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Li W, Cai B, Chen R, Cui J, Wang H, Li Z. Application of recombinase polymerase amplification with CRISPR/Cas12a and multienzyme isothermal rapid amplification with lateral flow dipstick assay for Bactrocera correcta. PEST MANAGEMENT SCIENCE 2024; 80:3317-3325. [PMID: 38375936 DOI: 10.1002/ps.8035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Revised: 01/13/2024] [Accepted: 02/20/2024] [Indexed: 02/21/2024]
Abstract
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.
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Affiliation(s)
- Weisong Li
- Key Laboratory of Surveillance and Management for Plant Quarantine Pests of MARA, Department of Plant Biosecurity, College of Plant Protection, China Agricultural University, Beijing, P. R. China
- Sanya Institute of China Agricultural University, Sanya, P. R. China
| | - Bo Cai
- Post-Entry Quarantine Station for Tropical Plant, Haikou Customs District, Haikou, P. R. China
| | - Ranran Chen
- National Agro-Tech Extension and Service Center, Beijing, P. R. China
| | - Jianchen Cui
- Beijing Plant Protection Station, Beijing, P. R. China
| | - Hui Wang
- Hainan Adminstration of Off-season Plant Breeding, Sanya, P. R. China
| | - Zhihong Li
- Key Laboratory of Surveillance and Management for Plant Quarantine Pests of MARA, Department of Plant Biosecurity, College of Plant Protection, China Agricultural University, Beijing, P. R. China
- Sanya Institute of China Agricultural University, Sanya, P. R. China
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Shivakumar N, Nanjundaiah SA, Thiruvengadam V, Channappa M, Thammayya SK, Aravindaram K, Sushil SN. Development of recombinase polymerase amplification-based colorimetric detection assay for rapid identification of invasive cassava mealybug, Phenacoccus manihoti Matile-Ferrero. Saudi J Biol Sci 2024; 31:104005. [PMID: 38741655 PMCID: PMC11089393 DOI: 10.1016/j.sjbs.2024.104005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Revised: 04/19/2024] [Accepted: 04/26/2024] [Indexed: 05/16/2024] Open
Abstract
Phenacoccus manihoti Matile-Ferrero (Hemiptera: Pseudococcidae), is an economically important invasive cassava pest responsible for the massive devastation of cassava in Asia and African continent. Initially, identifying this invasive pest posed challenges because it closely resembled native mealybug species. Additionally, the traditional morphological identification process is labor-intensive and time-consuming. Detecting invasive pests at an early stage is crucial, hence development of a rapid detection assay is essential. In the current study, we have developed a simple, rapid, sensitive, and efficient molecular detection assay for P. manihoti based on Recombinase Polymerase Amplification (RPA). The primers for the RPA assay were designed using unique nucleic acid sequences of P. manihoti, and the protocol was standardized. Specificity test demonstrated that the RPA assay could amplify DNA of P. manihoti only, and no amplification was observed in six other mealybug species. The specificity of assay was confirmed using SYBR green-based colorimetric detection and gel electrophoresis where positive samples showed 195 bp amplicon size in P. manihoti samples. The assay successfully amplified P. manihoti DNA in thirty minutes at an annealing temperature of 41° C in a water bath and displayed a sensitivity of 72.5 picograms per microliter. The assay's simplicity, rapidity, and high sensitivity make it a valuable tool for detecting and monitoring P. manihoti in quarantine stations and facilitating in development of a portable diagnostic kit.
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Affiliation(s)
- Nanditha Shivakumar
- ICAR-National Bureau of Agricultural Insect Resources, Bengaluru 560 024, India
| | | | | | | | | | - Kandan Aravindaram
- ICAR-National Bureau of Agricultural Insect Resources, Bengaluru 560 024, India
| | - Satya Nand Sushil
- ICAR-National Bureau of Agricultural Insect Resources, Bengaluru 560 024, India
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Eini O, Pfitzer R, Varrelmann M. Rapid and specific detection of Pentastiridius leporinus by recombinase polymerase amplification assay. BULLETIN OF ENTOMOLOGICAL RESEARCH 2024:1-8. [PMID: 38708571 DOI: 10.1017/s0007485324000099] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2024]
Abstract
Pentastiridius leporinus (Hemiptera: Cixiidae) is the main vector of an emerging and fast spreading sugar beet disease, the syndrome 'basses richesses' (SBR), in different European countries. The disease is caused by the γ-3-proteobacterium 'Candidatus Arsenophonus phytopathogenicus' and the phytoplasma 'Candidatus Phytoplasma solani' which are exclusively transmitted by planthoppers and can lead to a significant loss of sugar content and yield. Monitoring of this insect vector is important for disease management. However, the morphological identification is time consuming and challenging as two additional cixiid species Reptalus quinquecostatus and Hyalesthes obsoletus with a very close morphology have been reported in sugar beet fields. Further, identification of females and nymphs of P. leporinus at species level based on taxonomic key is not possible. In this study, an isothermal nucleic acid amplification based on recombinase polymerase amplification (RPA) was developed to specifically detect P. leporinus. In addition, real-time RPA was developed to detect both adults (male and female) and nymph stages using pure or crude nucleic acid extracts. The sensitivity of the real-time RPA for detection of P. leporinus was comparable to real-time PCR, but a shorter time (< 7 min) was required. This is a first report for real-time RPA application for P. leporinus detection using crude nucleic acid templates which can be applied for fast and specific detection of this vector in the field.
