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Özgünlük İ, Yücetepe AG, Çetiner B, Keskin O, Özyörük F. Development of a Multiplex PCR Assay for Rapid Differentiation of Fowlpox and Pigeonpox Viruses. Avian Dis 2024; 68:33-37. [PMID: 38687105 DOI: 10.1637/aviandiseases-d-23-00042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Accepted: 12/24/2023] [Indexed: 05/02/2024]
Abstract
The aim of this study was to develop a multiplex PCR assay capable of rapidly differentiating two major Avipoxvirus (APV) species, Fowlpox virus (FWPV) and Pigeonpox virus (PGPV), which cause disease in bird species. Despite the importance of a rapid differentiation assay, no such assay exists that can differentiate the APV species without sequencing. To achieve this, species-specific target DNA fragments were selected from the fpv122 gene of FWPV and the HM89_gp120 gene of PGPV, which are unique to each genome. Nine samples collected from unvaccinated chickens, pigeons, and a turkey with typical pox lesions were genetically identified as FWPV and PGPV. The designed primers and target DNA fragments were validated using in silico analyses with the nucleotide Basic Local Alignment Search Tool. The multiplex PCR assay consisted of species-specific primers and previously described PanAPV primers (genus-specific) and was able to differentiate FWPV and PGPV, consistent with the phylogenetic outputs. This study represents the first successful differentiation of FWPV and PGPV genomes using a conventional multiplex PCR test. This assay has the potential to facilitate the rapid diagnosis and control of APV infections.
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Affiliation(s)
- İrfan Özgünlük
- Harran University, Faculty of Veterinary Medicine, 63200 Şanlıurfa, Türkiye
| | | | - Burak Çetiner
- Harran University, Faculty of Veterinary Medicine, 63200 Şanlıurfa, Türkiye
| | - Oktay Keskin
- Harran University, Faculty of Veterinary Medicine, 63200 Şanlıurfa, Türkiye
| | - Fuat Özyörük
- Harran University, Faculty of Veterinary Medicine, 63200 Şanlıurfa, Türkiye,
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Marquez J, Hajihassani A. Identification, Diversity, and Distribution of Meloidogyne spp. in Vegetable Fields of South Georgia, U.S.A. Phytopathology 2023; 113:1093-1102. [PMID: 36449528 DOI: 10.1094/phyto-07-22-0246-r] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
Root-knot nematode (RKN; Meloidogyne spp.) is the most prevalent plant-parasitic nematode in vegetable fields of Georgia, with an incidence of 67.3%. Because aggressive RKN species are reported in the southeastern United States, molecular-based identification of RKN species was conducted on soil samples taken from a nematode surveillance study in 2018 from 292 RKN-infested vegetable fields in southern Georgia. The RKN-infested soil was potted with tomato cultivar Rutgers, and individual nematode females were isolated from galled roots and subjected to species-specific PCR and mitochondrial haplotype-based RKN species identification. The incidence (%), mean, and maximum relative abundance (second-stage juveniles per 100 cm3 of soil) of the five RKN species identified consisted of M. incognita (91.9, 486, 14,144), M. arenaria (36.0, 707, 14,144), M. floridensis (2.2, 909, 5,264), M. javanica (5.5, 352, 1,488), and M. haplanaria (0.7, 8, 14). A large proportion of fields (29%) had mixed populations of M. incognita and M. arenaria, which may reflect the region's long history of cotton and peanut cultivation. For unknown reasons, mixed populations of M. incognita and M. arenaria were associated with higher population densities. M. incognita is the most important RKN species in vegetable fields, followed by M. arenaria; therefore, pure or mixed populations of these species should be addressed in nematode management programs. Although at a lower incidence, the newly detected species, M. floridensis and M. haplanaria, have the potential to become a major threat since they reproduce on vegetables with Mi-resistant genes.
