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Journal articles on the topic 'Phytophthora specific DNA probes'

Author: Grafiati

Published: 2 June 2025

Last updated: 31 July 2025

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1

Bilodeau, Guillaume J., Frank N. Martin, Michael D. Coffey, and Cheryl L. Blomquist. "Development of a Multiplex Assay for Genus- and Species-Specific Detection of Phytophthora Based on Differences in Mitochondrial Gene Order." Phytopathology® 104, no. 7 (2014): 733–48. http://dx.doi.org/10.1094/phyto-09-13-0263-r.

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A molecular diagnostic assay for Phytophthora spp. that is specific, sensitive, has both genus- and species-specific detection capabilities multiplexed, and can be used to systematically develop markers for detection of a wide range of species would facilitate research and regulatory efforts. To address this need, a marker system was developed based on the high copy sequences of the mitochondrial DNA utilizing gene orders that were highly conserved in the genus Phytophthora but different in the related genus Pythium and plants to reduce the importance of highly controlled annealing temperature

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2

Sikora, Katarzyna, Els Verstappen, Odette Mendes, Cor Schoen, Jean Ristaino, and Peter Bonants. "A Universal Microarray Detection Method for Identification of Multiple Phytophthora spp. Using Padlock Probes." Phytopathology® 102, no. 6 (2012): 635–45. http://dx.doi.org/10.1094/phyto-11-11-0309.

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The genus Phytophthora consists of many species that cause important diseases in ornamental, agronomic, and forest ecosystems worldwide. Molecular methods have been developed for detection and identification of one or several species of Phytophthora in single or multiplex reactions. In this article, we describe a padlock probe (PLP)-based multiplex method of detection and identification for many Phytophthora spp. simultaneously. A generic TaqMan polymerase chain reaction assay, which detects all known Phytophthora spp., is conducted first, followed by a species-specific PLP ligation. A 96-well

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3

Miles, Timothy D., Frank N. Martin, Gregg P. Robideau, Guillaume J. Bilodeau, and Michael D. Coffey. "Systematic Development of Phytophthora Species-Specific Mitochondrial Diagnostic Markers for Economically Important Members of the Genus." Plant Disease 101, no. 7 (2017): 1162–70. http://dx.doi.org/10.1094/pdis-09-16-1224-re.

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The genus Phytophthora contains many invasive species to the U.S.A. that have the potential to cause significant damage to agriculture and native ecosystems. A genus and species-specific diagnostic assay was previously reported based on mitochondrial gene order differences that allowed for the systematic development of 14 species-specific TaqMan probes for pathogen detection ( Bilodeau et al. 2014 ). In this study, an additional 32 species-specific TaqMan probes for detection of primarily invasive species have been validated against 145 Phytophthora taxa as well as a range of Pythium and plant

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Vitas, Adomas, Tomasz Oszako, Justyna A. Nowakowska, Katarzyna Sikora, and Antanina Stankevičienėm. "First records of Phytophthora spp. based on DNA analysis in Lithuania." Folia Forestalia Polonica, Series A - Forestry 54(1) (March 1, 2012): 25–31. https://doi.org/10.5281/zenodo.30881.

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The assessment of alien invasive species of Phytophthora genus causing serious forest tree species diseases was carried out in Lithuania. The presence of Phytophthora DNA was recorded for the first time using real-time PCR analysis on 23 DNA samples. The sampling included wood from diseased trees, leaves from shrubs, leaves baited in water, and soil samples taken around diseased plants. Extracted DNA from soil and plant tissues was tested for the presence of Phytophthora. All analysed samples were positively recognized by Phytophthora-specific probe during real-time PCR which proved the presen

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5

McCoy, Austin G., Timothy D. Miles, Guillaume J. Bilodeau, et al. "Validation of a Preformulated, Field Deployable, Recombinase Polymerase Amplification Assay for Phytophthora Species." Plants 9, no. 4 (2020): 466. http://dx.doi.org/10.3390/plants9040466.

