Cross-kingdom RNA interference mediated by insect salivary microRNAs may suppress plant immunity

Communication between insects and plants relies on the exchange of bioactive molecules that traverse the species interface. Although proteinic effectors have been extensively studied, our knowledge of other molecules involved in this process remains limited. In this study, we investigate the role of salivary microRNAs (miRNAs) from the rice planthopper Nilaparvata lugens in suppressing plant immunity. A total of three miRNAs were confirmed to be secreted into host plants during insect feeding. Notably, the sequence-conserved miR-7-5P is specifically expressed in the salivary glands of N. lugens and is secreted into saliva, distinguishing it significantly from homologues found in other insects. Silencing miR-7-5P negatively affects N. lugens feeding on rice plants, but not on artificial diets. The impaired feeding performance of miR-7-5P-silenced insects can be rescued by transgenic plants overexpressing miR-7-5P. Through target prediction and experimental testing, we demonstrate that miR-7-5P targets multiple plant genes, including the immune-associated bZIP transcription factor 43 (OsbZIP43). Infestation of rice plants by miR-7-5P-silenced insects leads to the increased expression of OsbZIP43, while the presence of miR-7-5P counteracts this upregulation effect. Furthermore, overexpressing OsbZIP43 confers plant resistance against insects which can be subverted by miR-7-5P. Our findings suggest a mechanism by which herbivorous insects have evolved salivary miRNAs to suppress plant immunity, expanding our understanding of cross-kingdom RNA interference between interacting organisms.

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

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

A pipeline contributes to efficient identification of salivary proteins in short-headed planthopper, Epeurysa nawaii

Saliva, an oral secretion primarily originating from salivary glands (SGs), exert critical roles in the ongoing evolutionary interaction between insects and plants. However, identifying insect salivary components poses challenges due to the tiny size of insects, low secretion amounts, and the propensity for degradation after secretion. In this study, we developed a transcriptome-based approach to comprehensively analyze the salivary proteins of the short-headed planthopper, Epeurysa nawaii, a species with unique feeding habits on bamboo. A total of 165 salivary proteins were identified, with 114 secretory genes highly and specifically expressed in SGs. Consistent with most phloem-feeding insects, digestive enzymes, calcium-binding proteins, oxidoreductases, and a few previously reported salivary effectors were ubiquitously distributed in E. nawaii saliva. However, we also identified a substantial portion of salivary proteins exhibiting taxonomy specificity, including 60 E. nawaii-specific and 62 Delphacidae-specific proteins. These taxonomy-restricted proteins potentially play a role in insect adaptation to specific host plants. Our study provides an efficient pipeline for salivary protein identification and serves as a valuable resource for the functional characterization of effectors.

Salivary proteins potentially derived from horizontal gene transfer are critical for salivary sheath formation and other feeding processes

Herbivorous insects employ an array of salivary proteins to aid feeding. However, the mechanisms behind the recruitment and evolution of these genes to mediate plant-insect interactions remain poorly understood. Here, we report a potential horizontal gene transfer (HGT) event from bacteria to an ancestral bug of Eutrichophora. The acquired genes subsequently underwent duplications and evolved through co-option. We annotated them as horizontal-transferred, Eutrichophora-specific salivary protein (HESPs) according to their origin and function. In Riptortus pedestris (Coreoidea), all nine HESPs are secreted into plants during feeding. The RpHESP4 to RpHESP8 are recently duplicated and found to be indispensable for salivary sheath formation. Silencing of RpHESP4-8 increases the difficulty of R. pedestris in probing the soybean, and the treated insects display a decreased survivability. Although silencing the other RpHESPs does not affect the salivary sheath formation, negative effects are also observed. In Pyrrhocoris apterus (Pyrrhocoroidea), five out of six PaHESPs are secretory salivary proteins, with PaHESP3 being critical for insect survival. The PaHESP5, while important for insects, no longer functions as a salivary protein. Our results provide insight into the potential origin of insect saliva and shed light on the evolution of salivary proteins.

Comparative transcriptomic analysis of salivary glands between the zoophytophagous Cyrtorhinus lividipennis and the phytozoophagous Apolygus lucorum

BACKGROUND

Saliva plays a crucial role in shaping the feeding behavior of insects, involving processes such as food digestion and the regulation of interactions between insects and their hosts. Cyrtorhinus lividipennis serves as a predominant natural enemy of rice pests, while Apolygus lucorum, exhibiting phytozoophagous feeding behavior, is a destructive agricultural pest. In this study, a comparative transcriptome analysis, incorporating the published genomes of C.lividipennis and A.lucorum, was conducted to reveal the role of salivary secretion in host adaptation.