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Affiliation(s)
- Josiah Marquez
- Department of Plant Pathology, University of Georgia, Tifton, GA
| | - Abolfazl Hajihassani
- Department of Entomology and Nematology, Fort Lauderdale Research and Education Center, Institute of Food and Agricultural Sciences, University of Florida, Davie, FL
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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] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [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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Shin GY, Smith A, Coutinho TA, Dutta B, Kvitko BH. Validation of Species-Specific PCR Assays for the Detection of Pantoea ananatis, P. agglomerans, P. allii, and P. stewartii. Plant Dis 2022; 106:2563-2570. [PMID: 35171633 DOI: 10.1094/pdis-08-21-1810-sc] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Species of Pantoea represent a group of plant pathogenic bacteria that infect a variety of agro-economically important plant species. Among these, a complex of P. ananatis, P. allii, P. agglomerans, and P. stewartii subsp. indologenes cause center rot in onion, resulting in significant economic losses. As species of Pantoea are phenotypically closely related, identification of Pantoea species relies on the sequencing and phylogenetic analysis of housekeeping genes. To aid in rapid identification of Pantoea species, efforts have been made in developing species-specific primers to be used in PCR assays. In the current study, two P. ananatis, one P. allii, one P. agglomerans, and three P. stewartii published primers as well as newly developed P. agglomerans PagR primers were evaluated for their specificity against 79 Pantoea strains, belonging to 15 different species. To ensure that selected primers were evaluated against accurately identified species, sequencing and phylogenetic analysis of housekeeping gene infB were conducted. Thereafter, PCR assays using selected species-specific primers were performed. The results showed that previously described P. ananatis-specific PANA_1008; P. allii-specific allii-leuS; P. stewartii-specific PANST_rpoB, 3614galE, and DC283galE primers; and one newly designed P. agglomerans-specific PagR primer pair were highly specific for their target Pantoea species. They accurately identified these strains into their species and, in some cases, their subspecies level. The findings of the current study will facilitate rapid and reliable identification of P. ananatis, P. agglomerans, P. allii, and P. stewartii.
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Affiliation(s)
- Gi Yoon Shin
- Department of Plant Pathology, University of Georgia, Athens, GA 30602, U.S.A
| | - Amy Smith
- Department of Plant Pathology, University of Georgia, Athens, GA 30602, U.S.A
| | - Teresa A Coutinho
- Department of Biochemistry, Genetics, and Microbiology, University of Pretoria, Pretoria 0002, South Africa
| | - Bhabesh Dutta
- Department of Plant Pathology, University of Georgia, Tifton, GA 31793, U.S.A
| | - Brian H Kvitko
- Department of Plant Pathology, University of Georgia, Athens, GA 30602, U.S.A
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Van Dyk M, Spies CFJ, Mostert L, Halleen F. Detection of Pseudophaeomoniella globosa, an Olive Trunk Pathogen, on Olive Pruning Debris. Plant Dis 2022; 106:2330-2337. [PMID: 35380468 DOI: 10.1094/pdis-09-21-1903-re] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Pseudophaeomoniella globosa has recently been identified as a pathogen contributing to olive trunk diseases in South Africa. Little is known regarding the biology and epidemiology of this pathogen. The aim of this study was to investigate whether olive pruning debris act as an inoculum source of P. globosa in established orchards. A nested species-specific PCR was developed for the detection of this pathogen on 138 samples of pruning debris collected from Paarl (40 wood pieces), Stellenbosch (42 wood pieces), and Worcester (56 pieces) in the Western Cape Province, South Africa. Spore washes were made from the samples (5 to 10 cm in length), after which the nested species-specific primers were used to determine the presence of P. globosa on the wood. P. globosa was detected on 37.5% of the pruning debris collected from Paarl, 61.9% from Stellenbosch, and 39.3% from Worcester. The pruning debris that tested positive for P. globosa were evaluated visually by microscopic observations for P. globosa pycnidia. Dark-brown to black pycnidia were found. Conidia from these pycnidia were measured, cultured, and confirmed as P. globosa by sequencing the internal transcribed spacer region. In this study, the pruning debris in established olive orchards were identified as inoculum sources of P. globosa. This study emphasizes the importance of additional means focused on reducing the inoculum sources of this pathogen in these orchards as an additional management strategy against olive trunk diseases.
