Comparative transcriptional analysis of asexual and sexual morphs reveals possible mechanisms in reproductive polyphenism of the cotton aphid

Dual-role regulator of a novel miR-3040 in photoperiod-mediated wing dimorphism and wing development in green peach aphid

Wing dimorphism is regarded as an important phenotypic plasticity involved in the migration and reproduction of aphids. However, the signal transduction and regulatory mechanism of wing dimorphism in aphids are still unclear. Herein, the optimal environmental conditions were first explored for inducing winged offspring of green peach aphid, and the short photoperiod was the most important environmental cue to regulate wing dimorphism. Compared to 16 L:8 D photoperiod, the proportion of winged offspring increased to 90% under 8 L:16 D photoperiod. Subsequently, 5 differentially expressed microRNAs (miRNAs) in aphids treated with long and short photoperiods were identified using small RNA sequencing, and a novel miR-3040 was identified as a vital miRNA involved in photoperiod-mediated wing dimorphism. More specifically, the inhibition of miR-3040 expression could reduce the proportion of winged offspring induced by short photoperiod, whereas its activation increased the proportion of winged offspring under long photoperiod. Meanwhile, the expression level of miR-3040 in winged aphids was about 2.5 times that of wingless aphids, and the activation or inhibition of miR-3040 expression could cause wing deformity, revealing the dual-role regulator of miR-3040 in wing dimorphism and wing development. In summary, the current study identified the key environmental cue for wing dimorphism in green peach aphid, and the first to demonstrate the dual-role regulator of miR-3040 in photoperiod-mediated wing dimorphism and wing development.

Sexually dimorphic morphology, feeding behavior and gene expression profiles in cotton aphid Aphis gossypii

BACKGROUND

Sexual dimorphism exists in most insects; however, less is known about sexual dimorphism in aphids. In this study, we identified sexually dimorphic differences in morphology, feeding behavior and gene expression between sexual females and males of the cotton aphid through electron microscopy, electrical penetration graph techniques and RNA sequencing.

RESULTS

All males were alate with a slender reddish-yellow body and abdominal yellow-black stripes, whereas all sexual females were apterous with a pudgy green body. Sensillum types on the antennae were identical between the two sexes, although males had more sensilla, possibly because the antennae are significantly longer in males compared with sexual females. In terms of feeding behavior, males spent more time probing mesophyll cells and the phloem sieve, and salivating into the phloem sieve. By contrast, sexual females spent more time ingesting xylem sap. In total, 510 and 724 genes were specifically expressed in sexual females and males, respectively, and were significantly enriched in signaling pathways related to reproduction for sexual females (e.g. ovarian steroidogenesis, oxytocin signaling pathway) and energy and flight for males (e.g. thermogenesis, insulin signaling pathway). Moreover, 8551 differentially expressed genes were identified between the two sexes, of which the 3720 upregulated genes in sexual females were mostly enriched in signaling pathways of metabolism and energy, such as thermogenesis and the citrate cycle.

CONCLUSION

This study provides insight into sexual dimorphism in aphids and lays a foundation for revealing the molecular mechanism underlying differences between the two sexes in cotton aphid. © 2023 Society of Chemical Industry.

Variation of insulin-related peptides accompanying the differentiation of Aphis gossypii biotypes and their expression profiles

Insulin signaling plays a critical role in regulating various aspects of insect biology, including development, reproduction, and the formation of wing polyphenism. This leads to differentiation among insect populations at different levels. The insulin family exhibits functional variation, resulting in diverse functional pathways. Aphis gossypii Glover, commonly known as the cotton-melon aphid, is a highly adaptable aphid species that has evolved into multiple biotypes. To understand the genetic structure of the insulin family and its evolutionary diversification and expression patterns in A. gossypii, we conducted studies using genome annotation files and RNA-sequencing data. Consequently, we identified 11 insulin receptor protein (IRP) genes in the genomes of the examined biotypes. Among these, eight AgosIRPs were dispersed across the X chromosome, while two were found in tandem on the A1 chromosome. Notably, AgosIRP2 exhibited alternative splicing, resulting in the formation of two isoforms. The AgosIRP genes displayed a high degree of conservation between Hap1 and Hap3, although some variations were observed between their genomes. For instance, a transposon was present in the coding regions of AgosIRP3 and AgosIRP9 in the Hap3 genome but not in the Hap1 genome. RNA-sequencing data revealed that four AgosIRPs were expressed ubiquitously across different morphs of A. gossypii, while others showed specific expression patterns in adult gynopara and adult males. Furthermore, the expression levels of most AgosIRPs decreased upon treatment with the pesticide acetamiprid. These findings demonstrate the evolutionary diversification of AgosIRPs between the genomes of the two biotypes and provide insights into their expression profiles across different morphs, developmental stages, and biotypes. Overall, this study contributes valuable information for investigating aphid genome evolution and the functions of insulin receptor proteins.