RESULTS

In contrast to A.lucorum, C.lividipennis is a zoophytophagous insect. A de novo genome analysis of C.lividipennis yielded 19,706 unigenes, including 16,217 annotated ones. On the other hand, A.lucorum had altogether 20,111 annotated genes, as obtained from the published official gene set (20,353 unigenes). Functional analysis of the top 1,000 salivary gland (SG)-abundant genes in both insects revealed that the SG was a dynamically active tissue engaged in protein synthesis and secretion. Predictions of other tissues and signal peptides were compared. As a result, 94 and 157 salivary proteins were identified in C.lividipennis and A.lucorum, respectively, and were categorized into 68 and 81 orthogroups. Among them, 26 orthogroups were shared, potentially playing common roles in digestion and detoxification, including several venom serine proteases. Furthermore, 42 and 55 orthogroups were exclusive in C.lividipennis and A.lucorum, respectively, which were exemplified by a hyaluronidase in C.lividipennis that was associated with predation, while polygalacturonases in A.lucorum were involved in mesophyll-feeding patterns.

CONCLUSIONS

Findings in this study provide a comprehensive insight into saliva secretions in C.lividipennis and A.lucorum via a transcriptome approach, reflecting the intricate connections between saliva secretions and feeding behaviors. It is found that conserved salivary secretions are involved in shaping the overlapping feeding patterns, while a plethora of unique salivary secretions may drive the evolution of specific feeding behaviors crucial for their survival. These results enhance our understanding of the feeding mechanisms in different insects from the perspective of saliva and contribute to future environmentally friendly pest control by utilizing predatory insects.

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

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

Horizontally Transferred Salivary Protein Promotes Insect Feeding by Suppressing Ferredoxin-Mediated Plant Defenses

Herbivorous insects such as whiteflies, planthoppers, and aphids secrete abundant orphan proteins to facilitate feeding. Yet, how these genes are recruited and evolve to mediate plant-insect interaction remains unknown. In this study, we report a horizontal gene transfer (HGT) event from fungi to an ancestor of Aleyrodidae insects approximately 42 to 190 million years ago. BtFTSP1 is a salivary protein that is secreted into host plants during Bemisia tabaci feeding. It targets a defensive ferredoxin 1 in Nicotiana tabacum (NtFD1) and disrupts the NtFD1-NtFD1 interaction in plant cytosol, leading to the degradation of NtFD1 in a ubiquitin-dependent manner. Silencing BtFTSP1 has negative effects on B. tabaci feeding while overexpressing BtFTSP1 in N. tabacum benefits insects and rescues the adverse effect caused by NtFD1 overexpression. The association between BtFTSP1 and NtFD1 is newly evolved after HGT, with the homologous FTSP in its fungal donor failing to interact and destabilize NtFD1. Our study illustrates the important roles of horizontally transferred genes in plant-insect interactions and suggests the potential origin of orphan salivary genes.

Diversity of RNA viruses in agricultural insects

Recent advancements in next-generation sequencing (NGS) technology and bioinformatics tools have revealed a vast array of viral diversity in insects, particularly RNA viruses. However, our current understanding of insect RNA viruses has primarily focused on hematophagous insects due to their medical importance, while research on the viromes of agriculturally relevant insects remains limited. This comprehensive review aims to address the gap by providing an overview of the diversity of RNA viruses in agricultural pests and beneficial insects within the agricultural ecosystem. Based on the NCBI Virus Database, over eight hundred RNA viruses belonging to 39 viral families have been reported in more than three hundred agricultural insect species. These viruses are predominantly found in the insect orders of Hymenoptera, Hemiptera, Thysanoptera, Lepidoptera, Diptera, Coleoptera, and Orthoptera. These findings have significantly enriched our understanding of RNA viral diversity in agricultural insects. While further virome investigations are necessary to expand our knowledge to more insect species, it is crucial to explore the biological roles of these identified RNA viruses within insects in future studies. This review also highlights the limitations and challenges for the effective virus discovery through NGS and their potential solutions, which might facilitate for the development of innovative bioinformatic tools in the future.

Transcriptomic Analysis of Tobacco Plants in Response to Whitefly Infection

The whitefly Bemisia tabaci is one of the most destructive pests worldwide, and causes tremendous economic losses. Tobacco Nicotiana tabacum serves as a model organism for studying fundamental biological processes and is severely damaged by whiteflies. Hitherto, our knowledge of how tobacco perceives and defends itself against whiteflies has been scare. In this study, we analyze the gene expression patterns of tobacco in response to whitefly infestation. A total of 244 and 2417 differentially expressed genes (DEGs) were identified at 12 h and 24 h post whitefly infestation, respectively. Enrichment analysis demonstrates that whitefly infestation activates plant defense at both time points, with genes involved in plant pattern recognition, transcription factors, and hormonal regulation significantly upregulated. Notably, defense genes are more intensely upregulated at 24 h post infestation than at 12 h, indicating an increased immunity induced by whitefly infestation. In contrast, genes associated with energy metabolism, carbohydrate metabolism, ribosomes, and photosynthesis are suppressed, suggesting impaired plant development. Taken together, our study provides comprehensive insights into how plants respond to phloem-feeding insects, and offers a theoretical basis for better research on plant-insect interactions.

