Selection of Reference Genes for RT-qPCR Analysis in the Hawthorn Spider Mite, Amphitetranychus viennensis (Acarina: Tetranychidae), Under Acaricide Treatments

Study on the variations in acaricide sensitivity between two spider mite species, Amphitetranychus viennensis and Tetranychus urticae, in Chinese orchards

Amphitetranychus viennensis and Tetranychus urticae, are destructive agricultural and horticultural pests. Their management primarily relies on acaricides; however, little is known about the susceptibility of these two species to these chemicals. The current study assessed the susceptibility of A. viennensis and T. urticae to ten acaricides, investigated the detoxification enzyme activities, and conducted transcriptional analyses after bifenazate and cyetpyrafen exposure. The results showed that the LC50 values of most acaricides against T. urticae were notably higher than those for A. viennensis at different developmental stages. At the adult stage, A. viennensis was more tolerant to bifenazate than T. urticae, while A. viennensis showed increased sensitivity to cyetpyrafen than T. urticae. After cyetpyrafen exposure, glutathione S-transferases (GSTs) activity in T. urticae were markedly higher at 6 and 12 h, whereas that in A. viennensis increased only at 6 h. No notable differences in cytochrome P450 monooxygenases (P450s) levels were found in T. urticae between the control and treatment groups (cyetpyrafen or bifenazate). However, A. viennensis treated with either cyetpyrafen or bifenazate showed a marked decrease in P450 levels at 12 h. Furthermore, more detoxification genes in both species were activated in response to bifenazate or cyetpyrafen. Differential metabolic detoxification mediated by P450 and GST genes may primarily account for the distinct responses of these species to bifenazate and cyetpyrafen. These findings reveal the distinct detoxification capacities of the two species in response to acaricides and highlight the importance of applying species-specific management strategies for these pests.

Molecular target for sprayable double-stranded RNA-based biopesticide against Amphitetranychus viennensis (Acari, Tetranychidae)

Amphitetranychus viennensis, a destructive pest mite of fruit plants in Europe and Asia, poses a serious challenge due to its adaptability and resistance to multiple acaricides. RNA interference (RNAi)-based technologies offer a promising alternative to address this emerging issue. In this study, we screened for candidate genes that can be targeted for spray-induced gene silencing (SIGS). Suppression of AvSrp54k, AveIF4A-1, AvHel31B, AvCOPB2 and AvProsbeta5 led to a significantly higher mortality and caused minor damages to leaf discs in comparison to the controls. Among them, AvCOPB2 and AvProsbeta5 were the best candidates with the highest mortality (>95 %) and minimal leaf damages (<13 %). Given that LdProsbeta5 is the active ingredient of the first sprayable dsRNA-based biopesticide, Ledprona, against the Colorado Potato Beetle, Leptinotarsa decemlineata, we examined the suitability of AvProsbeta5 in managing A. viennensis. In comparison to the control, A. viennensis population was suppressed by >95 % at day-17, and the plant defoliation rate decreased to 0 at day-24. Our combined results not only provide two viable molecular targets for sprayable dsRNA-based biopesticides, but also confirm the practical implications of SIGS in managing A. viennensis, one of the most destructive arthropod pests in orchards and ornamental plants.

Determination of suitable reference genes for RT-qPCR normalisation in Bombyx mori (Lepidoptera: Bombycidae) infected by the parasitoid Exorista sorbillans (Diptera, Tachinidae)

The silkworm Bombyx mori (Lepidoptera: Bombycidae) is a lepidopteran model insect of great economic importance. The parasitoid Exorista sorbillans (Diptera, Tachinidae) is the major pest of B. mori and also a promising candidate for biological control. However, the molecular interactions between hosts and dipteran parasitoids have only partially been studied. Gene expression analysis by reverse-transcription quantitative real-time polymerase chain reaction (RT-qPCR) is indispensable to characterise their interactions. Accurate normalisation of RT-qPCR-based gene expression requires the use of reference genes that are constantly expressed irrespective of experimental conditions. In this study, the expression stability of 13 traditionally used reference genes was estimated by five statistical algorithms (ΔCt, geNorm, Normfinder, BestKeeper, and RefFinder) to determine the best reference genes for gene expression studies in different tissues of B. mori under E. sorbillans parasitism. Specifically, TATA-box-binding protein was the best reference gene in epidermis and testis, while elongation factor 1α was the most stable gene in prothoracic gland and midgut. Elongation factor 1γ, ribosomal protein L3, actin A1, ribosomal protein L40, glyceraldehyde-3-phosphate dehydrogenase and eukaryotic translation initiation factor 4A were the most suitable genes in head, silk gland, fat body, haemolymph, Malpighian tubule and ovary, respectively. Our study offers a set of suitable reference genes for gene expression normalisation in B. mori under the parasitic stress of E. sorbillans, which will benefit the in-depth exploration of host-dipteran parasitoid interactions, and also provide insights for further improvements of B. mori resistance against parasitoids and biocontrol efficacy of dipteran parasitoids.

