genes involved in tumor suppression and immune response. Loss of apparent signal of abiotic local adaptation post-disease suggests swamping by strong selection resulting from the rapid onset of DFTD.

Ovarian Transcriptomic Analyses in the Urban Human Health Pest, the Western Black Widow Spider

Due to their abundance and ability to invade diverse environments, many arthropods have become pests of economic and health concern, especially in urban areas. Transcriptomic analyses of arthropod ovaries have provided insight into life history variation and fecundity, yet there are few studies in spiders despite their diversity within arthropods. Here, we generated a de novo ovarian transcriptome from 10 individuals of the western black widow spider (Latrodectus hesperus), a human health pest of high abundance in urban areas, to conduct comparative ovarian transcriptomic analyses. Biological processes enriched for metabolism—specifically purine, and thiamine metabolic pathways linked to oocyte development—were significantly abundant in L. hesperus. Functional and pathway annotations revealed overlap among diverse arachnid ovarian transcriptomes for highly-conserved genes and those linked to fecundity, such as oocyte maturation in vitellogenin and vitelline membrane outer layer proteins, hormones, and hormone receptors required for ovary development, and regulation of fertility-related genes. Comparative studies across arachnids are greatly needed to understand the evolutionary similarities of the spider ovary, and here, the identification of ovarian proteins in L. hesperus provides potential for understanding how increased fecundity is linked to the success of this urban pest.

A comparative study of microbial community and dynamics of Asaia in the brown planthopper from susceptible and resistant rice varieties

BACKGROUND

The brown planthopper (BPH) is likely the most destructive, piercing and sucking monophagous insect pest of rice that causes substantial economic losses to farmers. Although yeast-like symbionts (YLS) and virus transmission have been observed in the BPH, the bacterial population inhabiting the BPH has received minimal research attention. Labelling BPH-associated bacterial species may shed light on BPH biology and the interaction between the BPH and rice to provide novel approaches for the efficient control of this insect pest.

RESULTS

We examined RNA-seq results to identify bacterial populations present in different generations of BPHs maintained on susceptible or resistant rice varieties. Overall, 87 operational taxonomic units (OTUs) were determined from the BPH-F0, F6 and F16 generations. These OTUs had Shannon and Simpson index values of 0.37-0.6 and 0.56-1.19, respectively. The evenness values of 0.7-1.00 showed the vastness of the bacterial diversity recovered from the BPH samples. The results showed high species diversity in the BPHs collected from susceptible rice and a high number of members of unclassified bacteria in the BPHs isolated from resistant rice. We noticed that Proteobacteria OTUs were predominant across all samples. Furthermore, PCR data of Asaia species showed variable DNA amplification across the BPH samples collected from susceptible or resistant varieties. The identification of Asaia in BPH eggs and BPH-egg-infected rice revealed its influence on the interaction between the BPH egg and rice.

CONCLUSIONS

The BPHs had clear differences in their microbiomes and in their ability to feed on different rice hosts. These variations could have an essential impact on host adaptation and interaction. These results provide a better understanding of the bacterial diversity and interaction of the microbiome of different generations of BPHs. Furthermore, PCR data of Asaia sp. variation across the BPH samples (isolated from different host genotypes selected from the field and laboratory, including BPH eggs and egg-infected rice tissues), suggest that Asaia could be an important member of the insect microbiome involved in adaptation, its interaction with rice and, most importantly, as a paratransgenic tool for insect control.

Transcriptomic and Expression Analysis of the Salivary Glands in Brown Planthoppers, Nilaparvata lugens (Hemiptera: Delphacidae)