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

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

Long-wave opsin involved in body color plastic development in Nilaparvata lugens

BACKGROUND

As one of the components of visual photopigments in photoreceptor cells, opsin exhibits different spectral peaks and plays crucial roles in visual function. Besides, it is discovered to evolve other functions despite color vision. However, research on its unconventional function is limited nowadays. With the increase in genome database numbers, various numbers and types of opsins have been identified in insects due to gene duplications or losses. The Nilaparvata lugens (Hemiptera) is a rice pest known for its long-distance migration capability. In this study, opsins were identified in N. lugens and characterized by genome and transcriptome analyses. Meanwhile, RNA interference (RNAi) was carried out to investigate the functions of opsins, and then the Illumina Novaseq 6000 platform-based transcriptome sequencing was performed to reveal gene expression patterns.

RESULTS

Four opsins belonging to G protein-coupled receptors were identified in the N. lugens genome, including one long-sensitive opsin (Nllw) together with two ultraviolet-sensitive opsins (NlUV1/2) and an additional new opsin with hypothesized UV peak sensitivity (NlUV3-like). A tandem array of NlUV1/2 on the chromosome suggested the presence of a gene duplication event, with similar exons distribution. Moreover, as revealed by spatiotemporal expression, the four opsins were highly expressed in eyes with age-different expression levels. Besides, RNAi targeting each of the four opsins did not significantly affect the survival of N. lugens in phytotron, but the silencing of Nllw resulted in the melanization of body color. Further transcriptome analysis revealed that silencing of Nllw resulted in up-regulation of a tyrosine hydroxylase gene (NlTH) and down-regulation of an arylalkylamine-N-acetyltransferases gene (NlaaNAT) in N. lugens, demonstrating that Nllw is involved in body color plastic development via the tyrosine-mediated melanism pathway.

CONCLUSIONS

This study provides the first evidence in a Hemipteran insect that an opsin (Nllw) takes part in the regulation of cuticle melanization, confirming a cross-talk between the gene pathways underlying the visual system and the morphological differentiation in insects.

Prevalence of Reversed Genome Organizations for Viruses in the Family Iflaviridae, Order Picornavirales

Viruses in the order Picornavirales possess a positive-strand RNA genome that encodes structural proteins (SPs) and nonstructural proteins (NSPs). According to the recent report of the International Committee on Taxonomy of Viruses (ICTV), there are 8 families in Picornavirales, and monopartite picornaviruses in each family exhibit distinct types of genome organizations with rearranged genes coding for SPs and NSPs, namely, TypeI (5'-SPs-NSPs-3') and TypeII (5'-NSPs-SPs-3'). In the present study, 2 iflaviruses with the 2 genome types were unexpectedly identified in a damselfly host species, suggesting that these 2 genome types coexisted in the same host species, and the families of order Picornavirales might be more complex than previously thought. The consequent systematic homologous screening with all the publicly available picornaviruses successfully revealed a considerable number of candidates rearranged genome types of picornaviruses in various families of Picornavirales. Subsequently, phylogenetic trees were reconstructed based on RNA dependent RNA polymerase and coat protein, which evidently confirmed the prevalence of the 10 typeII iflaviruses in the Iflaviridae family. This suggests that genome types may not be relevant to viral taxonomy in this family. However, candidate picornaviruses with reversed genome types in the Secoviridae and Dicistroviridae families require further investigation. All in all, as the number of newly discovered viruses increases, more viruses with non-canonical genome arrangements will be uncovered, which can expand our current knowledge on the genome complexity and evolution of picornaviruses. IMPORTANCE Monopartite viruses in the order Picornavirales exhibit distinct genome arrangement of nonstructural proteins and structural proteins for each of the 8 families. Recent studies indicated that at least 4 ifla-like viruses possessed reversed genome organization in the family Iflaviridae, raising the possibility that this phenomenon may commonly present in different families of picornaviruses. Since we discovered 2 iflaviruses with exchanged structural and nonstructural proteins simultaneously in the damselfly, a systematic screening was subsequently performed for all of the current available picornaviruses (1,543 candidates). The results revealed 10 picornaviruses with reversed genome organization in the family Iflaviridae, implying that this phenomenon might prevalence in the order Picornavirales. These results will contribute to a better understanding for the future study on the genome complexity and taxonomy of picornaviruses.

High-throughput sequencing yields a complete mitochondrial genome of the rice thrips, Stenchaetothrips biformis (Thysanoptera: Thripidae)

Rice thrips, Stenchaetothrips biformis (Bagnall, 1913), are one of the destructive pests of rice. Here, the complete mitochondrial genome of S. biformis was sequenced using high-throughput sequencing. The mitogenome is 15,359 bp long with an A + T content of 76.94%, which contains 13 protein-coding genes (PCGs), 22 transfer RNA (tRNAs), 2 ribosomal RNA genes (rRNAs) and 2 putative control regions (CRs). The phylogenetic analysis showed that S. biformis is closely related to Thrips imaginis and Thrips palmi. This new mitochondrial genome data can be better used to provide a basis for studies of the mitochondrial evolution of Thysanoptera.

