Genome-wide identification, expression profiling, and target gene analysis of microRNAs in the Onion thrips, Thrips tabaci Lindeman (Thysanoptera: Thripidae), vectors of tospoviruses (Bunyaviridae)

Regulatory networks of mRNAs and miRNAs involved in the immune response of diamondback moth, Plutella xylostella to fungal infection

BACKGROUND

The entomopathogenic fungus, Isaria fumosorosea, shows promise as a biological control agent in managing the diamondback moth (DBM) Plutella xylostella, a highly destructive global pest of cruciferous vegetables. To date, the miRNA-mRNA regulatory networks underlying the immune response of DBM to I. fumosorosea infection are still poorly understood. Here, we characterize the expression profiles of miRNA and mRNA, and construct the miRNA-gene regulatory network in DBM infected with I. fumosorosea.

RESULTS

We identified 580 differentially expressed genes (DEGs) and 55 differentially expressed miRNAs (DEMs) in I. fumosorosea-infected DBM. Among these DEGs, we found 28 immunity-related genes, which mainly include pattern recognition receptors, signal modulators, and immune effectors. Integrated analysis discovered 87 negative correlation pairs between miRNA and mRNA, involving 40 DEMs and 62 DEGs in infected DBM. Additionally, 13 miRNAs and 10 corresponding mRNAs were identified as candidate miRNA-mRNA pairs for DBM immunity against fungal infection. Gene functional enrichment analysis indicated that these miRNAs could target genes associated with various pathways, such as the immune system, infectious diseases, digestive system, endocrine system, nervous system, and signal transduction. Finally, the regulatory relationships of six miRNA-mRNA pairs were validated using quantitative reverse transcription PCR.

CONCLUSIONS

For the first time, we present integrated miRNA and mRNA data to elucidate the immune response of the DBM to fungal infection. Our findings enhance the understanding of the immune response of the DBM to entomopathogenic fungi infection.

Unveiling thrips morphology: A comparative analysis of microscopy-based ultrastructural, morphological, and molecular characterization of Thrips tabaci and Thrips parvispinus in onion

The present study unveils the intricate details on the morphology of thrips through optical, field emission scanning electron microscopy (FE-SEM) and mitochondrial cytochrome oxidase I gene-based molecular identification tools. The variation in the morphological characters namely, antennae (seven-segmented with forked sensorium on third, fourth segments), ctenidia (paired ctenidia were present in 5th-8th abdominal segments laterally), pronotum (two pairs of posteroangular setae) were observed in both Thrips tabaci and Thrips parvispinus, respectively. Similarly, ocelli color (brown and red colored), ocellar setae (two and three pairs of ocellar setae on the head of T. tabaci and T. parvispinus, respectively. Irregular reticulate striations on metascutum and medial striations are present in the metanotum of T. parvispinus; forewings with 6 distal setae in the first vein and 15 distal setae in the second vein in T. tabaci and forewings of T. parvispinus with complete rows of setae in the first and second vein in T. parvispinus; abdomen with median dorsal setae present in the tergite of T. tabaci and presence of 6-12 discal setae in sternites III-VI segments, absence of discal setae on sternites II and VII in T. parvispinus were observed, respectively. Further, FE-SEM studies revealed that similar type of sensilla namely, sensilla basiconica (SBI, SBII, SBIII), sensilla chaetica (SChI, SChII), sensilla trichodea (ST), sensilla campaniformia (SCa), and sensilla cavity (SCav) were recorded in both the species and variations were observed in length of above sensilla of T. tabaci and T. parvispinus. Additionally, Bohm bristles (Bb) and microtrichia (Mt) on the antennal surface contributed to a comprehensive understanding of their ultrastructural features. The molecular characterization revealed a single ~450 bp nucleotide fragment with over 98% similarity for the confirmation of T. tabaci and T. parvispinus in concurrence with NCBI data. RESEARCH HIGHLIGHTS: Microscopy-based morphological and ultrastructural characterization of Thrips tabaci Lindeman and Thrips parvispinus Karny.

Elucidating the ecophysiology of soybean pod-sucking stinkbug Riptortus pedestris (Hemiptera: Alydidae) based on de novo genome assembly and transcriptome analysis