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Affiliation(s)
- Meagan Van Dyk
- Plant Protection Division, Agricultural Research Council (ARC) Infruitec-Nietvoorbij, Private Bag X5026, Stellenbosch, 7599, South Africa
- Department of Plant Pathology, University of Stellenbosch, Private Bag X1, Matieland, 7602, South Africa
| | - Christoffel F J Spies
- Plant Protection Division, Agricultural Research Council (ARC) Infruitec-Nietvoorbij, Private Bag X5026, Stellenbosch, 7599, South Africa
- Department of Plant Pathology, University of Stellenbosch, Private Bag X1, Matieland, 7602, South Africa
- ARC-Plant Health and Protection, Private Bag X5017, Stellenbosch, 7599, South Africa
| | - Lizel Mostert
- Department of Plant Pathology, University of Stellenbosch, Private Bag X1, Matieland, 7602, South Africa
| | - Francois Halleen
- Plant Protection Division, Agricultural Research Council (ARC) Infruitec-Nietvoorbij, Private Bag X5026, Stellenbosch, 7599, South Africa
- Department of Plant Pathology, University of Stellenbosch, Private Bag X1, Matieland, 7602, South Africa
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Kaur H, Singh R, Doyle V, Valverde R. A Diagnostic TaqMan Real-Time PCR Assay for In Planta Detection and Quantification of Colletotrichum theobromicola, Causal Agent of Boxwood Dieback. Plant Dis 2021; 105:2395-2401. [PMID: 33630686 DOI: 10.1094/pdis-11-20-2439-re] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Boxwood dieback, caused by Colletotrichum theobromicola, is spreading at an alarming rate in the boxwood industry in the United States. Although C. theobromicola has been accepted as a distinct species within the C. gloeosporioides species complex, it is difficult to distinguish it from other closely related species based on morphology. Moreover, molecular identification of C. theobromicola requires amplification and sequencing of multiple loci, which can be expensive and time consuming. Therefore, a diagnostic TaqMan real-time PCR assay was developed for early and accurate detection and quantification of C. theobromicola in boxwood. The study involved the design of species-specific primers and a TaqMan probe to differentiate C. theobromicola from other closely related Colletotrichum species. The primers and probe discriminate between C. theobromicola and other species in the C. gloeosporioides species complex and can detect C. theobromicola at very low concentrations, illustrating the high specificity and sensitivity of the assay. This TaqMan real-time PCR assay accurately and rapidly distinguishes boxwood dieback from other diseases with similar symptomatology, including Macrophoma blight, Phytophthora root rot, and Volutella blight, as well as some disorders produced by abiotic agents.
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Affiliation(s)
- Harleen Kaur
- Department of Plant Pathology and Crop Physiology, Louisiana State University Agricultural Center, Baton Rouge, LA 70803
| | - Raghuwinder Singh
- Department of Plant Pathology and Crop Physiology, Louisiana State University Agricultural Center, Baton Rouge, LA 70803
| | - Vinson Doyle
- Department of Plant Pathology and Crop Physiology, Louisiana State University Agricultural Center, Baton Rouge, LA 70803
| | - Rodrigo Valverde
- Department of Plant Pathology and Crop Physiology, Louisiana State University Agricultural Center, Baton Rouge, LA 70803
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Chen MN, Santander RD, Talamas EJ, Jentsch PJ, Bon MC, Aćimović SG. Molecular Identification of Trissolcus japonicus, Parasitoid of the Brown Marmorated Stink Bug, by Species-Specific PCR. Insects 2021; 12:467. [PMID: 34069963 DOI: 10.3390/insects12050467] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 05/13/2021] [Accepted: 05/13/2021] [Indexed: 12/14/2022]
Abstract
The samurai wasp, Trissolcus japonicus (Ashmead), has been proposed as a biocontrol agent against brown marmorated stink bugs (BMSB), due to its ability to parasitize and kill BMSB eggs. However, the wasps' small size makes it challenging for those untrained in morphological identification to determine the wasps' species. To circumvent this problem, a molecular method was created to identify T. japonicus. The method uses species-specific primers, designed in this study, which target the variable region of the mitochondrial Cytochrome Oxidase 1 (CO1) locus. After confirming successful DNA extraction from samples, the PCR amplification using our primers produced 227-bp PCR products for all T. japonicus specimens and no amplification in other microhymenoptera candidates. Additionally, DNA from BMSB-parasitized eggs gave positive PCR amplification, while the control BMSB samples showed no amplification. This indicates that PCR with our primers specifically and sensitively differentiates T. japonicus specimens from other similar wasp species and discriminates between T. japonicus-parasitized and non-parasitized BMSB eggs. Finally, an in silico analysis of CO1 sequences demonstrated that our primers match the sequences of four different haplotypes of T. japonicus, indicating that our diagnostic method could potentially be applied to analyze T. japonicus populations throughout North America, Europe, and parts of Asia.