An RNA Virome Analysis of the Pink-Winged Grasshopper Atractomorpha sinensis

A large number of RNA viruses have been discovered in most insect orders using high-throughput sequencing (HTS) and advanced bioinformatics methods. In this study, an RNA virome of the grasshopper was systematically identified in Atractomorpha sinensis (Orthoptera: Pyrgomorphidae), an important agricultural pest known as the pink-winged grasshopper. These insect viruses were classified as the nege-like virus, iflavirus, ollusvirus, and chu-like virus using HTS and phylogenetic analyses. Meanwhile, the full sequences of four novel RNA viruses were obtained with RACE and named Atractomorpha sinensis nege-like virus 1 (ASNV1), Atractomorpha sinensis iflavirus 1 (ASIV1), Atractomorpha sinensis ollusvirus 1 (ASOV1), and Atractomorpha sinensis chu-like virus 1 (ASCV1), respectively. Moreover, the analysis of virus-derived small interfering RNAs showed that most of the RNA viruses were targeted by the host antiviral RNA interference pathway. Moreover, our results provide a comprehensive analysis on the RNA virome of A. sinensis.

Complete genome analysis of a novel chuvirus from a southern green stink bug (Nezara viridula)

A novel chuvirus from a southern green stink bug (Nezara viridula) was identified by RNA sequencing in this study and was tentatively named "Ningbo southern green stink bug chuvirus 1" (NBSGSBV-1). The complete genome sequence of NBSGSBV-1 consists of 11,375 nucleotides, and the genome was found to be circular by 'around-the-genome' reverse transcription polymerase chain reaction (RT-PCR) and Sanger sequencing. Three open reading frames (ORFs) were predicted in the NBSGSBV-1 genome, encoding a large polymerase protein (L protein), a glycoprotein (G protein), and a nucleocapsid protein (N protein). A phylogenetic tree was constructed based on all of the currently available RNA-dependent RNA polymerase amino acid sequences of viruses of the family Chuviridae, and NBSGSBV-1 was found to cluster together with Sanya chuvirus 2 and Hubei odonate virus 11, indicating that NBSGSBV-1 might belong to the genus Odonatavirus. Five conserved sites were identified in the L proteins of NBSGSBV-1 and other chuviruses. The abundance and characteristics of the NBSGSBV-1-derived small interfering RNAs suggested that NBSGSBV-1 actively replicates in the host insect. To the best of our knowledge, this is the first report of a chuvirus identified in a member of the insect family Pentatomidae. The discovery and characterization of NBSGSBV-1 will help us to understand the diversity of chuviruses in insects.

Complete genome analysis of a novel picorna-like virus from a ladybird beetle (Cheilomenes sexmaculata)

The ladybird beetle Cheilomenes sexmaculata (family Coccinellidae, order Coleoptera) is a common insect predator of agricultural pests. In this study, the full genome sequence of a novel picorna-like virus, tentatively named "Cheilomenes sexmaculata picorna-like virus 1" (CSPLV1), was identified in C. sexmaculata. The full-length sequence of CSPLV1 is 11,384 nucleotides (nt) in length (excluding the polyA tail), with one predicted open reading frame (ORF) encoding a polyprotein of 3727 amino acids, a 13-nt 5' untranslated region (UTR), and a 187-nt 3' UTR. The ORF of CSPLV1 consists of four distinct domains, including an RNA virus helicase domain (nt 3029-3319), a peptidase domain (nt 5555-6121), an RNA-dependent RNA polymerase domain (nt 7154-8101), and a picorna-like coat protein domain (nt 8606-9283). Phylogenetic analysis based on the conserved RdRP sequence showed that CSPLV1, together with Wuhan house centipede virus 3, Hypera postica associated virus 1, and Diabrotica undecimpunctata virus 1, forms an unclassified group that is closely related to members of the family Solinviviridae. To the best of our knowledge, CSPLV1 is the first picorna-like virus discovered in C. sexmaculata.

Complete genome analysis of a nege-like virus in aphids (Astegopteryx formosana)

Negeviruses are a group of insect-specific viruses that have a wide geographic distribution and broad host range. In recent years, nege-like viruses have been discovered in aphids of various genera of the family Aphididae, including Aphis, Rhopalosiphum, Sitobion, and Indomegoura. Here, we report the complete genome sequence of a nege-like virus isolated from Astegopteryx formosana aphids collected in Guangdong, China, which we have designated as "Astegopteryx formosana nege-like virus" (AFNLV). AFNLV has a genome length of 10,107 nt (excluding the polyA tail) and possesses the typical conserved domains of negeviruses. These include a viral methyltransferase, an S-adenosylmethionine-dependent methyltransferase, a viral helicase, and an RNA-dependent RNA polymerase (RdRP) domain in open reading frame 1 (ORF1), a DiSB-ORF2_chro domain in ORF2, and a SP24 domain in ORF3. The genome of AFNLV shares the highest nucleotide sequence identity (74.89%) with Wuhan house centipede virus, identified in a mixture of barley aphids. As clearly revealed by RdRP-based phylogenetic analysis, AFNLV, together with other negeviruses and nege-like viruses discovered in aphids, formed a distinct "unclassified clade" closely related to members of the proposed genus "Sandewavirus" and the family Kitaviridae. In addition, small interfering RNAs (siRNAs) derived from AFNLV did not exhibit typical characteristics of virus-derived siRNAs processed by the host RNAi-based antiviral pathway. However, the extremely high abundance of viral transcripts (average read coverage 73,403X) strongly suggested that AFNLV might actively replicate in the aphid host. AFNLV described in this study is the first nege-like virus discovered in aphids of the genus Astegopteryx, which will contribute to future study of the co-evolution of nege/nege-like viruses and their host aphids.

