DETECTION OF FUNGAL PATHOGENS

Abstract: Unique DNA sequences are provided which are useful in identifying different pathogenic fungi, such as those which infect grape plants. These unique DNA sequences can be used to provide oligonucleotide primers in PCR based analysis for the identification of fungal pathogens. The DNA sequences of the present invention include the internal transcribed spacer (ITS) of the ribosomal RNA gene regions of particular fungal pathogens, as well as oligonucleotide primers which are derived from these regions which are capable of identifying the particular pathogen.

Description: DETECTION OF FUNGAL PATHOGENS Field of the Invention The present invention relates to assays to detect pathogenic fungi. Description of the Related Art Significant crop damage to grape plants is caused by fungal pathogens. Prompt and accurate diagnosis of the causal agent is important to effectively combat such pathogens. In the past, traditional culture techniques have been used to detect and identify fungal pathogens. Recently, however, DNA-based methods of identifying fungi have become available. Polymerase chain reaction (PCR)-based techniques have been used to detect pathogens in infected animal tissues. This technique has also been applied to detect plant pathogens. For example, PCR has been used to detect the presence of Gaeumannomyces graminis in infected wheat by amplification of sequences specific to the pathogen mitochondrial genome (Schlesser et al. , Applied and Environ. Microbiol., 57:533-556, 1991); and numerous races of Gremmeniella abietina, the causal agent of scleroderris canker in conifers, were distinguished by random amplified polymorphic DNA (i.e. RAPD) markers. Ribosomal genes are suitable for use as molecular probe targets because of their high copy number. Non-transcribed and transcribed spacer sequences associated with ribosomal genes are usually poorly conserved and, thus, are advantageously used as target sequences for the detection of recent evolutionary divergence. Fungal rR A genes are organized in units. Each unit encodes mature subunits of 18S, 5.8S, and 28S rRNA. The internal transcribed spacer (ITS) region lies between the 18S and 28S rRNA genes and contains two variable non-coding spacers (referred to as ITS1 and ITS2) and the 5.8S rRNA gene (White et al., 1990; In: PCR Protocols; Eds. : Innes et al. ; pages 315-322). In addition, the transcriptional units are separated by non-transcribed spacer sequences (NTSs). The ITS and NTS sequences are particularly suitable for the detection of different fungal pathogens. Kumeda et al (Applied Environ. Micro. , 62(8): 2947-2952, 1996) describes use of PCR to amplify ribosomal DNA internal transcribed spacers in order to differentiate species of Aspergillus Section flavi. The ITS1-5.8S-ITS2 region was amplified using universal primers, and the PCR product analyzed by the principle of single-strand conformation polymorphism. In addition, Gardes et al (In: Methods in Molecular Biology, Vol. 50:Species Diagnostics Protocols: PCR and Other Nucleic Acid Methods, Ed. J.P. Clapp, Humana Press, Totowa, NJ, pp. 177-186) describes restriction fragment length polymorphism (RFLP) analysis of fungal ITS regions amplified by PCR. The PCR amplification of fungal ITS has also been described using other than universal primers. These methods allow for more specificity in identifying classes of fungi, or particular species of fungi. Thus, Gardes and Bruns (Molecular Ecology, 2: 113-118, 1993) identified ITS primers which allow differentiation of DNA from basidiomycetes against ascomycete DNA. Identification of specific species has been observed using PCR primers directed to unique sequences in the ITS1 and/or ITS2 regions of fungal pathogens. See, for example, Hamelin et al, Applied Environ. Micro. , 62(11): 4026-4031, 1996; Mazzola et al, Phytopathology, 86(4):354-360, 1996; O'Gorman et al, Can. J. Bot. , 72:342-346, 1994; and U.S. Patent No. 5,585,238 to Ligon et al. The present invention addresses the problem of detecting and identifying fungal pathogens by PCR-based techniques. Summary of the Invention The present invention is directed to the identification of different pathogenic fungi, particularly those which infect grape plants. The present invention provides DNA sequences which exhibit variability between different pathogenic fungi. In particular, the present invention identifies regions of DNA sequence located in the internal transcribed spacer (ITS) of the ribosomal RNA gene regions of various pathogenic fungi. Primers derived from the ITS can be used in polymerase