The brown planthopper (BPH), Nilaparvata lugens Stål (Hemiptera: Delphacidae), is a serious rice pest because of its destructive feeding. The salivary glands of the BPH play a key role in successful feeding. In this study, we explored the salivary gland transcriptome (sialotranscriptome) of adult BPHs using Illumina sequencing and a total of 55,913 transcripts and 45,421 unigenes were obtained. We identified one reference gene RPL9 (Ribosomal protein L9) and 19 salivary protein genes from the BPH sialotranscripome, which were categorized as those involved in sugar metabolism, extra-oral digestion of cell wall components, detoxification, and suppression of plant defenses. Tissue expression profiles of 19 salivary protein genes analysis revealed that the expression level of alpha-glucosidase family 31 had no difference in five tissues, suggesting that it may have functions in the whole-body parts. Glucose dehydrogenase (flavine adenine dinucleotide, quinone)-like was expressed highly in the salivary gland, which might play putative role in insect feeding. Glucose dehydrogenase (acceptor) was expressed the highest level in head without salivary gland. Other salivary protein genes were highly expressed in gut or malpighian tubule, suggesting that they may play roles in digestive and detoxification mechanism. Moreover, we detected RPL9 is one of the genes that is most consistently present for acquisition of gene expression in different tissues. Thus, RPL9 can be a new reference for expression studies of BPH. The obtained BPH sialotranscripome provides a list of genes that have potential roles in feeding and interaction between BPHs and rice plants.

Physiological and Evolutionary Changes in a Biological Control Agent During Prey Shifts Over Several Generations

Biological control agents usually suffer from a shortage of target prey or hosts in their post-release stage. Some predatory agents turn to attacking other prey organisms, which may induce physiological and evolutionary changes. In this study, we investigated life history traits, gene expression and genotype frequency in the predatory ladybird beetle Cryptolaemus montrouzieri during experimental prey shifts. C. montrouzieri were either continuously fed on aphids Megoura japonica as an alternative prey for four generations or were shifted back to the initial prey mealybugs Planococcus citri in each generation. In general, the utilization of aphids resulted in reduced performance and severe physiological adjustments, indicated by significant changes in development and fecundity traits and a large number of differentially expressed genes between the two offering setup prey treatments. Within the aphid-fed lines, performance regarding the developmental time, the adult weight and the survival rate recovered to some level in subsequent generations, possibly as a result of adaptive evolution. In particular, we found that a shift back to mealybugs caused a gradual increase in fecundity. Accordingly, a genotype of the fecundity-related gene vitellogenin, of which there were several minor alleles in the initial population, became the main genotype within four generations. The present study explored the short-term experimental evolution of a so-call specialist predator under prey shift conditions. This potential rapid adaptation of biological control agents to novel prey will increase environmental risks associated with non-target effects.

Regulation of NlE74A on vitellogenin may be mediated by angiotensin converting enzyme through a fecundity-related SNP in the brown planthopper, Nilaparvata lugens

The major yolk protein precursors (YPP) gene, vitellogenin (Vg), usually considered as a reproductive indicator and molecular marker for evaluating insect fecundity, is controlled by insect hormone (mainly ecdysteroids and juvenile hormone), transcription factors and many other fecundity-related genes. To better understand the underlying molecular regulation mechanisms of the NlVg in the brown planthopper Nilaparvata lugens (N. lugens), the correlation between one early ecdysone response gene E74 and one important fecundity-related gene angiotensin converting enzyme (ACE) on the regulation of Vg gene expression, was investigated. We first showed that the mRNA expression level of NlACE were significantly higher in a high-fecundity population (HFP) than a low-fecundity population (LFP) at different development stages, and knockdown of NlACE expression by RNA interference (RNAi) results in a reduced level of NlVg expression and N. lugens fecundity. Subsequently, we analyzed the promoter of NlACE and found an E74A binding site, which was also differentially expressed in HFP and LFP. Then a gene putatively encoding E74A, namely NlE74A, predominant in the ovary and fat body was cloned and characterized. Furthermore, the developmental profile during female adult and the tissue-specific expression pattern of NlACE and NlE74A were similar to the expression pattern of NlVg gene, implying that both NlACE and NlE74A may be involved in regulating the expression of NlVg. Finally, after injecting the dsRNA of NlE74A, the NlACE expression levels were significantly reduced simultaneously at 24 h and 48 h post-injection, and the NlVg expression level was significant reduced at 24 h post-injection and the downswing was more significant at 48 h post-injection. These results imply that regulation of NlE74A on NlVg transcription might be mediated by NlACE through the E74 binding site at the NlACE promoter region in N. lugens.

