Genetic Analyses of ENDOTHIA PARASITICA: Linkage Data for Four Single Genes and Three Vegetative Compatibility Types

Vegetative incompatibility loci with dedicated roles in allorecognition restrict mycovirus transmission in chestnut blight fungus

Vegetative incompatibility (vic), a form of nonself allorecognition, operates widely in filamentous fungi and restricts transmission of virulence-attenuating hypoviruses in the chestnut blight fungus Cryphonectria parasitica. We report here the use of a polymorphism-based comparative genomics approach to complete the molecular identification of the genetically defined C. parasitica vic loci with the identification of vic1 and vic3. The vic1 locus in the C. parasitica reference strain EP155 consists of a polymorphic HET-domain-containing 771-aa ORF designated vic1a-2, which shares 91% identity with the corresponding vic1a-1 allele, and a small (172 aa) idiomorphic DUF1909-domain-containing ORF designated vic1b-2 that is absent at the vic1-1 locus. Gene disruption of either vic1a-2 or vic1b-2 in strain EP155 eliminated restrictions on virus transmission when paired with a vic1 heteroallelic strain; however, only disruption of vic1a-2 abolished the incompatible programmed cell death (PCD) reaction. The vic3 locus of strain EP155 contains two polymorphic ORFs of 599 aa (vic3a-1) and 102 aa (vic3b-1) that shared 46 and 85% aa identity with the corresponding vic3a-2 and vic3b-2 alleles, respectively. Disruption of either vic3a-1 or vic3b-1 resulted in increased virus transmission. However, elimination of PCD required disruption of both vic3a and vic3b. Additional allelic heterogeneity included a sequence inversion and a 8.5-kb insertion containing a LTR retrotransposon sequence and an adjacent HET-domain gene at the vic1 locus and a 7.7-kb sequence deletion associated with a nonfunctional, pseudo vic locus. Combined gene disruption studies formally confirmed restriction of mycovirus transmission by five C. parasitica vic loci and suggested dedicated roles in allorecognition. The relevance of these results to the acquisition and maintenance of vic genes and the potential for manipulation of vic alleles for enhanced mycovirus transmission are discussed.

Δ(1)-pyrroline-5-carboxylate/glutamate biogenesis is required for fungal virulence and sporulation

Proline dehydrogenase (Prodh) and Δ¹-pyrroline-5-carboxylate dehydrogenase (P5Cdh) are two key enzymes in the cellular biogenesis of glutamate. Recombinant Prodh and P5Cdh proteins of the chestnut blight fungus Cryphonectria parasitica were investigated and showed activity in in vitro assays. Additionally, the C. parasitica Prodh and P5Cdh genes were able to complement the Saccharomyces cerevisiae put1 and put2 null mutants, respectively, to allow these proline auxotrophic yeast mutants to grow on media with proline as the sole source of nitrogen. Deletion of the Prodh gene in C. parasitica resulted in hypovirulence and a lower level of sporulation, whereas deletion of P5Cdh resulted in hypovirulence though no effect on sporulation; both Δprodh and Δp5cdh mutants were unable to grow on minimal medium with proline as the sole nitrogen source. In a wild-type strain, the intracellular level of proline and the activity of Prodh and P5Cdh increased after supplementation of exogenous proline, though the intracellular Δ¹-pyrroline-5-carboxylate (P5C) content remained unchanged. Prodh and P5Cdh were both transcriptionally down-regulated in cells infected with hypovirus. The disruption of other genes with products involved in the conversion of arginine to ornithine, ornithine and glutamate to P5C, and P5C to proline in the cytosol did not appear to affect virulence; however, asexual sporulation was reduced in the Δpro1 and Δpro2 mutants. Taken together, our results showed that Prodh, P5Cdh and related mitochondrial functions are essential for virulence and that proline/glutamate pathway components may represent down-stream targets of hypovirus regulation in C. parasitica.