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Recombinase polymerase amplification (RPA) assays are valuable molecular diagnostic tools that can detect and identify plant pathogens in the field without time-consuming DNA extractions. Historically, RPA assay reagents were commercially available as a lyophilized pellet in microfuge strip tubes, but have become available in liquid form more recently—both require the addition of primers and probes prior to use, which can be challenging to handle in a field setting. Lyophilization of primers and probes, along with RPA reagents, contained within a single tube limits the risk of contamination, e

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6

Tooley, Paul W., Frank N. Martin, Marie M. Carras, and Reid D. Frederick. "Real-Time Fluorescent Polymerase Chain Reaction Detection of Phytophthora ramorum and Phytophthora pseudosyringae Using Mitochondrial Gene Regions." Phytopathology® 96, no. 4 (2006): 336–45. http://dx.doi.org/10.1094/phyto-96-0336.

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A real-time fluorescent polymerase chain reaction (PCR) detection method for the sudden oak death pathogen Phytophthora ramorum was developed based on mitochondrial DNA sequence with an ABI Prism 7700 (TaqMan) Sequence Detection System. Primers and probes were also developed for detecting P. pseudosyringae, a newly described species that causes symptoms similar to P. ramorum on certain hosts. The species-specific primer-probe systems were combined in a multiplex assay with a plant primer-probe system to allow plant DNA present in extracted samples to serve as a positive control in each reactio

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7

Whisson, SC, BJ Howlett, ECY Liew, DJ Maclean, JM Manners, and JAG Irwin. "An Assessment of Genetic Relationships between Members of the Phytophthora megasperma Complex and Phytophthora vignae using Molecular Markers." Australian Systematic Botany 6, no. 4 (1993): 295. http://dx.doi.org/10.1071/sb9930295.

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Genetic relationships between Phytophora megasperma f. sp. glycinea (Pmg) and morphologically similar taxa, P. megasperma f. sp. medicaginis (Pmm), P. megasperma f. sp. trifolii (Pmt), P. megasperma from Douglas Fir (PmDF) and asparagus (PmAS) and Phytophthora vignae, were explored by restriction fragment length polymorphism (RFLP) analysis of nuclear DNA using random genomic multi-copy, cDNA, and ribosomal DNA probes as well as random amplified polymorphic DNA (RAPDs) and RFLP analysis of ribosomal intergenic spacer regions amplified by the polymerase chain reaction (PCR). Each method detecte

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8

Lievens, B., I. R. M. Hanssen, A. C. R. C. Vanachter, B. P. A. Cammue, and B. P. H. J. Thomma. "Root and Foot Rot on Tomato Caused by Phytophthora infestans Detected in Belgium." Plant Disease 88, no. 1 (2004): 86. http://dx.doi.org/10.1094/pdis.2004.88.1.86a.

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In January 2003, a severe root and foot rot was observed on 2-month-old wilted tomato (Lycopersicon esculentum Mill.) plants in a large-scale (2.5 ha) commercial greenhouse setting in Belgium. Tomato plants (10%) produced from healthy nursery-grown seedlings and planted to new, clean rockwool and drip irrigation with UV-disinfected water developed symptoms. Symptom development was restricted to lower plant parts with severe rotting of the entire root system and dark lesions girdling the stem base. No symptoms of disease were observed on the foliage or upper stems. Cross sections of the stem ba

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9

Oszako, Tomasz, Katarzyna Anna Kubiak, Marta Siebyła, and Justyna Anna Nowakowska. "Slow Sand Filters as a part of integrated protection of seedlings against disease in forest nurseries." Forest Research Papers 74 (1) (March 1, 2013): 49–56. https://doi.org/10.2478/frp-2013-0006.

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Slow Sand Filters (SSF) are a biological method used to protect nursery plants, from pathogen infections which can cause serious diseases in many forest tree species. Thanks to SSF application the number of phytopathogens in nurseries can be significantly reduced, as demonstrated by many field and greenhouse experiments (e.g. in Polish nurseries, and for horticultural crops in Germany and The Netherlands). In this study, the effect of pollution from fertilizers and fungicides used in agriculture (e.g. PCNB) on the efficiency of SSFs was assessed. A quantitative analysis was performed of the co

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10

Goodwin, P. H., B. C. Kirkpatrick, and J. M. Duniway. "Identification of Phytophthora citrophthora with Cloned DNA Probes." Applied and Environmental Microbiology 56, no. 3 (1990): 669–74. http://dx.doi.org/10.1128/aem.56.3.669-674.1990.

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11

Song, Jeong-Young, and Hong-Gi Kim. "Development of Repetitive DNA Probes for Genetic Analysis of Phytophthora capsici." Korean Journal of Mycology 30, no. 1 (2002): 66–72. http://dx.doi.org/10.4489/kjm.2002.30.1.066.