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Affiliation(s)
- Omid Eini
- Institute of Sugar Beet Research, Holtenser Landstraße 77, 37079 Göttingen, Germany
| | - René Pfitzer
- Institute of Sugar Beet Research, Holtenser Landstraße 77, 37079 Göttingen, Germany
- Agricultural Entomology, Department of Crop Sciences, Faculty of Agricultural Sciences, University of Göttingen, Grisebachstrasse 6, 37077 Göttingen, Germany
| | - Mark Varrelmann
- Institute of Sugar Beet Research, Holtenser Landstraße 77, 37079 Göttingen, Germany
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Wang R, Zhou R, Meng Y, Zheng J, Lu W, Yang Y, Yang J, Wu Y, Shan W. Specific Detection of Phytophthora parasitica by Recombinase Polymerase Amplification Assays Based on a Unique Multicopy Genomic Sequence. PLANT DISEASE 2024; 108:987-995. [PMID: 37884481 DOI: 10.1094/pdis-04-23-0722-re] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/28/2023]
Abstract
Phytophthora parasitica is a highly destructive oomycete plant pathogen that is capable of infecting a wide range of hosts including many agricultural cash crops, fruit trees, and ornamental garden plants. One of the most important diseases caused by P. parasitica worldwide is black shank of tobacco. Rapid, sensitive, and specific pathogen detection is crucial for early rapid diagnosis, which can facilitate effective disease management. In this study, we used a genomics approach to identify repeated sequences in the genome of P. parasitica by genome sequence alignment and identified a 203-bp P. parasitica-specific sequence, PpM34, that is present in 31 to 60 copies in the genome. The P. parasitica genome specificity of PpM34 was supported by PCR amplification of 24 genetically diverse strains of P. parasitica, 32 strains representing 12 other Phytophthora species, one Pythium species, six fungal species, and three bacterial species, all of which are plant pathogens. Our PCR and real-time PCR assays showed that the PpM34 sequence was highly sensitive in specifically detecting P. parasitica. Finally, we developed a PpM34-based high-efficiency recombinase polymerase amplification assay, which allowed us to specifically detect as little as 1 pg of P. parasitica total DNA from both pure cultures and infected Nicotiana benthamiana at 39°C using a fluorometric thermal cycler. The sensitivity, specificity, convenience, and rapidity of this assay represent a major improvement for early diagnosis of P. parasitica infection.
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Affiliation(s)
- Rongsheng Wang
- Liaoning Key Laboratory of Plant Pathology, College of Plant Protection, Shenyang Agricultural University, Shenyang 110866, Liaoning, China
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Agronomy, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Ran Zhou
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Agronomy, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Yuling Meng
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Agronomy, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Jie Zheng
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Agronomy, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Wenqin Lu
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Agronomy, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Yang Yang
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Agronomy, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Jiapeng Yang
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Agronomy, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Yuanhua Wu
- Liaoning Key Laboratory of Plant Pathology, College of Plant Protection, Shenyang Agricultural University, Shenyang 110866, Liaoning, China
| | - Weixing Shan
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Agronomy, Northwest A&F University, Yangling 712100, Shaanxi, China
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Deng W, Feng S, Stejskal V, Opit G, Li Z. An advanced approach for rapid visual identification of Liposcelis bostrychophila (Psocoptera: Liposcelididae) based on CRISPR/Cas12a combined with RPA. JOURNAL OF ECONOMIC ENTOMOLOGY 2023; 116:1911-1921. [PMID: 37463293 DOI: 10.1093/jee/toad139] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Revised: 07/02/2023] [Accepted: 07/10/2023] [Indexed: 07/20/2023]
Abstract
Liposcelis bostrychophila Badonnel (Psocoptera: Liposcelididae) is a booklouse pest that is a threat to commodity storage security worldwide. Accurate and sensitive methods of L. bostrychophila on-site identification are essential prerequisites for its effective management. Evidence suggests that L. bostrychophila contains 3 intraspecific biotypes that are morphologically indistinguishable but can be discriminated at the level of mitochondrial genome organization and sequences. The traditional molecular identification methods, such as DNA barcoding and PCR-RFLP, are instrumentally demanding and time-consuming, limiting the application of the identification in the field. Therefore, this study developed a new CRISPR/Cas12a-based visual nucleic acid system based on the mitochondrial gene coding for NADH dehydrogenase subunit 2 (nad2), combined with recombinase polymerase amplification (RPA) to accurately identify L. bostrychophila from 4 other common stored-product booklice, and also differentiate 3 biotypes of this species at the same time. The entire identification process could be completed at 37 °C within 20 min with high sensitivity. The system could stably detect at least 1 ng/μl of DNA template. The green fluorescence signal produced by the trans-cleaving of the single-stranded DNA reporter could be observed by the naked eye under blue light. Additionally, the suggested system combined with the crude DNA extraction method to extract DNA rapidly, enabled identification of all developmental stages of L. bostrychophila. With crude DNA, this novel diagnostic system successfully identified an unknown booklouse by holding the reaction tubes in the hand, thus can be considered as an accurate, rapid, highly sensitive, and instrument-flexible method for on-site visual identification of L. bostrychophila.