Hypovirus molecular biology: from Koch's postulates to host self-recognition genes that restrict virus transmission

The idea that viruses can be used to control fungal diseases has been a driving force in mycovirus research since the earliest days. Viruses in the family Hypoviridae associated with reduced virulence (hypovirulence) of the chestnut blight fungus, Cryphonectria parasitica, have held a prominent place in this research. This has been due in part to the severity of the chestnut blight epidemics in North America and Europe and early reports of hypovirulence-mediated mitigation of disease in European forests and successful application for control of chestnut blight in chestnut orchards. A more recent contributing factor has been the development of a hypovirus/C. parasitica experimental system that has overcome many of the challenges associated with mycovirus research, stemming primarily from the exclusive intracellular lifestyle shared by all mycoviruses. This chapter will focus on hypovirus molecular biology with an emphasis on the development of the hypovirus/C. parasitica experimental system and its contributions to fundamental and practical advances in mycovirology and the broader understanding of virus-host interactions and fungal pathogenesis.

A conceptual framework for restoration of threatened plants: the effective model of American chestnut (Castanea dentata) reintroduction

We propose a conceptual framework for restoration of threatened plant species that encourages integration of technological, ecological, and social spheres. A sphere encompasses ideas relevant to restoration and the people working within similar areas of influence or expertise. Increased capacity within a sphere and a higher degree of coalescing among spheres predict a greater probability of successful restoration. We illustrate this with Castanea dentata, a foundation forest tree in North America that was annihilated by an introduced pathogen; the species is a model that effectively merges biotechnology, reintroduction biology, and restoration ecology. Because of C. dentata's ecological and social importance, scientists have aggressively pursued blight resistance through various approaches. We summarize recent advancements in tree breeding and biotechnology that have emerged from C. dentata research, and describe their potential to bring new tools to bear on socio-ecological restoration problems. Successful reintroduction of C. dentata will also depend upon an enhanced understanding of its ecology within contemporary forests. We identify a critical need for a deeper understanding of societal influences that may affect setting and achieving realistic restoration goals. Castanea dentata may serve as an important model to inform reintroduction of threatened plant species in general and foundation forest trees in particular.

Molecular characterization of vegetative incompatibility genes that restrict hypovirus transmission in the chestnut blight fungus Cryphonectria parasitica

Genetic nonself recognition systems such as vegetative incompatibility operate in many filamentous fungi to regulate hyphal fusion between genetically dissimilar individuals and to restrict the spread of virulence-attenuating mycoviruses that have potential for biological control of pathogenic fungi. We report here the use of a comparative genomics approach to identify seven candidate polymorphic genes associated with four vegetative incompatibility (vic) loci of the chestnut blight fungus Cryphonectria parasitica. Disruption of candidate alleles in one of two strains that were heteroallelic at vic2, vic6, or vic7 resulted in enhanced virus transmission, but did not prevent barrage formation associated with mycelial incompatibility. Detailed characterization of the vic6 locus revealed the involvement of nonallelic interactions between two tightly linked genes in barrage formation, heterokaryon formation, and asymmetric, gene-specific influences on virus transmission. The combined results establish molecular identities of genes associated with four C. parasitica vic loci and provide insights into how these recognition factors interact to trigger incompatibility and restrict virus transmission.

Characterization of a Regional Population of Fusarium oxysporum f. sp. niveum by Race, Cross Pathogenicity, and Vegetative Compatibility

ABSTRACT Eighty-eight isolates of Fusarium oxysporum f. sp. niveum, collected from wilted watermelon plants and infested soil in Maryland and Dela-ware, were characterized by cross pathogenicity to muskmelon, race, and vegetative compatibility. Four isolates (4.5%) were moderately pathogenic to >/=2 of 18 muskmelon cultivars in a greenhouse test, and one representative isolate also was slightly pathogenic in field microplots. The four isolates all were designated as race 2, and were in vegetative compatibility group (VCG) 0082. Of the 74 isolates to which a VCG could be assigned, 41 were in VCG 0080, the VCG distributed most widely; 27 were in VCG 0082, and were distributed in half of the 20 watermelon fields surveyed; and 6 were in the newly described VCG 0083, and were restricted to three fields. Among the isolates in VCG 0080, 8 were designated as race 0, 21 as race 1, and 12 as race 2. Of the isolates in VCG 0082, 6 were designated as race 0, 11 as race 1, and 10 as race 2. All isolates in VCG 0083 were designated as race 2. Isolates from more than one race within the same VCG or isolates from more than one VCG were recovered from single plants and fields. No differences in aggressiveness on differential watermelon cultivars were observed among isolates from different VCGs of the same race. A diverse association between virulence and VCG throughout the Mid-Atlantic region suggests that the pathotypes of F. oxysporum f. sp. niveum may be of local origin or at least long existent in the region.