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12

Baumgartner, Adolf, Jingly Fung Weier, and Heinz-Ulrich G. Weier. "Chromosome-specific DNA Repeat Probes." Journal of Histochemistry & Cytochemistry 54, no. 12 (2006): 1363–70. http://dx.doi.org/10.1369/jhc.6a6974.2006.

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13

Rojas, J. Alejandro, Timothy D. Miles, Michael D. Coffey, Frank N. Martin, and Martin I. Chilvers. "Development and Application of qPCR and RPA Genus- and Species-Specific Detection of Phytophthora sojae and P. sansomeana Root Rot Pathogens of Soybean." Plant Disease 101, no. 7 (2017): 1171–81. http://dx.doi.org/10.1094/pdis-09-16-1225-re.

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Phytophthora root rot of soybean, caused by Phytophthora sojae, is one of the most important diseases in the Midwestern United States, and is estimated to cause losses of up to 1.2 million metric tons per year. Disease may also be caused by P. sansomeana; however, the prevalence and damage caused by this species is not well known, partly due to limitations of current diagnostic tools. Efficient, accurate, and sensitive detection of pathogens is crucial for management. Thus, multiplex qPCR and isothermal RPA (recombinase polymerase amplification) assays were developed using a hierarchical appro

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14

Oszako, Tomasz, Katarzyna Sikora, Lassaâd Belbahri, and Justyna A. Nowakowska. "Molecular detection of oomycetes species in water courses." Folia Forestalia Polonica 58, no. 4 (2016): 246–51. http://dx.doi.org/10.1515/ffp-2016-0028.

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Abstract In Poland, about 20% of forest nurseries use irrigation water coming from natural superficial reservoirs, presumed to be the first source of infection caused by harmful pathogens belonging to the Oomycota class, especially Phytophthora genus and Pythium genus. The forest nursery is the only place where forest managers can react before pathogens leave it with asymptomatic plants or soil attached to their roots. The aim of this research was detection and identification phytopathogens in water samples. In order to recognise genus Phytophthora or Pythium in water collected from 33 places

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15

Tomasz, Oszako, Sikora Katarzyna, Belbahri Lassaâd, and A. Nowakowska Justyna. "Molecular detection of oomycetes species in water courses." FOLIA FORESTALIA POLONICA, SERIES A – FORESTRY 58, no. 4 (2021): 246–51. https://doi.org/10.1515/ffp-2016-0028.

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In Poland, about 20% of forest nurseries use irrigation water coming from natural superficial reservoirs, presumed to be the first source of infection caused by harmful pathogens belonging to the Oomycota class, especially <em>Phytophthora</em> genus and<em> Pythium</em> genus. The forest nursery is the only place where forest managers can react before pathogens leave it with asymptomatic plants or soil attached to their roots. The aim of this research was detection and identification phytopathogens in water samples. In order to recognise genus <em>Phytophthora</em> or<em> Pythium</em> in wate

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16

Oakey, H. J., L. F. Gibson, and A. M. George. "DNA probes specific forAeromonas hydrophila(HG1)." Journal of Applied Microbiology 86, no. 2 (1999): 187–93. http://dx.doi.org/10.1046/j.1365-2672.1999.00647.x.

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17

Martin, Frank N., Paul W. Tooley, and Cheryl Blomquist. "Molecular Detection of Phytophthora ramorum, the Causal Agent of Sudden Oak Death in California, and Two Additional Species Commonly Recovered from Diseased Plant Material." Phytopathology® 94, no. 6 (2004): 621–31. http://dx.doi.org/10.1094/phyto.2004.94.6.621.

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Sudden oak death is a disease currently devastating forest ecosystems in several coastal areas of California. The pathogen causing this is Phy-tophthora ramorum, although species such as P. nemorosa and P. pseudo-syringae often are recovered from symptomatic plants as well. A molecular marker system was developed based on mitochondrial sequences of the cox I and II genes for detection of Phytophthora spp. in general, and P. ramorum, P. nemorosa, and P. pseudosyringae in particular. The first-round multiplex amplification contained two primer pairs, one for amplification of plant sequences to s

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18

Belbahri, L., G. Calmin, S. Wagner, E. Moralejo, S. Woodward, and F. Lefort. "Specific hybridization real-time PCR probes for Phytophthora ramorum detection and diagnosis." Forest Pathology 37, no. 6 (2007): 403–8. http://dx.doi.org/10.1111/j.1439-0329.2007.00517.x.