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Affiliation(s)
- Wenxin Deng
- Department of Plant Biosecurity, College of Plant Protection, China Agricultural University, Beijing 100193, China
- Sanya Institute of China Agricultural University, Yazhou Bay Science and Technology City, Yazhou District, Sanya 572025, Hainan, China
| | - Shiqian Feng
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Vaclav Stejskal
- Crop Research Institute, Drnovská 507, 161 06 Prague 6, Czech Republic
- Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences, Kamycka 129, 165 00 Prague, Czech Republic
| | - George Opit
- Department of Entomology and Plant Pathology, Oklahoma State University, Stillwater, OK 74078, USA
| | - Zhihong Li
- Department of Plant Biosecurity, College of Plant Protection, China Agricultural University, Beijing 100193, China
- Sanya Institute of China Agricultural University, Yazhou Bay Science and Technology City, Yazhou District, Sanya 572025, Hainan, China
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Wang L, Chen J, Zhao C, Jin H, Li F, Wu S. Production and quality of Hami melon (Cucumis melo var. reticulatus) and pest population of Thrips palmi in UV-blocking film greenhouses. PEST MANAGEMENT SCIENCE 2023; 79:4011-4017. [PMID: 37278523 DOI: 10.1002/ps.7597] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Revised: 05/19/2023] [Accepted: 06/06/2023] [Indexed: 06/07/2023]
Abstract
BACKGROUND Ultraviolet (UV) interferes with the vision, flight initiation, dispersal, host, and population dispersion of herbivorous insects. Hence, UV-blocking film has recently been developed as one of the most potential tools to control pests under tropical greenhouse conditions. In this study, we investigated the effects of UV-blocking film on the population dynamics of Thrips palmi Karny and the growth status of Hami melon (Cucumis melo var. reticulatus) in greenhouses. RESULTS By comparing thrips populations in greenhouses covered with UV-blocking films with those covered with ordinary polyethylene films, we found that the UV-blocking film effectively reduced the thrips population within 1 week and continued to control the population, meanwhile the quality and yield of melon in UV-blocking greenhouses also had a substantial increase. CONCLUSION The UV-blocking film remarkably inhibited the population growth of thrips and greatly improved the yield of Hami melon cultivated in UV-blocking greenhouse compared with the control greenhouse. Overall, UV-blocking film is a very powerful potential tool for green pest control in the field, enhancing the quality of tropical fruits, and providing a new wind vane for sustainable green agriculture in the future. © 2023 Society of Chemical Industry.