Markers linked to vegetative incompatibility (vic) genes and a region of high heterogeneity and reduced recombination near the mating type locus (MAT) in Cryphonectria parasitica

To find markers linked to vegetative incompatibility (vic) genes in the chestnut blight fungus, Cryphonectria parasitica, we constructed a preliminary linkage map. In general, this map is characterized by low levels of polymorphism, as evident from the more than 24 linkage groups observed, compared to seven expected from electrophoretic karyotyping. Nonetheless, we found markers closely linked to two vic genes (vic1 and vic2) making them candidates for positional cloning. Two markers were found to be linked to vic2: one cosegregated with vic2, i.e., it is 0.0 cM from vic2, the other was at a distance of 4.5 cM; a single marker was found 4.0 cM from vic1. The closest markers linked to three other vic genes (vic4, vic6, and vic7) were >15 cM away; additional markers are needed before efficient positional cloning of these three vic genes can be realized. In contrast to the low levels of polymorphism observed across most of the C. parasitica genome, the linkage group containing the MAT locus appears to harbor an extremely high level of RAPD heterogeneity and reduced recombination. Markers within this highly heterogeneous region are in linkage disequilibrium in some natural populations; however, recombination is clearly evident between this region and the MAT locus.

Mating-type heterokaryosis and selfing in Cryphonectria parasitica

Selfing in the chestnut blight fungus, Cryphonectria parasitica, occurs by two different genetic mechanisms. Most self-fertile isolates of C. parasitica are heterokaryotic for mating type, and the progeny from selfing segregate for mating type. Further, we resolved mating-type (MAT) heterokaryons into homokaryons of both mating types by isolating uninucleate asexual spores (conidia). However, because ascospore progeny, with rare exceptions, are not MAT heterokaryons, C. parasitica must lack a regular mechanism to maintain heterokaryosis by selfing. We hypothesize that heterokaryon formation may occur either because of recurrent biparental inbreeding, or by mating-type switching, possibly one involving some kind of parasexual process. The second mechanism found for selfing in C. parasitica occurred less frequently. Three single-conidial isolates (MAT-1 and MAT-2) selfed and produced progeny that did not segregate for mating type. It is currently not known if meiosis occurs during ascospore formation by this mechanism.

Characterization of South African Cryphonectria cubensis Isolates Infected with a C. parasitica Hypovirus

ABSTRACT Cryphonectria cubensis is the causal agent of a serious canker disease of Eucalyptus spp. in tropical and subtropical parts of the world. In this study, a South African C. cubensis isolate was transfected by electroporation with a synthetic RNA transcript corresponding to the full-length coding strand of the C. parasitica hypovirus (CHV1-EP713). Hypovirus infection resulted in pronounced morphological changes that included a striking increase in bright yellow-orange pigment production, a reduction in mycelial growth rate, and reduced sporulation. Greenhouse studies revealed that the virus-containing strain was significantly less virulent than the original virulent C. cubensis isolate. Although the hypovirus was not transmitted through conidia produced by infected C. cubensis, the virus was readily transmitted via hyphal anastomosis to C. cubensis isolates representing a broad range of vegetative compatibility groups. These results suggest that vegetative incompatibility may not pose a strong barrier against virus transmission in South African isolates of C. cubensis and that hypovirus-mediated biological control could provide opportunities to reduce the impact of Cryphonectria canker in South Africa.