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19

Johansen, I. E. "Specific Identification ofClavibacter michiganensesubsp.sepedonicumby DNA-Hybridization Probes." Phytopathology 79, no. 10 (1989): 1019. http://dx.doi.org/10.1094/phyto-79-1019.

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20

GILLAM, I. "Non-radioactive probes for specific DNA sequences." Trends in Biotechnology 5, no. 12 (1987): 332–34. http://dx.doi.org/10.1016/0167-7799(87)90017-5.

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21

Green, Michael R., and Joseph Sambrook. "Labeling of DNA Probes by Polymerase Chain Reaction." Cold Spring Harbor Protocols 2022, no. 3 (2021): pdb.prot100610. http://dx.doi.org/10.1101/pdb.prot100610.

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The polymerase chain reaction (PCR) can be used to produce both nonradiolabeled DNA probes and radiolabeled DNA probes with high specific activity. In this protocol, PCR is used to generate double-stranded probes. Related methods, including the generation of asymmetric probes by PCR, are also discussed.

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22

Man in 't Veld, Willem A., Wil J. Veenbaas-Rijks, Elena Ilieva, Arthur W. A. M. de Cock, Peter J. M. Bonants, and Rob Pieters. "Natural Hybrids of Phytophthora nicotianae and Phytophthora cactorum Demonstrated by Isozyme Analysis and Random Amplified Polymorphic DNA." Phytopathology® 88, no. 9 (1998): 922–29. http://dx.doi.org/10.1094/phyto.1998.88.9.922.

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Three similar isolates of Phytophthora (Phytophthora sp-h) were obtained from diseased Spathiphyllum and Primula plants. Cultural characteristics did not fit any known description of Phytophthora species. The Phytophthora sp-h isolates are papillate, are homothallic, possess 80 to 86% amphigynous antheridia, and have a maximum temperature for growth of 36.5°C. Isozyme analysis of the Phytophthora sp-h isolates revealed a three-banded pattern with malic enzyme and a three-banded pattern with malate dehydrogenase on the second putative locus. The fastest band at both enzyme loci comigrated with

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23

McFarlane, Robin G., and David G. Thawley. "DNA hybridization procedure to detect pseudorabies virus DNA in swine tissue." American Journal of Veterinary Research 46, no. 5 (1985): 1133–36. https://doi.org/10.2460/ajvr.1985.46.05.1133.

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SUMMARY A DNA hybridization technique was developed to detect the presence of pseudorabies virus (prv) DNA. 32P Nick translated probes of high specific activity were prepared from transformed Escherichia coli plasmids into which Bacillus amyloliquefaciens H (Bam H1) restriction fragments of prv DNA had been inserted. Swine cellular DNA and tissue culture prv DNA were digested with Bam H1, separated by agarosegel electrophoresis, transferred onto nitrocellulose paper, hybridized to the radioactive probes, and washed under high stringency conditions; autoradiographs were then prepared. Under the

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24

Miles, Timothy D., Frank N. Martin, and Michael D. Coffey. "Development of Rapid Isothermal Amplification Assays for Detection of Phytophthora spp. in Plant Tissue." Phytopathology® 105, no. 2 (2015): 265–78. http://dx.doi.org/10.1094/phyto-05-14-0134-r.

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Several isothermal amplification techniques recently have been developed that are tolerant of inhibitors present in many plant extracts, which can reduce the need for obtaining purified DNA for running diagnostic assays. One such commercially available technique that has similarities with real-time polymerase chain reaction (PCR) for designing primers and a labeled probe is recombinase polymerase amplification (RPA). This technology was used to develop two simple and rapid approaches for detection of Phytophthora spp.: one genus-specific assay multiplexed with a plant internal control and the

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25

Puertolas, Alexandra, Peter J. M. Bonants, Eric Boa, and Steve Woodward. "Application of Real-Time PCR for the Detection and Quantification of Oomycetes in Ornamental Nursery Stock." Journal of Fungi 7, no. 2 (2021): 87. http://dx.doi.org/10.3390/jof7020087.