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8
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Guo Y, Pooler M. Real-Time and Conventional PCR Tools for Detection and Discrimination of Calonectria pseudonaviculata and C. henricotiae Causing Boxwood Blight. Plant Dis 2021; 105:164-168. [PMID: 33197379 DOI: 10.1094/pdis-09-19-2053-re] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Calonectria pseudonaviculata and C. henricotiae are the causal agents of boxwood blight, a devastating disease of boxwood that has caused significant economic impact on the nursery and landscape industries in the U.S. and in Europe. The two species are genetically distinct and are found in different geographic areas but are difficult to distinguish based on morphology and pathogenicity. Fast, accurate, and inexpensive methods to detect and differentiate these species is critical in stopping the spread of the disease. We designed primer pairs based on available sequences of four conserved regions-calmodulin, histone H3, internal transcribed spacer, and β-tubulin-and tested their ability to differentiate the two Calonectria species. Here we report three primer pairs derived from sequence differences in the histone H3 region that can be used to specifically detect C. pseudonaviculata, C. henricotiae, or both species. Specificity of these primers was tested against nine isolates of C. pseudonaviculata, three isolates of C. henricotiae, 13 other Calonectria species, and five isolates from related genera using conventional and real-time PCR. These are the first primers available that can be used with either a multiplexed conventional PCR or SYBR-based real-time PCR to specifically detect and differentiate the two fungal species.
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Affiliation(s)
- Yonghong Guo
- U.S. National Arboretum - Floral and Nursery Plants Research Unit, U.S. Department of Agriculture/Agricultural Research Service, Beltsville, MD 20705
| | - Margaret Pooler
- U.S. National Arboretum - Floral and Nursery Plants Research Unit, U.S. Department of Agriculture/Agricultural Research Service, Beltsville, MD 20705
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Moumni M, Allagui MB, Mancini V, Murolo S, Tarchoun N, Romanazzi G. Morphological and Molecular Identification of Seedborne Fungi in Squash ( Cucurbita maxima, Cucurbita moschata). Plant Dis 2020; 104:1335-1350. [PMID: 32223640 DOI: 10.1094/pdis-04-19-0741-re] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Squash is one of the most important crops of tropical and temperate regions, and it can be affected by several fungal pathogens. Most of these pathogens infect the seeds, which become an efficient vehicle to disperse seedborne pathogens over long distances, with consequent severe crop losses. The main objective of this study was the identification of the principal seedborne fungi in seeds extracted from 66 samples of asymptomatic and symptomatic squash fruit (Cucurbita maxima, Cucurbita moschata) collected in two countries, Tunisia and Italy. The symptoms of fruit decay were identified and classified according to lesion size. Following the blotter test, 14 fungal species were detected from the seeds. Seedborne fungi were identified in all fruit samples tested, including asymptomatic fruit. The most frequent fungi from Tunisian seeds were Alternaria alternata (25.1%), followed by Stagonosporopsis cucurbitacearum (24.6%), Fusarium solani (16.6%), Rhizopus stolonifer (13.3%), F. fujikuroi (7.8%), Albifimbria verrucaria (3.3%), and Stemphylium vesicarium (2.3%). For the fruits from Italy, the most frequently identified fungal species in seed samples were Alternaria alternata (40.0%), followed by F. fujikuroi (20.8%), Stemphylium vesicarium (3.0%), and Curvularia spicifera (2.1%). Morphological identification was confirmed by molecular diagnosis using the available species-specific primers. Furthermore, specific primers were designed to identify Albifimbria verrucaria, Paramyrothecium roridum, and Stemphylium vesicarium. Application of seed-health testing methods, including such conventional and molecular diagnostic tools, will help to improve seed quality and crop yields.
