# Patent

## Title
Fungi and products thereof

## Abstract

The present invention provides substantially purified or isolated fungi of Nodulisporium spp. or Ascocoryne spp., plants infected with said fungi, organic compounds produced by said fungi, and related nucleic acids, polypeptides and methods.

## Background
FIELD OF THE INVENTION
The present invention relates to fungi, plants infected with fungi, products produced by fungi, and related nucleic acids, polypeptides and methods.
BACKGROUND OF THE INVENTION
Microbes represent an invaluable source of novel genes and compounds that have the potential to be utilised in a range of industrial sectors. Scientific literature gives numerous accounts of microbes being the primary source of antibiotics, immunosuppressants, anticancer agents and cholesterol-lowering drugs, in addition to their use in environmental decontamination and in the production of food and cosmetics. A relatively unexplored group of microbes known as endophytes, which reside in the tissues of living plants, offer a particularly diverse source of novel compounds and genes that may provide important benefits to society, and in particular, agriculture.
Endophytes often form mutualistic relationships with their hosts, with the endophyte conferring increased fitness to the host, often through the production of defence compounds. At the same time, the host plant offers the benefits of a protected environment and nutriment to the endophyte.
Recent discoveries highlight the diversity of applications of endophytes such as in the agricultural (e.g. bioprotectants) and energy (e.g. biofuels) sectors. For instance, the fungus Muscodor albus from Cinnamomum zeylanicum in Honduras produces a suite of volatile antimicrobial compounds that are effective against soil borne pathogens, and this has enabled development of a commercial preparation which has been utilised as a biological alternative (e.g. mycofumigant) to the ozone depleting fumigant methyl bromide. Furthermore, the discovery of the endophytic fungus Gliocladium roseum, which produces a variety of hydrocarbons commonly found in diesel, petrol and biodiesel, offers mankind a potential alternative to fossil fuels.
Bioprotectant endophytes that have been developed and commercialised include Neotyphodium species that produce insecticidal alkaloids, including peramine (a pyrrolopyrazine) and the lolines (pyrrolizidines). These compounds can accumulate to high levels in planta where they act as potent feeding deterrents against a range of insect pests, including a major pest of graminaceous species, Listronotus bonariensis (Argentine stem weevil). The gene responsible for peramine biosynthesis is a non-ribosomal peptide synthase (NRPS) and has been identified as perA.
The insecticidal compounds, destruxins, have also been well characterised as secondary metabolites of fungi. Their mode of action is still unclear however it is widely recognised that they induce cytological changes to the target organism, in particular Ca2+ dependent processes. It is thought that a NRPS is also responsible for the production of this compound. Another antimicrobial compound of fungi that is regulated by NRPS is the peptaibols. Trichoderma virens possesses a 62.8 kb NRPS gene (tex1) that codes for a 20,925 amino acid NRPS regulating the production of its peptaibol. Similarly, an endophyte of Quercus suber, Trichoderma citrinoviridae, produces another peptaibol that shows antifungal activity against a range of plant pathogens, including Biscogniauxia mediterranea and Apiognomonia quercine. 
In recent years molecular breeding of endophytes has also been employed to overcome pathogen and pest infections. The xylem limited bacterium Clavibacter xyli subsp cynodontis (Cxc) was inserted with the gene encoding the insectidal protein from Bacillus thuringiensis subsp kurstaki, the Bt-toxin. Similarly, Cxc was also engineered to encode β-1,3-glucanase which degrades an essential structural component of cell walls of fungal phytopathogens, β-1,3-glucan.
It is estimated that there are up to 1 million endophytic organisms which may possess genes and compounds that offer enormous benefits to agriculture, particularly in the area of disease management. As such, there exists a need to isolate and identify these endophytes, and characterise the compounds and genes responsible for the bioprotectant activity.
It is an objection of the present application to overcome, or at least alleviate, one or more of the difficulties or deficiencies associates with the prior art.
SUMMARY OF THE INVENTION
This patent application documents bioprotectant fungi of Nodulisporium spp. and Ascocoryne spp. that may exhibit broad spectrum activity against important plant pathogenic organisms. Antibiotic compounds responsible for the activity are characterised, along with the genes that regulate their production.
In a first aspect, the present invention provides a substantially purified or isolated fungus of Nodulisporium spp. or Ascocoryne spp. Preferably, the fungus is selected from the group consisting of Dandenong Ranges isolate 1 and Yarra Ranges isolates 7, 10, 11, 12, 13 and 15 and Otway Ranges isolates 1, 3, 4 and 5.
Representative samples, namely Dandenong Ranges isolate 1, Yarra Ranges isolate 11 and Otway Ranges isolate 4, were deposited at The National Measurement Institute on 3 May 2011 with accession number V11/011039 (Dandenong Ranges 1) and 17 Feb. 2010 with accession numbers V10/000244 (Yarra Ranges isolate 11) and V10/000245 (Otway Ranges isolate 4).
Preferably, the fungus is of a species selected from the group consisting of Nodulisporium sp. (asexual stage), Ascocoryne sarcoides (sexual stage) and Coryne sp. (asexual stage).
By ‘substantially purified’ is meant that the fungus is free of other organisms. The term therefore includes, for example, a fungus in axenic culture. Preferably, the fungus is at least approximately 90% pure, more preferably at least approximately 95% pure, even more preferably at least approximately 98% pure.
The term ‘isolated’ means that the fungus is removed from its original environment (e.g. the natural environment if it is naturally occurring). For example, a naturally occurring fungus present in a living plant is not isolated, but the same fungus separated from some or all of the coexisting materials in the natural system, is isolated.
In its natural environment, the fungus may be an endophyte, i.e. live mutualistically within a plant. Alternatively, the fungus may be an epiphyte, i.e. grow attached to or upon a plant.
The fungus of the present invention may in its natural environment be associated with a plant of the genus Lomatia, Nothofagus or Picea, more particularly Lomatia fraseri or Nothofagus cunninghamii. 
By ‘associated with’ in this context is meant that the fungus lives on, in or in close proximity to the plant. For example, it may be endophytic, for example living within the internal tissues of the plant, or epiphytic, for example growing externally on the plant.
The fungus may be a heterotroph that uses organic carbon for growth, more particularly a saprotroph that obtains nutrients by consuming detritus.
In a further aspect, the present invention provides a plant inoculated with a fungus as hereinbefore described, said plant comprising a fungus-free host plant stably infected with said fungus.
Preferably, the plant is an agricultural plant, including horticultural crops such as potato, tomato, broccoli and apple, grains and pulses such as wheat, barley, beans, peas and lentils, and pasture grasses and legumes such as ryegrass, fescue, clover and lucerne.
Preferably, the plant is infected with the fungus by a method selected from the group consisting of inoculation, breeding, crossing, hybridization and combinations thereof.
The fungus-infected plants may be cultured by known techniques. The person skilled in the art can readily determine appropriate culture conditions depending on the plant to be cultured.
In a further aspect, the present invention provides a method of culturing a fungus as hereinbefore described, said method including growing said fungus on a medium including a source of carbohydrates, for example a starch/sugar-based agar or broth such as potato dextrose agar or potato dextrose broth, or a cereal-based agar or broth such as oatmeal agar or oatmeal broth.
The fungus may be cultured under aerobic or anaerobic conditions.
In a particularly preferred embodiment, the fungus may be cultured in a culture medium including potato dextrose or oatmeal, for example potato dextrose agar, oatmeal agar, potato dextrose broth or oatmeal broth.
The fungus may be cultured for a period of approximately 1 to approximately 100 days, more preferably from approximately 1 to approximately 50 days more preferably from approximately 10 to approximately 25 days.
In a preferred embodiment, the fungus may be cultured in a bioreactor. By a ‘bioreactor’ is meant a device or system that supports a biologically active environment, such as a vessel in which is carried out a chemical process involving fungi of the present invention and/or products thereof. The chemical process may be aerobic or anaerobic. The bioreactor may have a volume ranging in size from milliliters to cubic meters, for example from approximately 50 ml to approximately 50,000 liters. The bioreactor may be operated via batch culture, batch feed culture, perfusion culture or continuous culture, for example continuous culture in a stirred-tank bioreactor. Fungi cultured in the bioreactor may be suspended or immobilized.
In a preferred embodiment, the method may include the further step of recovering an organic compound produced by the fungus from within fungal cells, including intracellular tissues (e.g. terpenes), from the culture medium (e.g. secreted liquids) or from the air space (e.g. secreted vapours) associated with the culture medium or fungus.
Vapours may arise directly from the fungus or from the secreted liquids which transition between vapour and liquid phases.
The step of recovering the organic compound is preferably done by separating cells from the culture medium or capturing vapours associated with the culture medium or fungus.
Preferably the organic compound is then isolated or purified by a method selected from the group consisting of gas chromatography, liquid chromatography, fractional distillation and absorption chromatography, such as pressure swing adsorption.
By an ‘organic compound’ is meant a chemical compound whose molecules contain carbon.
In a preferred embodiment, the organic compound may be a hydrocarbon such as a volatile hydrocarbon or a liquid hydrocarbon.