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Numerous Phytophthora and Pythium disease outbreaks have occurred in Europe following inadvertent introduction of contaminated ornamental plants. Detection and identification of pathogens are crucial to reduce risks and improve plant biosecurity in Europe and globally. Oomycete diversity present in roots and compost was determined in 99 hardy woody plants bought from nurseries, retailers and internet sellers, using both isolations and molecular analyses. Oomycete DNA was quantified using real-time PCR of environmental DNA from the plants using three loci: ITS, trnM-trnP-trnM and atp9-nad9. At

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26

El-Kharbotly, A., J. M. E. Jacobs, B. te Lintel Hekkert, et al. "Localization of Ds-transposon containing T-DNA inserts in the diploid transgenic potato: linkage to the R1 resistance gene against Phytophthora infestans (Mont.) de Bary." Genome 39, no. 2 (1996): 249–57. http://dx.doi.org/10.1139/g96-034.

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The Dissociation transposable element (Ds) of maize containing NPTII was introduced into the diploid potato (Solanum tuberosum) clone J91-6400-A16 through Agrobacterium tumefaciens mediated transformation. Genomic DNA sequences flanking the T-DNAs from 312 transformants were obtained with inverse polymerase chain reaction or plasmid rescue techniques and used as probes for RFLP linkage analysis. The RFLP map location of 60 T-DNAs carrying Ds–NPTII was determined. The T-DNA distribution per chromosome and the relative distance between them appeared to be random. All 12 chromosomes have been cov

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27

ole-MoiYoi, O. K. "DNA probes in the field; Trypanosome Species-specific DNA probes to detect infection in Tsetse Flies." Parasitology Today 3, no. 12 (1987): 371–74. http://dx.doi.org/10.1016/0169-4758(87)90246-8.

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28

WANG, RONG-FU, MICHAEL F. SLAVIK, WEI-WEN CAO, and P. J. BLORE. "DEVELOPMENT of DNA PROBES SPECIFIC FOR CAMPYLOBACTER JEJUNI." Journal of Rapid Methods and Automation in Microbiology 1, no. 1 (1992): 83–92. http://dx.doi.org/10.1111/j.1745-4581.1992.tb00072.x.

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29

Shaohua Zhao and Richard Yamamoto. "Species-specific recombinant DNA probes for Mycoplasma meleagridis." Veterinary Microbiology 35, no. 1-2 (1993): 179–85. http://dx.doi.org/10.1016/0378-1135(93)90124-p.

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30

Khan, M. I., B. C. Kirkpatrick, and R. Yamamoto. "Mycoplasma gallisepticumspecies and strain‐specific recombinant DNA probes." Avian Pathology 18, no. 1 (1989): 135–46. http://dx.doi.org/10.1080/03079458908418586.

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31

KÖHRER, KARL, TONI M. KUTCHAN, and HORST DOMDEY. "Specific Oligodeoxynucleotide Probes Obtained through RNA Sequencing." DNA 8, no. 2 (1989): 143–47. http://dx.doi.org/10.1089/dna.1.1989.8.143.

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32

Kim, Hyun-Joong, and Byron F. Brehm-Stecher. "Design and Evaluation of Peptide Nucleic Acid Probes for Specific Identification of Candida albicans." Journal of Clinical Microbiology 53, no. 2 (2014): 511–21. http://dx.doi.org/10.1128/jcm.02417-14.

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Candida albicansis an important cause of systemic fungal infections, and rapid diagnostics for identifying and differentiatingC. albicansfrom otherCandidaspecies are critical for the timely application of appropriate antimicrobial therapy, improved patient outcomes, and pharmaceutical cost savings. In this work, two 28S rRNA-directed peptide nucleic acid-fluorescencein situhybridization (PNA-FISH) probes, P-Ca726 (targeting a novel region of the ribosome) and P-CalB2208 (targeting a previously reported region), were evaluated. Hybridization conditions were optimized by using both fluorescence

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33

Ma, Wenbo, Yuanchao Wang, and John McDowell. "Focus on Effector-Triggered Susceptibility." Molecular Plant-Microbe Interactions® 31, no. 1 (2018): 5. http://dx.doi.org/10.1094/mpmi-11-17-0275-le.