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Affiliation(s)
- Marwa Moumni
- Department of Agricultural, Food and Environmental Sciences, Marche Polytechnic University, 60131 Ancona, Italy
- National Agricultural Institute of Tunisia, 1082 Tunis, Tunisia
- Laboratory of Plant Protection, National Institute for Agronomic Research of Tunisia, University of Carthage, 2080 Ariana, Tunisia
| | - Mohamed Bechir Allagui
- Laboratory of Plant Protection, National Institute for Agronomic Research of Tunisia, University of Carthage, 2080 Ariana, Tunisia
| | - Valeria Mancini
- Department of Agricultural, Food and Environmental Sciences, Marche Polytechnic University, 60131 Ancona, Italy
| | - Sergio Murolo
- Department of Agricultural, Food and Environmental Sciences, Marche Polytechnic University, 60131 Ancona, Italy
| | - Neji Tarchoun
- Laboratory of Vegetable Crops, High Agronomic Institute of Chott Mariem, Sousse, Tunisia
| | - Gianfranco Romanazzi
- Department of Agricultural, Food and Environmental Sciences, Marche Polytechnic University, 60131 Ancona, Italy
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Hafez M, Abdelmagid A, Adam LR, Daayf F. Specific Detection and Identification of Fusarium graminearum Sensu Stricto Using a PCR-RFLP Tool and Specific Primers Targeting the Translational Elongation Factor 1α Gene. Plant Dis 2020; 104:1076-1086. [PMID: 32031910 DOI: 10.1094/pdis-03-19-0572-re] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Fusarium graminearum is a toxigenic plant pathogen that causes Fusarium head blight (FHB) disease on cereal crops. It has recently shown to have cross-pathogenicity on noncereals (i.e., Fusarium root rot [FRR] on soybean) in Canada and elsewhere. Specific detection and differentiation of this potent toxigenic, trichothecene-producing pathogen among other closely related species is extremely important for disease control and mycotoxin monitoring. Here, we designed a PCR restriction fragment length polymorphism protocol based on the DNA sequence of the translational elongation factor 1α (TEF1α) gene. A unique restriction site to the enzyme HpaII is only found in F. graminearum sensu stricto strains among different Fusarium strains in the F. graminearum species complex (FGSC) and other Fusarium spp. associated with FHB in cereals and FRR in soybean. Partial amplification of the TEF1α gene with newly designed primers mh1/mh2 generated a 459-bp PCR fragment. Restriction digestion of the generated fragments with the HpaII enzyme generated a unique restriction pattern that can rapidly and accurately differentiate F. graminearum sensu stricto among all other Fusarium spp. A primer pair (FgssF/FgssR) specific to F. graminearum sensu stricto also was designed and can distinguish F. graminearum sensu stricto from all other Fusarium spp. in the FGSC and other closely related Fusarium spp. involved in FHB and FRR. This finding will be very useful for the specific detection of F. graminearum sensu stricto for diagnostic purposes as well as for the accurate detection of this pathogen in breeding and other research purposes.
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Affiliation(s)
- Mohamed Hafez
- Department of Plant Science, University of Manitoba, Winnipeg, Manitoba, R3T2N2, Canada
- Department of Botany and Microbiology, Faculty of Science, Suez University, Suez, Egypt
| | - Ahmed Abdelmagid
- Department of Plant Science, University of Manitoba, Winnipeg, Manitoba, R3T2N2, Canada
- Department of Plant Pathology, Assiut University, Assiut,71515, Egypt
| | - Lorne R Adam
- Department of Plant Science, University of Manitoba, Winnipeg, Manitoba, R3T2N2, Canada
| | - Fouad Daayf
- Department of Plant Science, University of Manitoba, Winnipeg, Manitoba, R3T2N2, Canada
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11
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Kunadiya MB, Dunstan WD, White D, Hardy GESJ, Grigg AH, Burgess TI. A qPCR Assay for the Detection of Phytophthora cinnamomi Including an mRNA Protocol Designed to Establish Propagule Viability in Environmental Samples. Plant Dis 2019; 103:2443-2450. [PMID: 31313641 DOI: 10.1094/pdis-09-18-1641-re] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Phytophthora cinnamomi causes root and collar rot in many plant species in natural ecosystems and horticulture. A species-specific primer and probe PCIN5 were designed based on a mitochondrial locus encoding subunit 2 of cytochrome c oxidase (cox2). Eight PCR primers, including three forward and five reverse, were designed and tested in all possible combinations. Annealing temperatures were optimized for each primer pair set to maximize both specificity and sensitivity. Each set was tested against P. cinnamomi and two closely related clade 7 species, P. parvispora and P. niederhauseri. From these tests, five primer pairs were selected based on specificity and, with a species-specific P. cinnamomi probe, used to develop quantitative real-time PCR (qPCR) assays. The specificity of the two most sensitive qPCR assays was confirmed using the genomic DNA of 29 Phytophthora isolates, including 17 isolates of 11 species from clade 7, and representative species from nine other clades (all except clade 3). The assay was able to detect as little as 150 ag of P. cinnamomi DNA and showed no cross-reaction with other Phytophthora species, except for P. parvispora, a very closely related species to P. cinnamomi, which showed late amplification at high DNA concentrations. The efficiency of the qPCR protocol was evaluated with environmental samples including roots and associated soil from plants artificially infected with P. cinnamomi. Different RNA isolation kits were tested and evaluated for their performance in the isolation of RNA from environmental samples, followed by cDNA synthesis, and qPCR assay. Finally, a protocol was recommended for determining the presence of P. cinnamomi in recalcitrant environmental samples.