Food security is important for the ever-growing global population. Soybean, Glycine max (L.) Merr., is cultivated worldwide providing a key source of food, protein and oil. Hence, it is imperative to maintain or to increase its yield under different conditions including challenges caused by abiotic and biotic stresses. In recent years, the soybean pod-sucking stinkbug Riptortus pedestris has emerged as an important agricultural insect pest in East, South and Southeast Asia. Here, we present a genomics resource for R. pedestris including its genome assembly, messenger RNA (mRNA) and microRNA (miRNA) transcriptomes at different developmental stages and from different organs. As insect hormone biosynthesis genes (genes involved in metamorphosis) and their regulators such as miRNAs are potential targets for pest control, we analyzed the sesquiterpenoid (juvenile) and ecdysteroid (molting) hormone biosynthesis pathway genes including their miRNAs and relevant neuropeptides. Temporal gene expression changes of these insect hormone biosynthesis pathways were observed at different developmental stages. Similarly, a diet-specific response in gene expression was also observed in both head and salivary glands. Furthermore, we observed that microRNAs (bantam, miR-14, miR-316, and miR-263) of R. pedestris fed with different types of soybeans were differentially expressed in the salivary glands indicating a diet-specific response. Interestingly, the opposite arms of miR-281 (-5p and -3p), a miRNA involved in regulating development, were predicted to target Hmgs genes of R. pedestris and soybean, respectively. These observations among others highlight stinkbug's responses as a function of its interaction with soybean. In brief, the results of this study not only present salient findings that could be of potential use in pest management and mitigation but also provide an invaluable resource for R. pedestris as an insect model to facilitate studies on plant-pest interactions.

Genomic and Transcriptomic Insights into the Genetic Basis of Foam Secretion in Rice Spittlebug Callitettix versicolor

Many animal species produce protective foams, the majority of which exhibit evolutionary adaptability. Although the function and composition of foams have been widely studied, the genetic basis of foam secretion remains unknown. Unlike most species that produce foam under specific situations, spittlebugs continuously secrete foams throughout all nymphal stages. Here, we capitalize on the rice spittlebug (Callitettix versicolor) to explore the genetic basis of foam secretion through genomic and transcriptomic approaches. Our comparative genomic analysis for C. versicolor and eight other insect species reveals 606 species-specific gene families and 66 expanded gene families, associated with carbohydrate and lipid metabolism. These functions are in accordance with the composition of foams secreted by spittlebugs. Transcriptomic analyses of malpighian tubules across developmental stages detected 3192 differentially expressed genes. Enrichment analysis of these genes highlights functions also revealed by our comparative genomic analysis and aligns with previous histochemical and morphological observations of foam secretion. This consistency suggests the important roles of these candidate genes in foam production. Our study not only provides novel insights into the genetic basis of foam secretion in rice spittlebugs but also contributes valuable knowledge for future evolutionary studies of spittlebugs and the development of pest control strategies for C. versicolor.

Predicting the potential geographical distribution of onion thrips, Thrips tabaci in India based on climate change projections using MaxEnt

Onion thrips, Thrips tabaci Lindeman, an economically important onion pest in India, poses a severe threat to the domestic and export supply of onions. Therefore, it is important to study the distribution of this pest in order to assess the possible crop loss, which it may inflict if not managed in time. In this study, MaxEnt was used to analyze the potential distribution of T. tabaci in India and predict the changes in the suitable areas for onion thrips under two scenarios, SSP126 and SSP585. The area under the receiver operating characteristic curve values of 0.993 and 0.989 for training and testing demonstrated excellent model accuracy. The true skill statistic value of 0.944 and 0.921, and the continuous Boyce index of 0.964 and 0.889 for training and testing, also showed higher model accuracy. Annual Mean Temperature (bio1), Annual Precipitation (bio12) and Precipitation Seasonality (bio15) are the main variables that determined the potential distribution of T. tabaci, with the suitable range of 22-28 °C; 300-1000 mm and 70-160, respectively. T. tabaci is distributed mainly in India's central and southern states, with 1.17 × 10⁶ km², covering 36.4% of land area under the current scenario. Multimodal ensembles show that under a low emission scenario (SSP126), low, moderate and optimum suitable areas of T. tabaci is likely to increase, while highly suitable areas would decrease by 17.4% in 2050 20.9% in 2070. Whereas, under the high emission scenario (SSP585), the high suitability is likely to contract by 24.2% and 51.7% for 2050 and 2070, respectively. According to the prediction of the BCC-CSM2-MR, CanESM5, CNRM-CM6-1 and MIROC6 model, the highly suitable area for T. tabaci would likely contract under both SSP126 and SSP585. This study detailed the potential future habitable area for T. tabaci in India, which could help monitor and devise efficient management strategies for this destructive pest.

The variation of a cytochrome P450 gene, CYP6G4, drives the evolution of Musca domestica L. (Diptera: Muscidae) resistance to insecticides in China

Long term and excessive insecticide use has resulted in some environmental problems and especially, insecticide resistance evolution in insect pests. The variation of cytochrome P450 monooxygenases (P450s), associated with the metabolic detoxification of toxic xenobiotics, is often involved in insecticide resistance. Here, we found that the variation in a P450 gene, CYP6G4, is the most important driver of carbamates resistance in the house fly (Musca domestica). Deciphering the detailed molecular mechanisms of the insecticide resistance is critical for performing suitable insecticide resistance management strategies. Our research results revealed that the combination of amino acid mutations (110C-330E-360N/S, 110C-330E-360S) of CYP6G4 could improve the resistance to propoxur. The nucleotide variations in the promoter region of CYP6G4 significantly increased the luciferase activity by the reporter gene assays. Additionally, miR-281-1-5p was confirmed to post-transcriptionally down-regulate the expression of CYP6G4. These findings suggest that three independent mechanisms; amino acid mutations of the P450 protein, mutations in the promoter region and low expression of post-trans-regulatory factors, as the powerful strategies for the insect resistance to toxic compounds, play a crucial role in the evolutionary processes of insecticide resistance.