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Affiliation(s)
- Likui Wang
- Department of Entomology, College of Plant Protection and Sanya Institute of China Agricultural University, Beijing, China
| | - Jianwen Chen
- School of Tropical Crops, Hainan University, Haikou, China
| | - Chenyang Zhao
- School of Plant Protection, Hainan University, Haikou, China
| | - Haifeng Jin
- School of Plant Protection, Hainan University, Haikou, China
- Sanya Nanfan Research Institute, Hainan University, Sanya, China
| | - Fen Li
- School of Plant Protection, Hainan University, Haikou, China
- Sanya Nanfan Research Institute, Hainan University, Sanya, China
| | - Shaoying Wu
- School of Plant Protection, Hainan University, Haikou, China
- Sanya Nanfan Research Institute, Hainan University, Sanya, China
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Liu Y, Hao J, Guo Q, Yan J, Yao Q. Establishment of a recombinase polymerase amplification detection method for Puccinia striiformis f. sp. tritici. Sci Rep 2023; 13:16133. [PMID: 37752159 PMCID: PMC10522615 DOI: 10.1038/s41598-023-42663-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2023] [Accepted: 09/13/2023] [Indexed: 09/28/2023] Open
Abstract
Wheat stripe rust caused by Puccinia striiformis f. sp. tritici (Pst) is an airborne disease that endangers wheat during its entire growth period. In this study, the Pst134EA_003354 uncharacterized protein (GenBank: XM_047941824.1) of Pst was used as the target sequence, and the primers PS-RPA-F and PS-RPA-R, as well as the probe PS-LF-probe, were designed for recombinase polymerase amplification (RPA) technology. Flow chromatography was combined with the process to establish an RPA detection method for Pst. This method successfully established visual detection within 10 min under a constant temperature of 39 °C, and the detection results were consistent with those of ordinary PCR analysis. However, it only had high specificity for Pst, and the detection limit was 10 fg/μL. In addition, this rapid method successfully detected Pst from wheat leaves during the field incubation period, indicating substantial benefits for applied use. In summary, the RPA detection method established in this study has the favourable characteristics of high efficiency, simple functionality, and rapid and universal practicability, providing a theoretical basis for the early detection and prevention of Pst.
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Affiliation(s)
- Yaoxia Liu
- Qinghai Provincial Key Laboratory of Agricultural Integrated Pest ManagementScientific Observing and Experimental Station of Crop Pest in Xining, Ministry of Agriculture, Academy of Agriculture and Forestry Science, Qinghai University, Xining, 810016, Qinghai, People's Republic of China
| | - Jianyun Hao
- Qinghai Provincial Key Laboratory of Agricultural Integrated Pest ManagementScientific Observing and Experimental Station of Crop Pest in Xining, Ministry of Agriculture, Academy of Agriculture and Forestry Science, Qinghai University, Xining, 810016, Qinghai, People's Republic of China
| | - Qingyun Guo
- Qinghai Provincial Key Laboratory of Agricultural Integrated Pest ManagementScientific Observing and Experimental Station of Crop Pest in Xining, Ministry of Agriculture, Academy of Agriculture and Forestry Science, Qinghai University, Xining, 810016, Qinghai, People's Republic of China
| | - Jiahui Yan
- Qinghai Provincial Key Laboratory of Agricultural Integrated Pest ManagementScientific Observing and Experimental Station of Crop Pest in Xining, Ministry of Agriculture, Academy of Agriculture and Forestry Science, Qinghai University, Xining, 810016, Qinghai, People's Republic of China
| | - Qiang Yao
- Qinghai Provincial Key Laboratory of Agricultural Integrated Pest ManagementScientific Observing and Experimental Station of Crop Pest in Xining, Ministry of Agriculture, Academy of Agriculture and Forestry Science, Qinghai University, Xining, 810016, Qinghai, People's Republic of China.
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Shen XJ, Chen JC, Cao LJ, Ma ZZ, Sun LN, Gao YF, Ma LJ, Wang JX, Ren YJ, Cao HQ, Gong YJ, Hoffmann AA, Wei SJ. Interspecific and intraspecific variation in susceptibility of two co-occurring pest thrips, Frankliniella occidentalis and Thrips palmi, to nine insecticides. PEST MANAGEMENT SCIENCE 2023. [PMID: 37042232 DOI: 10.1002/ps.7502] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/26/2022] [Revised: 03/19/2023] [Accepted: 04/12/2023] [Indexed: 06/19/2023]
Abstract
BACKGROUND Field control of pest thrips mainly relies on insecticides, but the toxicity of insecticides can vary among thrips species and populations. In this study, we examined the susceptibility of multiple field populations of two thrips pests, Frankliniella occidentalis, and Thrips palmi, that often co-occur on vegetables, to nine insecticides belonging to seven subgroups. RESULTS The highest level of variation in susceptibility among F. occidentalis populations was for spinetoram (73.92 fold difference between most resistant and most susceptible population), followed by three neonicotinoids (8.06-15.99 fold), while among T. palmi populations, it was also for spinetoram (257.19 fold), followed by emamectin benzoate, sulfoxaflor, and acetamiprid (23.64-45.50 fold). These findings suggest evolved resistance to these insecticides in some populations of the two thrips. One population of F. occidentalis had a particularly high level of resistance overall, being the most resistant for five of the nine insecticides tested. Likewise, a population of T. palmi had high resistance to all nine insecticides, again suggesting the evolution of resistance to multiple chemicals. For F. occidentalis, the LC95 values of most populations were higher than the field-recommended dosage for all insecticides except chlorfenapyr and emamectin benzoate. For several T. palmi populations, the LC95 values also tended to be higher than recommended dosages, except in the case of emamectin benzoate and spinetoram. CONCLUSIONS Our study found interspecific and intraspecific variations in the susceptibility of two thrips to nine insecticides and multiple resistance in some populations, highlighting the need for ongoing monitoring and resistance management. © 2023 Society of Chemical Industry.