chain reaction (PCR) based diagnostic assays to determine the presence or absence of specific pathogenic fungi in plants, including grape plants. The primers can also be used as molecular probes to detect the presence of target DNA. Thus, in one aspect, the present invention provides an isolated double stranded nucleic acid of the full length ITS1 or ITS2 region of a fungal pathogen known to infect plants. More particularly, the DNA sequence is selected from among Sequence ID NOS: 6 to 15. In another aspect, the present invention provides an oligonucleotide primer for identification of a fungal pathogen, wherein the primer is a divergent portion of the ITS1 or ITS2 region of a fungal pathogen known to infect plants. More particularly, the oligonucleotide primer is selected from among Sequence ID NOS: 26 to 36. Furthermore, the oligonucleotide primers may be selected from among sequences which contain one of SEQ ID NOS: 26 to 36 and from 1 to 15 nucleotides in the 5' and/or 3' direction of the corresponding Sequence ID NOS: 16 to 25. A pair of the foregoing oligonucleotide primers for use in the amplification-based detection of an ITS of a fungal pathogen which infects plants is also provided. In yet another aspect, a method is provided for detection of a fungal pathogen which comprises: (a) obtaining DNA from an organism, or part thereof, infected with a pathogen, or from a fungal culture isolated from a symptomatic or asymptomatic diseased organism; (b) amplifying a part of the ITS of the fungal pathogen using the DNA as a template in a polymerase chain reaction with the aforementioned oligonucleotide primers; and (c) visualizing the amplified part of the ITS sequence to determine whether the fungal pathogen is present. In still another aspect, kits are provided which are useful in detecting fungal pathogens. Brief Description of the Sequences in the Sequence Listing; SEQ ID NO: 1 DNA sequence for the internal transcribed spacer of Eutypella vitis. SEQ ID NO: 2 DNA sequence for the internal transcribed spacer of Eutypa lot a. SEQ ID NO: 3 DNA sequence for the internal transcribed spacer of Phomopsis viticola (variant 1). SEQ ID NO: 4 DNA sequence for the internal transcribed spacer of Phomopsis viticola (variant 2). SEQ ID NO: 5 DNA sequence for the internal transcribed spacer of Diplodia gossypina. SEQ ID NO: 6 DNA sequence for the ITSl of Eutypella vitis. SEQ ID NO: 7 DNA sequence for the ITS2 of Eutypella vitis. SEQ ID NO: 8 DNA sequence for the ITSl of Eutypa lata. SEQ ID NO: 9 DNA sequence for the ITS2 of Eutypa lata. SEQ ID NO: 10 DNA sequence for the ITSl of Phomopsis viticola (variant 1). SEQ ID NO: 11 DNA sequence for the ITS2 of Phomopsis viticola (variant 1). SEQ ID NO: 12 DNA sequence for the ITSl of Phomopsis viticola (variant 2). SEQ ID NO: 13 DNA sequence for the ITS2 of Phomopsis viticola (variant 2). SEQ ID NO: 14 DNA sequence for the ITSl of Diplodia gossypina. SEQ ID NO: 15 DNA sequence for the ITS2 of Diplodia gossypina. SEQ ID NO: 16 Oligonucleotide Sequence EVUITS1. SEQ ID NO: 17 Oligonucleotide Sequence EVLITS2. SEQ ID NO: 18 Oligonucleotide Sequence ELUITS1. SEQ ID NO: 19 Oligonucleotide Sequence ELLITS2. SEQ ID NO: 20 Oligonucleotide Sequence PVUITSla. SEQ ID NO: 21 Oligonucleotide Sequence PVLITS2a. SEQ ID NO: 22 Oligonucleotide Sequence PVUITSlb. SEQ ID NO: 23 Oligonucleotide Sequence PVLITS2b. SEQ ID NO: 24 Oligonucleotide Sequence DGUITS1. SEQ ID NO: 25 Oligonucleotide Sequence DGLITS2. SEQ ID NO: 26 Oligonucleotide Sequence EVU129. SEQ ID NO: 27 Oligonucleotide Sequence EVL422. SEQ ID NO: 28 Oligonucleotide Sequence ELU 141. SEQ ID NO: 29 Oligonucleotide Sequence ELL430. SEQ ID NO: 30 Oligonucleotide Sequence ELL465. SEQ ID NO: 31 Oligonucleotide Sequence PVU 182. SEQ ID NO: 32 Oligonucleotide Sequence PVL463. SEQ ID NO: 33 Oligonucleotide Sequence PVU 191. SEQ ID NO: 34 Oligonucleotide Sequence PVL464. SEQ ID NO: 35 Oligonucleotide Sequence DGU70. SEQ ID NO: 36 Oligonucleotide Sequence DGL384. SEQ ID NO: 37 Oligonucleotide Sequence ITS5. SEQ ID NO: 38 Oligonucleotide Sequence ITS4. Detailed Description Of The Invention The present invention provides unique DNA sequences which are useful in identifying pathogenic fungi. These unique DNA sequences can be used as primers in PCR-based analysis for the identification of fungal pathogens, or as molecular probes to detect the presence of DNA from fungal pathogens. The DNA sequences of the present invention include the internal transcribed spacer (ITS) of the ribosomal RNA gene regions of specific fungal pathogens, as well as primers that are derived from these regions