Genetics of vegetative incompatibility in cryphonectria parasitica

Vegetative incompatibility in the chestnut blight fungus, Cryphonectria parasitica, in Europe is controlled by six unlinked vic loci, each with two alleles. Four previously identified vic loci (vic1, vic2, vic3, and vic4) were polymorphic in European vegetative compatibility (vc) types. Two new loci, vic6 and vic7, also were identified among European vc types. In one cross, vic genes segregated independently at five loci, and 194 progeny were assigned to 32 vc types; none of these loci were linked. A total of 64 vc types were identified from all crosses. All 64 genotypes possible from six vic loci, each with two alleles (2(6) = 64), were identified and assigned to vc types. Based on our model, vc types v-c 5 and v-c 10, which had been used in previous genetic studies, differ by only five vic genes. Future studies of vc types in C. parasitica can use knowledge of vic genotypes for analysis of population genetic structure based on vic allele frequencies and to determine the effect of each vic gene on virus transmission between vc types.

Genetic heterogeneity of leucostoma species in michigan peach orchards

ABSTRACT The pathogens causing perennial canker of peach, Leucostoma spp., were characterized in Michigan orchards to identify which species and subgroups (cryptic species) were prevalent on a highly susceptible peach cultivar, Loring, and a less susceptible cultivar, Redhaven. Four hundred and three strains of Leucostoma were isolated from cankers in three southwest Michigan orchards where 'Loring' occurred adjacent to 'Redhaven' in side-by-side plots. Based on colony morphology and small nuclear rDNA size polymorphisms, three cryptic species were detected; 89% of the isolates were identified as L. persoonii phenetic group 1, 10% were L. cincta group 4, and 1% were L. persoonii group 2. Pathogen profiles differed significantly between cankers on small branches of 'Loring' and 'Redhaven', and between cankers on small branches and trunks. Of 1,232 random pairings among isolates of L. persoonii group 1, 95% were vegetatively incompatible. A minimum of 11 and a maximum of 17 maternal lines were identified based upon mitochondrial DNA restriction fragment length polymorphisms among 69 isolates of L. persoonii group 1 from one split-cultivar block of 72 trees. Vegetative compatibility loci were randomly associated with maternal lines. Evidence of clonality was absent in L. persoonii group 1, as no correlation occurred between these two sets of independent genetic markers and no genotype was over-represented. The number of cryptic species, the number of maternal lines, and the frequency of incompatibility within maternal lines indicate that considerable genetic variation exists within the Leucostoma populations in Michigan peach orchards, and that sexual recombination is common.

Comparison of RAPD technique and somatic incompatibility tests for the identification of Phlebiopsis gigantea strains

Somatic incompatibility assays and random amplified polymorphic DNA (RAPD) analysis were assessed and compared for use in monitoring the survival of introduced strains of Phlebiopsis gigantea, a fungal biocontrol agent used against Heterobasidion annosum root rot. Overall there was concordance between the two methods. All incompatible strains exhibited different RAPD profiles whilst compatible ones, with two exceptions, had the same RAPD profile. Somatic incompatibility tests and RAPD profiles generated by three primers, from which 11 markers were retained, could distinguish field-tested strains from among 60 strains from a population collected in Quebec and Ontario. Furthermore, both methods allowed us to clearly demonstrate the presence of inoculated strains 1 year after treatment. The combined use of these techniques provides a valuable tool for discriminating between different P. gigantea strains and conducting epidemiological studies. Key words: Heterobasidion annosum, vegetative incompatibility, random amplified polymorphic DNA, biological control, Pinus resinosa.

Variation in Pathogenicity and Genetic Structure in the Eutypa lata Population of a Single Vineyard