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Effector biology exhibits diversity at every level. Effector proteins play key roles in the molecular interplay between plants and plant-associated organisms, and effector biology remains one of the most active areas in the research field of molecular plant-microbe interactions. Using effectors as probes, much has been learned about pathogen virulence and host immunity, which has broad implications in developing disease-resistant crops that are essential for global food security. Thus, the MPMI Editorial Board is publishing this Focus Issue to showcase recent progress in this area. Additional

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34

Leung, F. C., M. Welt, R. D. Quesenberry, and X.-Z. Shen. "DNA Fingerprinting and Cloning of Hypervariable Minisatellite Repeats in Salmonids." Canadian Journal of Fisheries and Aquatic Sciences 51, S1 (1994): 258–66. http://dx.doi.org/10.1139/f94-312.

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We used heterologous Jeffreys' 33.6 core sequence and microsatellites (CAC)5 and (CA)12 as probes and compared them with probes based on the minisatellite sequences from tilapia (Oreochromis niloticus) and Atlantic salmon (Salmo salar) in fingerprinting assays. DNA fingerprints generated with the Jeffreys' 33.6 core sequence and the microsatellite (CAC)5 and (CA)12 probes showed complex profiles with high background, but DNA fingerprints using the tilapia and Atlantic salmon probes showed clear, less complex, informative, individual-specific DNA fingerprints suitable for analysis. We cloned an

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35

Weier, H. U., R. Segraves, D. Pinkel, and J. W. Gray. "Synthesis of Y chromosome-specific labeled DNA probes by in vitro DNA amplification." Journal of Histochemistry & Cytochemistry 38, no. 3 (1990): 421–26. http://dx.doi.org/10.1177/38.3.2406338.

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We describe the use of in vitro DNA amplification for production of double-stranded, biotin-labeled DNA probes. Specifically, a 124 BP DNA segment of the Y chromosome-specific 3.4 KB repeat was amplified in preparations of human genomic DNA using the polymerase chain reaction (PCR) and a thermostable DNA polymerase. The PCR products were amplified further in the presence of a molar excess of biotin-11-dUTP. The resulting double-stranded DNA segments showed a high amount of incorporated biotin-11-dUTP. The probes were used in DNA-DNA hybridization experiments without further purification. When

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36

Modi, Nishtaa, Jeffrey Guo, Ryan A. Lee, Alisha Greenstein, and Richard S. Lee. "Targeted DNA Methylation Using Modified DNA Probes: A Potential Therapeutic Tool for Depression and Stress-Related Disorders." International Journal of Molecular Sciences 26, no. 12 (2025): 5643. https://doi.org/10.3390/ijms26125643.

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: Epigenetic modifications play a crucial role in gene regulation and have been implicated in various physiological processes and disease conditions. DNA methylation (DNAm) has been implicated in the etiology and progression of many stress-related psychiatric behaviors, such as depression. The ability to manipulate DNAm may provide a means to reverse and treat such disorders. Although CRISPR-based technologies have enabled locus-specific DNAm editing, their clinical applicability may be limited due to immunogenicity concerns and off-target effects. In this study, we introduce a novel approach

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37

Rudi, Knut, Janneke Treimo, Hilde Nissen, and Gerd Vegarud. "Protocols for 16S rDNA Array Analyses of Microbial Communities by Sequence-Specific Labeling of DNA Probes." Scientific World JOURNAL 3 (2003): 578–84. http://dx.doi.org/10.1100/tsw.2003.44.

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Analyses of complex microbial communities are becoming increasingly important. Bottlenecks in these analyses, however, are the tools to actually describe the biodiversity. Novel protocols for DNA array-based analyses of microbial communities are presented. In these protocols, the specificity obtained by sequence-specific labeling of DNA probes is combined with the possibility of detecting several different probes simultaneously by DNA array hybridization. The gene encoding 16S ribosomal RNA was chosen as the target in these analyses. This gene contains both universally conserved regions and re

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38

Křivánková, Anna, David Kopecký, Štěpán Stočes, Jaroslav Doležel, and Eva Hřibová. "Repetitive DNA: A Versatile Tool for Karyotyping in Festuca pratensis Huds." Cytogenetic and Genome Research 151, no. 2 (2017): 96–105. http://dx.doi.org/10.1159/000462915.