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Affiliation(s)
- Xiu-Jing Shen
- Institute of Plant Protection, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Jin-Cui Chen
- Institute of Plant Protection, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Li-Jun Cao
- Institute of Plant Protection, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Zhong-Zheng Ma
- Institute of Plant Protection, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Li-Na Sun
- Institute of Plant Protection, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Yong-Fu Gao
- Institute of Plant Protection, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Li-Jun Ma
- Institute of Plant Protection, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Jia-Xu Wang
- Institute of Plant Protection, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Ya-Jing Ren
- Institute of Plant Protection, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Hua-Qian Cao
- Institute of Plant Protection, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Ya-Jun Gong
- Institute of Plant Protection, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Anthony Ary Hoffmann
- Bio21 Institute, School of BioSciences, University of Melbourne, Parkville, Australia
| | - Shu-Jun Wei
- Institute of Plant Protection, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
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Pfitzer R, Varrelmann M, Hesse G, Eini O. Molecular Detection of Pentastiridius leporinus, the Main Vector of the Syndrome 'Basses Richesses' in Sugar Beet. INSECTS 2022; 13:992. [PMID: 36354816 PMCID: PMC9695866 DOI: 10.3390/insects13110992] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Revised: 10/22/2022] [Accepted: 10/26/2022] [Indexed: 06/16/2023]
Abstract
Monitoring of Pentastiridius leporinus (Hemiptera: Auchenorrhyncha: Cixiidae), representing the main vector of the syndrome 'basses richesses' (SBR) disease in sugar beet is based on morphological identification. However, two other cixiid species, Reptalus quinquecostatus and Hyalesthes obsoletus with similar external characters are known to appear in sugar beet fields and are challenging to be distinguished from P. leporinus. We present a PCR-based method for species-specific detection of both male and female P. leporinus, directly after sweep net collection or after up to 18 months long term storage on sticky traps. Two methods of DNA template preparation, based on a commercial extraction kit or on simple grinding in phosphate-buffered saline (PBS) were compared. The latter method was also established for eggs and all five nymphal instars of P. leporinus from a rearing. Furthermore, in silico primer analysis showed that all Auchenorrhyncha species including far related species reported from sugar beet fields can be differentiated from P. leporinus. This was PCR-confirmed for the most common Auchenorrhyncha species from different German sugar beet fields. Sequence analysis of the P. leporinus mitochondrial cytochrome oxidase I gene (COI) amplicon showed a close relationship to COI from P. beieri but separated from the Reptalus and Hyalesthes species which are grouped into the same family Cixiidae. We present a sensitive, cost- and time-saving PCR-based method for reliable and specific detection of eggs and all nymphal instars, as well as male and female P. leporinus, after different methods of planthopper collection and template DNA template preparation that can be used in large scale monitoring assays.
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Affiliation(s)
- René Pfitzer
- Institute of Sugar Beet Research, Holtenser Landstraße 77, 37079 Göttingen, Germany
- Agricultural Entomology, Department of Crop Sciences, Faculty of Agricultural Sciences, University of Göttingen, Grisebachstrasse 6, 37077 Göttingen, Germany
| | - Mark Varrelmann
- Institute of Sugar Beet Research, Holtenser Landstraße 77, 37079 Göttingen, Germany
| | - Georgia Hesse
- Institute of Sugar Beet Research, Holtenser Landstraße 77, 37079 Göttingen, Germany
| | - Omid Eini
- Institute of Sugar Beet Research, Holtenser Landstraße 77, 37079 Göttingen, Germany
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Rapid and zero-cost DNA extraction from soft-bodied insects for routine PCR-based applications. PLoS One 2022; 17:e0271312. [PMID: 35839213 PMCID: PMC9286237 DOI: 10.1371/journal.pone.0271312] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2021] [Accepted: 06/28/2022] [Indexed: 11/30/2022] Open
Abstract
Nucleic acid extraction is the first and foremost step in molecular biology studies. Extraction of DNA from small, soft-bodied insects is often time-consuming and costly. A fast, easy, and cost-effective DNA extraction method with greater yield and purity of DNA would aid in the rapid diagnostics, screening of large populations, and other routine PCR-based applications. The present study evaluated and standardized a rapid and zero-cost DNA extraction from soft-bodied small insects for routine molecular studies. Five rapid DNA extraction methods viz. extraction in sterile distilled water (SDW), 1X phosphate-buffered saline (PBS, pH 7.4), 1.4 M sodium chloride (NaCl), 20 mM ethylenediaminetetraacetic acid (EDTA, pH 8.0), and elution from blotted nitrocellulose membrane (NCM) were compared with standard CTAB extraction buffer and DNeasy® Blood and Tissue Kit methods. The average yield, purity, storage stability, time, and cost of extraction were assessed for all the methods and compared. A method of DNA extraction by simply crushing the soft-bodied insects in SDW was ideal in terms of yield, purity, storability, and performing routine PCR-based applications including detection of pathogens from vector species. The extraction could be accomplished in 2.5 min only with zero-reagent cost. The method would be useful in rapid molecular diagnostics and screening large populations of soft-bodied insects.