Identification of salivary proteins in the whitefly Bemisia tabaci by transcriptomic and LC-MS/MS analyses

The whitefly Bemisia tabaci is a notorious agricultural pest of many crops worldwide. Although it is thought that B. tabaci secretes saliva into the host plant to counter plant defenses, knowledge on the whitefly salivary proteome is limited. Here, we characterized the gene/protein repertoires of B. tabaci salivary glands and secreted saliva by transcriptomic and liquid chromatography tandem mass spectroscopy analyses. A total of 698 salivary gland-enriched unigenes and 171 salivary proteins were identified. Comparative analysis between the B. tabaci salivary proteins and those of different arthropod species revealed numerous similarities in proteins associated with binding, hydrolysis, and oxidation-reduction, which demonstrates a degree of conservation across herbivorous saliva. There were 74 proteins only identified in B. tabaci saliva, of which 34 were B. tabaci-specific. In addition, 13 salivary proteins, of which 11 were B. tabaci-specific, were differentially regulated when B. tabaci fed on different hosts. Our results provide a good resource for future functional studies of whitefly salivary effectors, and might be useful in pest management.

Chromosome-level genome assembly of the bean bug Riptortus pedestris

The bean bug (Riptortus pedestris) causes great economic losses of soybeans by piercing and sucking pods and seeds. Although R. pedestris has become the focus of numerous studies associated with insect-microbe interactions, plant-insect interactions, and pesticide resistance, a lack of genomic resources has limited deeper insights. Here, we report the first R. pedestris genome at the chromosomal level using PacBio, Illumina, and Hi-C technologies. The assembled genome was 1.080 Gb in size with a contig N50 of 2.882 Mb. More than 96.3% of the total genome bases were successfully anchored to six unique chromosomes. Genome resequencing of male and female individuals and chromosomic staining demonstrated that the sex chromosome system of R. pedestris is XO, and the shortest chromosome is the X chromosome. In total, 19,026 protein-coding genes were predicted, 18,745 of which were validated as being expressed. Temporospatial expression of R. pedestris genes in six tissues and 37 development stages revealed 4,657 and 7,793 genes mainly expressed in gonads and egg periods, respectively. Evolutionary analysis demonstrated that R. pedestris and Oncopeltus fasciatus formed a sister group and split ∼80 million years ago (Mya). Additionally, a 5.04 Mb complete genome of symbiotic Serratia marcescens Rip1 was assembled, and the virulence factors that account for successful colonization in the host midgut were identified. The high-quality R. pedestris genome provides a valuable resource for further research, as well as for the pest management of bug pests.

Complete genome sequence of a novel nege-like virus in aphids (genus Indomegoura)

Background

Aphids are important vectors of numerous plant viruses. Besides plant viruses, a number of insect specific viruses (ISVs), such as nege/nege-like viruses, have been recently discovered in aphids of the genera Aphis, Rhopalosiphum, and Sitobion.

Findings

In this study, the complete genome sequence of a novel nege-like virus, tentatively named “Indomegoura nege-like virus 1” (INLV1), was identified in aphids of the genus Indomegoura. INLV1 possessed a single positive-stranded RNA genome with 8945 nucleotides, which was predicted to contain three typical open reading frames (ORFs) of negeviruses (including ORF1, ORF2, and ORF3), a 44-nt 5′ untranslated region (UTR) and a 98-nt 3′ UTR. Five conserved domains were predicted for INLV1, including an Alphavirus-like methyltransferase domain, a RNA virus helicase core domain, and a RNA-dependent RNA polymerase domain (RdRP) in ORF1, a DISB-ORF2_chro domain in ORF2, and a SP24 domain in ORF3. According to the maximum likelihood phylogenetic tree based on RdRP, INLV1 was grouped with barley aphid RNA virus 1 and Hubei virga-like virus 4, together with another two invertebrate viruses, which formed a distinct clade in the proposed group Centivirus. The alignment of RdRP domains for INLV1 and other nege/kita-like viruses suggested that RdRP of INLV1 contained the permuted C (GDD)- A [DX(4–5)D] –B [GX(2–3)TX(3)N] motifs, which were conserved in the Centivirus and Sandewavirus groups. Furthermore, the high abundance and typical characteristics of INLV1 derived small interfering RNAs clearly showed the active replication of INLV1 in the aphid Indomegoura.

Conclusion

INLV1 is the first nege-like virus infecting aphids of the genus Indomegoura. As far as we know, it is also the first ISV revealed in this aphid genus.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12985-021-01552-w.