Dynamic changes in species richness and community diversity of symbiotic bacteria in five reproductive morphs of cotton aphid Aphis gossypii Glover (Hemiptera: Aphididae)

Introduction

Reproductive polymorphism and symbiotic bacteria are commonly observed in aphids, but their interaction remains largely unclear. In polymorphic aphid species (Aphis gossypii), offspring of parthenogenetic females (PFs) develops into sexuparae which produces gynoparae and males successively. Gynoparae further produces sexual females (SFs), and these sexual females mate with males to produce offspring.

Methods

In this study, we investigated the dynamic changes of symbiotic bacteria during the above-mentioned five reproductive morph switch in A. gossypii via 16S rRNA sequencing technology.

Results

The results showed that species richness and community diversity of symbiotic bacteria in males were the highest. Proteobacteria was absolutely dominant bacterial phylum (with relative abundance of more than 90%) in the five reproductive morphs of A. gossypii, and Buchnera was absolutely dominant genus (with relative abundance of >90%), followed by Rhodococcus, Pseudomonas, and Pantoea. Male-killing symbiont Arsenophonus presented the highest relative abundance in gynoparae, a specific morph whose offsprings were exclusively sexual females. Both principal component analysis (PCA) and clustering analysis showed trans-generation similarity in microbial community structure between sexuparae and sexual females, between PFs and gynoparae. PICRUSt 2 analysis showed that symbiotic bacteria in the five reproductive morphs were mainly enriched in metabolic pathways.

Discussion

Reproductive morph switch induced by environmental changes might be associated with bacterial community variation and sexual polymorphism of aphids. This study provides a new perspective for further deciphering the interactions between microbes and reproductive polymorphism in host aphids.

Reproduction Evaluation and Transcription Analysis of Aphis gossypii under Various Photoperiods

Aphis gossypii Glover (Hemiptera, Aphidoidae) is a polyphagous pest, whose complex phenotypic form, combined with its high fecundity and short reproductive cycle, has caused serious economic losses to agriculture worldwide. Photoperiod plays an important role in the reproduction of aphids. However, the molecular mechanisms underlying its response to seasonal photoperiodic changes are not known. In this study, the effects of different photoperiod treatments (8 L:16 D, 10 L:14 D, 12 L:12 D and 14 L:10 D) on A. gossypii reproduction in the first, third, and fifth generations at low temperatures were investigated. Then, transcriptome sequencing analysis was performed after the fifth generation of A. gossypii, exposed to different photoperiods (8 L:16 D and 12 L:12 D), using high-throughput sequencing technology. The results showed that (I) the effect of photoperiod on aphids was gradually evident with increasing exposure generations. In general, daylight extension help the A. gossypii to reproduce with the optimum photoperiod of L:D 12:12. (II) The transcriptome analysis results showed that 170 differentially expressed genes (DEGs) (123 downregulated and 47 upregulated genes) were identified between aphids under 8 h daylight and 12 h daylight. (III) Gene Ontology (GO) enrichment analysis showed that the DEGs involved in "proteolysis", "metabolic process", "peptidase activity" and "structural molecule activity" were significantly enriched; Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis showed that there were more DEGs in "Longevity regulating pathway-multiple species", "Lysosome", "Endocytosis", "Spliceosome" and "Protein processing in endoplasmic reticulum". (IV) Ten related genes were chosen for validation of statistical analysis based on RNA-Seq by the reverse transcription quantitative (RT-qPCR). The comparison was consistent with the expression pattern and supported the accuracy and reliability of RNA-Seq. In summary, the genes involved in these pathways play an important role in the reproduction of A. gossypii under photoperiodical changes. These will contribute to the sustainable management of cotton aphids through the disruption of their reproduction by the method of RNA interference in the future.