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Jangra S, Ghosh A, Mukherjee S, Baranwal VK, Dietzgen RG. Development of a Polymerase Spiral Reaction-Based Isothermal Assay for Rapid Identification of Thrips palmi. Front Mol Biosci 2022; 9:853339. [PMID: 35586189 PMCID: PMC9108268 DOI: 10.3389/fmolb.2022.853339] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Accepted: 03/23/2022] [Indexed: 12/03/2022] Open
Abstract
Thrips cause considerable economic losses to a wide range of food, feed, and forest crops. They also transmit several plant viruses. Being cryptic, it is often difficult to distinguish thrips species in crops and large consignments by conventional methods. Melon thrips (Thrips palmi Karny, Thysanoptera: Thripidae) is an invasive insect pest of vegetables, legumes, and ornamentals besides being vector to several viruses. It poses a threat to domestic and international plant biosecurity and can invade and establish in new areas. Here, we report a polymerase spiral reaction (PSR)-based isothermal assay for rapid, sensitive, specific, low-cost, and on-site detection of T. palmi. To the best of our knowledge, this is the first application of PSR in the identification of any insect species. A primer pair designed based on 3′-polymorphism of mtCOIII region can specifically identify T. palmi without any cross-reactivity with predominant thrips species. The assay uses crude lysate of a single thrips saving time and reagents involved in nucleic acid extraction. The presence of T. palmi is visualized by the appearance of bright fluorescence under ultraviolet light or a change in reaction color thus avoiding gel electrophoresis steps. The entire process can be completed in 70 min on-site using only an ordinary water bath. The assay is sensitive to detecting as little as 50 attograms of T. palmi template. The assay was validated with known thrips specimens and found to be efficient in diagnosing T. palmi under natural conditions. The described method will be useful for non-expert personnel to detect an early infestation, accidental introduction to a new area, restrict the spread of diseases and formulate appropriate management strategies.
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Affiliation(s)
- Sumit Jangra
- Insect Vector Laboratory, Advanced Centre for Plant Virology, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Amalendu Ghosh
- Insect Vector Laboratory, Advanced Centre for Plant Virology, ICAR-Indian Agricultural Research Institute, New Delhi, India
- *Correspondence: Amalendu Ghosh, , orcid.org/0000-0001-6634-5771
| | - Sunil Mukherjee
- Insect Vector Laboratory, Advanced Centre for Plant Virology, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Virendra Kumar Baranwal
- Insect Vector Laboratory, Advanced Centre for Plant Virology, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Ralf G. Dietzgen
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Saint Lucia, QLD, Australia
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Warmt C, Fenzel CK, Henkel J, Bier FF. Using Cy5-dUTP labelling of RPA-amplicons with downstream microarray analysis for the detection of antibiotic resistance genes. Sci Rep 2021; 11:20137. [PMID: 34635776 PMCID: PMC8505619 DOI: 10.1038/s41598-021-99774-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Accepted: 09/29/2021] [Indexed: 11/09/2022] Open
Abstract
In this report we describe Cy5-dUTP labelling of recombinase-polymerase-amplification (RPA) products directly during the amplification process for the first time. Nucleic acid amplification techniques, especially polymerase-chain-reaction as well as various isothermal amplification methods such as RPA, becomes a promising tool in the detection of pathogens and target specific genes. Actually, RPA even provides more advantages. This isothermal method got popular in point of care diagnostics because of its speed and sensitivity but requires pre-labelled primer or probes for a following detection of the amplicons. To overcome this disadvantages, we performed an labelling of RPA-amplicons with Cy5-dUTP without the need of pre-labelled primers. The amplification results of various multiple antibiotic resistance genes indicating great potential as a flexible and promising tool with high specific and sensitive detection capabilities of the target genes. After the determination of an appropriate rate of 1% Cy5-dUTP and 99% unlabelled dTTP we were able to detect the blaCTX-M15 gene in less than 1.6E-03 ng genomic DNA corresponding to approximately 200 cfu of Escherichia coli cells in only 40 min amplification time.