[Establishment and primary clinical application of metabolic evaluation database of urolithiasis]

Objective: To establish the metabolic evaluation database of urolithiasis, perform metabolic evaluation, and provide instructions for treatment and prevention of urolithiasis. Methods: This metabolic evaluation database was developed by JAVA and was established by Oracle11g database and Browser/Server framework. We extracted the clinical data of all patients who had complete information, and analyzed their risk factors of stone formation, stone-related medical history, blood and urine tests results and 24-hour urine analysis. Results: A total of 360 patients diagnosed as urolithiasis were included in this research. Male to female ratio was 1.9∶1, and the urolithiasis was first diagnosed at (35.5±13.5) years old. Family history was positive in 39.7% of patients. Metabolic syndrome occurred in 35.0% of patients. Overweight or obesity occurred in 73.2% and 50.0% of male patients, respectively. Abdominal obesity in 62.3% and 56.1% of male and female patients, respectively. Among all patients, 67.5% had high urine sodium, 53.6% had hypercalciuria, 41.1% had hypocitraturia, 29.7% had hyperuricosuria, 22.5% had hypomagnesuria, 15.8% had hyperoxaluria, 11.7% had hyperphosphoraturia, and 36.4% had low urinary volume. Conclusions: The prevalence of overweight or obesity, abdominal obesity, hypertension, diabetes, and metabolic syndrome in stone patients were significantly higher than those in general population. The number of 24-hour urinary abnormalities was positively associated with body mass index. The interventions on high urinary sodium, low urinary volume, obesity and metabolic syndrome were important to the treatment of urolithiasis. This database would facilitate the metabolic evaluation, provide evidence for the treatment and prevention of urolithiasis, and lay foundation for finding important controllable risk factors of urinary stone.

Clinicoradiological features associated with epidermal growth factor receptor exon 19 and 21 mutation in lung adenocarcinoma

AIM

To retrospectively identify clinicopathological and radiological characteristics that could be independent predictors of epidermal growth factor receptor (EGFR) exon 19 and 21 mutation in surgically resected lung adenocarcinomas in a cohort of Asian patients.

MATERIALS AND METHODS

Demographics, histopathology data, and preoperative chest computed tomography (CT) images were evaluated retrospectively in 471 surgically resected lung adenocarcinomas. A total of 24 CT descriptors were assessed. Univariate analyses and multivariate logistic regression analyses were performed to identify independent predicted factors of harbouring EGFR mutations.

RESULTS

EGFR mutations were existed in 252 (53.5%) of 471 patients, and associated with 11 clinicoradiological features. For the model with both clinical and radiological features, the independent predictors of harbouring EGFR mutation were small maximum diameter (≤3.9 cm), non-smokers, micropapillary pattern, pleural retraction, vascular convergence, and absence of solid pattern. The area under the receiver operating characteristic (ROC) curve (AUC) was 0.784. Multivariable logistic regression analysis indicated that non-smokers, vascular convergence, and absence of solid pattern were important independent predictors of EGFR exon 19 mutation, while non-smokers and vascular convergence were independent predictors of EGFR exon 21 mutation. The AUCs were 0.807 and 0.794, respectively. A lepidic growth pattern appeared more frequently in exon 21 mutant tumours than in exon 19 mutant group (p<0.001).

CONCLUSION

CT imaging features of lung adenocarcinomas in combination with clinical variables could be used to prognosticate EGFR mutation status. The separate analysis of EGFR exon 19 or 21 mutation could further improve diagnostic performance.

[The prevalence of temporomandibular disorder symptoms in 898 university students and its relationship with psychological distress and sleep quality]

OBJECTIVE

To investigate the prevalence of temporomandibular disorders(TMD) symptoms, psychological distress and sleep quality in a population of Chinese university students, and discuss the relationship between psychological distress, sleep quality and TMD symptoms.

METHODS

A total of 898 stomatological university students from 5 Chinese universities(342 males and 556 females with a mean age of 20.5 years) were included in the study. Self-reported TMD symptoms using diagnostic criteria for temporomandibular disorders symptom questionnaire were collected. Depression, anxiety and stress scales-21(DASS-21) and Pittsburgh sleep quality index(PSQI) were used to measure psychological distress and sleep quality.

RESULTS

61.9% (556/898) of the students had TMD symptoms. The most common symptoms were pain and clicking of joint, with a prevalence of 42.3% (380/898) and 34.2% (307/898), respectively. The prevalence of depression, anxiety, stress and sleep quality among the students who had TMD symptoms was 33.5%(186/556), 63.1%(351/556), 29.5%(164/556) and 30.2%(243/556), respectively, which was significantly higher than those who had no TMD symptoms(24.3% [83/342], 48.5% [166/342], 21.6%[74/342] and 21.9%[75/342])(P<0.05). Stepwise logistic regression analysis demonstrated that anxiety (OR 1.57, 95%CI 1.14-2.15) and female(OR 1.57, 95%CI 1.19-2.08) were possible risk indicators for TMD symptoms(P<0.05).