Transcriptional regulation of the vitellogenin gene through a fecundity-related single nucleotide polymorphism within a GATA-1 binding motif in the brown planthopper, Nilaparvata lugens

Identifying the Single Nucleotide Polymorphisms (SNPs) with functions in insect fecundity promises to provide novel insight into genetic mechanisms of adaptation and to aid in effective control of insect populations. We previously identified several SNPs within the vitellogenin (Vg) promoter region between a high-fecundity population (HFP) and a low-fecundity population (LFP) of the brown planthopper, Nilaparvata lugens Stål (Hemiptera: Delphacidae). Here, we found that an A-to-T (HFP allele to LFP allele) transversion at nucleotide -953 upstream of Vg in a Nilaparvata lugens GATA-1 (NlGATA-1) binding motif is associated with the level of Vg transcription. We also characterized NlGATA-1, containing a double CX₂ CX₁₇ CX₂ C zinc finger, which has been implicated in the activation of Vg gene expression. Knockdown of the NlGATA-1 gene results in a reduced basal level of expression of the Vg gene and fewer offspring of N. lugens in vivo, whereas overexpression of NlGATA-1 in cells increased Vg promoter activity. Moreover, upon cotransfection with NlGATA-1 expression vector, the luciferase activities of Vg reporter vectors with the A allele were significantly higher than those with the T allele. These findings support a mechanism in which a SNP within the promoter of Vg is associated with the level of Vg transcription by altering the binding activity of NlGATA-1 and subsequently affecting fecundity in N. lugens.

Navigating the Interface Between Landscape Genetics and Landscape Genomics

As next-generation sequencing data become increasingly available for non-model organisms, a shift has occurred in the focus of studies of the geographic distribution of genetic variation. Whereas landscape genetics studies primarily focus on testing the effects of landscape variables on gene flow and genetic population structure, landscape genomics studies focus on detecting candidate genes under selection that indicate possible local adaptation. Navigating the transition between landscape genomics and landscape genetics can be challenging. The number of molecular markers analyzed has shifted from what used to be a few dozen loci to thousands of loci and even full genomes. Although genome scale data can be separated into sets of neutral loci for analyses of gene flow and population structure and putative loci under selection for inference of local adaptation, there are inherent differences in the questions that are addressed in the two study frameworks. We discuss these differences and their implications for study design, marker choice and downstream analysis methods. Similar to the rapid proliferation of analysis methods in the early development of landscape genetics, new analytical methods for detection of selection in landscape genomics studies are burgeoning. We focus on genome scan methods for detection of selection, and in particular, outlier differentiation methods and genetic-environment association tests because they are the most widely used. Use of genome scan methods requires an understanding of the potential mismatches between the biology of a species and assumptions inherent in analytical methods used, which can lead to high false positive rates of detected loci under selection. Key to choosing appropriate genome scan methods is an understanding of the underlying demographic structure of study populations, and such data can be obtained using neutral loci from the generated genome-wide data or prior knowledge of a species' phylogeographic history. To this end, we summarize recent simulation studies that test the power and accuracy of genome scan methods under a variety of demographic scenarios and sampling designs. We conclude with a discussion of additional considerations for future method development, and a summary of methods that show promise for landscape genomics studies but are not yet widely used.

Discovery and functional identification of fecundity-related genes in the brown planthopper by large-scale RNA interference

Recently, transcriptome and proteome data have increasingly been used to identify potential novel genes related to insect phenotypes. However, there are few studies reporting the large-scale functional identification of such genes in insects. To identify novel genes related to fecundity in the brown planthopper (BPH), Nilaparvata lugens, 115 genes were selected from the transcriptomic and proteomic data previously obtained from high- and low-fecundity populations in our laboratory. The results of RNA interference (RNAi) feeding experiments showed that 91.21% of the genes were involved in the regulation of vitellogenin (Vg) expression and may influence BPH fecundity. After RNAi injection experiments, 12 annotated genes were confirmed as fecundity-related genes and three novel genes were identified in the BPH. Finally, C-terminal binding protein (CtBP) was shown to play an important role in BPH fecundity. Knockdown of CtBP not only led to lower survival, underdeveloped ovaries and fewer eggs laid but also resulted in a reduction in Vg protein expression. The novel gene resources gained from this study will be useful for constructing a Vg regulation network and may provide potential target genes for RNAi-based pest control.