By a ‘hydrocarbon’ is meant an organic compound comprising the elements carbon and hydrogen.
In another preferred embodiment, the organic compound may be a terpene, more preferably a monoterpene or a sesquiterpene.
By a ‘terpene’ is meant a molecule formed from units of isoprene and having a molecular formula (C5H8)n where n is the number of linked isoprene units. The isoprene units may be linked together ‘head to tail’ to form linear chains or they may be arranged to form rings.
In a preferred embodiment, the organic compound may be selected from the group consisting of (C10H16, C10H14, C7H10, C9H12, C10H18O, C9H18O2, C10H14O, C15H24), or a derivative and/or salt thereof.
In a particularly preferred embodiment, the organic compound may be selected from the group consisting of α-Thujene, β-Sabinene, β-Myrcene, α-Phellendrene, α-Terpinene, p-Cymene, (R)-(+)-Limonene, Eucalyptol, α-Ocimene, 1,4-Cyclohexadiene,1-methyl-, Cyclohexane,1,2,4-tris(methylene)-, β-Ocimene, γ-Terpinene, α-Terpinolene, Allo-Ocimene, (−)-Terpinen-4-ol, α-Terpineol, 2H-pyran,tetrahydro-2-(propan-2-ylidene)-5-methoxy, 2H-pyran,tetrahydro-2-isopropyl-5-methoxy, 3-Cyclohexene-1-acetaldehyde,4-methyl-α-methylene-, 1-Cyclohexene-1-carboxaldehyde,4-(1-methylethenyl)-, p-Mentha-1,4(8)-dien-3-one (isomers), Bicyclo[2.2.2]octan-1-ol-ethyl, β-Elemene, α-Guajene, Bicyclo[5.3.0]decane,2 methylene-5-(1-methylvinyl)-8-methyl, δ-Guaijene, cyclohexane derivatives, cyclohexene derivatives and pyran derivatives.
By a ‘derivative’ is meant an organic compound obtained from, or regarded as derived from, a compound of the present invention. Examples of derivatives include compounds where the degree of saturation of one or more bonds has been changed (e.g., a single bond has been changed to a double or triple bond) or wherein one or more atoms are replaced with a different atom or functional group. Examples of different atoms and functional groups may include, but are not limited to hydrogen, halogen, oxygen, nitrogen, sulphur, hydroxy, alkoxy, alkyl, alkenyl, alkynyl, amine, amide, ketone and aldehyde.
Preferably, said organic compound is produced by a method as hereinbefore described.
In a preferred embodiment, derivatives of the organic compound of the present invention may be obtained by chemical dehydration (for example using a strong acid) and/or hydrogenation.
The organic compound of the present invention may also be converted to lower molecular weight alkanes and alkenes, for example by cracking (e.g., catalytic or thermal).
In a preferred embodiment, the organic compound may be obtained from a fungus of the present invention.
In a still further aspect of the present invention, there is provided use of an organic compound according to the present invention as a biofuel or biofuel precursor, in biofumigation or bioprotection, or in the cosmetic or pharmaceutical industry, for example as a surfactant.
In a further aspect of the present invention, there is provided a method of producing an organic compound, said method including culturing a fungus as hereinbefore described under conditions suitable to produce said organic compound. Preferably the conditions are as hereinbefore described.
Preferably the organic compound is a hydrocarbon or terpene, including a hydrocarbon or terpene as hereinbefore described.
In a preferred embodiment, the method may include the further step of recovering an organic compound produced by the fungus as hereinbefore described.
On the basis of the deposits referred to above, the entire genome of a fungus of Nodulisporium spp. or Ascocoryne spp., selected from the group consisting of Dandenong Ranges isolate 1 and Yarra Ranges isolates 7, 10, 11, 12, 13 and 15 and Otway Ranges isolates 1, 3, 4 and 5, is incorporated herein by reference.
In a preferred embodiment, the entire genomes of Dandenong Ranges isolate 1, Yarra Ranges isolate 11 and Otway Ranges isolate 4, which were deposited at The National Measurement Institute on 3 May 2010 and 17 Feb. 2010 with accession numbers V11/011039, V10/000244 and V10/000245, respectively, are incorporated herein by reference.
Thus, in a further aspect, the present invention includes identifying and/or cloning nucleic acids including genes encoding polypeptides that are involved in the production of organic compounds of the present invention, for example genes encoding enzymes from one or more biochemical pathways which result in the synthesis of said organic compounds.
By a ‘biochemical pathway’ is meant a plurality of chemical reactions occurring within a cell which are catalysed by more than one enzyme or enzyme subunit and result in the conversion of a substrate into a product. This includes, for example, a situation in which two or more enzyme subunits (each being a discrete protein coded by a separate gene) combine to form a processing unit that converts a substrate into a product. A ‘biochemical pathway’ is not constrained by temporal or spatial sequentiality.
Methods for identifying and/or cloning nucleic acids encoding such genes are known to those skilled in the art and include creating nucleic acid libraries, such as cDNA or genomic libraries, and screening such libraries, for example using probes, for genes encoding enzymes from synthetic pathways for said organic compounds; or mutating the genome of the fungus of the present invention, for example using chemical or transposon mutagenesis, identifying changes in the production of an organic compound of the present invention, and thus identifying genes encoding enzymes from synthetic pathways for said organic compound.
Thus, in a further aspect of the present invention, there is provided a substantially purified or isolated nucleic acid encoding a polypeptide involved in the production of an organic compound of the present invention.
In a preferred embodiment, the nucleic acid may encode a polypeptide involved in the production of a terpene, or a hydrocarbon such as a volatile hydrocarbon or a liquid hydrocarbon. Preferably, the organic compound is a terpene or hydrocarbon as hereinbefore described.
In a preferred embodiment, the nucleic acid may encode a polypeptide involved in the production of an organic compound. Preferably, the organic compound is a terpene, more preferably a monoterpene or a sesquiterpene. In a particularly preferred embodiment, the nucleic acid may encode a terpene synthase.
More preferably, the organic compound is selected from the group consisting of C10H16, C10H14, C7H10, C9H12, C10H18O, C9H18O2, C10H14O, C15H24 and derivatives and salts thereof.
More preferably the organic compound is selected from the group consisting from the group consisting α-Thujene, β-Sabinene, β-Myrcene, α-Phellendrene, α-Terpinene, p-Cymene, (R)-(+)-Limonene, Eucalyptol, α-Ocimene, 1,4-Cyclohexadiene,1-methyl-, Cyclohexane, 1,2,4-tris(methylene)-, β-Ocimene, γ-Terpinene, α-Terpinolene, Allo-Ocimene, (−)-Terpinen-4-ol, α-Terpineol, 2H-pyran,tetrahydro-2-(propan-2-ylidene)-5-methoxy, 2H-pyran,tetrahydro-2-isopropyl-5-methoxy, 3-Cyclohexene-1-acetaldehyde,4-methyl-α-methylene-, 1-Cyclohexene-1-carboxaldehyde,4-(1-methylethenyl)-, p-Mentha-1,4(8)-dien-3-one (isomers), Bicyclo[2.2.2]octan-1-ol,4-ethyl, β-Elemene, α-Guajene, Bicyclo[5.3.0]decane,2 methylene-5-(1-methylvinyl)-8-methyl, δ-Guaijene, cyclohexane derivatives, cyclohexene derivatives and pyran derivatives.
In a particularly preferred embodiment, the nucleic acid may encode a polypeptide including an amino acid sequence selected from the group consisting of sequences shown in FIGS. 12 to 19 hereto and functionally active fragments and variants thereof.
In a particularly preferred embodiment, the nucleic acid may include a nucleotide sequence selected from the group consisting of shown in FIGS. 20 to 27 hereto and functionally active fragments and variants thereof.
By ‘nucleic acid’ is meant a chain of nucleotides capable of carrying genetic information. The term generally refers to genes or functionally active fragments or variants thereof and or other sequences in the genome of the organism that influence its phenotype. The term ‘nucleic acid’ includes DNA (such as cDNA or genomic DNA) and RNA (such as mRNA or microRNA) that is single- or double-stranded, optionally containing synthetic, non-natural or altered nucleotide bases, synthetic nucleic acids and combinations thereof.
By a ‘nucleic acid encoding a polypeptide involved in the production of an organic compound of the present invention’ is meant a nucleic acid encoding an enzyme normally present in a fungus of the present invention, which catalyses a step in the pathway that results in synthesis of the organic compound of the present invention.
The present invention encompasses functionally active fragments and variants of the nucleic acids of the present invention. By ‘functionally active’ in relation to the nucleic acid is meant that the fragment or variant (such as an analogue, derivative or mutant) is capable of manipulating synthesis of an organic compound of the present invention, for example by being translated into an enzyme that is able to participate in the pathway that results in synthesis of the organic compound. Such variants include naturally occurring allelic variants and non-naturally occurring variants. Additions, deletions, substitutions and derivatizations of one or more of the nucleotides are contemplated so long as the modifications do not result in loss of functional activity of the fragment or variant. Preferably the functionally active fragment or variant has at least approximately 80% identity to the relevant part of the above mentioned sequence to which the fragment or variant corresponds, more preferably at least approximately 90% identity, even more preferably at least approximately 95% identity, most preferably at least approximately 98% identity. Such functionally active variants and fragments include, for example, those having conservative nucleic acid changes.
Preferably the fragment has a size of at least 20 nucleotides, more preferably at least 50 nucleotides, more preferably at least 100 nucleotides, more preferably at least 200 nucleotides, more preferably at least 500 nucleotides.
By ‘conservative nucleic acid changes’ is meant nucleic acid substitutions that result in conservation of the amino acid in the encoded protein, due to the degeneracy of the genetic code. Such functionally active variants and fragments also include, for example, those having nucleic acid changes which result in conservative amino acid substitutions of one or more residues in the corresponding amino acid sequence.
By ‘conservative amino acid substitutions’ is meant the substitution of an amino acid by another one of the same class, the classes being as follows:

    
    
        Nonpolar: Ala, Val, Leu, Ile, Pro, Met Phe, Trp
        Uncharged polar: Gly, Ser, Thr, Cys, Tyr, Asn, Gln
        Acidic: Asp, Glu
        Basic: Lys, Arg, His
    
    


Other conservative amino acid substitutions may also be made as follows:

    
    
        Aromatic: Phe, Tyr, His
        Proton Donor: Asn, Gln, Lys, Arg, His, Trp
        Proton Acceptor: Glu, Asp, Thr, Ser, Tyr, Asn, Gln
    
    


In a further aspect of the present invention, there is provided a genetic construct including a nucleic acid according to the present invention.
By ‘genetic construct’ is meant a recombinant nucleic acid molecule.
In a preferred embodiment, the genetic construct according to the present invention may be a vector.
By a ‘vector’ is meant a genetic construct used to transfer genetic material to a target cell.
The vector may be of any suitable type and may be viral or non-viral. The vector may be an expression vector. Such vectors include chromosomal, non-chromosomal and synthetic nucleic acid sequences, e.g. derivatives of plant viruses; bacterial plasmids; derivatives of the Ti plasmid from Agrobacterium tumefaciens; derivatives of the Ri plasmid from Agrobacterium rhizogenes; phage DNA; yeast artificial chromosomes; bacterial artificial chromosomes; binary bacterial artificial chromosomes; vectors derived from combinations of plasmids and phage DNA. However, any other vector may be used as long as it is replicable or integrative or viable in the target cell.
In a preferred embodiment of this aspect of the invention, the genetic construct may further include a promoter and a terminator; said promoter, gene and terminator being operatively linked.
By a ‘promoter’ is meant a nucleic acid sequence sufficient to direct transcription of an operatively linked nucleic acid sequence.
By ‘operatively linked’ is meant that the nucleic acid(s) and a regulatory sequence, such as a promoter, are linked in such a way as to permit expression of said nucleic acid under appropriate conditions, for example when appropriate molecules such as transcriptional activator proteins are bound to the regulatory sequence. Preferably an operatively linked promoter is upstream of the associated nucleic acid.
By ‘upstream’ is meant in the 3′→5′ direction along the nucleic acid.
The promoter and terminator may be of any suitable type and may be endogenous to the target cell or may be exogenous, provided that they are functional in the target cell.
A variety of terminators which may be employed in the genetic constructs of the present invention are also well known to those skilled in the art. The terminator may be from the same gene as the promoter sequence or a different gene. Particularly suitable terminators are polyadenylation signals, such as the (CaMV) 35S polyA and other terminators from the nopaline synthase (nos) and the octopine synthase (ocs) genes.
The genetic construct, in addition to the promoter, the gene and the terminator, may include further elements necessary for expression of the nucleic acid, in different combinations, for example vector backbone, origin of replication (ori), multiple cloning sites, spacer sequences, enhancers, introns (such as the maize Ubiquitin Ubi intron), antibiotic resistance genes and other selectable marker genes [such as the neomycin phosphotransferase (nptll) gene, the hygromycin phosphotransferase (hph) gene, the phosphinothricin acetyltransferase (bar or pat) gene], and reporter genes (such as beta-glucuronidase (GUS) gene (gusA)]. The genetic construct may also contain a ribosome binding site for translation initiation. The genetic construct may also include appropriate sequences for amplifying expression.
Those skilled in the art will appreciate that the various components of the genetic construct are operably linked, so as to result in expression of said nucleic acid. Techniques for operably linking the components of the genetic construct of the present invention are well known to those skilled in the art. Such techniques include the use of linkers, such as synthetic linkers, for example including one or more restriction enzyme sites.
Preferably, the genetic construct is substantially purified or isolated. By ‘substantially purified’ is meant that the genetic construct is free of the genes, which, in the naturally-occurring genome of the organism from which the nucleic acid or promoter of the invention is derived, flank the nucleic acid or promoter. The term therefore includes, for example, a genetic construct which is incorporated into a vector; into an autonomously replicating plasmid or virus; or into the genomic DNA of a prokaryote or eukaryote; or which exists as a separate molecule (e.g. a cDNA or a genomic or cDNA fragment produced by PCR or restriction endonuclease digestion) independent of other sequences. It also includes a genetic construct which is part of a hybrid gene encoding additional polypeptide sequence. Preferably, the substantially purified genetic construct is at least approximately 90% pure, more preferably at least approximately 95% pure, even more preferably at least approximately 98% pure.
The term “isolated” means that the material is removed from its original environment (e.g. the natural environment if it is naturally occurring). For example, a naturally occurring nucleic acid present in a living plant is not isolated, but the same nucleic acid separated from some or all of the coexisting materials in the natural system, is isolated. Such nucleic acids could be part of a vector and/or such nucleic acids could be part of a composition, and still be isolated in that such a vector or composition is not part of its natural environment.
As an alternative to use of a selectable marker gene to provide a phenotypic trait for selection of transformed host cells, the presence of the genetic construct in transformed cells may be determined by other techniques well known in the art, such as PCR (polymerase chain reaction), Southern blot hybridisation analysis, histochemical assays (e.g. GUS assays), thin layer chromatography (TLC), northern and western blot hybridisation analyses.
The genetic constructs of the present invention may be introduced into plants or fungi by any suitable technique. Techniques for incorporating the genetic constructs of the present invention into plant cells or fungal cells (for example by transduction, transfection, transformation or gene targeting) are well known to those skilled in the art. Such techniques include Agrobacterium-mediated introduction, Rhizobium-mediated introduction, electroporation to tissues, cells and protoplasts, protoplast fusion, injection into reproductive organs, injection into immature embryos and high velocity projectile introduction to cells, tissues, calli, immature and mature embryos, biolistic transformation, Whiskers transformation, and combinations thereof. The choice of technique will depend largely on the type of plant or fungus to be transformed, and may be readily determined by an appropriately skilled person. For transformation of protoplasts, PEG-mediated transformation is particularly preferred. For transformation of fungi electroporation is particularly preferred.
Cells incorporating the genetic constructs of the present invention may be selected, as described below, and then cultured in an appropriate medium to regenerate transformed plants or fungi, using techniques well known in the art. The culture conditions, such as temperature, pH and the like, will be apparent to the person skilled in the art. The resulting plants may be reproduced, either sexually or asexually, using methods well known in the art, to produce successive generations of transformed plants or fungi.
Accordingly, in a further aspect of the present invention there is provided a transgenic plant cell, plant, plant seed or other plant part, or a transgenic fungus, fungal cell or other fungal part, capable of producing an organic compound as hereinbefore defined in greater quantities than an untransformed control plant cell, plant, plant seed or other plant part, or an untransformed fungus, fungal cell or other fungal part.
In a preferred embodiment the a transgenic plant cell, plant, plant seed or other plant part or the transgenic fungus, fungal cell or other fungal part has an increase in the quantity of the organic compound produced of at least approximately 10%, more preferably at least approximately 20%, more preferably at least approximately 30%, more preferably at least approximately 40% relative to the untransformed control.
For example, the quantity of the organic compound may be increased by between approximately 10% and 300%, more preferably between approximately 20% and 200%, more preferably between approximately 30% and 100%, more preferably between approximately 40% and 80% relative to the untransformed control.
Preferably the transgenic plant cell, plant, plant seed or other plant part or the transgenic fungus, fungal cell or other fungal part includes a nucleic acid, genetic construct or vector according to the present invention. Preferably the transgenic plant cell, plant, plant seed or other plant part, or the transgenic fungus, fungal cell or other fungal part, is produced by a method according to the present invention.
The present invention also provides a transgenic plant, plant seed or other plant part, or a transgenic fungus, fungal cell or other fungal part, derived from a plant or fungal cell of the present invention and including a nucleic acid, genetic construct or vector of the present invention.
The present invention also provides a transgenic plant, plant seed or other plant part, or a transgenic fungus, fungal cell or other fungal part, derived from a plant or fungus of the present invention and including a nucleic acid, genetic construct or vector of the present invention.
By ‘plant cell’ is meant any self-propagating cell bounded by a semi-permeable membrane and containing a plastid. Such a cell also requires a cell wall if further propagation is desired. Plant cell, as used herein includes, without limitation, algae, cyanobacteria, seeds suspension cultures, embryos, meristematic regions, callus tissue, leaves, roots, shoots, gametophytes, sporophytes, pollen and microspores.
By ‘fungal cell’ is meant any cell of a fungus. The term ‘fungus’ refers to whole fungi, fungal organs and tissues (e.g., asci, hyphae, pseudohyphae, rhizoid, sclerotia, sterigmata, spores, sporodochia, sporangia, synnemata, conidia, ascostroma, cleistothecia, mycelia, perithecia, basidia and the like), spores, fungal cells and the progeny thereof. Fungi may either exist as single cells or make up a multicellular body called a mycelium, which consists of filaments known as hyphae. Most fungal cells are multinucleate and have cell walls, composed chiefly of chitin.
Preferably, the fungus is of Nodulisporium spp. or Ascocoryne spp.
By ‘transgenic’ is meant any cell which includes a DNA sequence which is inserted by artifice into a cell and becomes part of the genome of the organism which develops from that cell.
The present invention also provides a substantially purified or isolated polypeptide involved in the production of an organic compound of the present invention.
In a preferred embodiment, the polypeptide may be involved in the production of a terpene, or a hydrocarbon such as a volatile hydrocarbon or a liquid hydrocarbon. Preferably, the organic compound is a terpene or hydrocarbon as hereinbefore described.
In a particularly preferred embodiment, the polypeptide may include an amino acid sequence selected from the group consisting of sequences shown in FIGS. 12 to 19 hereto and functionally active fragments and variants thereof. In a particularly preferred embodiment, the polypeptide may be a terpene synthase.
In a particularly preferred embodiment, the polypeptide may be encoded by a nucleic acid including a sequence selected from the group consisting of sequences shown in FIGS. 20 to 27 hereto and functionally active fragments and variants thereof. The present invention encompasses functionally active fragments and variants of the polypeptides of the present invention. By functionally active’ in this context is meant that the fragment or variant has one or more of the biological properties of the corresponding protein from which the fragment or variant is derived. Additions, deletions, substitutions and derivatizations of one or more of the amino acids are contemplated so long as the modifications do not result in loss of functional activity of the fragment or variant. Preferably the fragment or variant has at least approximately 80% identity to the relevant part of the above mentioned sequence to which the fragment or variant corresponds, more preferably at least approximately 90% identity, more preferably at least approximately 95% identity, most preferably at least approximately 98% identity. Such functionally active variants and fragments include, for example, those having conservative amino acid substitutions of one or more residues in the corresponding amino acid sequence.
Preferably the fragment has a size of at least 10 amino acids, more preferably at least 20 amino acids, more preferably at least 50 amino acids, more preferably at least 100 amino acids, more preferably at least 200 amino acids. As used herein, except where the context requires otherwise, the term “comprise” and variations of the term, such as “comprising”, “comprises” and “comprised”, are not intended to exclude further additives, components, integers or steps.
In a further aspect of the present invention, there is provided use of an organic compound, nucleic acid, genetic construct, vector, polypeptide, fungus, transgenic plant cell, plant, plant seed or other plant part, or transgenic fungus, fungal cell or other fungal part, according to the present invention in biofumigation or bioprotection.
Reference to any prior art in the specification is not, and should not be taken as, an acknowledgment or any form of suggestion that this prior art forms part of the common general knowledge in Australia or any other jurisdiction or that this prior art could reasonably be expected to be ascertained, understood and regarded as relevant by a person skilled in the art.
DETAILED DESCRIPTION OF THE EMBODIMENTS
Eleven fungal isolates were collected from two plant species at cool temperate rainforests within the Dandenong Ranges, Yarra Ranges and the Otway Ranges (Victoria, Australia). One isolate was collected from foliar tissue of Lomatia fraseri in the Dandenong Ranges, while the other 10 isolates were collected from decaying wood of Nothafagus cunninghamii in the Yarra Ranges and Otway Ranges. All isolates were morphologically and genetically (5.8S-ITS rRNA gene) identified. The isolate from L. fraserii was identified as Nodulisporium sp. (teleomorph: Hypoxylon sp., Xylariaceae), while the 10 isolates from N. cunninghamii were identified as Ascocoryne sarcoides (anamorph: Coryne sp., Helotiaceae). Molecular markers based on single sequence repeats from expressed sequence tags (EST-SSR markers) detected genetic diversity amongst A. sarcoides isolates, separating them according to origin (i.e. either Yarra Ranges or Otway Ranges). All eleven isolates exhibited bioactivity in in vitro bioassays against a range of plant pathogenic fungi, including Fusarium oxysporum, Sclerotinia minor and Pythium ultimum. The in vitro bioassays indicated that the isolate of Nodulisporium produced volatile bioactive compounds, while isolates of A. sarcoides produced liquid bioactive compounds. GC/MS analysis of Nodulisporium identified 58 volatile organic compounds, including many monoterpenes (e.g. eucalyptol) and, sesquiterpenes (e.g. β-Elemene), which may be produced by plants as defence compounds (e.g. eucalyptol—eucalyptus oil). The genes regulating the production of the terpenes were identified following the sequencing of the genome of the Nodulisporium isolate. A total of 8 terpene synthases were identified that are thought to regulate the production of the mono- and sesquiterpene compounds in Nodulisporium. 
The two fungi were morphologically characterised via micro- and macroscopic features of in vitro states and identified as Nodulisporium sp. and A. sarcoides (and in vivo state). The identification of the isolates were supported by comparing sequences of the rRNA gene (5.8S/ITS) to closely related Ascocoryne and Nodulisporium species from around the world (closest matches from Genbank). Isolates of A. sarcoides clustered together with a bootstrap support of 81.0%. Similarly, the isolate of Nodulisporium clustered closest to species of Nodulisporium and Hypoxylon (the teleomorph of Nodulisporium), with a bootstrap support of 80.0%.
Isolates of A. sarcoides were genotyped using EST-SSR markers derived from Neotyphodium species. Amplification was expected as markers were derived from expressed genes, some of which were likely to be universally found across the fungal kingdom. Isolates clustered according to origin.
In vitro bioassays were established to determine the bioactivity of Nodulisporium and A. sarcoides isolates against 3 plant pathogenic fungi, F. oxysporum, S. minor and P. ultimum. Both Nodulisporium and A. sarcoides reduced the growth of the plant pathogenic fungi by up to 100%. Bioassays indicated that volatile compounds were responsible for the bioactivity observed with Nodulisporium, whereas the bioactive compounds of A. sarcoides were liquid.
To evaluate the production of volatile compounds from Nodulisporium, growth conditions were chosen to enhance the production (diversity and quantity) of these compounds. For example, high nutrient media (e.g. potato dextrose agar) was used as the carbon source for growth. As a result a total of 58 compounds were produced by Nodulisporium including a range of terpenes, which are low molecular weight organic compounds that may be produced by plants as defence compounds. These terpenoid compounds included 21 monoterpenes (α-Thujene, β-Sabinene, β-Myrcene, α-Phellendrene, α-Terpinene, p-Cymene, (R)-(+)-Limonene, Eucalyptol, α-Ocimene, β-Ocimene, γ-Terpinene, α-Terpinolene, Allo-Ocimene, (−)-Terpinen-4-ol, α-Terpineol, 2H-pyran,tetrahydro-2-(propan-2-ylidene)-5-methoxy, 2H-pyran,tetrahydro-2-isopropyl-5-methoxy, 3-Cyclohexene-1-acetaldehyde,4-methyl-α-methylene-, 1-Cyclohexene-1-carboxaldehyde,4-(1-methylethenyl)-, p-Mentha-1,4(8)-dien-3-one (isomers), Bicyclo[2.2.2]octan-1-ol,4-ethyl,) and four sesquiterpenes (β-Elemene, α-Guajene, Bicyclo[5.3.0]decane,2 methylene-5-(1-methylvinyl)-8-methyl, δ-Guaijene). A further 16 monoterpene-like compounds and seven sesquiterpene-like compounds were produced by Nodulisporium. These terpenes had masses consistent with mono and sesquiterpenes, and were structurally similar based on their ion fragmentation (cyclohexane-, cyclohexene- and pyran-derivatives). A major constituent of the volatile metabolome of Nodulisporium was eucalyptol which is major component of eucalyptus oil, a potent antimicrobial extract found within leaves of Eucalyptus species. While the applicant does not wish to be restricted by theory, it is proposed that the volatile terpene compounds of Nodulisporium are acting synergistically to deliver the biocidal activity in in vitro bioassays.
The genome of the Nodulisporium isolate was sequenced in an effort to determine the genes responsible for the regulation of the bioactive terpenes. Mono- and sesqui-terpenes are produced via the mevalonate pathway through a series of condensation and phosphorylation reactions to yield prenyl pyrophosphate chains with 10 or 15 carbons. These products are then converted to monoterpenes (10 carbons) or sesquiterpenes (15 carbons) by a terpene synthase. Terpene synthases promote the metal (e.g. Mg2+) ion-dependent expulsion of pyrophosphate and catalyse the formation of acyclic and cyclic terpenes from the prenyl groups via a common ionization reaction, followed by various reactions such as isomerisation, cyclization, rearrangement (hydride shifts, methyl shifts, alkyl shifts, Wagner-Meerwein shifts), hydration and deprotonation. The majority of sesquiterpene synthases have been functionally characterised from microbes, unlike monoterpene synthases that have predominantly been characterised from plants. The enormous diversity of terpenes can be attributed to the unique ability of terpene synthases to synthesise multiple products from the one enzyme. While some terpenes synthases produce a single product, a large majority of mono- and sesqui-terpene synthases catalyse the formation of multiple terpene structures, often with high regio- and stereo-selectivity. For instance, in Arabidopsis thaliana, the enzyme At-TPS-Cin was responsible for catalysing the formation of 10 acyclic (e.g. myrcene and (E)-β-ocimene) and cyclic (e.g. sabinene, α-pinene) monoterpenes, with eucalyptol predominating (52%). The genome of Nodulisporium contained 8 terpene synthases, as these genes possessed structural domains specific to terpene synthases, including aspartate rich regions that form the substrate binding site. It is proposed that these 8 terpene synthases regulate the production of the volatile bioactive mono- and sesqui-terpenes of Nodulisporium. 
Nodulisporium and A. sarcoides represent a highly valuable microbial resource, principally due to there unique metabolism and ability to produce organic bioactive compounds via novel genes. These organisms, metabolites and genes are of commercial interest in the agricultural sector, particularly in the area of plant protection.