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FISH is a useful method to identify individual chromosomes in a karyotype and to discover their structural changes accompanying genome evolution and speciation. DNA probes for FISH should be chromosome specific and/or exhibit specific patterns of distribution along each chromosome. Such probes are not available in many plants including meadow fescue (Festuca pratensis Huds.), an important forage grass species. In the present study, various DNA repeats identified in Illumina shotgun sequences specific to chromosome 4F of F. pratensis were used as probes for FISH to develop the molecular karyoty

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39

Zhang, Ruoyu, Ryan T. K. Kwok, Ben Zhong Tang, and Bin Liu. "Hybridization induced fluorescence turn-on of AIEgen–oligonucleotide conjugates for specific DNA detection." RSC Advances 5, no. 36 (2015): 28332–37. http://dx.doi.org/10.1039/c5ra00322a.

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40

Hu, Qiong, Xianbao Deng, Jinming Kong, Yuanyuan Dong, Qianrui Liu, and Xueji Zhang. "Simple and fast electrochemical detection of sequence-specific DNA via click chemistry-mediated labeling of hairpin DNA probes with ethynylferrocene." Analyst 140, no. 12 (2015): 4154–61. http://dx.doi.org/10.1039/c5an00566c.

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In this work, the azido-containing hairpins were exploited as the capture probes; after hybridization, labeling of electroactive probes, ethynylferrocene, was conveniently and efficiently achieved via the Cu(i)-catalyzed azide–alkyne cycloaddition.

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Somers, Daryl J., and Goewin Demmon. "Identification of repetitive, genome-specific probes in crucifer oilseed species." Genome 45, no. 3 (2002): 485–92. http://dx.doi.org/10.1139/g02-006.

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Direct amplification of minisatellite DNA by PCR (DAMD PCR) was used to amplify and subsequently clone several fragments of DNA from crucifer species. The PCR-derived fragments of DNA were generated using known minisatellite core sequences as PCR primers. Southern hybridization of these putative minisatellite DNA fragments revealed that many were genome-specific; they hybridized with high affinity only to the genomic DNA of the species from which they were cloned. The DNA fragments were believed to be dispersed in the genome, based on smear-like hybridization signals on EcoRI-, BamHI-, and Hin

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Hieno, Ayaka, Mingzhu Li, Auliana Afandi, Kayoko Otsubo, Haruhisa Suga, and Koji Kageyama. "Detection of the Genus Phytophthora and the Species Phytophthora nicotianae by LAMP with a QProbe." Plant Disease 104, no. 9 (2020): 2469–80. http://dx.doi.org/10.1094/pdis-12-19-2523-re.

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Phytophthora is an oomycete genus with worldwide distribution, and many of its species cause destructive diseases. In Japan, Phytophthora species are listed as quarantine organisms with the exception of Phytophthora nicotianae. For effective quarantine control, we designed a Phytophthora genus-specific loop-mediated isothermal amplification (LAMP) primer set and a P. nicotianae species-specific quenching probe (QProbe) to establish a simultaneous LAMP-based detection method. We confirmed the specificity of the genus-specific primers, and all 161 taxa were detected. No other species in the clos

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Wesley, I. V., L. Schroeder-Tucker, A. L. Baetz, F. E. Dewhirst, and B. J. Paster. "Arcobacter-specific and Arcobacter butzleri-specific 16S rRNA-based DNA probes." Journal of clinical microbiology 33, no. 7 (1995): 1691–98. http://dx.doi.org/10.1128/jcm.33.7.1691-1698.1995.

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Elie, Cheryl M., Timothy J. Lott, Errol Reiss, and Christine J. Morrison. "Rapid Identification of Candida Species with Species-Specific DNA Probes." Journal of Clinical Microbiology 36, no. 11 (1998): 3260–65. http://dx.doi.org/10.1128/jcm.36.11.3260-3265.1998.

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Rapid identification of Candida species has become more important because of an increase in infections caused by species other than Candida albicans, including species innately resistant to azole antifungal drugs. We previously developed a PCR assay with an enzyme immunoassay (EIA) format to detect amplicons from the five most common Candida species by using universal fungal primers and species-specific probes directed to the ITS2 region of the gene for rRNA. We designed probes to detect seven additional Candidaspecies (C. guilliermondii, C. kefyr,C. lambica, C. lusitaniae,C. pelliculosa, C. r

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Vainstein, A., and H. Ben-Meir. "DNA Fingerprint Analysis of Roses." Journal of the American Society for Horticultural Science 119, no. 5 (1994): 1099–103. http://dx.doi.org/10.21273/jashs.119.5.1099.