ABSTRACT Fifty-five isolates of Eutypa lata were collected in 1994 from a single vineyard, each from a different vine that showed either shoot and foliar symptoms of Eutypa dieback or only abnormalities during the period of 1990 to 1994. These isolates showed a large variation in pathogenicity after inoculation on cuttings in the greenhouse. Variability also was observed for cultural traits and radial growth rate on potato dextrose agar (PDA) medium, but no relation was found between these characteristics and pathogenicity. The isolates were paired on PDA medium, and a barrage reaction was observed for all pairings, indicating the isolates were vegetatively incompatible. Thirty-two random amplified polymorphic DNA (RAPD) markers were used to study the genetic relatedness of the isolates and the genetic structure of the population. Fifty-five different RAPD patterns were observed, confirming the genetic uniqueness of each isolate. Gametic disequilibrium values were calculated among all pairs of the 32 putative RAPD loci, and only one value was significant. Unweighted pair-group method with arithmetic averages analysis of distance data, as well as a heterogeneity statistic (Fst), did not indicate any population substructure. The results strongly suggest that isolates originated from a random-mating population and that the disease was propagated in this vineyard by ascospores produced from diverse outside sources. Southern hybridization performed for five markers indicated that the two-allele assumption made to interpret RAPD data may be violated for markers that are similar in size. However, the exclusion of such markers did not change the conclusions of the study.

Population biology of the chestnut blight fungus,Cryphonectria parasitica

Interest in the population biology of the chestnut blight fungus Cryphonectria parasitica has been motivated largely by the potential for biological control of chestnut blight with fungal viruses that cause hypovirulence. Earlier studies gave valuable insights into the correlation between diversity of vegetative compatibility groups and transmission of hypovirulence viruses. However, inferences about evolutionary processes affecting populations were not possible because vegetative compatibility groups are not genetically defined. Using restriction fragment length polymorphism markers, however, progress has been made in studying the origin of C. parasitica in North America, gene flow among populations, dispersal within populations, and recombination and the mating system. Cryphonectria parasitica populations in North America are genetically more similar to populations in Japan than in China, which is consistent with previous speculations that this fungus was introduced from Japan. Populations in China and Japan are quite different, suggesting little or no gene flow between these areas. Restricted gene flow and genetic drift are probably the dominant evolutionary forces shaping North American populations, with approximately 20% of gene diversity due to differences among populations (GST = 0.20). Two populations of C. parasitica in Michigan and one population in Italy are primarily clonal in structure. In contrast, sexual reproduction appears to be common in populations in eastern North America, although most of these populations deviate significantly from random mating. Deviations from random mating are most likely due to self-fertilization (uniparental inbreeding), restricted dispersal of male gametes, and mating between individuals that are more closely related genetically than would be expected by chance (biparental inbreeding). Aggregations of similar genotypes in space suggest that populations of C. parasitica may be structured into genetic neighborhoods by restricted dispersal. Future research efforts in this system will explore isolation by distance and address questions of hypovirulence virus coevolution with its fungal host. Key words: Cryphonectria parasitica, Endothia parasitica, chestnut blight, genetic neighbourhoods, inbreeding.

Spatial analysis of nuclear and mitochondrial RFLP genotypes in populations of the chestnut blight fungus, Cryphonectria parasitica

Spatial structure of both nuclear and mitochondrial RFLPs were studied in several populations of the chestnut blight fungus, Cryphonectria parasitica, using a variety of spatial autocorrelation tests designed to detect nonrandom patterns. Fungal individuals were sampled from cankers on infected chestnut trees, and the location of each tree was mapped. Single-locus nuclear RFLPs, nuclear fingerprints, and mitochondrial DNA haplotypes were determined for each individual. Individuals with the same DNA fingerprint genotypes occurred closer together than would be expected at random in four of the five plots, while mitochondrial DNA haplotypes were aggregated in all five plots. Genetic distances between individuals, expressed as one minus the proportion of shared restriction fragment size classes for fingerprints and mitochondrial haplotypes, were significantly correlated with Euclidean distances between individuals in four of the five populations, but these correlations were very weak (r < 0.18). The same DNA fingerprint and single-copy nuclear RFLP alleles occurred on the same trees or immediately neighbouring trees more often than would be expected at random. Most of the aggregation for all three genetic markers occurred among individuals within the same cluster of chestnut stems or on neighbouring trees. Lack of spatial autocorrelation in one population was probably due to sampling on a larger scale that was too coarse to detect any patterns. Significant aggregation of genotypes in C. parasitica is most likely caused by some degree of restricted dispersal within populations. The implications of restricted dispersal are discussed in relation to the breeding system and isolation by distance in populations of C. parasitica.

