A rapid diagnostic technique of Bactrocera cucurbitae and Bactrocera zonata (Diptera: Tephritidae) for quarantine application

Application of recombinase polymerase amplification with CRISPR/Cas12a and multienzyme isothermal rapid amplification with lateral flow dipstick assay for Bactrocera correcta

BACKGROUND

Bactrocera correcta is a quarantine pest that negatively impacts the fruit and vegetable industry. Differentiating B. correcta from similar species, especially in non-adult stages, remains challenging. Rapid molecular identification techniques, such as recombinase polymerase amplification (RPA) combined with CRISPR/Cas12a and multienzyme isothermal rapid amplification with lateral flow dipstick (MIRA-LFD), play a crucial role in early monitoring and safeguarding agricultural production. Our study introduces two methods for the rapid visual identification of B. correcta.

RESULTS

Bactrocera correcta specific RPA primers, CRISPR RNA (crRNA), and the LFD probe were designed based on the cox1 genes. The RPA reaction conditions were optimized (at 37 °C for 8 min) for effective template DNA amplification. Two nucleic acid detection methods were established to visualize RPA. In the RPA-CRISPR/Cas12a system, the optimal LbCas12a/crRNA concentration ratio was 200:400 nmol L-1 . Successful amplification was determined by the presence or absence of green fluorescence following 15 min incubation at 37 °C. The MIRA-LFD system achieved precise identification of the target species within 4 min at 37 °C. Both methods exhibited high specificity and sensitivity, allowing for detection from 1.0 × 10-1  ng μL-1 of DNA. Combined with rapid DNA extraction, rapid identification of individual B. correcta at different developmental stages was achieved, enhancing the practicality and convenience of the established methods.

CONCLUSION

Our research findings demonstrate that both the RPA-CRISPR/Cas12a and MIRA-LFD methods for B. correcta detection was accurate and rapid (within 30 min and 10 min, respectively), at 37 °C. Our methods do not rely on expensive equipment, thus possess high practical value, providing improved identification solutions for port quarantine pests and field applications. © 2024 Society of Chemical Industry.

New and rapid visual detection assay for Trogoderma granarium everts based on recombinase polymerase amplification and CRISPR/Cas12a

BACKGROUND

Khapra beetle (Trogoderma granarium Everts), one of the most important quarantine pests globally, is capable of causing severe infestation and huge economic loss to stored grain, and its interception rate has increased in major global trade countries over the past few years. However, difficulties remain in distinguishing this species with similar ones. In order to assist border ports and warehouses in khapra beetle's effective rapid identification as well as pest control at the early stages of monitoring or interception, we herein developed a new and rapid visual detection assay for T. granarium based on recombinase polymerase amplification (RPA) and the CRISPR/Cas12a system.

RESULTS

We designed and selected the first khapra beetle-specific RPA primers and crRNA, and optimized the visualization reaction system (Cas12a/CrRNA = 100 nM/500 nM). With only a 37 °C-heat-source and a blue light torch, RPA and CRISPR/CAS12a-based visualization assays can be completed within 40 min to differentiate between khapra beetle and nine similar Dermestidae species. After DNA extraction using a kit (4-5 h) or a simple method (5 min), the specific amplicons were obtained after a 15 min RPA reaction at 37 °C, followed by a 15 min color reaction under 37 °C in dark conditions using a CRISPR/CAS12a system and a fluorescent probe (5'-FAM/3'-BHQ1 labeled). This method is ingenious to low levels of DNA (10-1  ng μL-1 ) and meets the sensitivity requirements for detecting a single khapra beetle's egg (≈0.7 mm).

CONCLUSION

Our specificity and sensitivity analysis inferred that the present visualization system is effective to quickly and uniquely detect khapra beetle at room temperature (37 °C), thereby preventing this species before they spread widely. Our study is suitable for being pushed forward in storage pest management, and provides value as a reference for monitoring and identification of other pests. © 2023 Society of Chemical Industry.

LAMP Assay as a Rapid Identification Technique of Chinese Citrus Fly and Japanese Orange Fly (Diptera: Tephritidae)

Bactrocera tsuneonis and Bactrocera minax are the most destructive pests that damage citrus in China. These key pests hinder the citrus trade, cause significant financial losses, drastically lower citrus production and quality, and decrease farmer enthusiasm for citrus planting. Bactrocera minax and B. tsuneonis are very similar in all life stages. There are limited morphological characteristics to differentiate the adult species, and it is nearly impossible to differentiate these two species in the egg and larval stages. Loop-mediated isothermal amplification (LAMP) is a rapid and robust diagnostic tool used to identify these two species accurately. We designed two sets of primers to distinguish B. minax and B. tsuneonis using DNA barcoding region of the COI gene. Only 50 min was needed under a constant temperature of 65ºC to determine the species of the two flies. The reaction system has high specificity and sensitivity, in which these two species can be accurately distinguished between different geographical populations and 1.0 ng/μL was the lowest DNA concentration that could be detected. Our primers can quickly identify these key pests without knowing their morphology, which could facilitate plant protection workers at the primary level to solve problems in plant quarantine.