which are capable of identifying the particular pathogen. The DNA sequences of the invention are from the ITS of the ribosomal RNA gene region of fungal pathogens known to infect plants. However, the present invention is not limited to detecting the presence of the pathogens in plants, i.e. , the invention can be used to detect the presence of such pathogens in any infected organism. There is variability in the ITS DNA sequences from different pathogens. The ITS sequences can be aligned and compared. Primers can be designed based on regions within the ITS regions that contain the greatest differences in sequence among the fungal pathogens. The sequences and primers based on these sequences can be used to identify specific pathogens. DNA sequences of particular interest include ITS DNA sequences from Eutypella sp. , especially Eutypella vitis; Eutypa sp., especially Eutypa lata; Phomopsis sp. , especially Phomopsis viticola; and Diplodia sp. , especially Diplodia gossypina. The ITS DNA sequences, as well as primers of interest, are set forth in SEQUENCE ID NOS: 1-38. The sequences are useful in PCR-based identification of fungal pathogens. Methods for use of the primer sequences of the invention in PCR analysis are well known in the art. For example, see U.S. Patent No. 4,683,195; 4,683,202 and 5,585,238, the contents of all of which are hereby incorporated by reference. The primer sequences of the invention can also be used as molecular probes to detect the presence of target DNA. The Tm for the primers ranges from about 48-58° C at 50 mM salt. The hybridization temperature is approximately 5-10° C below the melting temperature. Thus, the primers are hybridized to target DNA typically at a temperature ranging from about 43-55° C. Final wash conditions generally range from about 45-55° C at about 36 mM salt concentration. Specific hybridization as used herein means the use of a final high stringency wash in about 0.2X SSPE (salt concentration of about 36 mM) at a temperature appropriate for the particular primer. IX SSPE contains 10 mM NaH 2 PO 4 , 180 mM NaCl, 1 mM EDTA, pH 7.4. The ITS DNA sequences of the present invention can be cloned from fungal pathogens by methods known in the art. In general, the methods for the isolation of DNA from fungal isolates are known. See, Raeder & Broda (1985) Letters in Applied Microbiology 2:17-20; Lee et al. (1990) Fungal Genetics Newsletter 35:23- 24; and Lee and Taylor (1990) In: PCR Protocols: A Guide to Methods and Applications, Innes et al. (Eds.); pages 282-287; the contents of all of which are hereby incorporated by reference. Alternatively, the ITS regions of interest can be identified by PCR amplification. Primers to amplify the entire ITS region can be designed according to White et al. (1990; In PCR Protocols; Eds.: Innes et al., pages 315-322, the contents of which are hereby incorporated by reference). The ITS sequences were determined and the sequences were compared to locate divergences which might be useful to test in PCR to distinguish the different fungal pathogens. The sequences of the ITS regions which were determined are shown as Sequence ID NOS: 1 to 5. The DNA sequences for the ITSl and ITS2 regions are shown as Sequence ID NOS: 6 to 15. From the identification of divergences, numerous primers were synthesized and tested in PCR-amplification. Purified pathogen DNA and DNA isolated from infected host plant tissue were used as templates for PCR-amplification. Thus, pairs of diagnostic primers were identified, i.e. , those which identified one particular fungal pathogen species. Preferred primer combinations are able to distinguish between the different fungal pathogens in infected host tissue. Primer sequences are set forth in Sequence ID NOS: 26 to 36, with flanking sequences depicted in Sequence ID NOS: 16 to 25. Thus, while oligonucleotide primers selected from among Sequence ID NOS: 26 to 36 are preferred, primers may also be used which contain at least 10 contiguous nucleotide bases from one of SEQ ID NOS: 26 to 36. Additionally, primers may be used which contain at least 10 contiguous nucleotide bases from one of SEQ ID NOS: 26 to 36 contiguous with 1 to 15 nucleotide bases in the 5' and/or 3' direction of corresponding SEQ ID NOS: 16 to 25, and primers of 10 nucleotide bases or longer which contain at least 5 contiguous nucleotide bases from one of SEQ ID NOS: 26 to 36 contiguous with from 1 to 15 nucleotide bases in the 5' and/or 3' direction of corresponding SEQ ID NOS: 16 to 25. The present invention provides numerous diagnostic primer combinations. The primers of the