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Affiliation(s)
- Christian Warmt
- Fraunhofer Institute for Cell Therapy and Immunology - Bioanalytics and Bioprocesses (IZI-BB), 14476, Potsdam, Germany.
| | - Carolin Kornelia Fenzel
- Fraunhofer Institute for Cell Therapy and Immunology - Bioanalytics and Bioprocesses (IZI-BB), 14476, Potsdam, Germany.,Institute for Biochemistry and Biology, University of Potsdam, 14476, Potsdam, Germany
| | - Jörg Henkel
- Fraunhofer Institute for Cell Therapy and Immunology - Bioanalytics and Bioprocesses (IZI-BB), 14476, Potsdam, Germany.
| | - Frank Fabian Bier
- Institute for Biochemistry and Biology, University of Potsdam, 14476, Potsdam, Germany.,Institute for Molecular Diagnostics and Bioanalysis, IMDB, 16761, Hennigsdorf, Germany
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Ghosh A, Jangra S, Dietzgen RG, Yeh WB. Frontiers Approaches to the Diagnosis of Thrips (Thysanoptera): How Effective Are the Molecular and Electronic Detection Platforms? INSECTS 2021; 12:insects12100920. [PMID: 34680689 PMCID: PMC8540714 DOI: 10.3390/insects12100920] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/04/2021] [Revised: 10/01/2021] [Accepted: 10/04/2021] [Indexed: 11/23/2022]
Abstract
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.
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Affiliation(s)
- Amalendu Ghosh
- Insect Vector Laboratory, Advanced Centre for Plant Virology, ICAR-Indian Agricultural Research Institute, New Delhi 110012, India; (A.G.); (S.J.)
| | - Sumit Jangra
- Insect Vector Laboratory, Advanced Centre for Plant Virology, ICAR-Indian Agricultural Research Institute, New Delhi 110012, India; (A.G.); (S.J.)
| | - Ralf G. Dietzgen
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St. Lucia, Brisbane, QLD 4072, Australia
- Correspondence:
| | - Wen-Bin Yeh
- Department of Entomology, National Chung Hsing University, Taichung City 402, Taiwan;
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Bragard C, Dehnen‐Schmutz K, Di Serio F, Gonthier P, Jacques M, Jaques Miret JA, Justesen AF, MacLeod A, Magnusson CS, Navas‐Cortes JA, Parnell S, Potting R, Reignault PL, Thulke H, Van der Werf W, Vicent Civera A, Yuen J, Zappalà L, Lucchi A, Loomans A, Mosbach‐Schulz O, de la Peña E, Milonas P. Commodity risk assessment of Momordica charantia fruits from Thailand. EFSA J 2021; 19:e06399. [PMID: 33613742 PMCID: PMC7881712 DOI: 10.2903/j.efsa.2021.6399] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
The European Commission requested the EFSA Panel on Plant Health to prepare and deliver risk assessments for commodities listed in Commission Implementing Regulation (EU) 2018/2019 as 'High risk plants, plant products and other objects'. Momordica fruits originating from countries where Thrips palmi is known to occur qualify as high-risk plants. This Scientific Opinion covers the introduction risk for T. palmi posed by fruits of Momordica charantia L. imported from Thailand, taking into account the available scientific information, including the technical information provided by the Department of Agriculture of Thailand. The risk mitigation measures proposed in the technical dossier from Thailand were evaluated taking into account the possible limiting factors. An expert judgement is given on the likelihood of pest freedom taking into consideration the potential pest pressure in the field, the risk mitigation measures acting on the pest in the field and in the packing house, including uncertainties associated with the assessment. For T. palmi on M. charantia fruits from Thailand, an expert judgement is given on the likelihood of pest freedom following the evaluation of the risk mitigation measures acting on T. palmi, including any uncertainties. The Expert Knowledge Elicitation indicated, with 95% certainty that between 9,496 and 10,000 M. charantia fruits/10,000 will be free from T. palmi.