Transcriptomic and Expression Analysis of the Salivary Glands in White-Backed Planthoppers, Sogatella furcifera

The white-backed planthopper (WBPH), Sogatella furcifera (Horváth), is one of the serious rice pests because of its destructive feeding. The salivary glands of the WBPH play an important role in the feeding behaviour. Currently, however, very little is known about the salivary glands at the molecular level. We sequenced the salivary gland transcriptome (sialotranscripome) of adult WBPHs using the Illumina sequencing. A total of 65,595 transcripts and 51,842 unigenes were obtained from salivary glands. According to annotations against the Nr database, many of the unigenes identified were associated with the most studied enzymes in hemipteran saliva. In the present study, we identified 32 salivary protein genes from the WBPH sialotranscripome, which were categorized as those involved in sugar metabolism, detoxification, suppression of plant defense responses, immunity-related responses, general digestion, and other phytophagy processes. Tissue expression profiles analysis revealed that four of 32 salivary protein genes (multicopper oxidase 4, multicopper oxidase 6, carboxylesterase and uridine phosphorylase 1 isform X2) were primarily expressed in the salivary gland, suggesting that they played putative role in insect-rice interactions. 13 of 32 salivary protein genes were primarily expressed in gut, which might play putative role in digestive and detoxify mechanism. Development expression profiles analysis revealed that the expression level of 26 of 32 salivary protein genes had no significant difference, suggesting that they may play roles in every developmental stages of salivary gland of WBPH. The other six genes have a high expression level in the salivary gland of adult. 31 of 32 genes (except putative acetylcholinesterase 1) have no significant difference in male and female adult, suggesting that their expression level have no difference between sexes. This report analysis of the sialotranscripome for the WBPH, and the transcriptome provides a foundational list of the genes involved in feeding. Our data will be useful to investigate the mechanisms of interaction between the WBPH and the host plant.

Nutritional Signaling Regulates Vitellogenin Synthesis and Egg Development through Juvenile Hormone in Nilaparvata lugens (Stål)

Insect female reproduction which comprises the synthesis of vitellogenein (Vg) in the fat body and its incorporation into developing oocytes, needs a large amount of energy and food resources. Our previous studies found that juvenile hormone (JH) regulates vitellogenesis in the brown planthopper, Nilaparvata lugens. Here, we report on the role of JH in nutrient-regulated Vg synthesis and egg development. We first cloned the genes coding for juvenile hormone acid methyltransferase (JHAMT) which is involved in JH biosynthesis and methoprene-tolerant (Met) for JH action. Amino acids (AAs) induced the expression of jmtN, while showing no effects on the expression of met using an artificial diet culture system. Reduction in JH biosynthesis or its action by RNA interference (RNAi)-mediated silencing of jmtN or met led to a severe inhibition of AAs-induced Vg synthesis and oocyte maturation, together with lower fecundity. Furthermore, exogenous application of JH III partially restored Vg expression levels in jmtN RNAi females. However, JH III application did not rescue Vg synthesis in these met RNAi insects. Our results show that AAs induce Vg synthesis in the fat body and egg development in concert with JH biosynthesis in Nilaparvata lugens (Stål), rather than through JH action.

Functional screen for microRNAs of Nilaparvata lugens reveals that targeting of glutamine synthase by miR-4868b regulates fecundity

Insect fecundity is regulated by the interaction of genotypes and the environment. MicroRNAs (miRNAs) also act in insect development and reproduction by regulating genes involved in these physiological processes. Although hundreds of insect miRNAs have been identified, the biological roles of most remain poorly understood. Here, we used a multi-algorithm approach for miRNA target prediction in 3'UTRs of fecundity-related genes in the brown planthopper (BPH) Nilaparvata lugens and identified 38 putative miRNAs targeting 9 fecundity-related genes. High-ranked miRNAs were selected for target validation. Using a dual luciferase reporter assay in S2 cells, we experimentally verified N. lugens glutamine synthetase (NlGS) as an authentic target of microRNA-4868b (miR-4868b). In the females, NlGS protein expression was down-regulated after injection of a miR-4868b mimic but up-regulated after injection of a miR-4868b inhibitor. In addition, overexpression of miR-4868b reduced fecundity, and disrupted ovary development and Vg expression in N. lugens. These findings showed that miR-4868b is involved in regulating N. lugens fecundity by targeting NlGS. Moreover, this study may lead to better understanding of the fecundity of this important agricultural insect pest.