CONCLUSIONS

Chinese university students reported a high prevalence of TMD symptoms, which may have a correlation with psychological distress symptoms such as anxiety.

Seasonal variation and source apportionment of organic tracers in PM10 in Chengdu, China

Organic compound tracers including n-alkanes, triterpane, sterane, polycyclic aromatic hydrocarbons (PAHs) and dicarboxylic acids of airborne particulate matter (PM10) were characterized for samples collected at five sites from July 2010 to March 2011 using GC/MS. Spatial and temporal variations of these organic tracers in PM10 were studied, and their sources were then identified respectively. Average daily concentrations of PM10 varied in different seasons with the trend of PM10 in winter (0.133 mg/m(3)) > autumn (0.120 mg/m(3)) > spring (0.103 mg/m(3)) > summer (0.098 mg/m(3)). Daily concentrations of n-alkanes (C11-C36) ranged from 12.11 to 163.58 ng/m(3) with a mean of 61.99 ng/m(3). The C max and CPI index of n-alkanes indicated that vehicle emissions were the major source in winter, while the contributions of high plant wax emissions became significant in other seasons. It was discovered that the main sources of triterpenoid and steranes were gasoline and diesel engine emissions. Concentrations of ∑15PAHs in PM10 also varied (12.25-58.56 ng/m(3)) in different seasons, and chrysene, benzo(a)pyrene, benzo(b)fluoranthene, benzo(k)fluoranthene, benzo(ghi) perylene and fluoranthene were the dominant components. In the four seasons, the concentration of ∑15PAHs was relatively higher at the northern site because of traffic congestion. The main source of airborne PAHs was traffic emissions and coal combustion. Average daily concentrations of dicarboxylic acids (C4-C10) in PM10 ranged from 12.11 to 163.58 ng/m(3), of which azeleic acid was the major compound (0.49-52.04 ng/m(3), average 14.93 ng/m(3)), followed by succinic acid (0.56-19.08 ng/m(3), average 6.84 ng/m(3)). The ratio of C6/C9 showed that the major source in winter was biological, while the contributions of emissions from anthropogenic activities were much higher in summer.

Vascular stiffness in familial hypercholesterolaemia is associated with C-reactive protein and cholesterol burden

BACKGROUND

Familial hypercholesterolaemia (FH) is characterized by very high serum cholesterol and premature coronary atherosclerosis. Arterial stiffness and atherosclerosis are two major underlying pathophysiologies of arterial disease that are predictive of future cardiovascular events. The aims of this study were to quantify atherosclerosis and arterial stiffness and to evaluate their relationship with high sensitive C-reactive protein (hs-CRP) and the level of exposure to high serum cholesterol in FH patients.

MATERIALS AND METHODS

We measured traditional risk factors, hs-CRP, intima-media thickness (IMT) of carotid artery, and brachial-ankle pulse wave velocity (baPWV) in 35 heterozygous FH subjects and 17 healthy control subjects. Cholesterol-year score (CYS) was calculated to estimate the lifetime cholesterol burden in FH subjects.

RESULTS

FH subjects had significantly elevated total cholesterol, low-density lipoprotein cholesterol, and carotid IMT compared with those without mutations. Among FH patients, the baPWV and carotid IMT were higher in cases with high cholesterol burden than those without. Similarly, the baPWV and carotid IMT were also higher in cases with elevated hs-CRP (> 1 mg L(-1)) than those without. Multiple linear regression analysis demonstrated CYS and hs-CRP were significant independent predictors of baPWV and IMT in FH patients.

CONCLUSIONS

Both high cholesterol burden and vascular inflammation are not only associated with atherosclerosis, but also contribute to the development of arterial stiffness in FH patients. Early detection of hypercholesterolaemia in FH patients is warranted to prevent the untoward pathophysiologies.

Identification and characterization of novel low-density lipoprotein receptor mutations of familial hypercholesterolaemia patients in Taiwan

BACKGROUND

Familial hypercholesterolaemia (FH) is an autosomal dominant disease associated with a very high risk of coronary vascular disease. The study objective was to identify patients with FH in Taiwan and characterize novel mutations.

MATERIALS AND METHODS

Fifty-one patients with suspected FH living in Taiwan were screened for mutations in both the low-density lipoprotein (LDL) receptor and the apolipoprotein (apoB) genes using the multiplex polymerase chain reaction and exon-by-exon DNA sequencing technique. Functional consequences on LDL receptor activity were characterized in vitro for novel mutations and family pedigree was also analyzed.

RESULTS

Thirteen different functional mutations in the LDL receptor gene and one mutation in the apoB gene were found in 21 patients. Among the 13 mutations in the LDL receptor gene, 10 were single-point missense mutations, one was a two-point mutation in the same allele, one was a non-sense mutation and one was a frame-shift mutation. There were three novel mutations, including two missense mutations (M510K and W512R) and one frame-shift mutation (1953 delTA mutation). The characterization of missense M510K retained 36.2% of the activity of the normal receptor. Conversely, frame-shift 1953 delTA and missense W512R led to defective proteins, with only 0-6% of normal receptor activity.