New Species-Specific Primers for Molecular Diagnosis of Bactrocera minax and Bactrocera tsuneonis (Diptera: Tephritidae) in China Based on DNA Barcodes

Tephritidae fruit flies (Diptera: Tephritidae) are regarded as important damage-causing species due to their ability to cause great economic losses in fruit and vegetable crops. Bactrocera minax and Bactrocera tsuneonis are two sibling species of the subgenus Tetradacus of Bactrocera that are distributed across a limited area of China, but have caused serious impacts. They share similar morphological characteristics. These characteristics can only be observed in the female adult individuals. The differences between them cannot be observed in preimaginal stages. Thus, it is difficult to distinguish them in preimaginal stages morphologically. In this study, we used molecular diagnostic methods based on cytochrome c oxidase subunit I and species-specific markers to identify these two species and improve upon the false-positive results of previous species-detection primers. DNA barcode sequences were obtained from 900 individuals of B. minax and 63 individuals of B. tsuneonis. Based on these 658 bp DNA barcode sequences of the cytochrome c oxidase subunit I gene, we successfully designed the species-specific primers for B. minax and B. tsuneonis. The size of the B. minax specific fragment was 422 bp and the size of the B. tsuneonis specific fragment was 456 bp. A series of PCR trials ensured the specificity of these two pairs of primers. Sensitivity assay results demonstrated that the detection limit for the DNA template concentration was 0.1~1 ng/μL for these two species. In this study, we established a more reliable, rapid, and low-cost molecular identification method for all life stages of B. minax and B. tsuneonis. Species-specific PCR can be applied in plant quarantine, monitoring and control of B. minax and B. tsuneonis.

Geographical Distribution of Ectropis grisescens (Lepidoptera: Geometridae) and Ectropis obliqua in China and Description of an Efficient Identification Method

Ectropis grisescens Warren 1894 (Lepidopotera: Geometridae) and Ectropis obliqua Prout 1915 (Lepidopotera: Geometridae) are the most destructive chewing pests in China's tea plantations. Ectropis grisescens sex pheromone lures and E. obliqua nucleopolyhedrosis virus (EoNPV) are two species-specific and effective bio-control technologies to control these pests. Because these two species are morphologically similar, tea growers are unable to discriminate them by visual inspection. Hence, determining whether to use E. grisescens sex pheromone lures or EoNPV is difficult without knowledge on the geographical distribution of these two Ectropis species in China. In this study, we developed an efficient identification method, which is considerably cheaper and faster than sequencing the cytochrome c oxidase I gene. Overall, 2,588 E. grisescens and E. obliqua samples, collected from 13 provinces and municipalities in China covering the major regions where these pests have been reported, were identified. All insect samples from southern Jiangsu Province were identified as E. obliqua. Both Ectropis species were mix-distributed at the Anhui-Zhejiang Province border areas, whereas E. grisescens was mostly collected from the other sampling sites. Thus, E. obliqua might be mainly distributed at the junction of Jiangsu, Anhui, and Zhejiang Provinces. In contrast, E. grisescens has a considerably wide distribution area and is the main lepidopteran pest in the tea plantations of China. Our results contribute to improve the management of E. grisescens and E. obliqua populations and provide new insights for further studies on these two species.

Molecular Identification of Two Vector Species, Cacopsylla melanoneura and Cacopsylla picta (Hemiptera: Psyllidae), of Apple Proliferation Disease and Further Common Psyllids of Northern Italy

The psyllid species Cacopsylla melanoneura (Förster) and Cacopsylla picta (Förster) are vectors of 'Candidatus Phytoplasma mali', the causal agent of apple proliferation, one of the economically most important apple diseases in Europe. Both vectors are present in apple orchards of South Tyrol and Trentino provinces in Northern Italy. As no direct treatment of the disease is possible, monitoring of the psyllids provides information about the vector presence in the orchards and enables targeted control. Thus, fast and reliable identification of the various psyllids occurring in the apple orchards is required. Morphological differentiation is problematic due to extensive resemblance of some psyllid species especially among females and is error-prone for nymphs. Here we present a rapid and cost-effective polymerase chain reaction-restriction fragment length polymorphism method based on the cytochrome c oxidase subunit I region for the molecular identification of the vector species as well as eight further Cacopsylla species present in the orchards. This method was verified through 98.9% consensus with morphologically identified males, through sequencing and subsequent phylogenetic analysis. In case of doubtful morphological identification of females, the method was able to provide a refined species assignment and could also remarkably facilitate the identification of nymphs.

A Rapid Diagnostic Technique to Discriminate between Two Pests of Palms, Brontispa longissima and Octodonta nipae (Coleoptera: Chrysomelidae), for Quarantine Applications

Octodonta nipae (Maulik) is morphologically and biologically similar to Brontispa longissima (Gestro), one of the most damaging pests of coconut. The two species share several palm hosts and produce similar symptoms. They are easily confused when they invade a new area, and without professional taxonomic expertise accurate identification is arduous and time-consuming. Thus, a method of rapidly distinguishing these two invasive insects rapidly is critical for quarantine. Based on the first internal transcribed spacer and the mitochondrial cytochrome oxidase I gene, two pairs of special primers and corresponding polymerase chain reaction processes have been developed to enhance a single objective band only from the O. nipae DNA template. This will quickly discriminate between these two species. The present results provide a rapid method of distinguishing O. nipae from B. longissima to help avoid misidentification, and furthermore, to facilitate rapid and appropriate quarantine decisions and effective treatments to the pest.