Frontiers Approaches to the Diagnosis of Thrips (Thysanoptera): How Effective Are the Molecular and Electronic Detection Platforms?

Simple Summary

Thrips are important agricultural and forest pests. They cause damage by sucking plant sap and transmitting several plant viruses. Correct identification is the key for epidemiological studies and formulating appropriate management strategies. The application of molecular and electronic detection platforms has improved the morphological character-based diagnosis of thrips species. This article reviews research on molecular and automated identification of thrips species and discusses future research strategies for rapid and high throughput thrips diagnosis.

Abstract

Thrips are insect pests of economically important agricultural, horticultural, and forest crops. They cause damage by sucking plant sap and by transmitting several tospoviruses, ilarviruses, carmoviruses, sobemoviruses, and machlomoviruses. Accurate and timely identification is the key to successful management of thrips species. However, their small size, cryptic nature, presence of color and reproductive morphs, and intraspecies genetic variability make the identification of thrips species challenging. The use of molecular and electronic detection platforms has made thrips identification rapid, precise, sensitive, high throughput, and independent of developmental stages. Multi-locus phylogeny based on mitochondrial, nuclear, and other markers has resolved ambiguities in morphologically indistinguishable thrips species. Microsatellite, RFLP, RAPD, AFLP, and CAPS markers have helped to explain population structure, gene flow, and intraspecies heterogeneity. Recent techniques such as LAMP and RPA have been employed for sensitive and on-site identification of thrips. Artificial neural networks and high throughput diagnostics facilitate automated identification. This review also discusses the potential of pyrosequencing, microarrays, high throughput sequencing, and electronic sensors in delimiting thrips species.

Omics approaches in Allium research: Progress and way ahead

BACKGROUND

The genus Allium (Family: Amaryllidaceae) is an economically important group of crops cultivated worldwide for their use as a vegetable and spices. Alliums are also well known for their nutraceutical properties. Among alliums, onion, garlic, leek, and chives cultivated worldwide. Despite their substantial economic and medicinal importance, the genome sequence of any of the Allium is not available, probably due to their large genome sizes. Recently evolved omics technologies are highly efficient and robust in elucidating molecular mechanisms of several complex life processes in plants. Omics technologies, such as genomics, transcriptomics, proteomics, metabolomics, metagenomics, etc. have the potential to open new avenues in research and improvement of allium crops where genome sequence information is limited. A significant amount of data has been generated using these technologies for various Allium species; it will help in understanding the key traits in Allium crops such as flowering, bulb development, flavonoid biosynthesis, male sterility and stress tolerance at molecular and metabolite level. This information will ultimately assist us in speeding up the breeding in Allium crops.

METHOD

In the present review, major omics approaches, and their progress, as well as potential applications in Allium crops, could be discussed in detail.

RESULTS

Here, we have discussed the recent progress made in Allium research using omics technologies such as genomics, transcriptomics, micro RNAs, proteomics, metabolomics, and metagenomics. These omics interventions have been used in alliums for marker discovery, the study of the biotic and abiotic stress response, male sterility, organ development, flavonoid and bulb color, micro RNA discovery, and microbiome associated with Allium crops. Further, we also emphasized the integrated use of these omics platforms for a better understanding of the complex molecular mechanisms to speed up the breeding programs for better cultivars.

CONCLUSION

All the information and literature provided in the present review throws light on the progress and potential of omics platforms in the research of Allium crops. We also mentioned a few research areas in Allium crops that need to be explored using omics technologies to get more insight. Overall, alliums are an under-studied group of plants, and thus, there is tremendous scope and need for research in Allium species.

Spectral sensitivity of L2 biotype in the Thrips tabaci cryptic species complex

The onion thrips, Thrips tabaci (Lindeman, 1889), is a cosmopolitan pest of economic importance on a wide range of crops. Despite being one of the most studied thrips species, there is very limited knowledge available about its ability to perceive light. The T. tabaci cryptic species complex consists of a tobacco-associated (T) and two leek-associated (L1, L2) biotypes. We made electroretinogram recordings on the most widespread thelytokous (where unfertilized eggs produce females) T. tabaci L2 biotype and measured attraction to light sources in this biotype as a function of wavelength in behavioural experiments. The spectral sensitivity of the T. tabaci L2 biotype shows a unimodal curve peaking at λ_max = 521 nm. Contrary to this spectral sensitivity curve, L2 biotype attraction in an arena is bimodal with local maxima at 368 nm (UV) and 506-520 nm (green) being practically of the same magnitude. Although being similar to the arrhenotokous (where unfertilized eggs produce males) L1 biotype in phototaxis, significant differences regarding photoreceptor cell responses emerged. This study contributes to our understanding of light perception in Thysanoptera as well as to the development of more effective monitoring tools for this economically important pest species.