invention are designed based on sequence differences among the fungal ITS regions. A minimum of one base pair difference between sequences can permit design of a discriminatory primer. In general, primers should have a theoretical melting temperature between about 55 °C to about 65 °C to achieve good sensitivity, and should be void of significant secondary structure and 3' overlaps between primer combinations. Primers are generally at least about 10 nucleotide bases, more preferably at least about 15 to about 20 nucleotide bases. The oligonucleotide primers of the present invention are particularly useful in detecting infection of grape plants with fungal pathogens, in particular, fungal pathogens selected from among Eutypella vitis, Eutypa lata, Phomopsis viticola and Diplodia gossypina. However, the primers of the present invention can also be used to detect infection by the foregoing fungal pathogens in any organism which will act as a host. In the case of plants, for example, Eutypa lata (also known as Eutypa armeniacae) can infect plants other than grape plants, including apricot, black currant, red currant, almond, walnut, apple, prune, peach, pear, European plum, gooseberry and lemon plants. See Carter et al (1983) Review of Plant Pathology, Vol. 62, No. 7, incorporated herein by reference. The present invention also relates to the preparation of "kits" containing elements for detecting fungal pathogens. Such a kit may comprise a carrier to receive therein one or more containers, such as tubes or vials. Unlabeled or detectably labeled oligonucleotide primers may be contained in one or more of the containers. The oligonucleotide primers may be present in lyophilized form, or in an appropriate buffer. One or more enzymes or reagents for use in PCR reactions may be contained in one or more of the containers. The enzymes or reagents may be present alone or in admixture, and in lyophilized form or in appropriate buffers. The kit may also contain any other component necessary for carrying out the present invention, such as buffers, extraction agents, enzymes, pipettes, plates, nucleic acids, nucleoside triphosphates, filter paper, gel materials, transfer materials, and autoradiography supplies. The examples below illustrate typical experimental protocols which can be used in the isolation of ITS sequences, the selection of suitable primer sequences, the testing of primers for selective and diagnostic efficacy, and die use of such primers to detect the presence of a fungal pathogen. Such examples are provided by way of illustration and not by way of limitation. Examples Example 1 Culture of Fungal Isolates and Genomic DNA Extraction Viable fungal isolates of Eutypella vitis, Eutypa lata, Phomopsis viticola, and Diplodia gossypina were obtained from the E. & J. Gallo Genetics Research Fungal Culture Collection. Fungi were grown in 40 ml of Malt Yeast Extract Broth in 250 ml flasks inoculated with mycelial fragments from two week-old, cultures grown on Malt Yeast Extract Agar (MYEA). Liquid cultures were incubated at room temperature for 14 days without shaking. DNA was extracted as follows: 1. Collect 2-3 mycelial mats from culture flasks (250 ml flask/40 ml media). Grind mycelial mats using a mortar and pestle in the presence of liquid nitrogen. Transfer the powder to 45 ml polypropylene centrifuge tubes and add 15 ml of prewarmed extraction buffer (IX extraction buffer; 50 mM sodium ethylene diaminetetraacetic acid (EDTA), 100 mM tris-HCl (pH 8.0), 500 mM NaCl). Add 0.2% β-mercaptoethanol just prior to use. Mix by inversion and/or break up clumps with spatula. 2. Add 1.0 ml of 20% sodium dodecyl sulfate (SDS), mixing gently by inversion, incubate at 65 °C for 10 min. 3. Add 5.0 ml of 5.0 M potassium acetate and mix gently, but thoroughly, by inverting the tubes. Incubate in freezer for 20 min. 4. Centrifuge at 25000 x g for 20 min at 4 °C. Pour supernatant through a Miracloth * filter into a clean 35 ml Corex * centrifuge tube containing 10 ml ice- cold isopropanol; mix and incubate tubes in freezer for 30 min. 5. Spool out DNA on glass hooks or pellet by centrifugation at 20,000 x g for 15 min. Gently pour off supernatant and lightly dry pellets by inverting over a paper towel for 10 min. 6. Resuspend pellets in 0.75 ml of TE (10 mM Tris_HCl, 1 mM EDTA). Transfer to a 1.7 ml microcentrifuge tube. Add 375 μl of phenol and 375 μl of chloroform: isoamyl alcohol (24: 1). Shake the tubes until an emulsion forms. Spin the samples at 14,000 RPM for 10 min. Remove the aqueous (top) layer using a PI 000 ® pipet and put into a new 1.7 ml