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Mini- and microsatellite probes were hybridized to DNA of 24 rose (Rosa×hybrida) genotypes. The resultant DNA fingerprints were shown to be genotype-specific, thereby enabling cultivar identification at the DNA level. Restriction enzyme Dra I yielded the most informative band patterns. Full-sib family analysis of DNA fingerprints revealed 32 parental-specific bands out of the 128 observed in the parents. These bands were revealed cumulatively by phage (M13), human (33.6), and oligonucleotide (GACA)4 probes. Only one pair of these loci was found to be allelic, and no linked pairs were detected

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Berka, Miroslav, Marie Greplová, Iñigo Saiz-Fernández, et al. "Peptide-Based Identification of Phytophthora Isolates and Phytophthora Detection in Planta." International Journal of Molecular Sciences 21, no. 24 (2020): 9463. http://dx.doi.org/10.3390/ijms21249463.

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Phytophthora is arguably one of the most damaging genera of plant pathogens. This pathogen is well suited to transmission via the international plant trade, and globalization has been promoting its spread since the 19th century. Early detection is essential for reducing its economic and ecological impact. Here, a shotgun proteomics approach was utilized for Phytophthora analysis. The collection of 37 Phytophthora isolates representing 12 different species was screened for species-specific peptide patterns. Next, Phytophthora proteins were detected in planta, employing model plants Solanum tube

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Wyroba, Elzbieta, and Birgit H. Satir. "A comparative hybridization analysis of yeast DNA with Paramecium parafusin- and different phosphoglucomutase-specific probes." Biochemistry and Cell Biology 78, no. 6 (2000): 683–90. http://dx.doi.org/10.1139/o00-080.

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Molecular probes designed for the parafusin (PFUS), the Paramecium exocytic-sensitive phospho glyco protein, gave distinct hybridization patterns in Saccharomyces cerevisiae genomic DNA when compared with different phosphoglucomutase specific probes. These include two probes identical to segments of yeast phosphoglucomutase (PGM) genes 1 and 2. Neither of the PGM probes revealed the 7.4 and 5.9 kb fragments in Bgl II-cut yeast DNA digest detected with the 1.6 kb cloned PFUS cDNA and oligonucleotide constructed to the PFUS region (insertion 3 I-3) not found in other species. PCR amplification

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Gregory Matera, A., and Christine L. O'Keefe. "Haplotype-Specific Alphoid Oligonucleotides Can Distinguish Normal Homologous Chromosomes by Fish." Microscopy and Microanalysis 3, S2 (1997): 197–98. http://dx.doi.org/10.1017/s143192760000787x.

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The field of molecular cytogenetics is presently hampered by the need for allele- and homologue-specific hybridization probes. Vast stretches of the human genome display a considerable amount of polymorphic variation between individuals. Alpha satellite DNA is a tandemly repeated sequence located at the centromeres of all primate chromosomes and is a rich source of polymorphisms. These DNA variants are phenotypically silent; they are also stable and heritable in Mendelian fashion. We have shown that we can use this genetic diversity to create homologue-specific probes using fluorescence in sit

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Figueroa, F., E. Neufeld, U. Ritte, and J. Klein. "t-Specific DNA polymorphisms among wild mice from Israel and Spain." Genetics 119, no. 1 (1988): 157–60. http://dx.doi.org/10.1093/genetics/119.1.157.

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Abstract Lehrach and his coworkers have isolated a series of DNA probes that specifically hybridize with different regions of mouse chromosome 17 within the t complex. The probes display restriction fragment length polymorphisms, RFLPs, which are specific for the t haplotypes in all laboratory mouse strains tested thus far. Some of these probes have been used to test wild mice populations for these t-associated DNA forms. It is demonstrated that populations from Germany, Switzerland, Italy, Greece, Yugoslavia, Australia, Costa Rica, and Venezuela contain chromosomes in which all the tested DNA

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Sotiropoulos, C., S. C. Smith, and P. J. Coloe. "Characterization of two DNA probes specific for Serpulina hyodysenteriae." Journal of Clinical Microbiology 31, no. 7 (1993): 1746–52. http://dx.doi.org/10.1128/jcm.31.7.1746-1752.1993.

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