DESCRIPTION OF THE FIGURES
FIG. 1 shows apothecia (A) and conidiomata (B) of Ascocoryne sarcoides growing on fallen logs of Nothafagus cunninghamii. 
FIG. 2 shows Conidiophore ex-culture (Nodulisporium).
FIG. 3 shows Conidiophore ex culture (A. sarcoides).
FIG. 4 shows Conidia ex culture (A. sarcoides).
FIG. 5 shows A MP phenogram (1 of 8631) based on 5.8S/ITS rRNA gene sequences from 55 isolates of Nodulisporium and Hypoxylon species. Highlighted area (red) shows Victorian Nodulisporium isolate. The phenogram was obtained using the Close-Neighbour-Interchange algorithm of MEGA4.1 (deletion of gaps and missing data). Numbers on the nodes represent frequency (in per cent) with which a cluster appears in 1000 bootstrap tests. Scale bar equals 5 changes per 100 bases.
FIG. 6 shows A MP phenogram (199 of 330) based on 5.8S/ITS rRNA gene sequences from 26 isolates of Ascocoryne species. Highlighted area (grey) shows Victorian A. sarcoides isolates. The phenogram was obtained using the Close-Neighbour-Interchange algorithm of MEGA4.1 (deletion of gaps and missing data). Numbers on the nodes represent frequency (in per cent) with which a cluster appears in 1000 bootstrap tests. Scale bar equals 5 changes per 100 bases.
FIG. 7 shows UPGMA phenogram for Victorian Ascocoryne isolates using measurements of average taxonomic distance based on EST-SSRs.
FIG. 8 shows images of in vitro bioassays of Ascocoryne isolates from the Yarra Ranges (Victoria) against S. minor (including an untreated control).
FIG. 9 shows a GC/MS headspace analysis of volatile compounds produced by Nodulisporium sp. (Dandenong Ranges 1) when grown on PDA for 1, 4, 7, 10, 13, 16, 19 and 22 days growth. Each total ion chromatograph (TIC) represents one day.
FIG. 10 shows the chemical structures of volatile compounds produced by Nodulisporium sp. (Dandenong Ranges 1). Names of compounds (from left to right, line by line) are as follows:

    1-Butanol, 3-methyl—(4.098 min)
    1,4 Cyclohexadiene, 1-methyl (5.032 min)
    α-Thujene (9.312 min)
    β-Sabinene (10.868 min)
    β-Myrcene (11.425 min)
    α-Phellandrene (11.806 min)
    p-Cymene (12.578 min)
    (R)-(+)-Limonene (12.575 min)
    Eucalyptol (12.825 min)
    α-Ocimene (12.941 min)
    Cyclohexane, 1,2,4-tris(methylene)—(13.075 min)
    β-Ocimene (13.249 min)
    γ-Terpinene (13.558 min)
    α-Terpinolene (14.469 min)
    Phenylethyl alcohol (14.469 min)
    Allo-Ocimene (15.725 min)
    Benzoic acid ethyl ester (16.972 min)
    (−)-Terpinen-4-ol (17.159 min)
    α-Terpineol (17.566 min)
    2H-pyran, tetrahydro-2-(propan-2-ylidene)-5-methoxy (19.987 min)
    2H-pyran, tetrahydro-2-isopropyl-5-methoxy (20.124 min)
    3-Cyclohexene-1-acetaldehyde, 4-methyl-α-methylene—(20.506 min)
    1-Cyclohexene-1-carboxaldehyde, 4-(1-methylethenyl)—(20.676 min)
    p-Mentha-1,4(8)-dien-3-one (and isomer) (21.744/22.849 min)
    Bicyclo[2.2.2]octan-1-ol4-ethyl (22.526 min)
    β Elemene (23.129 min)
    α-Guajene (24.297 min)
    Bicyclo[5.3.0]decane,2 methylene-5-(1-methylvinyl)-8-methyl (25.580 min)
    δ-Guaijene (25.998 min)