Patterns of gene expression in ovaries of sexual vs. asexual lineages of a freshwater snail

Why sexual reproduction is so common when asexual reproduction should be much more efficient and less costly remains an open question in evolutionary biology. Comparisons between otherwise similar sexual and asexual taxa allow us to characterize the genetic architecture underlying asexuality, which can, in turn, illuminate how this reproductive mode transition occurred and the mechanisms by which it is maintained or disrupted. Here, we used transcriptome sequencing to compare patterns of ovarian gene expression between actively reproducing obligately sexual and obligately asexual females from multiple lineages of Potamopyrgus antipodarum, a freshwater New Zealand snail characterized by frequent separate transitions to asexuality and coexistence of otherwise similar sexual and asexual lineages. We also used these sequence data to evaluate whether population history accounts for variation in patterns of gene expression. We found that source population was a major source of gene expression variation, and likely more influential than reproductive mode. This outcome for these common garden-raised snails is strikingly similar to earlier results from field-collected snails. While we did not identify a likely set of candidate genes from expression profiles that could plausibly explain how transitions to asexuality occurred, we identified around 1,000 genes with evidence of differential expression between sexual and asexual reproductive modes, and 21 genes that appear to exhibit consistent expression differences between sexuals and asexuals across genetic backgrounds. This second smaller set of genes provides a good starting point for further exploration regarding a potential role in the transition to asexual reproduction. These results mark the first effort to characterize the causes of asexuality in P. antipodarum, demonstrate the apparently high heritability of gene expression patterns in this species, and hint that for P. antipodarum, transitions to asexuality might not necessarily be strongly associated with broad changes in gene expression.

Transitions to asexuality and evolution of gene expression in Artemia brine shrimp

While sexual reproduction is widespread among many taxa, asexual lineages have repeatedly evolved from sexual ancestors. Despite extensive research on the evolution of sex, it is still unclear whether this switch represents a major transition requiring major molecular reorganization, and how convergent the changes involved are. In this study, we investigated the phylogenetic relationship and patterns of gene expression of sexual and asexual lineages of Eurasian Artemia brine shrimp, to assess how gene expression patterns are affected by the transition to asexuality. We find only a few genes that are consistently associated with the evolution of asexuality, suggesting that this shift may not require an extensive overhauling of the meiotic machinery. While genes with sex-biased expression have high rates of expression divergence within Eurasian Artemia, neither female- nor male-biased genes appear to show unusual evolutionary patterns after sexuality is lost, contrary to theoretical expectations.

Transcriptomic Analysis Suggests Genes Expressed Stage-Independently and Stage-Dependently Modulating the Wing Dimorphism of the Brown Planthopper

Wing dimorphism is considered as an adaptive trait of insects. Brown planthoppers (BPHs) Nilaparvata lugens, a serious pest of rice, are either macropterous or brachypterous. Genetic and environmental factors are both likely to control wing morph determination in BPHs, but the hereditary law and genes network are still unknown. Here, we investigated changes in gene expression levels between macropterous and brachypterous BPHs by creating artificially bred morphotype lines. The nearly pure-bred strains of macropterous and brachypterous BPHs were established, and their transcriptomes and gene expression levels were compared. Over ten-thousand differentially expressed genes (DEGs) between macropterous and brachypterous strains were found in the egg, nymph, and adult stages, and the three stages shared 6523 DEGs. The regulation of actin cytoskeleton, focal adhesion, tight junction, and adherens junction pathways were consistently enriched with DEGs across the three stages, whereas insulin signaling pathway, metabolic pathways, vascular smooth muscle contraction, platelet activation, oxytocin signaling pathway, sugar metabolism, and glycolysis/gluconeogenesis were significantly enriched by DEGs in a specific stage. Gene expression trend profiles across three stages were different between the two strains. Eggs, nymphs, and adults from the macropterous strain were distinguishable from the brachypterous based on gene expression levels, and genes that were related to wing morphs were differentially expressed between wing strains or strain × stage. A proposed mode based on genes and environments to modulate the wing dimorphism of BPHs was provided.