microcentrifuge tube. Try not to pull off any of the cloudy/slimy interface between the upper and lower layers. Add 750 μl of chloroform: isoamyl alcohol (24: 1) to the sample, mix well, and spin at 14,000 RPM for 10 min. 7. Remove the aqueous (top) layer and put into a 15 ml plastic centrifuge tube. Add DDH 2 O to bring volume up to 2 ml and then add 2 ml of 5M NaCl. Mix well and add 8 ml of cold 100% ethanol. Mix gently and spool out the DNA using a glass hook. If the DNA cannot be recovered with a glass hook, spin at a low speed (2-3000 RPM) in the centrifuge. Dry the DNA and resuspend in 500 μl of DDH 2 O. 8. Add 50 μl of 7.5M ammonium acetate and 1100 μl of cold 100% ethanol. Mix well and place in-freezer for at least one h. Spin the samples at 14,000 RPM for 10 min and dry the pellet in the Speed-Vac ® . Resuspend in 3-500 μl of DDH 2 O. Direct Amplification of DNA from Fungal Mycelia 1. Malt Yeast Extract Agar plates are inoculated with mycelia and grown for 2 weeks. 2. A sterile pipette tip is used to scrape a small amount of aerial mycelia off of the plate and deposited into a 250 μl microcentrifuge tube containing all of the components required for the polymerase chain reaction as stated in Example 6. Example 2 Amplification and Sequencing of the Internal Transcribed Spacer (ITS) Regions An — 600 bp internal transcribed spacer region was amplified from genomic DNA isolated from 28 isolates of Eutypa lata, two isolates of E. armeniacae, three isolates of Libertella viticola, one isolate of Eutypella vitis, six isolates of Phomopsis viticola, and four isolates of Diplodia gossypina (see Table 1) using ITS5 (5'- GGAAGTAAAAGTCGTAACAAGG-3'; SEQ ID NO: 37) and ITS4 (5'- TCCTCCGCTTATTGATATGC-3'; SEQ ID NO: 38). The 50-μl reactions contained 5-20 ng of genomic template, 5 μl each of GeneAmp* 10X PCR Buffer II and MgC- 2 solution (PE Applied Biosystems, Foster City, CA; part no. N808-0161), 0.2 mM each of dATP, dCTP, dGTP, and dTTP (GeneAmp * dNTPs; PE Applied Biosystems, Foster City, CA; part no. N808-0007), ~ 25 pM/μl each of ITS5 and ITS4, and 2.5 Units AmpliTaq * DNA polymerase (PE Applied Biosystems; part no. N808-0161). Reactions were run for 35 cycles of 30 s at 94 °C, 40 s at 58 °C, and 2 min at 72 °C, followed by a final elongation step at 72 °C for 10 min, on a Perkin Elmer GeneAmp * PCR System 9600 (PE Applied Biosystems). PCR products were purified using QIAquick * PCR Purification Kits (Qiagen Inc., Santa Clarita, CA) to remove any excess primers, nucleotides, and polymerases. Five microliters of the purified PCR products were run on a 1.2% agarose gel with 5 μl of pGEM -3Zf(+) double-stranded DNA Control Template (0.2 g/L, PE Applied Biosystems) to approximate concentrations. All products were sequenced using the primers ITS5 and ITS4 (see sequences above; White et al., 1990; In: PCR Protocols; Eds. : Innes et al. pp. 315-322). Sequencing was performed on an PE Applied Biosystems 377 Automated DNA Sequencer * using ABI PRISM™ Dye Terminator Cycle Sequencing Ready Reaction Kits * (PE Applied Biosystems; part no. 402079). Cycle sequencing products were run over Centri-Sep * spin columns (Princeton Separations, Inc. , Adelphia, NJ) to remove excess primers, dye-labeled terminators, nucleotides, and polymerases before being run on the automated sequencer. Example 3 Selection of Species-Specific Primers The ITS sequences of the Eutypa lata, Eutypella vitis, Phomopsis viticola, and Diplodia gossypina isolates were aligned and primers were designed using Oligo 5.0 (National Biosciences, Inc. , Plymouth, MN) in regions of maximum sequence difference between the target species. Example 4 Primer Synthesis Primers were synthesized on an Applied Biosystems 394 DNA/RNA Synthesizer ® using phosphoramidite chemistry. Example 5 Extraction of DNA from Plant Tissue for Use with Diagnostic Primers 1. Excise 10 mg fresh weight of plant tissue. Place in a microcentrifuge mbe with 100 μl of 0.5 N NaOH and grind for 30 s with a small, motor powered pestle. 2. Immediately transfer 5 μl of this extract to a microcentrifuge tube containing 495 μl of 100 mM Tris, pH 8.0. 