FIG. 11 shows a representative terpene synthase sequence from Nodulisporium (g9560, 313 amino acids; SEQ ID NO: 1), aligned against a “type” terpene synthase from the Conserved Domain Database (NCBI; SEQ ID NO: 2). The highlighted areas represent common domains associated with terpene synthases. The medium grey area identifies the aspartate rich regions that form the substrate binding site. The dark grey area identifies the regions that form the substrate binding pocket. The light grey area identifies the regions that form the active site lid residues.
FIG. 12 shows an amino acid sequence of a terpene synthase of Nodulisporium (g226.t1, 339 amino acids; SEQ ID NO: 3).
FIG. 13 shows an amino acid sequence of a terpene synthase of Nodulisporium (g1080.t1, 365 amino acids; SEQ ID NO: 4).
FIG. 14 shows an amino acid sequence of a terpene synthase of Nodulisporium (g2861.t1, 293 amino acids; SEQ ID NO: 5).
FIG. 15 shows an amino acid sequence of a terpene synthase of Nodulisporium (g4788.t1, 541 amino acids; SEQ ID NO: 6).
FIG. 16 shows an amino acid sequence of a terpene synthase of Nodulisporium (g5351.t1, 373 amino acids; SEQ ID NO: 7).
FIG. 17 shows an amino acid sequence of a terpene synthase of Nodulisporium (g6654.t1, 348 amino acids; SEQ ID NO: 8).
FIG. 18 shows an amino acid sequence of a terpene synthase of Nodulisporium (g9560.t1, 313 amino acids; SEQ ID NO: 9).
FIG. 19 shows an amino acid sequence of a terpene synthase of Nodulisporium (g11102.t1, 417 amino acids; SEQ ID NO: 10).
FIG. 20 shows a nucleic acid sequence of a gene encoding terpene synthase from Nodulisporium (g226.t1, 1017 base pairs; SEQ ID NO: 11).
FIG. 21 shows a nucleic acid sequence of a gene encoding terpene synthase from Nodulisporium (g1080.t1, 1095 base pairs; SEQ ID NO: 12).
FIG. 22 shows a nucleic acid sequence of a gene encoding terpene synthase from Nodulisporium (g2861.t1, 879 base pairs; SEQ ID NO: 13).
FIG. 23 shows a nucleic acid sequence of a gene encoding terpene synthase from Nodulisporium (g4788.t1, 1623 base pairs; SEQ ID NO: 14).
FIG. 24 shows a nucleic acid sequence of a gene encoding terpene synthase from Nodulisporium (g5351.t1, 1119 base pairs; SEQ ID NO: 15).
FIG. 25 shows a nucleic acid sequence of a gene encoding terpene synthase from Nodulisporium (g6654.t1, 1044 base pairs; SEQ ID NO: 16).
FIG. 26 shows a nucleic acid sequence of a gene encoding terpene synthase from Nodulisporium (g9560.t1, 939 base pairs; SEQ ID NO: 17).
FIG. 27 shows a nucleic acid sequence of a gene encoding terpene synthase from Nodulisporium (g11102.t1, 1251 base pairs; SEQ ID NO: 18).



EXAMPLE 1
Fungal Isolates
Pieces of leaf and stem of Lomatia fraserii were collected during surveys in the Dandenong Ranges. Sections of leaf and stem were surface sterilised (70% Ethanol for 30 secs, flame sterilisation) prior to the excision of internal tissues, which were then plated onto potato dextrose agar (PDA) (39 g/L) (Amyl Media, Dandenong, Australia) amended with achromycin (50 ppm). Endophytic fungi growing from the plant tissue were removed by excising a hyphal tip from each colony, and plated onto PDA. Each hyphal tip constituted one endophytic fungal isolate. Isolates then underwent a preliminary screen for bioactivity by challenging them against Rhizoctonia solani on PDA. One isolate inhibited the growth of R. solani and was selected for further analysis.
In addition, pieces of wood from fallen logs of Nothafagus cunninghamii containing apothecia (gelatinous purple discs, sexual stage) or coniodamata (gelatinous purple fingers, asexual stage) characteristic of Ascocoryne sarcoides (FIG. 1) were collected during surveys in the Yarra Ranges and the Otway Ranges respectively. Sections of apothecia or conidiomata were surface sterilised (2% NaOCl for 30 secs, 2 washes in sterile distilled water, SDW) and plated onto PDA (39 g/L) (Amyl Media, Dandenong, Australia) amended with achromycin (50 ppm). Each apothecium or conidioma section comprised one isolate, with ten isolates collected in total, 6 from the Yarra Ranges and 4 from the Otway Ranges.
Pure cultures of the eleven fungal isolates (i.e. hyphal plugs) were placed in SDW and stored at room temperature and at 4° C., and in 15% glycerol at −70° C. Sections of conidiomata were placed in SDW and stored at room temperature.
EXAMPLE 2
Morphology
Isolates were removed from storage and placed onto PDA and allowed to grow at 25° C. (in the dark) until the formation of conidiophores. Sections of hyphae containing conidiophores were mounted in lactic acid and examined under light microscopy (in vitro description). In addition, sections of conidiomata from the Ascocoryne isolates were mounted in lactic acid and examined under light microscopy (in vivo description).
Nodulisporium State of Hypoxylon 
Description in Vitro
Colonies on PDA initially white, becoming pale yellow to grey yellow. Conidiophores branching loosely, pale brown, paler towards the apex, verruculose, 2.5-3 um wide. Conidiogenous cells usually produced singly, pale brown, verruculose, 12-20×2.5-3 um. Conidia borne from minutely visible denticles, pale brown, more or less smooth, ellipsoidal, 6-8×3-4 um (FIG. 2).
By evaluating the microscopic features of the isolates growing in culture (in vitro stage) we confirmed that they were characteristic of an undescribed species of Nodulisporium. 
Coryne State of Ascocoryne sarcoides 
Description in Vitro
Colonies on PDA initially white, becoming dark violet to grey violet, forming violet crystals in the medium. Conidiophores complex, branching 3-5 times, hyaline, thin walled (FIG. 3). Phialides hyaline, narrowly obclavate to cylindrical, straight to slightly curved, thin walled, 10-14×1.5-2 μm. Conidia hyaline, subglobose to ellipsoid, sometimes slightly curved, 2-5×1-2 μm (FIG. 4).
Description in Vivo
Conidiomata synemmatous, determinate, 3-5 mm×1-5 mm, dark purple, gelatinous, unbranched, subulate to capitate, gregarious. Hyphae of the stipe in two zones; the ectal excipulum a textura angularis, the medullary excipulum a textura intricata. Conidiophores complex, branching 3-4 times, hyaline, thin walled. Phialides hyaline, narrowly obclavate to cylindrical, straight to slightly curved, thin walled, 10-14×1.5-2 μm. Conidia hyaline, subglobose to ellipsoid, sometimes slightly curved, 2-5×1-2 μm.
By evaluating the microscopic features of the gelatinous purple fingers (conidomata, in vivo stage) and the isolates growing in culture (in vitro stage) we confirmed that they were characteristic of A. sarcoides. 
EXAMPLE 3
Genotyping
A. DNA Sequencing—Ribosomal RNA
Genomic DNA was extracted from cultures of the Nodulisporium and A. sarcoides isolates grown in either PDA or potato dextrose broth (PDB) using a DNeasy Plant Mini Kit (Qiagen). A section of the ribosomal RNA loci (5.8S/ITS) was amplified with primers ITS4 and ITS5 (White et al., 1990). PCR amplifications were performed in 25 μL reaction volumes containing 1.0 U of Platinum Taq DNA Polymerase (Invitrogen), ×1 PCR buffer, 0.2 mM of each dNTP, 1.5 mM MgCl2, 0.5 μM of each primer, and 15-25 μg DNA. Reactions were performed in a thermocycler (Gradient Palm-Cycler, Corbett Research) with cycling conditions consisting of denaturation at 94° C. (3 min), followed by 35 cycles at 94° C. (30 s), 50° C. (30 s), and 72° C. (2 min), with a final extension step at 72° C. (3 min) to complete the reaction. PCR products were separated by electrophoresis at 100 V for 45 min in a 1.5% (w/v) agarose gel (containing ethidium bromide, 0.1 ppm) in 0.5×TBE running buffer and visualised under UV light. Amplification products were purified using a PCR Purification Kit (Qiagen), and sequenced using the BigDye Terminator Cycle v 3.1 sequencing kit (Applied Biosystems) on the ABI 3730xl Capillary Sequencer (Applied Biosystems), according to manufacturers' instructions.
Sequences of Victorian isolates were compared to reference sequences from known Nodulisporium (or related teleomorphs, i.e. Hypoxylon and Daldinia) and Ascocoryne species (A. sarcoides or A. cylichnium) from around world (closest matches from GenBank). A total of 55 Nodulisporium-related sequences were aligned with MUSCLE (Edgar, 2004), while 26 Ascocoryne-related sequences were aligned. Aligned sequences were adjusted with ClustalW/Alignment Explorer in MEGA 4.1 (Tamura et al, 2007). Based on these sequences phylogenetic relationships were inferred using distance and maximum parsimony (MP) analyses. For distance analysis, phenograms were obtained using the neighbour-joining (NJ) algorithm (Saitou et al, 1987), applying the Kimura-2-parameter model (Kimura, 1980), as implemented in MEGA4.1. For MP analysis, phenograms were obtained using the Close-Neighbour-Interchange algorithm (search level 3) (Nei et al, 2000), as implemented in MEGA4.1. To find the global optimum phenogram 10 random sequences were added. Measurements calculated for MP included tree length, consistency index, retention index and rescaled consistency index (TL, CI, RI, RCI). In both analyses, alignment gaps and missing data were eliminated from the dataset (Complete deletion option) and the confidence of branching was assessed by computing 1000 bootstrap replications (Felsenstein, 1985).
Of the 55 Nodulisporium-related isolates the size of the rRNA (5.8S/ITS) gene sequence ranged from 436-664 base pairs, of which 371 were included in the final data set for analysis. In the NJ analysis the optimal phenogram had a sum of branch length of 0.525. The MP analysis yielded 8631 most parsimonious phenograms (TL=211, CI=0.654 RI=0.916, RCI=0.569, for the parsimony informative sites). NJ and MP analyses yielded phenograms with similar topology and bootstrap values. Therefore, only the MP phenogram is presented (1 of 8631, FIG. 5).
Isolates tended to cluster according to the teleomorph of Nodulsporium species, Hypoxylon and Daldinia. The Dandenong Ranges isolate clustered with Hypoxylon species, with an 80% bootstrap support. This group formed a cluster with other Nodulisporium and Hypoxylon isolates, with a bootstrap support of 14% (Clade 1) This cluster was alongside another group of Hypoxylon isolates with a bootstrap support of 41% (Clade 2). A large group of Daldinia isolates formed the next related cluster with a 37% bootstrap support (Clade 3).
Of the 26 Ascocoryne isolates the average size of the rRNA (5.8S/ITS) gene sequence was approximately 569 base pairs, of which 436 were included in the final data set for analysis. In the NJ analysis the optimal phenogram had a sum of branch length of 0.103. The MP analysis yielded 330 most parsimonious phenograms (TL=46, CI=0.921, RI=0.964, RCI=0.888, for the parsimony informative sites). NJ and MP analyses yielded phenograms with similar topology and bootstrap values. Therefore, only the MP phenogram is presented (199 of 330, FIG. 6).
Isolates tended to cluster according to Ascocoryne species. All Victorian isolates clustered together, with 64% bootstrap support (Clade 1). They clustered alongside a group of A. sarcoides isolates from Lithuania, Sweden and New Zealand, with 81% bootstrap support (Clade 2). Gliocladium roseum also clustered with these A. sarcoides isolates. Finally, six isolates of A. cylichnium from Latvia, Lithuania and Sweden clustered together, with 90% bootstrap support (Clade 3).
B. Microsatellites—Simple Sequence Repeats (SSR)
Expressed sequence tag-simple sequence repeat (EST-SSR) markers developed by van Zijll de Jong (2003) were used to evaluate genetic diversity amongst ten Victorian Ascocoryne isolates. A total of 34 EST-SSR markers were initially evaluated, of which four were selected for routine genotyping based on their ability to detect levels of polymorphism between isolates (Table 1). PCR amplifications were performed in 20 μL reaction volumes containing 0.5 U Immolase (Bioline), 1×PCR buffer, 0.2 mM of each dNTP, 0.25 μM each primer, and 10 ng fungal genomic DNA. The forward primer was 5′-end labelled with a fluorescent phosphoramidite dye (6-FAM, HEX, or NED). Amplification was performed in a thermocycler using an appropriate touchdown profile depending on the Tm value of the primer pairs: (Program 1, P1) 95° C. (10 min), 10 cycles at 94° C. (30 s), 55° C. (30 s) and 72° C. (1 min) with a reduction of annealing temperature of 1° C. every cycle, followed by 20 cycles at 94° C. (30 s), 45° C. (30 s), 72° C. (1 min); (Program 2, P2) a similar profile to (P1) with an initial annealing temperature of 60° C. and final annealing temperature of 50° C.; (Program 3, P3) a similar profile to (P1) with an initial annealing temperature of 65° C. and final annealing temperature of 55° C. PCR products (2 mL) were diluted 1:99 (P1 and P3) or 1:199 (P2), and analysed on the ABI 3730xl Capillary Sequencer (Applied Biosystems), according to manufacturers instructions.