Transcriptomic Analysis of Oryza sativa Leaves Reveals Key Changes in Response to Magnaporthe oryzae MSP1

Rice blast disease, caused by Magnaporthe oryzae, results in an extensive loss of rice productivity. Previously, we identified a novel M. oryzae secreted protein, termed MSP1 which causes cell death and pathogen-associated molecular pattern (PAMP)-triggered immune (PTI) responses in rice. Here, we report the transcriptome profile of MSP1-induced response in rice, which led to the identification of 21,619 genes, among which 4,386 showed significant changes (P < 0.05 and fold change > 2 or < 1/2) in response to exogenous MSP1 treatment. Functional annotation of differentially regulated genes showed that the suppressed genes were deeply associated with photosynthesis, secondary metabolism, lipid synthesis, and protein synthesis, while the induced genes were involved in lipid degradation, protein degradation, and signaling. Moreover, expression of genes encoding receptor-like kinases, MAPKs, WRKYs, hormone signaling proteins and pathogenesis-related (PR) proteins were also induced by MSP1. Mapping these differentially expressed genes onto various pathways revealed critical information about the MSP1-triggered responses, providing new insights into the molecular mechanism and components of MSP1-triggered PTI responses in rice.

Extensive Differential Splicing Underlies Phenotypically Plastic Aphid Morphs

Phenotypic plasticity results in a diversity of phenotypes from a single genotype in response to environmental cues. To understand the molecular basis of phenotypic plasticity, studies have focused on differential gene expression levels between environmentally determined phenotypes. The extent of alternative splicing differences among environmentally determined phenotypes has largely been understudied. Here, we study alternative splicing differences among plastically produced morphs of the pea aphid using RNA-sequence data. Pea aphids express two separate polyphenisms (plasticity with discrete phenotypes): a wing polyphenism consisting of winged and wingless females and a reproduction polyphenism consisting of asexual and sexual females. We find that pea aphids alternatively splice 34% of their genes, a high percentage for invertebrates. We also find that there is extensive use of differential spliced events between genetically identical, polyphenic females. These differentially spliced events are enriched for exon skipping and mutually exclusive exon events that maintain the open reading frame, suggesting that polyphenic morphs use alternative splicing to produce phenotype-biased proteins. Many genes that are differentially spliced between polyphenic morphs have putative functions associated with their respective phenotypes. We find that the majority of differentially spliced genes is not differentially expressed genes. Our results provide a rich candidate gene list for future functional studies that would not have been previously considered based solely on gene expression studies, such as ensconsin in the reproductive polyphenism, and CAKI in the wing polyphenism. Overall, this study suggests an important role for alternative splicing in the expression of environmentally determined phenotypes.

Assembling large genomes: analysis of the stick insect (Clitarchus hookeri) genome reveals a high repeat content and sex-biased genes associated with reproduction

BACKGROUND

Stick insects (Phasmatodea) have a high incidence of parthenogenesis and other alternative reproductive strategies, yet the genetic basis of reproduction is poorly understood. Phasmatodea includes nearly 3000 species, yet only the genome of Timema cristinae has been published to date. Clitarchus hookeri is a geographical parthenogenetic stick insect distributed across New Zealand. Sexual reproduction dominates in northern habitats but is replaced by parthenogenesis in the south. Here, we present a de novo genome assembly of a female C. hookeri and use it to detect candidate genes associated with gamete production and development in females and males. We also explore the factors underlying large genome size in stick insects.

