A novel single-stranded RNA virus in Nesidiocoris tenuis

Rich diversity of RNA viruses in the biological control agent, Orius laevigatus

Orius laevigatus (Hemiptera, Anthocoridae) is a generalist predator extensively used for the biocontrol of diverse agricultural pests. Previous studies on O. laevigatus have focused on the improvement of insect genetic traits, but little is known about its association with microbes, especially viruses that may influence its production and efficacy. More than 280 RNA viruses have been described in other Hemiptera insects, in line with the continuous discovery of insect-specific viruses (ISVs) boosted by next-generation sequencing. In this study, we characterized the repertoire of RNA viruses associated with O. laevigatus. Its virome comprises 27 RNA viruses, classified within fourteen viral families, of which twenty-three viruses are specific to O. laevigatus and four are likely associated with fungal microbiota. The analysis of viral abundance in five O. laevigatus populations confirmed the presence of simultaneous viral infections and highlighted the ubiquitous presence and high abundance of one solinvivirus and three totiviruses. Moreover, we identified 24 non-retroviral endogenous viral elements (nrEVEs) in the genome of O. laevigatus, suggesting a long-term relationship between the host and its virome. Although no symptoms were described in the insect populations under study, the high diversity of viral species and the high abundance of certain RNA viruses identified indicate that RNA viruses may be significant for the applicability and efficacy of O. laevigatus in biocontrol programs.

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.

Effects of PVY-Infected Tobacco Plants on the Adaptation of Myzus persicae (Hemiptera: Aphididae)

The indirect interaction between viruses and their insect vectors via the host plants can mediate viral transmission. Thus, elucidating these tripartite interactions is crucial for controlling the occurrence of viral diseases. This study examined the feeding behavior and life table parameters of the green peach aphid, Myzus persicae, using electropenetrography and an age-stage, two-sex life table on PVY-infected and uninfected tobacco plants. Furthermore, the amino acid and soluble sugar contents in tobacco tissue at different stages of PVY infection were determined. The results showed that PVY-infected plants exerted remarkable effects on the feeding activities of M. persicae. Aphids exhibited a reduced non-probing duration and increased phloem sap ingestion on infected plants. Although the nymph development time on the PVY-infected plants was significantly shorter than that of uninfected plants, M. persicae reared on infected plants had reduced fecundity and significantly shortened adult longevity. On day 12, the sugar: amino acid ratio of the PVY-infected plants was significantly higher than that of uninfected plants, whereas the opposite was observed on day 24. Our results demonstrated that PVY could alter the adaptability of M. persicae by modifying the nutritional quality of tobacco plants. In addition, divergent effects on aphids were observed at different infection stages, which are crucial to consider while exploring the interactions between viruses, insect vectors, and host plants. These results provided significant information for comprehending PVY spread and outbreaks.

The evolution of opsin genes in five species of mirid bugs: duplication of long-wavelength opsins and loss of blue-sensitive opsins

BACKGROUND

Color vision and phototactic behavior based on opsins are important for the fitness of insects because of their roles in foraging and mate choice. Related topics, including the duplication and loss of opsin genes, have been well investigated in insect orders such as Coleoptera, Lepidoptera, Hymenoptera, Odonata and Orthoptera, and the findings have been used to develop pest management strategies involving light trapping. Mirid bugs of Hemiptera, which are pests that cause heavy economic losses, show capacity for color discrimination and phototaxis. However, the opsins in mirid bugs remain uncharacterized. Herein, we examined five species to investigate the evolution of opsins in the family Miridae.

RESULTS

Using RNA-seq, we identified several contigs showing high identity with opsins, including four contigs in Apolygus lucorum and three contigs each in Adelphocoris suturalis, Adelphocoris fasciaticollis, Adelphocoris lineolatus and Nesidiocoris tenuis. Phylogenetic analyses indicated that one of these genes clustered with ultraviolet-sensitive (UV) opsins and that the others clustered with long-wavelength (LW) opsins, suggesting that duplication of LW opsins and loss of blue light-sensitive (B) opsins occurred in mirid bugs. The existence of introns in the LW opsins of mirid bugs suggested that the duplication events were DNA based. Both LW1 and LW2 opsins of mirid bugs were found to be under strong purifying selection. The LW1 opsins were significantly more highly expressed than the LW2 and UV opsins.

CONCLUSIONS

We identified the opsins of mirid bugs using five selected mirid species as a representative sample. Phylogenetic analyses clustered one of the genes with UV opsins and the others with LW opsins, suggesting the occurrence of LW opsin duplication and B opsin loss during the evolution of mirid bugs. Intron detection suggested that the identified duplication event was DNA based. The evidence of strong purifying selection and the relatively high expression levels suggested that these opsins exhibit fundamental functions in mirid bugs.

Sequencing and phylogenetic characterization of a novel Polerovirus from Nicotiana tabacum

In this study, we reported the complete genome of a novel Polerovirus, named Tobacco yellow virus (TYV), which can be transmitted by Myzus persicae. TYV had a single-stranded RNA genome of 5735 nucleotides in length and contained six putative open reading frames (ORFs). Phylogenetic analysis with whole genome nucleotide sequences and amino acid sequences deduced from the conserved domain of the RNA-dependent RNA polymerase, clustered TYV with Potato leafroll virus from the genus Polerovirus with high bootstrap values. However, TYV clustered with Brassica yellow virus using amino acid sequences deduced from the conserved domain of the coat protein. Taken together with the identities between ORFs in TYV and related ORFs in species from Polerovirus, our results strongly suggested TYV is a novel species of the genus Polerovirus.