3. Immediately mix the extract with the Tris by vortexing the mbe contents. This is critical to prevent damage to the DNA. Use 1-2 μl of this mixture as the template DNA for PCR. Example 6 Polymerase Chain Reaction Amplification Polymerase chain reactions were performed with the GeneAmp * kit from PE Applied Biosystems (Foster City, CA.; part no. N801-0055) using 50 mM KC1, 1.5 mM MgCl 2 , 10 mM Tris, pH 8.3, containing 200 μM of each TTP, dATP, dCTP, and dGTP, 50 pM of each primer, 2.5 units of Taq polymerase and 25 ng of genomic DNA, or barely visible amount of mycelia, in a final volume of 50 μl. The following thermocycler program was used: initial denaturation at 94 °C for 2 min; 35 cycles of three temperatures consisting of denaturing at 94 °C for 30 s followed by annealing for 40 s at 45, 50, 55, 58, 60, or 62 °C and elongation for 2 min at 72 °C; then a final elongation step for 10 min at 72 °C. The products were analyzed by loading 25 μl of each PCR sample on a 1.0% agarose gel and electrophoresing. Example 7 Verification of Primer Specificity to Extracted fungal genomic DNA from target species. Purified fungal genomic DNAs were obtained as described in Example 1 and PCR assayed as described in Example 6 using the species-specific primers. Different annealing temperatures were tested to determine the optimal temperamre for PCR for individual primers. In cases with multiple species-specific primers, different primer combinations were used to determine die best primer combination and annealing temperamre to amplify a single species-specific DNA fragment (Table 4). Species-specific amplification products were produced from primers designed from the ITS region between the 18S and 25S ribosomal DNA subunits of each fungal strain of interest. Example 8 Determination of Cross-reactivity of Species-specific Primers with Non-target Species. Purified fungal genomic DNAs obtained as described in Example 1 and/or direct amplification from mycelia as described in Example 1 were used with the PCR assay as described in Example 8 using the species-specific primers. Table 5 lists the results of the cross-reactivity tests with the species-specific primers and non-target fungal species. A 60 °C annealing temperamre was sufficient to prevent cross-reactivity between species-specific primers and non-target species. Example 9 Verification of Primer Specificity to Detect Presence of Grape Pathogenic Fungi in Plant Tissue DNA was isolated from woody and green plant tissue using the method outlined in Example 5. PCR was performed as described in Example 6. The species-specific primer combinations detected me target grape fungal pathogen in all plant tissues tested. Controls consisting of non-infected plant tissue tested negative for all species-specific primer pairs examined. Example 10 Utilization of ITS sequences as diagnostic probes to hybridize with target DNA i. Put chosen concentration of target DNA sample in 100 ul of TE, pH 7.0. ii. Add 0.1 volume [10 μl] of 3.0 M NaOH, vortex to mix and incubate at 65 °C for 20 min. This destroys the RNA and denatures the DNA. iii. Spin down condensation. Allow samples to cool to room temp. Neutralize by adding 1.0 volume [110 μl] of 2M ammonium acetate, pH 7.0, vortex to mix. Spin down to remove solution off of cap. Refrigerate until slot blot apparatus is ready. iv. Apply to slot-blot apparams according to manufacturers protocol; about 220 μl to slot blot. v. Label ITS sequence probe according to kit manufacturer's recommendation. vi. The blots are prehybridized in 1.0% BSA; ImM EDTA, 0.5 M NaHPO4, pH 7.2, 7.0% sodium dodecyl sulfate for a minimum of two hr prior to adding the probe, and then hybridized for 16 hr at 45 °C. Initial washes consist of two 30-min washes in IX SSPE/0.1% SDS at 50 °C. The blots are then transferred to a plastic tray and washed in IX SSPE for one hr, at 50 °C with shaking. The final wash consisted of 15 min at 50 °C in 0.2X SSPE. Table 1 Source of Test Isolates Isolate Species Origin Source ATCC #64171 Eutypella vitis Illinois ATCC 1 ATCC #28120 Eutypa armeniacae Australia ATCC ATCC #28900 Eutypa armeniacae South Africa ATCC 1 E100 Eutypa lata California G. Munkvold 2 E101 Eutypa lata California G. Munkvold 2 E102 Eutypa lata California G. Munkvold 2 E103 Eutypa lata California G. Munkvold 2 E104 Eutypa lata California G. Munkvold 2 E105 Eutypa lata California G. Munkvold 2 E106 Eutypa lata California G. Munkvold 2 E107 Eutypa lata California G. Munkvold 2 E108 Eutypa lata California G. Munkvold 2 E109 Eutypa lata California G. Munkvold 2 E110 Eutypa lata California G. Munkvold 2 Elll Eutypa lata California G. Munkvold 2 E112 Eutypa lata California G. Munkvold 2 E113 Eutypa lata California G. Munkvold 2 E114 Eutypa lata California G. Munkvold 2 E115 Eutypa lata California G. Munkvold 2 E116 Eutypa lata California G. Munkvold 2 E117 Eutypa lata New York G. Munkvold 2 E118 Eutypa lata California G. Munkvold 2 E119 Eutypa lata California G. Munkvold 2 E120 Eutypa lata California N. Irelan 3 E121 Eutypa lata California N. Irelan 3 E122 Eutypa lata California N. Irelan 3 