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Affiliation(s)
- Manisha B Kunadiya
- Centre for Phytophthora Science and Management, School of Veterinary and Life Sciences, Murdoch University, Murdoch, WA 6150, Australia
| | - William D Dunstan
- Centre for Phytophthora Science and Management, School of Veterinary and Life Sciences, Murdoch University, Murdoch, WA 6150, Australia
| | - Diane White
- Centre for Phytophthora Science and Management, School of Veterinary and Life Sciences, Murdoch University, Murdoch, WA 6150, Australia
| | - Giles E St J Hardy
- Centre for Phytophthora Science and Management, School of Veterinary and Life Sciences, Murdoch University, Murdoch, WA 6150, Australia
| | - Andrew H Grigg
- Alcoa of Australia Ltd., Huntly Mine, Pinjarra, WA 6208, Australia
| | - Treena I Burgess
- Centre for Phytophthora Science and Management, School of Veterinary and Life Sciences, Murdoch University, Murdoch, WA 6150, Australia
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12
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Xu Y, Zhang S, Wang H, Wang M, Li G. Mitochondrial Gene Sequence ( COI) Reveals the Genetic Structure and Demographic History of Lymantria dispar (Lepidoptera: Erebidae: Lymantriinae) in and around China. Insects 2019; 10:E146. [PMID: 31121918 DOI: 10.3390/insects10050146] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/06/2019] [Revised: 05/16/2019] [Accepted: 05/18/2019] [Indexed: 11/17/2022]
Abstract
The gypsy moth, Lymantria dispar, is among the most destructive quarantine pests of forests. Here, we reconstructed the genetic structure and determined the population differentiation of gypsy moths across its distribution range at different times. This information could be used to both improve the prevention and detection of gypsy moths in the field. Using 31 newly designed species-specific primers targeting fragments of 216-1102 bp, we identified 103 full-length cytochrome oxidase subunit I (COI) gene sequences from eight fresh samples and 95 L. dispar specimens collected between 1955 and 1996, mainly in China. Combining 103 full-length COI gene sequences with 146 COI gene sequences from Genbank or DNA barcode libraries, we analyzed the genetic differentiation, gene flow and haplotypes between gypsy moth populations in order to reflect the genetic structure and population dynamics of gypsy moths. We discovered 25 previously unknown haplotypes from old gypsy moth specimens. We found that the genetic diversity among gypsy moth populations (collected in the same region at different time points) was relatively high. Furthermore, the genetic structure of Chinese geographical populations (Heilongjiang, Liaoning, Beijing) in different years was distinct. Our results suggested that some gypsy moths in China showed the genetic affinity with European gypsy moths (a sub-species of gypsy moths found mainly in Europe).
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Eaton S, Zúñiga C, Czyzewski J, Ellis C, Genney DR, Haydon D, Mirzai N, Yahr R. A method for the direct detection of airborne dispersal in lichens. Mol Ecol Resour 2017; 18:240-250. [PMID: 29091345 DOI: 10.1111/1755-0998.12731] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2017] [Revised: 09/29/2017] [Accepted: 10/11/2017] [Indexed: 11/27/2022]
Abstract
This study sets out a novel method to determine dispersal distances in lichens. Direct measurement of dispersal often remains difficult for lichens and other small inconspicuous species because of the need to track microscopic reproductive propagules, which even if they can be captured, cannot be identified using traditional morphological approaches. A low-cost device (<£200) was developed to trap the reproductive propagules of lichens, capable of sampling around 0.1 m3 of air per minute. In parallel, molecular techniques were developed to enable species-specific detection of propagules caught by the devices, with identification using novel species-specific primers and optimization of a standard DNA extraction and nested PCR protocol. The methods were tested for both their sensitivity and specificity against a suite of lichen epiphytes, differing in their reproductive mechanisms, dispersal structures and rarity. Sensitivity tests showed that the molecular techniques could detect a single asexual propagule (soredium or isidium), or as few as 10 sexual spores. As proof of concept, propagule traps were deployed into a wooded landscape where the target epiphytes were present. Extractions from deployed propagule traps were sequenced, showing that the method was able to detect the presence of the target species in the atmosphere. As far as we are aware, this is the first attempt to use mechanized propagule traps in combination with DNA diagnostics to detect dispersal of lichens. The tests carried out here point the way for future dispersal studies of lichen epiphytes and other passively dispersed microscopic organisms including fungi or bryophytes.