Selection and Validation of Optimal RT-qPCR Reference Genes for the Normalization of Gene Expression under Different Experimental Conditions in Lindera megaphylla

Lindera megaphylla, a broad-leaved evergreen that is used as a landscape ornamental plant and medicinal plant, is an ecologically important and dominant tree species. However, little is known about the molecular mechanisms of its growth, development, and metabolism. The selection of suitable reference genes is critical for molecular biological analyses. To date, no research on reference genes as a foundation for gene expression analysis has been undertaken in L. megaphylla. In this study, 14 candidate genes were selected from the transcriptome database of L. megaphylla for RT-qPCR assay under different conditions. Results showed that helicase-15 and UBC28 were most stable in different tissues of seedlings and adult trees. For different leaf developmental stages, the best combination of reference genes was ACT7 and UBC36. UBC36 and TCTP were the best under cold treatment, while PAB2 and CYP20-2 were the best under heat treatment. Finally, a RT-qPCR assay of LmNAC83 and LmERF60 genes were used to further verify the reliability of selected reference genes above. This work is the first to select and evaluate the stability of reference genes for the normalization of gene expression analysis in L. megaphylla and will provide an important foundation for future genetic studies of this species.

Identification and validation of the reference genes in the echiuran worm Urechis unicinctus based on transcriptome data

BACKGROUND

Real-time quantitative PCR (RT-qPCR) is a crucial and widely used method for gene expression analysis. Selecting suitable reference genes is extremely important for the accuracy of RT-qPCR results. Commonly used reference genes are not always stable in various organisms or under different environmental conditions. With the increasing application of high-throughput sequencing, transcriptome analysis has become an effective method for identifying novel stable reference genes.

RESULTS

In this study, we identified candidate reference genes based on transcriptome data covering embryos and larvae of early development, normal adult tissues, and the hindgut under sulfide stress using the coefficient of variation (CV) method in the echiuran Urechis unicinctus, resulting in 6834 (15.82%), 7110 (16.85%) and 13880 (35.87%) candidate reference genes, respectively. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses revealed that the candidate reference genes were significantly enriched in cellular metabolic process, protein metabolic process and ribosome in early development and normal adult tissues as well as in cellular localization and endocytosis in the hindgut under sulfide stress. Subsequently, ten genes including five new candidate reference genes and five commonly used reference genes, were validated by RT-qPCR. The expression stability of the ten genes was analyzed using four methods (geNorm, NormFinder, BestKeeper, and ∆Ct). The comprehensive results indicated that the new candidate reference genes were more stable than most commonly used reference genes. The commonly used ACTB was the most unstable gene. The candidate reference genes STX12, EHMT1, and LYAG were the most stable genes in early development, normal adult tissues, and hindgut under sulfide stress, respectively. The log2(TPM) of the transcriptome data was significantly negatively correlated with the Ct values of RT-qPCR (Ct =  - 0.5405 log2(TPM) + 34.51), which made it possible to estimate the Ct value before RT-qPCR using transcriptome data.

CONCLUSION

Our study is the first to select reference genes for RT-qPCR from transcriptome data in Echiura and provides important information for future gene expression studies in U. unicinctus.

Identification and Validation of Common Reference Genes for Normalization of Esophageal Squamous Cell Carcinoma Gene Expression Profiles

Esophageal squamous cell carcinoma (ESCC) is one of the subtypes of esophageal cancer with Chinese characteristics, and its five-year survival rate is less than 20%. Early diagnosis is beneficial to improving the survival rate of ESCC significantly. Quantitative Real-Time Polymerase Chain Reaction is a high-throughput technique that can quantify tumor-related genes for early diagnosis. Its accuracy largely depends on the stability of the reference gene. There is no systematic scientific basis to demonstrate which reference gene expression is stable in ESCC and no consensus on the selection of internal reference. Therefore, this research used four software programs (The comparative delta-Ct method, GeNorm, NormFinder, and BestKeeper) to evaluate the expression stability of eight candidate reference genes commonly used in other tumor tissues and generated a comprehensive analysis by RefFinder. Randomly selected transcriptome sequencing analysis confirmed the SPP1 gene is closely related to ESCC. It was found that the expression trend of SPP1 obtained by RPS18 and PPIA as internal reference genes were the same as that of sequencing. The results show that RPS18 and PPIA are stable reference genes, and PPIA + RPS18 are a suitable reference gene combination. This is a reference gene report that combines transcriptome sequencing analysis and only focuses on ESCC, which makes the quantification more precise, systematic, and standardized, and promotes gene regulation research and the early diagnosis of ESCC in the future.