E123 Eutypa lata Michigan G. Munkvold 2 E124 Eutypa lata Michigan G. Munkvold 2 E125 Eutypa lata Italy S. Di Marco 4 E126 Eutypa lata California G. Munkvold 2 E127 Eutypa lata California G. Munkvold 2 LI Libertella viticola Italy S. Serra 5 L2 Libertella viticola Italy S. Serra 3 L3 Libertella viticola Italy S. Serra 5 ATCC #12685 Phomposis viticola unknown ATCC 1 ATCC #28595 Phomposis viticola unknown ATCC 1 ATCC #28596 Phomposis viticola unknown ATCC 1 ATCC #38931 Phomposis viticola Australia ATCC 1 ATCC #48153 Phomposis viticola California ATCC 1 ATCC #76192 Phomposis viticola New York ATCC 1 ATCC #9055 Diplodia gossypina Unknown ATCC 1 ATCC #10936 Diplodia gossypina Florida ATCC 1 ATCC #1639 Diplodia gossypina Central America ATCC 1 ATCC #20571 Diplodia gossypina unknown ATCC 1 A150 Aureobasidium sp. California GGRFCC 6 A250 Alternaria sp. California GGRFCC 6 B002 Botrytis cinerea Italy S. Di Marco 4 C200 Cladospoήum sp. California GGRFCC 6 F100 Fusarium sp. California GGRFCC 6 1 American Type Culture Collection, Rockville, Maryland USA Dr. Gary Munkvold, Dept. of Plant Pathology, Iowa State University, Ames, IA, USA 3 Dr. Nancy Irelan, Genetics Research, E. & J. Gallo Winery, Modesto, CA, USA 4 Dr. Stefano Di Marco, Consiglio Nazionale Delle Ricerche, Bologna, Italy 5 Dr. Salvatorica Serra, Istimto Sperimentale per la Viticolmra, Conegliano, Italy 6 Gallo Genetics Research Fungal Culture Collection, E. & J. Gallo Winery, Modesto, CA USA Table 2 Primer Template Primer Name Primer Sequence E. vitis ΕVU129 5 '-GCTACCCTGTAGCTACCCTGTA AGG-3 ' (SEQ ID NO: 26) E. vitis EVL422 5'-GGAGTTATCCCGCAAGTCCAG-3' (SEQ ID NO: 27) E. lata ELU141 5 '-GGGAGCGAGCTACCCTGTAGC-3 ' (SEQ ID NO: 28) E. lata ELL430 5'-AGCTATCCGGAGATAGGCTCC-3' (SEQ ID NO: 29) E. lata ELL465 5'-CACCGCGACTCCGCC-3' (SEQ ID NO: 30) P. viticola PVU182 5'- AACTCTTGTTTTTACACTGAA-3' (SEQ ID NO: 31) P. viticola PVL463 5'-GGTCCTGGCGAGCT-3' (SEQ ID NO: 32) P. viticola PVU191 5 '-TTTTACACTGAAACTCTGAGAA-3 ' (SEQ ID NO: 33) P. viticola PVL464 5'-GGGTCCTGGCGAGCT-3' (SEQ ID NO: 34) D. gossypina DGU70 5 '-TCGGCTCGACTCTCCC-3 ' (SEQ ID NO: 35) D. gossypina DGL 384 5'-CGCGTCCGCAGTGAG-3' (SEQ ID NO: 36) 18S rDNA ITS5 5'-GGAAGTAAAAGTCGTAACAAGG-3' (SEQ ID NO: 37) 28S rDNA ITS4 5 '-TCCTCCGCTTATTGATATGC-3 ' (SEQ ID NO: 38) Table 3 ITS-derived diagnostic PCR primers Approximate size of Source of template amplified fragment DNA 5' Primer 3' Primer (bp) Eutypa lata ELU141 ELL430 310 ELU141 ELL465 338 ITS5 ELL430 472 ITS5 ELL465 501 ELU141 ITS4 497 Eutypella viήs EVU129 EVL422 314 ITS5 EVL422 464 EVU129 ITS4 496 Phomopsis viticola PVU182 PVL463 294 PVU182 PVL464 295 PVU191 PVL463 285 PVU191 PVL464 286 ITS5 PVL463 498 ITS5 PVL464 499 PVU182 ITS4 392 PVU191 ITS4 383 Diplodia gossypina DGU70 DGL384 328 ITS5 DGL384 418 DGU70 ITS4 457 Table 4 Verification of species-specific primers to target species Target Species Species-specific Primers Temp (°C) Reaction Eutypella vitis EVU129/EVL422 54 (+) 58 (+) 60 (+) 62 (+) Eutypa lata ELU141/ELL430 54 (+) 58 (+) 60 (+) 62 (+) ELU141/ELL465 54 (+) 58 (+) 60 (+) 62 (+) Diplodia gossypina DGU70/DGL384 60 (+) Phomopsis viticola PVU182/PVL463 60 (+) PVU182/PVL464 60 (+) PVU191/PVL463 60 (+) PVU191/PVL464 60 (+) Table 5 Cross-reactivity with species-specific primers and non-target species Target species Species-specific Primers Temp Non-target Species Reaction (°C) Eutypella vitis EVU129/EVL422 60 Eutypa lata (-) 60 Libertella viticola (-) 60 Phomopsis viticola (-) 60 Diplodia gossypina (-) Eutypa lata ELU141/ELL430 62 Eutypella vitis (-) 60 Eutypa armeniacae (+) 60 Libertella viticola (+) 60 Phomopsis viticola (-) 60 Diplodia gossypina (-) 60 Aureobasidium sp. (-) 60 Cladosporium sp. (-) 60 Fusarium sp. (-) 60 Botrytis cinerea (-) 60 Alternaria sp. (-) ELU141/ELL465 62 Eutypella vitis (-) 60 Eutypa armeniacae (+) 60 Libertella viticola (+) 60 Phomopsis viticola (-) 60 Diplodia gossypina (-) 60 Aureobasidium sp. (-) 60 Cladosporium sp. (-) 60 Fusarium sp. (-) 60 Botrytis cinerea (-) 60 Alternaria sp. (-) Diplodia gossypina DGU70/DGL384 60 Phomopsis viticola (-) 60 Eutypa lata (-) Phomopsis viticola PVU182/PVL463 60 Eutypa lata (-) 60 Diplodia gossypina (-) PVU182/PVL464 60 Eutypa lata (-) 60 Diplodia gossypina (-) PVU191/PVL463 60 Eutypa lata (-) 60 Diplodia gossypina (-) PVU191/PVL464 60 Eutypa lata (-) 60 Diplodia gossypina (-) 60 Fusarium sp. (-)