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Affiliation(s)
- Sally Eaton
- Royal Botanic Garden Edinburgh, Edinburgh, UK
| | | | - Jakub Czyzewski
- College of Medical, Veterinary & Life Sciences (MVLS), University of Glasgow, Glasgow, UK
| | | | - David R Genney
- Scottish Natural Heritage, Great Glen House, Inverness, UK
| | - Daniel Haydon
- College of Medical, Veterinary & Life Sciences (MVLS), University of Glasgow, Glasgow, UK
| | - Nosrat Mirzai
- College of Medical, Veterinary & Life Sciences (MVLS), University of Glasgow, Glasgow, UK
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Liu Y, Wang XY, Gao ZT, Han JP, Xiang L. Detection of Ophiocordyceps sinensis and Its Common Adulterates Using Species-Specific Primers. Front Microbiol 2017; 8:1179. [PMID: 28680424 PMCID: PMC5478735 DOI: 10.3389/fmicb.2017.01179] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2017] [Accepted: 06/09/2017] [Indexed: 11/30/2022] Open
Abstract
Ophiocordyceps sinensis is a fungus that infects Hepialidae caterpillars, mummifying the larvae and producing characteristic fruiting bodies (stromata) that are processed into one of the most valued traditional Chinese medicines (TCM). The product commands a very high price due to a high demand but a very limited supply. Adulteration with other fungi is a common problem and there is a need to test preparation for the presence of the correct fungus. In the current study, a PCR-based approach for the identification of O. sinensis based on a segment of the internal transcribed spacer (ITS) region was developed. The segments is 146-bp in size and is likely to be amplified even in materials where processing led to DNA fragmentation. Primer development was based on the alignment of sequence data generated from a total of 89 samples of O. sinensis and potential adulterants as well as sequences date from 41 Ophiocordyceps species and 26 Cordyceps species available in GenBank. Tests with primer pair, DCF4/DCR4, demonstrated generation of an amplicon from DNA extracted from O. sinensis stromata, but not from extracts derived from adulterants. Species-specific primer pairs were also developed and tested for detection of the common adulterants, Cordyceps gunnii, Cordyceps cicadae, Cordyceps militaris, Cordyceps liangshanensis and Ophiocordyceps nutans. The collection of primers developed in the present study will be useful for the authentication of preparation claiming to only contain O. sinensis and for the detection of fungi used as adulterants in these preparations.
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Affiliation(s)
- Yang Liu
- Identification Center, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical CollegeBeijing, China
| | - Xiao-Yue Wang
- Identification Center, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical CollegeBeijing, China
| | - Zi-Tong Gao
- Identification Center, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical CollegeBeijing, China
| | - Jian-Ping Han
- Identification Center, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical CollegeBeijing, China
| | - Li Xiang
- Artemisinin Research Center, Institute of Chinese Materia Medica, China Academy of Chinese Medical SciencesBeijing, China
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Li J, Yang F, Wang Q, Pan H, Yuan H, Lu Y. Predation by generalist arthropod predators on Apolygus lucorum (Hemiptera: Miridae): molecular gut-content analysis and field-cage assessment. Pest Manag Sci 2017; 73:628-635. [PMID: 27349598 DOI: 10.1002/ps.4346] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2016] [Revised: 06/22/2016] [Accepted: 06/23/2016] [Indexed: 06/06/2023]
Abstract
BACKGROUND The mirid bug Apolygus lucorum (Meyer-Dür) is a principal pest of cotton that also causes great damage to many other crops in China. A study was conducted to assess the mortality of A. lucorum from generalist arthropod predators using both molecular methods and a field-cage trial. The species-specific primer pair for the detection of A. lucorum tissues in predators was designed according to the sequences of the cytochrome oxidase subunit I (COI) gene. RESULTS A total of 2096 generalist predators that consisted of ladybeetles, lacewings and spiders were collected, and A. lucorum remains were detected using the designed primers. Only 1.6% of these predators contained A. lucorum DNA, with the highest positive proportion (6.1%) for Harmonia axyridis larvae. In the field-cage experiment, the daily predation rates of second-instar A. lucorum nymphs by H. axyridis adults and larvae were 4.7 and 5.2% respectively. CONCLUSIONS The overall low positive proportion of generalist predators with A. lucorum DNA detected using the molecular method, combined with the low predation rate in the field-cage experiment, indicated that the primary generalist predators likely had a limited role in the suppression of A. lucorum in the field. © 2016 Society of Chemical Industry.