Vegetative incompatibility in filamentous fungi: het genes begin to talk

Somatic or vegetative incompatibility is widespread in filamentous fungi. It prevents the coexistence of genetically different nuclei within a common cytoplasm. Cloning the het genes that control this process has been achieved in several species. This has provided essential information on the function of the genes in the biology of fungi and has also led to the formulation of models that may explain similar phenomena in other organisms.

Isolation and characterization of a virus-resistant mutant of Cryphonectria parasitica

Hypovirulent strain NB58 of Cryphonectria parasitica contains a dsRNA virus with a genome size of approximately 12.5 kb. Although NB58 is very stable in culture, a phenotypically-distinct sector arose which was found to be dsRNA-free. Attempts to infect the mutant strain, termed NB58F, by pairing with the parent strain (NB58) or other conversion-compatible, virus-containing strains have been unsuccessful. DNA fingerprint analysis showed that NB58, NB58F, and a representative dsRNA-free single-conidial isolate of NB58 termed NB58-19, were isogenic. The mutant culture was phenotypically stable, and all single-conidial progeny had the NB58F morphology. NB58F was intermediate between NB58 and NB58-19 in laccase production and virulence. Pigmentation and sporulation of NB58F, however, were reduced to near the level of NB58. In mating studies, NB58F functioned only as the male in sexual crosses. The mutant phenotype (F) predominated by a ratio of 5:2 among the ascospore progeny of F-type x wild-type crosses. These data suggest the lesion is nuclear and may be associated with a chromosomal abnormality. Attempts to infect the NB58F-type ascospore progeny failed, whereas the wild-type progeny were successfully infected with strains compatible with one or the other parent at a frequency of about 34%. Hyphal anastomosis and movement of cytoplasmic material occurred when NB58F was paired with a compatible strain, suggesting that the lesion is involved in viral maintenance as opposed to initial virus infection. NB58F represents the first virus-resistant isolate of C. parasitica to be described.

Biological control of chestnut blight: an example of virus-mediated attenuation of fungal pathogenesis

Environmental concerns have focused attention on natural forms of disease control as potentially safe and effective alternatives to chemical pesticides. This has led to increased efforts to develop control strategies that rely on natural predators and parasites or that involve genetically engineered microbial pest control agents. This review deals with a natural form of biological control in which the virulence of a fungal pathogen is attenuated by an endogenous viral RNA genetic element: the phenomenon of transmissible hypovirulence in the chestnut blight fungus, Cryphonectria parasitica. Recent progress in the molecular characterization of a hypovirulence-associated viral RNA has provided an emerging view of the genetic organization and basic expression strategy of this class of genetic elements. Several lines of evidence now suggest that specific hypovirulence-associated virus-encoded gene products selectively modulate the expression of subsets of fungal genes and the activity of specific regulatory pathways. The construction of an infectious cDNA clone of a hypovirulence-associated viral RNA represents a major advancement that provides exciting new opportunities for examining the molecular basis of transmissible hypovirulence and for engineering hypovirulent strains for improved biocontrol. These developments have significantly improved the prospects of using this system to identify molecular determinants of virulence and elucidate signal transduction pathways involved in pathogenic responses. In addition, novel approaches are now available for extending the application of transmissible hypovirulence for management of chestnut blight and possibly other fungal diseases.

Hypovirulence of chestnut blight fungus conferred by an infectious viral cDNA

Strains of the chestnut blight fungus Cryphonectria parasitica that contain viral double-stranded RNAs often exhibit reduced virulence. Such hypovirulent strains act as biocontrol agents by virtue of their ability to convert virulent strains to hypovirulence after anastomosis. Transformation of virulent C. parasitica strains with a full-length complementary DNA copy of a hypovirulence-associated viral RNA conferred the complete hypovirulence phenotype. Cytoplasmic double-stranded RNA was resurrected from the chromosomally integrated complementary DNA copy and was able to convert compatible virulent strains to hypovirulence. These results establish viral double-stranded RNA as the casual agent of hypovirulence and demonstrate the feasibility of engineering hypovirulent fungal strains.