RESULTS

The C. hookeri genome assembly was 4.2 Gb, similar to the flow cytometry estimate, making it the second largest insect genome sequenced and assembled to date. Like the large genome of Locusta migratoria, the genome of C. hookeri is also highly repetitive and the predicted gene models are much longer than those from most other sequenced insect genomes, largely due to longer introns. Miniature inverted repeat transposable elements (MITEs), absent in the much smaller T. cristinae genome, is the most abundant repeat type in the C. hookeri genome assembly. Mapping RNA-Seq reads from female and male gonadal transcriptomes onto the genome assembly resulted in the identification of 39,940 gene loci, 15.8% and 37.6% of which showed female-biased and male-biased expression, respectively. The genes that were over-expressed in females were mostly associated with molecular transportation, developmental process, oocyte growth and reproductive process; whereas, the male-biased genes were enriched in rhythmic process, molecular transducer activity and synapse. Several genes involved in the juvenile hormone synthesis pathway were also identified.

CONCLUSIONS

The evolution of large insect genomes such as L. migratoria and C. hookeri genomes is most likely due to the accumulation of repetitive regions and intron elongation. MITEs contributed significantly to the growth of C. hookeri genome size yet are surprisingly absent from the T. cristinae genome. Sex-biased genes identified from gonadal tissues, including genes involved in juvenile hormone synthesis, provide interesting candidates for the further study of flexible reproduction in stick insects.

Comparative Transcriptional Analysis of the Host-Specialized Aphids Aphis gossypii (Hemiptera: Aphididae)

Host specialization is an ubiquitous character in aphid populations. Many polyphagous aphid populations usually consist of several subpopulations that have strong fidelity to a specific host or a subset of host range. Host specialization is an evolutional result of food habit of insects. However, genetic basis and molecular mechanism of host specialization are still unclear. In this study, we presented a comparative analysis on global gene expression profiles of three lineages of Aphis gossypii Glover: cotton-specialized (CO), cucurbit-specialized (CU), and CU reared on cowpea (CU-cowpea), using RNA-Seq method. More than 157 million clean reads and 38,398 different unigenes were generated from transcriptomes of these three aphid lineages. The 1,106 down- and 2,835 up-regulated genes were found between CO and CU, and 812 down- and 14,492 up-regulated genes between CU-cowpea and CU. Differentially expressed genes between CO and CU were enriched in sugar metabolism, immune system process, pathogen infection or symbiosis, and salivary secretion. Genes associated with cytochrome P450, major facilitator superfamily, and salivary effector were differentially expressed between CO and CU, which might be involved in determining host specialization. UDP-glycosyltransferases genes were sensitive to host shift. Carboxylesterases and digestion-related protease genes were related to both the host specialization and host shift of aphids. Expression levels of 22 out of 24 genes of CO and CU measured by RT-qPCR method were as similar as the results from RNA-seq method. This study provides a road map for future study on molecular mechanism of host specialization in aphids.

Exploration of molecular pathways mediating electric field-directed Schwann cell migration by RNA-seq

In peripheral nervous systems, Schwann cells wrap around axons of motor and sensory neurons to form the myelin sheath. Following spinal cord injury, Schwann cells regenerate and migrate to the lesion and are involved in the spinal cord regeneration process. Transplantation of Schwann cells into injured neural tissue results in enhanced spinal axonal regeneration. Effective directional migration of Schwann cells is critical in the neural regeneration process. In this study, we report that Schwann cells migrate anodally in an applied electric field (EF). The directedness and displacement of anodal migration increased significantly when the strength of the EF increased from 50 mV/mm to 200 mV/mm. The EF did not significantly affect the cell migration speed. To explore the genes and signaling pathways that regulate cell migration in EFs, we performed a comparative analysis of differential gene expression between cells stimulated with an EF (100 mV/mm) and those without using next-generation RNA sequencing, verified by RT-qPCR. Based on the cut-off criteria (FC > 1.2, q < 0.05), we identified 1,045 up-regulated and 1,636 down-regulated genes in control cells versus EF-stimulated cells. A Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis found that compared to the control group, 21 pathways are down-regulated, while 10 pathways are up-regulated. Differentially expressed genes participate in multiple cellular signaling pathways involved in the regulation of cell migration, including pathways of regulation of actin cytoskeleton, focal adhesion, and PI3K-Akt.