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Affiliation(s)
- Jinhua Li
- College of Agronomy, Jilin Agricultural University, Changchun, China
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Fan Yang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Qian Wang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Hongsheng Pan
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
- Institute of Plant Protection, Xinjiang Academy of Agricultural Sciences, Urumqi, China
| | - Haibin Yuan
- College of Agronomy, Jilin Agricultural University, Changchun, China
| | - Yanhui Lu
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
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Qiming C, Tingting T, Xiaomei B, Yingjian L, Fengxia L, Ligong Z, Zhaoxin L. Mining for sensitive and reliable species-specific primers for PCR for detection of Cronobacter sakazakii by a bioinformatics approach. J Dairy Sci 2016; 98:5091-101. [PMID: 26074237 DOI: 10.3168/jds.2015-9304] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2015] [Accepted: 04/24/2015] [Indexed: 11/19/2022]
Abstract
Although several studies have reported PCR assays for distinguishing Cronobacter sakazakii from other species in the genus, reports regarding assay sensitivity and specificity, as well as applications for food testing, are lacking. Hence, the objective of this study was to develop a sensitive and reliable PCR-based method for detection of C. sakazakii by screening for specific target genes. The genome sequence of C. sakazakii in the GenBank database was compared with that of other organisms using BLAST. Thirty-eight DNA fragments unique to C. sakazakii were identified, and primers targeting these sequences were designed. Finally, 3 primer sets (CS14, CS21, and CS38) were found to be specific for C. sakazakii by PCR verification. The detection limit of PCR assays using the 3 pairs of primers was 1.35 pg/μL, 135 fg/μL, and 135 fg/μL, respectively, for genomic DNA, and 5.5×10(5), 5.5×10(3), 5.5×10(3) cfu/mL, respectively, using pure cultures of the bacteria, compared with 13.5 pg/μLand 5.5×10(5) cfu/mLfor primer set SpeCronsaka, which has been previously described. Cronobacter sakazakii were detected in artificially contaminated powdered infant formula (PIF) by PCR using primer sets CS21 and CS38 after 8h of enrichment. The detection limit was 5.5×10(-1) cfu/10g of PIF. Thus, the PCR assay can be used for rapid and sensitive detection of C. sakazakii in PIF.
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Affiliation(s)
- Chen Qiming
- College of Food Science and Technology, Nanjing Agricultural University, 1 Weigang, Nanjing 210095, People's Republic of China
| | - Tao Tingting
- College of Food Science and Technology, Nanjing Agricultural University, 1 Weigang, Nanjing 210095, People's Republic of China
| | - Bie Xiaomei
- College of Food Science and Technology, Nanjing Agricultural University, 1 Weigang, Nanjing 210095, People's Republic of China
| | - Lu Yingjian
- Department of Nutrition and Food Sciences, University of Maryland, College Park 20742
| | - Lu Fengxia
- College of Food Science and Technology, Nanjing Agricultural University, 1 Weigang, Nanjing 210095, People's Republic of China
| | - Zhai Ligong
- College of Food Science and Technology, Nanjing Agricultural University, 1 Weigang, Nanjing 210095, People's Republic of China
| | - Lu Zhaoxin
- College of Food Science and Technology, Nanjing Agricultural University, 1 Weigang, Nanjing 210095, People's Republic of China.
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Al-Banna L, Ploeg AT, Williamson VM, Kaloshian I. Discrimination of six pratylenchus species using PCR and species-specific primers. J Nematol 2004; 36:142-146. [PMID: 19262799 PMCID: PMC2620765] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/27/2023] Open
Abstract
A PCR-based assay for identification of six species of Pratylenchus common in California is described. In this assay, five forward species-specific primers were designed from the internal variable portion of the D3 expansion region of the 26S rDNA and were each used with a single, common reverse primer. The optimized species-specific primers produced unique amplicons from their respective target and did not amplify DNA from other Pratylenchus species. With this assay we were able to identify single females to species level. This method obviates the need for subsequent RFLP or sequence analysis of the PCR product and can be used as a rapid diagnostic tool in epidemiological and management studies.
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