CONCLUSIONS

The study identified 13 LDL receptor gene mutations and characterized three novel mutations causing FH in Taiwan. This facilitated a better understanding of FH among the Chinese population and may enable diagnosis of FH at the molecular level at a presymptomatic, early age.

[Study of cardiovascular and cerebrovascular disease in Chinese traditional medicines on Pb, Cr, Cd by AAS]

Cardiovascular and cerebrovascular disease are the common and frequently-occurring disease for the old man and are the main cause of death in the world. The Z-8000 polarized zeeman atomic absorption spectrophotometer was used for the determination of Pb, Cr, Cd in seventeen kinds of Chinese traditional medicines. And studied on Pb, Cr, Cd in Zhennao Ning, Di Ao Xinxue Kang, Linao Xin, Xueshuan Xinmai Ning et al. thirteen kinds of Chinese traditional medicines. The result shows that Chinese traditional medicines of cardiovascular and cerebrovascular drugs contain Pb, Cr, Cd and their efficacies are related to Pb, Cr, Cd.

Mechanisms of tolerance induction: splenocytes from total lymphoid irradiated mice inhibit the IL-2 pathway in TCR-activated CD4 cells

Mice given total lymphoid irradiation (TLI) can be tolerized by an incompletely understood mechanism to foreign Ags given during a brief window of time immediately after completing radiation. We previously showed that splenocytes taken from mice immediately after completing TLI treatment (TLI cells) block the ability of control cells to proliferate or to produce IL-2 in response to alloantigen, suggesting that TLI cells interfere with the IL-2 pathway in responder lymphocytes. To further characterize the mechanism by which TLI cells affect IL-2, we utilized an in vitro system of T cell activation. Adding TLI cells into cultures decreased the ability of TCR-stimulated T cells to proliferate and to secrete IL-2 by 40 to 60%. Exogenous IL-2 did not restore the proliferative response. The inhibition of IL-2 secretion resulted both from a decrease in the number of IL-2-producing cells and a decrease in IL-2 mRNA transcription. TLI cells directly inhibited IL-2 secretion by TCR-stimulated CD4 cells, as determined by ELISPOT. Competitive PCR demonstrated that TLI cells decreased IL-2 transcription of TCR-stimulated CD4 cells by 75%. In situ hybridization confirmed that unfractionated spleen and sorted CD4 cells from TCR-stimulated cultures transcribed less IL-2 RNA in the presence of TLI cells. The results show that TLI cells directly inhibit IL-2 transcription and protein secretion of normal TCR-stimulated CD4 cells.

Mechanisms of tolerance induction: splenocytes from total lymphoid irradiated mice inhibit the IL-2 pathway in TCR-activated CD4 cells

Mice given total lymphoid irradiation (TLI) can be tolerized by an incompletely understood mechanism to foreign Ags given during a brief window of time immediately after completing radiation. We previously showed that splenocytes taken from mice immediately after completing TLI treatment (TLI cells) block the ability of control cells to proliferate or to produce IL-2 in response to alloantigen, suggesting that TLI cells interfere with the IL-2 pathway in responder lymphocytes. To further characterize the mechanism by which TLI cells affect IL-2, we utilized an in vitro system of T cell activation. Adding TLI cells into cultures decreased the ability of TCR-stimulated T cells to proliferate and to secrete IL-2 by 40 to 60%. Exogenous IL-2 did not restore the proliferative response. The inhibition of IL-2 secretion resulted both from a decrease in the number of IL-2-producing cells and a decrease in IL-2 mRNA transcription. TLI cells directly inhibited IL-2 secretion by TCR-stimulated CD4 cells, as determined by ELISPOT. Competitive PCR demonstrated that TLI cells decreased IL-2 transcription of TCR-stimulated CD4 cells by 75%. In situ hybridization confirmed that unfractionated spleen and sorted CD4 cells from TCR-stimulated cultures transcribed less IL-2 RNA in the presence of TLI cells. The results show that TLI cells directly inhibit IL-2 transcription and protein secretion of normal TCR-stimulated CD4 cells.

Mechanisms of total lymphoid irradiation-induced immunosuppression. II. Failure of con A-stimulated splenocytes from TLI-treated mice to express IL-2 and IL-2 receptor RNA

Total lymphoid irradiation is a radiotherapy procedure used as an alternative immunosuppressive regimen in organ transplantation. Following TLI mature lymphocytes are depleted, and splenocytes do not proliferate to mitogens, produce IL-2, or express IL-2 receptors. We now show that mitogen stimulated splenocytes from TLI-treated mice do not secrete IL-2 protein by an IL-2 ELISA assay. Northern blot analysis and RNase protection assays reveal that TLI splenocytes do not make IL-2 RNA or IL-2 receptor RNA following mitogen stimulation. TLI splenocytes produce at least 1000 times less IL-2 RNA after Con A stimulation than normal splenocytes. TLI therapy resembles anti-CD4 therapy and CsA in that each results in an IL-2-"depleted" state.