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Bragard C, Dehnen‐Schmutz K, Di Serio F, Gonthier P, Jacques M, Jaques Miret JA, Justesen AF, MacLeod A, Magnusson CS, Navas‐Cortes JA, Parnell S, Potting R, Reignault PL, Thulke H, Van der Werf W, Vicent Civera A, Yuen J, Zappalà L, Lucchi A, Loomans A, Mosbach‐Schulz O, de la Peña E, Milonas P. Commodity risk assessment of Momordica charantia fruits from Honduras. EFSA J 2021; 19:e06395. [PMID: 33613738 PMCID: PMC7881708 DOI: 10.2903/j.efsa.2021.6395] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
The European Commission requested the EFSA Panel on Plant Health to prepare and deliver risk assessments for commodities listed in Commission Implementing Regulation (EU) 2018/2019 as 'High risk plants, plant products and other objects'. Momordica fruits originating from countries where Thrips palmi is known to occur qualify as high risk plants. This Scientific Opinion covers the introduction risk for T. palmi posed by fruits of Momordica charantia L. imported from Honduras, taking into account the available scientific information, including the technical information provided by the National Service of Agrifood Health and Safety (SENASA) of Honduras. The risk mitigation measures proposed in the technical dossier from Honduras were evaluated taking into account the possible limiting factors. An expert judgement is given on the likelihood of pest freedom taking into consideration the potential pest pressure in the field, the risk mitigation measures acting on the pest in the field and in the packinghouse, including uncertainties associated with the assessment. For T. palmi on M. charantia fruits from Honduras, an expert judgement is given on the likelihood of pest freedom following the evaluation of the risk mitigation measures acting on T. palmi, including any uncertainties. The Expert Knowledge Elicitation indicated, with 95% certainty that between 9,406 and 10,000 M. charantia fruits per 10,000 will be free from T. palmi.
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Bragard C, Dehnen‐Schmutz K, Di Serio F, Gonthier P, Jacques M, Jaques Miret JA, Justesen AF, MacLeod A, Magnusson CS, Navas‐Cortes JA, Parnell S, Potting R, Reignault PL, Thulke H, Van der Werf W, Civera AV, Yuen J, Zappalà L, Lucchi A, Loomans A, Mosbach‐Schulz O, de la Peña E, Milonas P. Commodity risk assessment of Momordica charantia fruits from Suriname. EFSA J 2021; 19:e06396. [PMID: 33613739 PMCID: PMC7881711 DOI: 10.2903/j.efsa.2021.6396] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
The European Commission requested the EFSA Panel on Plant Health to prepare and deliver risk assessments for commodities listed in Commission Implementing Regulation (EU) 2018/2019 as 'High risk plants, plant products and other objects'. M. charantia fruits originating from countries where Thrips palmi is known to occur qualify as high-risk plants. This Scientific Opinion covers the introduction risk for T. palmi posed by fruits of Momordica charantia L. imported from Suriname, taking into account the available scientific information, including the technical information provided by the National Plant Protection Organization of Suriname. The risk mitigation measures proposed in the technical dossier from Suriname were evaluated taking into account the possible limiting factors. An expert judgement is given on the likelihood of pest freedom taking into consideration the potential pest pressure in the field, the risk mitigation measures acting on the pest in the field and in the packinghouse, including uncertainties associated with the assessment. For T. palmi on M. charantia fruits from Suriname, an expert judgement is given on the likelihood of pest freedom following the evaluation of the risk mitigation measures acting on T. palmi, including any uncertainties. The Expert Knowledge Elicitation indicated, with 95% certainty that between 8,652 and 10,000 M. charantia fruits per 10,000 will be free from T. palmi.
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Bragard C, Dehnen‐Schmutz K, Di Serio F, Gonthier P, Jacques M, Jaques Miret JA, Justesen AF, MacLeod A, Magnusson CS, Navas‐Cortes JA, Parnell S, Potting R, Reignault PL, Thulke H, Van der Werf W, Vicent Civera A, Yuen J, Zappalà L, Lucchi A, Loomans A, Mosbach‐Schulz O, de la Peña E, Milonas P. Commodity risk assessment of Momordica charantia fruits from Sri Lanka. EFSA J 2021; 19:e06397. [PMID: 33613740 PMCID: PMC7881710 DOI: 10.2903/j.efsa.2021.6397] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
The European Commission requested the EFSA Panel on Plant Health to prepare and deliver risk assessments for commodities listed in Commission Implementing Regulation (EU) 2018/2019 as 'High risk plants, plant products and other objects'. Momordica fruits originating from countries where Thrips palmi is known to occur qualify as high-risk plants. This Scientific Opinion covers the introduction risk for T. palmi posed by fruits of Momordica charantia L. imported from Sri Lanka, taking into account the available scientific information, including the technical information provided by the National Plant Quarantine Service of Sri Lanka. The risk mitigation measures proposed in the technical dossier from Sri Lanka were evaluated taking into account the possible limiting factors. An expert judgement is given on the likelihood of pest freedom taking into consideration the potential pest pressure in the field, the risk mitigation measures acting on the pest in the field and in the packing house, including uncertainties associated with the assessment. For T. palmi on M. charantia fruits from Sri Lanka, an expert judgement is given on the likelihood of pest freedom following the evaluation of the risk mitigation measures acting on T. palmi, including any uncertainties. The Expert Knowledge Elicitation indicated, with 95% certainty that between 9831 and 10,000 M. charantia fruits/10,000 will be free from T. palmi.
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