TABLE 1







EST-SSR markers for determining genetic variation in Ascocoryne


isolates from Victoria, Australia.


















SEQ










ID



No. of
Size of


Primer

Primer sequence (5′ → 3′)
No
Label
PCR
Motif
alleles
products





NCESTA1DH04
F
CAGTCCAAATCAGGCGGTAGCAGA
19
FAM
1
(GTC)8
2
150/397


 



R
TGAGAAGGATCGGAATCGAGTGGT
20







 


NCESTA1HA02
F
TGCTCCTCGTCGACAGTTTCAAGT
21
HEX
1
(CAG)5
1
259


 



R
CTTCATATTGGTTGTGCTGGACCC
22







 


NLESTA1NF04
F
AACCCGCTCCTACACTCGCCCAAT
23
NED
2
(TGC)8(TGA)3
3
 366/416/








(TGG)1(TGA)3

450


 



R
TCGGTAGCCGAGCAGCCTGCCTTG
24







 


NLESTA1TA10
F
TTTCCGACCCGCCAGACACC
25
FAM
3
(TC)11
2
252/313


 



R
CCGGTCCTGCGATTCCTCCA
26









Products or alleles for each of the Victorian Ascocoryne isolates were characterised by size (i.e. number of base pairs) using GeneMapper version 3.7 software (Applied Biosystems). Isolates were then scored for the presence (1) and absence (0) of each allele. A similarity matrix was generated with this data using the Dice coefficient (Dice, 1945; NTSYSpc version 2.10t). Phenograms were constructed by the unweighted pair group method of arithmetic averages (SAHN program—UPGMA clustering method, NTSYSpc version 2.10t). The resulting genetic relationships were evaluated by cophenetic correlation and principle coordinate analysis (MXCOMP and EIGEN programs, NTSYSpc version 2.10t).
Of the 34 EST-SSR markers initially evaluated, 18 (53%) produced amplification products, but only four (12%) detected genetic polymorphism between the Victorian Ascocoryne isolates. Analysis of SSR polymorphism across the 10 Victorian isolates identified 8 different alleles.
A UPGMA phenogram constructed using the average taxonomic distance based on SSR polymorphism across the ten Victorian isolates, showed a separation largely based on the origin of the isolate (e.g. Otway Ranges cluster or Yarra Ranges cluster) (FIG. 7). Within the Yarra Ranges cluster the Yarra Ranges 7 isolate branched apart from the core cluster. Similarly, the Otway Ranges cluster branched apart leaving Otway Ranges 1 separated from the remaining Otway Ranges isolates. The cophonetic correlation between distance matrices was high (r=0.90).
EXAMPLE 4
Bioactivity
In vitro bioassays were established to test the bioactivity of Victorian Nodulisporium and A. sarcoides (Yarra Ranges only) isolates against a range of plant pathogenic fungi, Fusarium oxysporum, Sclerotinia minor and Pythium ultimum. Nodulisporium was compared against the bioactive endophytes Muscodor albus (CZ620) and Endophyte A. The bioassays used two types of Petri plates—standard 90 mm Petri plates for A. sarcoides, and 90 mm split Petri plates for Nodulisporium. The split plates consisted of an impermeable barrier through the centre of the plate, which completely separated the plate into two halves, with only volatile compounds capable of passing over the septum (i.e. no direct contact between test fungi or their liquid exudates). The isolates were inoculated on to Petri plates containing PDA by placing a 6 mm agar plug containing actively growing mycelia, 13 mm from the edge of the plate (i.e. on one half of the plate). Isolates were allowed to grow at 25 C (in the dark) for 7 days for Nodulisporium and 20 days for A. sarcoides. Subsequently, the plant pathogenic fungi were inoculated on to the other half of the plate by placing a 6 mm agar plug containing actively growing mycelia, 13 mm from the edge of the plate. Plates were sealed with LDPE plastic film (approximately 0.01 mm thick). After 5 days the growth of the plant pathogenic fungi were determined by measuring the radius of the colony (toward the centre of the plate). Measurements were compared to the control and expressed as percentage inhibition versus the control. Data were analysed using ANOVA as performed in GenStat, version 11 (Payne et al, 2008). The experiment was fully randomised with 3 replicates for Nodulisporium and A. sarcoides. 
The Nodulisporium isolate showed strong levels of activity against the 3 horticultural crop pathogens, completely inhibiting the mycelial growth of P. sulcatum and S. minor, and inhibited the growth of F. oxysporum by up to 46.4% (Table 2). Nodulisporium also provided equivalent (or better) control of pathogens to the bioactive endophytes, Muscodor albus (CZ620) and Endophyte A.







TABLE 2







Percent inhibition of 3 plant pathogens (Pythium sulcatum,


Fusarium oxysporum and Sclerotinia minor) following exposure 


(5 days) to volatile secondary metabolites produced by an isolate 


of Nodulisporium from the Dandenong Ranges, Victoria, 


compared to Muscodor albus and Endophyte A.











Pythium
Fusarium
Sclerotinia



sulcatum
oxysporum
minor


Isolate
(% Inhibition)
(% Inhibition)
(% Inhibition)





Dandenong Ranges 1
100.0% a
46.4% a
100.0% a


Muscodor albus
100.0% a
32.3% b
100.0% a


(CZ620)





Endophyte A
 55.5% b
 2.9% c
 44.7% b


LSD (5%)
 5.9%
 8.5%
 18.2%


F Pr.
 0.01
 0.01
 0.01









Isolates of A. sarcoides from the Yarra Ranges inhibited mycelial growth of F. oxysporium and S. minor (Table 3, FIG. 8). Yarra Ranges 11 was the most active isolate against F. oxysorum and S. minor, inhibiting mycelial growth by 31.8% and 85.0% respectively. Yarra Ranges 11 had significantly greater activity against F. oxysporum than all other isolates. Yarra Ranges 11, 12, 13 and 15 were the most active isolates against S. minor, significantly greater than Yarra Ranges 7 and 10.







TABLE 3







Percent inhibition of two plant pathogenic fungi (F. oxysporum and 


S. minor) following exposure (5 days) to isolates of A. sarcoides


from the Yarra Ranges, Victoria.










Fusarium oxysporum
Sclerotinia minor



(% Inhibition)
(% Inhibition)