Claims: We claim: 1. An isolated double stranded nucleic acid selected from the group consisting of SEQ ID NOS: 6 to 15. 2. An isolated nucleic acid which specifically hybridizes with the nucleic acid of claim 1. 3. An oligonucleotide sequence for identification of a fungal pathogen, wherein said sequence is selected from the group consisting of SEQ ID NOS: 16 to 25. 4. An oligonucleotide primer which is a fragment of the sequences according to claim 3, and which specifically hybridizes to the ITSl or ITS2 of Eutypella vitis, Eutypa lata, Phomopsis viticola, or Diplodia gossypina. 5. An oligonucleotide primer for identification of a fungal pathogen, wherein said primer is selected from the group consisting of primers which contain at least 10 contiguous nucleotide bases from one of SEQ ID NOS: 26 to 36, primers which contain at least 10 contiguous nucleotide bases from one of SEQ ID NOS: 26 to 36 contiguous with 1 to 15 nucleotide bases in the 5' and/ or 3' direction of corresponding SEQ ID NOS: 16 to 25, and primers of 10 nucleotide bases or longer which contain at least 5 contiguous nucleotide bases from one of SEQ ID NOS: 26 to 36 contiguous with from 1 to 15 nucleotide bases in the 5' and/or 3' direction of corresponding SEQ ID NOS: 16 to 25. 6. A pair of oligonucleotide primers for use in the amplification-based detection of an internal transcribed spacer sequence of a fungal pathogen, wherein the primers are selected from the group consisting of primers which contain at least 10 contiguous nucleotide bases from one of SEQ ID NOS: 26 to 36, primers which contain at least 10 contiguous nucleotide bases from one of SEQ ID NOS: 26 to 36 contiguous with 1 to 15 nucleotide bases in the 5' and/or 3' direction of corresponding SEQ ID NOS: 16 to 25, and primers of 10 bases or longer which contain at least 5 contiguous nucleotide bases from one of SEQ ID NOS: 26 to 36 contiguous with from 1 to 15 nucleotide bases in the 5' and/or 3' direction of corresponding SEQ ID NOS: 16 to 25. 7. The pair of oligonucleotide primers according to claim 6 which comprises SEQ ID NO: 26 and SEQ ID NO: 27. 8. The pair of oligonucleotide primers according to claim 6 which comprises SEQ ID NO: 28 and SEQ ID NO: 29. 9. The pair of oligonucleotide primers according to claim 6 which comprises SEQ ID NO: 28 and SEQ ID NO: 30. 10. The pair of oligonucleotide primers according to claim 6 which comprises SEQ ID NO: 31 and SEQ ID NO: 32. 11. The pair of oligonucleotide primers according to claim 6 which comprises SEQ ID NO: 33 and SEQ ID NO: 34. 12. The pair of oligonucleotide primers according to claim 6 which comprises SEQ ID NO: 35 and SEQ ID NO: 36. 13. A method for detection of a fungal pathogen comprising: (a) obtaining DNA from an organism, or part thereof, infected with a pathogen, or from a fungal culture isolated from a symptomatic or asymptomatic diseased organism; (b) amplifying a part of the internal transcribed spacer sequence of said fungal pathogen using said DNA as a template in a polymerase chain reaction with a pair of oligonucleotide primers according to claim 6; and (c) visualizing said amplified part of the internal transcribed spacer sequence to determine whether said fungal pathogen is present. 14. The method according to claim 13, wherein said fungal pathogen is selected from the group consisting of Eutypella vitis, Eutypa lata, Phomopsis viticola and Diplodia gossypina. 15. The method according to claim 13, wherein said organism or diseased organism is a grape plant. 16. The method according to claim 13, wherein the pair of oligonucleotide primers comprises SEQ ID NO: 26 and SEQ ID NO: 27. 17. The method according to claim 13, wherein the pair of oligonucleotide primers comprises SEQ ID NO: 28 and SEQ ID NO: 29. 18. The method according to claim 13, wherein the pair of oligonucleotide primers comprises SEQ ID NO: 28 and SEQ ID NO: 30. 19. The method according to claim 13, wherein the pair of oligonucleotide primers comprises SEQ ID NO: 31 and SEQ ID NO: 32. 20. The method according to claim 13, wherein the pair of oligonucleotide primers comprises SEQ ID NO: 33 and SEQ ID NO: 34. 21. The method according to claim 13, wherein the pair of oligonucleotide primers comprises SEQ ID NO: 35 and SEQ ID NO: 36. 22. A kit comprising a carrier to receive therein one or more containers, at least one of said containers comprising an oligonucleotide primer according to claim 5. 23. A kit comprising a carrier to receive therein one or more containers, at least one of said containers comprising a pair of oligonucleotide primers according to claim 6.

Inventors: DESCENZO RICHARD A, ENGEL STACIA R, IRELAN NANCY A, DESCENZO, RICHARD, A., ENGEL, STACIA, R., IRELAN, NANCY, A.
Applicants: GALLO WINERY E & J, E. & J. GALLO WINERY
Application year: 1998
Main classification: C12Q1
IPC codes: C12Q1