Sequencing and phylogenetic characterization of a novel RNA virus genome from Harmonia axyridis

As a natural predator of many insect pests on its native Asian range, Harmonia axyridis remains amongst the insects whose pathogenic or beneficial microorganisms are yet to be studied. The genome nucleotide (nt) and amino acid sequences of open reading frames (ORFs) of the novel RNA virus were identified. Neighbor-joining (NJ) were constructed using MEGA7 software packages with nt sequences and conserved amino acid sequences of predicted RNA-dependent RNA polymerase (RdRp).The complete genome of a novel virus named Harmonia axyridis virus 1 was determined by RNA-seq and rapid amplification of cDNA ends from H. axyridis, which had a single-stranded RNA genome of 8868 nts in length and contains two putative ORFs. ORF1 encodes a polypeptide of 2182 amino acids, which contained conserved domains for 2 picornavirus-like capsid proteins and one RNA helicase. ORF2 encodes a polypeptide of 655 amino acids, which contained 1 RdRp domain. Phylogenetic analysis of whole genome nt sequences and RdRp deduced amino acid sequences suggested that the virus clustered with several unclassified Hubei picorna-like virus. To our knowledge, this is the first full annotated genome of a novel member of the unclassified group of RNA viruses, infecting H. axyridis in natural field conditions.

Preference of the aphid Myzus persicae (Hemiptera: Aphididae) for tobacco plants at specific stages of potato virus Y infection

Potato virus Y (PVY) is a common pathogen affecting agricultural production worldwide and is mainly transmitted by Myzus persicae in a non-persistent manner. Insect-borne plant viruses can modify the abundance, performance, and behavior of their vectors by altering host plant features; however, most studies have overlooked the fact that the dynamic progression of virus infection in plants can have variable effects on their vectors. We addressed this point in the present study by dividing the PVY infection process in tobacco into three stages (early state, steady state and late state); delineated by viral copy number. We then compared the differential effects of PVY-infected tobacco (Nicotiana tabacum) plants on the host selection and feeding behavior of M. persicae. We used Y-shaped olfactory apparatus and electrical penetration graph (EPG) methods to evaluate host selection and feeding behavior, respectively. Interestingly, we found that PVY-infected plants at the steady state attracted more aphids than healthy plants, whereas no differences were observed for those at the early and late states. In terms of feeding behavior, intracellular punctures (closely related to PVY acquisition and transmission) were more abundant on PVY-infected tobacco plants at the early and steady states of infection than in uninfected plants. These results indicate that PVY-infected host plants can alter the host selection and feeding behavior of aphids in a stage-dependent manner, which is an important consideration when studying the interactions among host plants, viruses, and insect vectors.

Duplication and expression of horizontally transferred polygalacturonase genes is associated with host range expansion of mirid bugs

BACKGROUD

Horizontal gene transfer and gene duplication are two major mechanisms contributing to the evolutionary adaptation of organisms. Previously, polygalacturonase genes (PGs) were independently horizontally transferred and underwent multiple duplications in insects (e.g., mirid bugs and beetles). Here, we chose three phytozoophagous mirid bugs (Adelphocoris suturalis, A. fasciaticollis, A. lineolatus) and one zoophytophagous mirid bug (Nesidiocoris tenuis) to detect whether the duplication, molecular evolution, and expression levels of PGs were related to host range expansion in mirid bugs.

RESULTS

By RNA-seq, we reported 30, 20, 19 and 8 PGs in A. suturalis, A. fasciaticollis, A. lineolatus and N. tenuis, respectively. Interestingly, the number of PGs was significantly positive correlation to the number of host plants (P = 0.0339) in mirid bugs. Most PGs (> 17) were highly expressed in the three phytozoophagous mirid bugs, while only one PG was relatively highly expressed in the zoophytophagous mirid bug. Natural selection analysis clearly showed that a significant relaxation of selection pressure acted on the PGs in zoophytophagous mirid bugs (K = 0.546, P = 0.0158) rather than in phytozoophagous mirid bugs (K = 1, P = 0.92), suggesting a function constraint of PGs in phytozoophagous mirid bugs.

CONCLUSION

Taken together with gene duplication, molecular evolution, and expression levels, our results suggest that PGs are more strictly required by phytozoophagous than by zoophytophagous mirid bugs and that the duplication of PGs is associated with the expansion of host plant ranges in mirid bugs.

Characterization of a novel RNA virus from Nesidiocoris tenuis related to members of the genus Iflavirus

The complete genome of a novel virus from Nesidiocoris tenuis was determined by RNA-seq and rapid amplification of cDNA ends. This virus has a single-stranded RNA genome of 10633 nucleotides (nt) in length, not including the poly(A) tail, and contains two putative open reading frames (ORFs). ORF1 encodes a polypeptide of 1320 amino acids (aa) with a predicted molecular mass of 147.92 kDa and theoretical isoelectric point (pI) of 6.96. ORF2 encodes a polypeptide of 1728 aa with a predicted molecular mass of 197.09 kDa and pI of 6.73. Phylogenetic analysis with the deduced aa sequences of the conserved RNA dependent RNA polymerase domain as well as whole genome nt sequences indicated that the virus clusters with viruses classified within the genus Iflavirus, with a high bootstrap value in the maximum-likelihood and neighbor-joining trees. However, this virus has a distinct genome structure with two ORFs, iflaviruses normally having one, suggesting the virus might be a prototype of a new genus. We named the virus isolate Nesidiocoris tenuis virus 1 (NtV-1). The prevalence of NtV-1 infection in wild samples of N. tenuis was at a low level (7.32%, 6 positive in 82 samples), suggesting a possible harmful effect to its host.