Yarra Ranges 7
  22.7% ab
  77.3% b


Yarra Ranges 10
  26.1% cd
  71.0% a


Yarra Ranges 11
  31.8% e
  85.0% c


Yarra Ranges 12
  22.7% ab
  81.2% bc


Yarra Ranges 13
  21.6% a
  83.1% c


Yarra Ranges 15
  23.9% abc
  81.2% bc


LSD (p = 0.05) 
   3.1%
   3.9%


F Pr.
 <0.001
 <0.001









EXAMPLE 5
Metabolite Production
A. Qualitative Analysis of Major Non-Polar Fungal Gases
Gases were analysed in the head space above cultures of Nodulisporium. The isolate was cultured under microaerophilic conditions, which consisted of growing the fungus on PDA slopes (39 g/L) (Amyl Media Pty Ltd) in 20 ml glass vials, with an agar:air ratio of 1:2.5. Vials were sealed with a screw cap lid with PTFE septum, and grown for 22 days at room temperature.
A head space solid phase microextraction (SPME) was performed to capture volatiles produced by Nodulisporium. A StableFlex fibre (Supelco) consisting of a matrix of divinylbenzene/carboxen (DVB/CAR) on polydimethylsiloxane (PDMS) (50/30 um) was used to absorb volatiles from the head space of vials. Automated sampling was performed by an Agilent GC Sampler combined with Gerstel Maestro software. The fibre was conditioned (baked at 250° C.) daily for 20 minutes prior to commencement of activities and for 2 minutes between each sample. For each sample the fibre was inserted into the vial and incubated at room temperature for 5 minutes to absorb volatiles, after which the fibre was inserted into a splitless injection port of an Agilent 7890 GC System where the contents was thermally desorbed (250° C. for 6 mins) onto a capillary column (Agilent HP-5 ms, 30 m×250 um id., 0.25 um film thickness) coupled with a deactivated fused silica guard (Agilent, 6.02 m.×250 um id.). The column oven was programmed as follows: 40° C. (3.5 min), 5° C./min to 200° C., hold at 200° C. (2 min). The carrier gas was helium with a constant flow rate of 1.2 mL/min. The GC was interfaced with an Agilent 7000 GC/MS triple quadruple mass selective detector (mass spectrometer, MS) operating in electron impact ionization mode at 70 eV. The temperature of the transfer line was held at 280° C. during the chromatographic run. The source temperature was 280° C. Acquisitions were carried out over a mass range of 35-450 mz, with a scan time of 300 ms.
Initial identification of the volatiles produced by the Nodulisporium isolates was made through library comparison using standard chemical databases. Secondary confirmatory identification was made by comparing mass spectral data of authentic standards with data of the fungal volatiles. All chemical names in this patent application follow the nomenclature of the standard chemical databases. In all cases, uninoculated control vials were also analysed and the compounds found therein were subtracted from those appearing in the vials supporting fungal growth. Tentative identification of the fungal volatiles was based on observed mass spectral data as compared to those in these chemical databases and those of authentic standards (where possible).
The GC-MS analysis (0-37.5 mins) identified 58 volatile metabolites produced by Nodulisporium when grown for 1-22 days on PDA at room temperature (Table 4, FIGS. 9 and 10). The metabolites produced by Nodulisporium were representatives of a number of structural classes, with the terpenes predominating, accounting for over 82% of the compounds produced by Nodulisporium. There were 21 monoterpenes (α-Thujene, β-Sabinene, β-Myrcene, α-Phellendrene, α-Terpinene, p-Cymene, (R)-(+)-Limonene, Eucalyptol, α-Ocimene, β-Ocimene, γ-Terpinene, α-Terpinolene, Allo-Ocimene, (−)-Terpinen-4-ol, α-Terpineol, 2H-pyran,tetrahydro-2-(propan-2-ylidene)-5-methoxy, 2H-pyran,tetrahydro-2-isopropyl-5-methoxy, 3-Cyclohexene-1-acetaldehyde,4-methyl-α-methylene-, 1-Cyclohexene-1-carboxaldehyde,4-(1-methylethenyl)-, p-Mentha-1,4(8)-dien-3-one (isomers), Bicyclo[2.2.2]octan-1-ol,4-ethyl,) and four sesquiterpenes (β-Elemene, α-Guajene, Bicyclo[5.3.0]decane,2 methylene-5-(1-methylvinyl)-8-methyl, δ-Guaijene) produced by Nodulisporium. A further 16 monoterpene-like compounds and seven sesquiterpene-like compounds were produced by Nodulisporium. (Table 4 FIGS. 9 and 10). These terpenes had masses consistent with mono and sesquiterpenes, and were structurally similar based on their ion fragmentation. Fragmentation patterns also indicated the presence of a cyclohexane, cyclohexene or pyran ring as the primary structure), which is consistent with cyclic monoterpenes.







TABLE 4







GC-MS headspace analysis of the volatile compounds


produced by Nodulisporium (Dandenong Ranges 1) when grown on


PDA for 1-22 days at room temperature.














RT
Peak Name
Standard
Formula
Mass
Area
















 1
4.098
1 Butanol, 3-methyl-

C5H12O
88
+


 2
5.032
1,4-Cyclohexadiene, 1-methyl-

C7H10
94
+


 3
9.312
α-Thujene

C10H16
136
+


 4
10.868
β-Sabinene

C10H16
136
+


 5
11.198
Unknown


126
+


 6
11.425
β-Myrcene
Y
C10H16
136
+++


 7
11.806
α-Phellandrene
Y
C10H16
136
+


 8
12.217
α-Terpinene
Y
C10H16
136
+


 9
12.578
ρ-Cymene
Y
C10H14
134
+


10
12.575
(R)-(+)-Limonene
Y
C10H16
136
+


11
12.825
Eucalyptol
Y
C10H18O
154
++++


12
12.941
α-Ocimene

C10H16
136
+


13
13.075
Cyclohexane, 1,2,4-tris(methylene)-

C9H12
120
+


14
13.249
β-Ocimene
Y
C10H16 
136
+


15
13.558
γ-Terpinene
Y
C10H16 
136
+++


16
13.906
Unknown#


138
+


17
13.969
Unknown#


136
+


18
14.268
Unknown#


140
+


19
14.469
α-Terpinolene
Y
C10H16 
136
+


20
14.581
Unknown#


142
+


21
14.787
Unknown#


138
+


22
14.934
Unknown#


136
+


23
15.261
Phenylethyl alcohol

C8H10O 
122
++++


24
15.546
Unknown#


138
+


25
15.725
Allo-Ocimene

C10H16 
136
+


26
16.864
Unknown#


136
+


27
16.972
Benzoic acid ethyl ester

C9H10O2
150
+


28
17.159
(−)-Terpinen-4-ol

C10H18O
154
+


29
17.566
α-Terpineol
Y
C10H18O
154
+++


30
18.679
Unknown#


180
+


31
19.171
Unknown#


150
++


32
19.470
Unknown#


152
+


33
19.899
Unknown#


152
+


34
19.987
2H-pyran, tetrahydro-2-(propan-2-ylidene)-5-methoxy

C9H16O2 
156
++++


35
20.124
2H-pyran, tetrahydro-2-isopropyl-5-methoxy

C9H18O2 
158
++++


36
20.287
Unknown#


152
+


37
20.457
Unknown#


154
+


38
20.506
3-Cyclohexene-1-acetaldehyde, 4-methyl-α-methylene-

C10H14O
150
++++


39
20.676
1-Cyclohexene-1-carboxaldehyde, 4-(1-methylethenyl)-

C10H14O
150
++++


40
21.074
Unknown#


152
+


41
21.159
Unknown#


148
+


42
21.744
ρ-Mentha-1,4(8)-dien-3-one (isomer)

C10H14O
150
++++


43
22.526
Bicyclo[2.2.2]octan-1-ol,4-ethyl

C10H18O
154
+++++


44
22.849
ρ-Mentha-1,4(8)-dien-3-one (isomer)

C10H14O
150
+++


45
23.086
Unknown


168
+


46
23.129
β-Elemene
Y
C15H24
204
+


47
24.297
α-Guajene

C15H24
204
+


48
25.203
Unknown{circumflex over ( )}


204
+


49
25.364
Unknown{circumflex over ( )}


204
+


50
25.440
Unknown{circumflex over ( )}


204
+


51
25.493
Unknown{circumflex over ( )}


204
+


52
25.580
Bicyclo[5.3.0]decane, 2 methylene-5-(1-methylvinyl)-8-methyl

C15H24
204
+


53
25.712
Unknown{circumflex over ( )}


204
+


54
25.806
Unknown{circumflex over ( )}


204
+


55
25.998
δ-Guaijene

C15H24
204
++


56
26.262
Unknown{circumflex over ( )}


204
+


57
26.870
Unknown


238
+


58
26.959
Unknown


238
+





#Fragmentation pattern suggests a monoterpene-like compound derived from of a cyclohexane/ene or pyran substructure


{circumflex over ( )}Fragmentation pattern suggests a sesquiterpene-like compound






EXAMPLE 6
Gene Regulation
Genome Sequencing
The genome of Nodulisporium sp. (Dandenong Ranges 1) was sequenced using the Genome Sequencer FLX Titanium (GS FLX Titanium), using standard and modified protocols for this technology. A shotgun library of the fungal isolate was prepared from 5 μg of intact genomic DNA, as per the DNeasy Plant Mini Prep (Qiagen) protocol. Following library preparation, the resulting single stranded (ss) DNA library showed a fragment distribution between 500 and 2000 bp, with an average of 750 bp. The optimal amount of ssDNA library input for the emulsion PCR (emPCR) was determined empirically through two small-scale titrations leading to 1.7 molecules per bead used for the large-scale approach. The large-scale emPCR generated 4,602,000 DNA-carrying beads for the two-region-sized 70×75 mm PicoTiterPlate (PTP). One region was subsequently loaded with 2,000,000 DNA-carrying beads. During the sequencing run a total of 200 cycles of nucleotide flows (flow order TACG) were performed, which were assessed via a pipeline of 454 Life Sciences/Roche Diagnostics software Version 1.1.03. The output consisted of a Standard Flowgram Format (sff) file that provided information about read flowgrams, basecalls, and per base quality scores. The sff file was subsequently used to assemble (de novo) high quality reads into contiguous sequences using the 454 Life Sciences/Roche Diagnostics software, Newbler v2.3 (gsAssembler).
The GS FLX Titanium sequencing run yielded 663,514 high quality reads, with an average read length of over 420 bp. A total of 6,938 contigs were assembled de novo, of which 6,165 were larger than 500 bp. Overall, contigs contained around 33.9 Mb of sequence, at sequencing depth of ×6.0. The contig size ( x/n50) was 5.4/8.6 kbp. The largest contig was 47.4 kbp.
In addition, the genome of Nodulisporium sp. (Dandenong Ranges 1) was sequenced using the Illumina HiSeq platform using standard and adapted protocols for this technology. A paired end library of the isolate was prepared from 2 ug of intact genomic DNA as per the DNeasy Plant Mini Prep (Qiagen) protocol. DNA was sheared to fragments of 200-700 bp, end-repaired, A-tailed and ligated to Illumina paired end adaptors. The ligated fragments were size selected at 400 and 600 bp on agarose gels, ligated again with multiplex adaptors and amplified to the desired concentration by qPCR and PCR. Finally, libraries were titrated (KAPA) to accurately measure the number of competent molecules present. Library concentrations were adjusted and sequenced on the Illumina HiSeq 2000, with read lengths of 90-100 bp. Raw sequences were filtered for low quality and short length, and trimmed of adapter sequence and paired-end read overlap. The Illumina HiSeq sequencing run yielded 23,354,002 raw reads, of which 11,677,001 were deemed of high quality.
High quality reads from both the GS FLX Titanium and Illumina HiSeq sequencing runs were then assembled with Velvet to construct contigs. A total of 4299 contigs were assembled de novo, of which 1543 were greater than 1 kb (large contigs). The total number of bases in large contigs totalled 37.8 MB with an estimated sequencing depth of ×25.0. The contig n50 was 101.5 kbp with the largest contig measuring 397.3 kbp.
Gene Prediction
The gene prediction program Augustus was used to predict coding domains in the contigs of Nodulisporium, according to manufacturer's instructions. In Augustus, trained models of a closely related species, Aspergillus oryzae, was used to predict coding regions in contigs of Nodulisporium. A total of 9,958 coding regions were predicted for Nodulisporium from the assembly.
Gene Annotation
The predicted genes were then compared against the Conserved Domain Database (CDD) and the non-redundant protein database (NRPD) to determine putative function. The comparison was completed using the NCBI alignment tools RPS-BLAST (CDD) and BLAST-P (NRPD) Of the 9958 predicted genes for Nodulisporium 6525 were found to contain functional coding domains when compared against the CDD (evalue>1e-5).
An analysis of the specific function of coding domains identified a number of unique genes in Nodulisporium, which are involved in the regulation of key secondary metabolites. A total of 8 putative genes were found to contain non-plant terpene synthase domains (FIG. 11, Table 6). The average length of the putative non-plant terpene synthase genes from Nodulisporium was 376 amino acids. The eight gene sequences are represented in FIGS. 12-19 (amino acid sequences) and FIGS. 20-27 (nucleic acid sequences).







TABLE 6







Features of putative non-plant terpene synthase genes from 


Nodulisporium (bp—base pairs; aa—amino acid).













Contig

Gene
Gene




Length 

Length 
Length 



Contig
(bp)
Gene
(bp)
(aa)
Evalue*















297
15247
g226
1017
339
4.66 × 10−58


58
91070
g1080
1095
365
8.06 × 10−16


1132
179839
g2861
879
293
2.75 × 10−19


4952
55485
g4788
1623
541
5.15 × 10−7 


334
34511
g5351
1119
373
3.66 × 10−28


4952
55485
g6654
1044
348
1.81 × 10−8 


364
85750
g9560
939
313
5.99 × 10−51


789
225983
g11102
1251
417
3.76 × 10−23





*Evalue represents sequence similarity between amino acid gene sequences of Nodulisporium and sequences within the Conserved Domain Database (NCBI), generated via a RPS-BLAST comparison






When the 8 putative terpene synthase genes were compared against the NRPD, sequences were found to be highly similar to terpene synthases from the fungi Leptosphaeria maculans, Trichoderma reesei, Aspergillus species and Penicillium species, and the bacterium Nostoc punctiforme (Table 7). Sequences from Penicillium rocquerfortii and Aspergillus terreus are known to regulate the production of sesquiterpenes, providing evidence to suggest g226 and g9560 may regulate the production of the sesquiterpenes identified in the volatile bioactive compounds. The remaining genes may regulate the production of the monoterpenes in Nodulisporium.







TABLE 7







Sequence similarity between the 8 putative terpene synthase genes from Nodulisporium and 


sequences from the Non-redundant Protein Database. The top two matches are presented.











Gene
Genbank Accession
Terpene Synthase
Organism
E value





g226
Q03471.1
Terpene Synthase (Sesqui-)
Penicillium rocquertfortii
1.6 × 10−118


g226
1D|1|A
Terpene Synthase (Sesqui-)
Penicillium rocquertfortii
2.8 × 10−116


g1080
|XP_002849193.1
Hypothetical Protein
Arthroderma otae
4.6 × 10−29


g1080
CBY01604.1
Terpene Synthase
Leptosphaeria maculans
7.9 × 1020


g2681
XP_002479429.1
Hypothetical Protein
Talaromyces stipitatus
3.2 × 1044


g2681
XP_001826046.2
Terpene Synthase
Aspergillus oryzae
7.4 × 1038


g4788
XP_001400832.2
Hypothetical Protein
Aspergillus niger
5.9 × 10−47


g4788
|XP_001262485.1
Hypothetical Protein
Neosartorya fischeri
2.9 × 10−46


g5351
EGR44655.1
Terpene Synthase
Trichoderma reesei
8.9 × 10−166


g5351
XP_002149866.1
Terpene Synthase
Penicillium marneffei
3.2 × 10−130


g6654
XP_002390417.1
Hypothetical Protein
Moniliophthora perniciosa
5.0 × 10−72


g6654
XP_001550978.1
Hypothetical Protein
Botryotinia fuckeliana
1.6 × 10−41


g9560
2E4O|A
Terpene Synthase (Sesqui-)
Aspergillus terreus
6.2 × 10−125


g9560
Q03471.1
Terpene Synthase (Sesqui-)
Penicillium rocquertfortii
1.9 × 10−100


g11102
EGR47124.1
Hypothetical Protein
Trichoderma reesei
8.0 × 10−51


g11102
EFQ28833.1
Hypothetical Protein
Glomerella graminicola
8.9 × 10−40





*Evalue represents sequence similarity between amino acid gene sequences of Nodulisporium and sequences within the Non-redundant Protein Database (NCBI), generated via a BLAST-P comparison






It is widely regarded genes regulating fungal secondary metabolism are commonly found in clusters, including those regulating terpene synthesis (e.g. gibberellin—7 genes, trichothecene—11 genes). All of the putative terpene synthases identified in Nodulisporium were located on large contigs (>15247 bp) enabling flanking genes to be comprehensively evaluated. The putative function of common flanking genes included cytochrome p450 oxidases (add oxygen functional groups), transporters (transmembrane proteins for antibiotic resistance) and protein kinases (gene regulation). For instance, g5351 is located alongside a putative p450, a transporter and a polyprenyl synthase (precursor compounds to terpenes). Similarly g4788 and 6654 are located on the same contig, 3 genes apart. One of the genes separating the putative terpene synthases is a putative transporter. These flanking genes provide further evidence to suggest that the putative terpene synthases are regulating mono- and sesquiterpene synthesis.
REFERENCES


    1. Edgar R C (2004) MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Research 32, 1792-1797.
    2. Felsenstein J (1985) Confidence limits on phylogenies: An approach using the bootstrap. Evolution 39:783-791.
    3. Kimura M. (1980). A simple method for estimating evolutionary rates of base substitution through comparative studies of nucleotide sequences. Journal of Molecular Evolution. 16:111-120.
    4. Marchler-Bauer A, Anderson J, Chitsaz F, Derbyshire M, DeWeese-Scott C, Fong J, Geer L, Geer R, Gonzales N, Gwadz M, He S, Hurwitz D, Jackson J, Ke Z, Lanczycki C, Liebert C, Liu C, Lu F, Lu S, Marchler G, Mullokandov M, Song J, Tasneem A, Thanki N, Yamashita R, Zhang D, Zhang N and Bryant S (2009) CDD: specific functional annotation with the Conserved Domain Database. Nucleic Acids Research 37, D205-10.
    5. Nei M and Kumar S (2000) Molecular Evolution and Phylogenetics. Oxford University Press, New York.
    6. Payne R W, Murray D A, Harding S A, Baird D B. and Soutar D M. (2008). GenStat for Windows (11th Edition) Introduction. VSN International, Hemel Hempstead.
    7. Pruitt K D, Tatusova T and Maglott D R (2007) NCBI reference sequences (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins. Nucleic Acids Research 35, D61-D65.
    8. Saitou N, Nei M. (1987). The Neighbor-joining Method: A New Method for Reconstructing Phylogenetic Trees. Molecular Biology and Evolution. 4:406-425.
    9. Stanke M, Keller O, Gunduz I, Hayes A, Waack S and Morgerstern B (2006) AUGUSTUS: ab initio prediction of alternative transcripts. Nucleic Acids Research 34, W435-W439.
    10. Tamura K, Dudley J, Nei M. and Kumar S. (2007) MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0. Molecular Biology and Evolution. 24:1596-1599.
    11. van Zijll de Jong E, Guthridge K M, Spangenberg G C and Forster J W (2003). Development and characterization of EST-derived simple sequence repeats (SSR) for pasture grass endophytes. Genome. 46:277-290.
    12. White T J, Bruns T Lee S, and Taylor J. 1990. Amplification and direct sequencing of fungal ribosomal RNA genes for phylogenetics, p. 315-322. In M. A. Innis, D. H. Gelfand, J. J. Sninsky, and T. J. White (ed.), PCR protocols: a guide to methods and applications. Academic Press, Inc., New York, N.Y.

## Claims

1. A genetic construct including a nucleic acid encoding a terpene synthase, said terpene synthase-encoding nucleic acid including a nucleic acid sequence selected from the group consisting of SEQ ID NOS: 11 to 18 and functionally active terpene synthase-encoding variants thereof having at least 90% identity to one of SEQ ID NOS: 11 to 18.

2. The genetic construct according to claim 1, wherein said functionally active variants have at least 95% identity to one of SEQ ID NOS: 11 to 18.

3. The genetic construct according to claim 1, wherein said functionally active variants have at least 98% identity to one of SEQ ID NOS: 11 to 18.

4. A genetic construct including a nucleic acid encoding a terpene synthase, wherein said terpene synthase-encoding nucleic acid includes a nucleic acid sequence selected from the group consisting of SEQ ID NOS: 11 to 18.

5. The genetic construct according to claim 4, wherein said terpene synthase encoding nucleic acid includes the nucleic acid sequence of SEQ ID NO: 14.

6. A fungus transformed with the genetic construct according to claim 1.

7. The fungus according to claim 6, wherein said fungus is selected from the group consisting of Nodulisporiumi spp. and Ascocoryne spp.

8. The fungus according to claim 6, wherein said fungus consists of a Nodulisporiumi spp. that produces at least one volatile terpenoid compound when grown in potato dextrose culture medium.

9. The fungus according to claim 6, wherein said fungus consists of an Ascocoryne spp. that produces at least organic compound that is liquid at room temperature when grown in potato dextrose culture medium.

10. The fungus according to claim 7, wherein said fungus is selected from the group consisting of Dandenong Ranges isolate 1, Yana Ranges isolates 7, 10, 11, 12, 13 and 15 and Otway Ranges isolates 1, 3, 4 and 5.

11. A plant inoculated with the fungus according to claim 6, said plant comprising a fungus-free host plant stably infected with said fungus.

12. A method of producing an organic compound, said method including growing the fungus according to claim 6 in a culture medium under conditions suitable to produce said organic compound, and recovering the organic compound produced by the fungus.

13. The method according to claim 12, wherein said culture medium includes a source of carbohydrates, and wherein said fungus is grown under aerobic or anaerobic conditions.

14. The method according to claim 13, wherein said culture medium includes potato dextrose.

15. The method according to claim 12, wherein said organic compound is recovered from fungal cells, from the culture medium, or from air space associated with the culture medium or fungus.

16. The method according to claim 12, wherein said organic compound is a terpene selected from the group consisting of monoterpenes and sesquiterpenes.

17. The method according to claim 16, wherein said organic compound is selected from the group consisting of α-Thujene, β-Sabinene, β-Myrcene, α-Phellendrene, α-Terpinene, p-Cymene, (R)-(+)-Limonene, Eucalyptol, α-Ocimene, β-Ocimene, γ-Terpinene, α-Terpinolene, Allo-Ocimene, (−)-Terpinen-4-ol, α-Terpineol, 2H-pyran,tetrahydro-2-(propan-2-ylidene)-5-methoxy, 2H-pyran,tetrahydro-2-isopropyl-5-methoxy, 3-Cyclohexene-1-acetaldehyde,4-methyl-α-methylene-, 1-Cyclohexene-1-carboxaldehyde,4-(1-methylethenyl)-, p-Mentha-1,4(8)-dien-3-one (isomers), Bicyclo[2.2.2]octan-1-ol,4-ethyl, β-Elemene, α-Guajene, Bicyclo[5.3.0]decane,2 methylene-5-(1-methylvinyl)-8-methyl and 6-Guaijene, and derivatives and salts thereof.