Correction to: A comparative genomic analysis of putative pathogenicity genes in the host-specific sibling species Colletotrichum graminicola and Colletotrichum sublineola.

Following the publication of this article [1], the authors informed us of the following error.

A comparative genomic analysis of putative pathogenicity genes in the host-specific sibling species Colletotrichum graminicola and Colletotrichum sublineola.

BACKGROUND: Colletotrichum graminicola and C. sublineola cause anthracnose leaf and stalk diseases of maize and sorghum, respectively. In spite of their close evolutionary relationship, the two species are completely host-specific. Host specificity is often attributed to pathogen virulence factors, including specialized secondary metabolites (SSM), and small-secreted protein (SSP) effectors. Genes relevant to these categories were manually annotated in two co-occurring, contemporaneous strains of C. graminicola and C. sublineola. A comparative genomic and phylogenetic analysis was performed to address the evolutionary relationships among these and other divergent gene families in the two strains. RESULTS: Inoculation of maize with C. sublineola, or of sorghum with C. graminicola, resulted in rapid plant cell death at, or just after, the point of penetration. The two fungal genomes were very similar. More than 50% of the assemblies could be directly aligned, and more than 80% of the gene models were syntenous. More than 90% of the predicted proteins had orthologs in both species. Genes lacking orthologs in the other species (non-conserved genes) included many predicted to encode SSM-associated proteins and SSPs. Other common groups of non-conserved proteins included transporters, transcription factors, and CAZymes. Only 32 SSP genes appeared to be specific to C. graminicola, and 21 to C. sublineola. None of the SSM-associated genes were lineage-specific. Two different strains of C. graminicola, and three strains of C. sublineola, differed in no more than 1% percent of gene sequences from one another. CONCLUSIONS: Efficient non-host recognition of C. sublineola by maize, and of C. graminicola by sorghum, was observed in epidermal cells as a rapid deployment of visible resistance responses and plant cell death. Numerous non-conserved SSP and SSM-associated predicted proteins that could play a role in this non-host recognition were identified. Additional categories of genes that were also highly divergent suggested an important role for co-evolutionary adaptation to specific host environmental factors, in addition to aspects of initial recognition, in host specificity. This work provides a foundation for future functional studies aimed at clarifying the roles of these proteins, and the possibility of manipulating them to improve management of these two economically important diseases.

A novel test for host-symbiont codivergence indicates ancient origin of fungal endophytes in grasses.

Significant phylogenetic codivergence between plant or animal hosts (H) and their symbionts or parasites (P) indicates the importance of their interactions on evolutionary time scales. However, valid and realistic methods to test for codivergence are not fully developed. One of the systems where possible codivergence has been of interest involves the large subfamily of temperate grasses (Pooideae) and their endophytic fungi (epichloae). These widespread symbioses often help protect host plants from herbivory and stresses and affect species diversity and food web structures. Here we introduce the MRCALink (most-recent-common-ancestor link) method and use it to investigate the possibility of grass-epichloë codivergence. MRCALink applied to ultrametric H and P trees identifies all corresponding nodes for pairwise comparisons of MRCA ages. The result is compared to the space of random H and P tree pairs estimated by a Monte Carlo method. Compared to tree reconciliation, the method is less dependent on tree topologies (which often can be misleading), and it crucially improves on phylogeny-independent methods such as ParaFit or the Mantel test by eliminating an extreme (but previously unrecognized) distortion of node-pair sampling. Analysis of 26 grass species-epichloë species symbioses did not reject random association of H and P MRCA ages. However, when five obvious host jumps were removed, the analysis significantly rejected random association and supported grass-endophyte codivergence. Interestingly, early cladogenesis events in the Pooideae corresponded to early cladogenesis events in epichloae, suggesting concomitant origins of this grass subfamily and its remarkable group of symbionts. We also applied our method to the well-known gopher-louse data set.

Prevalence of interspecific hybrids amongst asexual fungal endophytes of grasses.

Epichloë endophytes are fungal symbionts of grasses that span a continuum including asexual mutualists that are vertically transmitted, obligately sexual pathogens that are horizontally transmitted, and mixed-strategy symbionts with both mutualistic and pathogenic capabilities. Here we show that processes of genome evolution differ markedly for the different symbiont types. Genetic and phylogenetic analysis was conducted of a broad taxonomic, ecological and geographical sample of sexual and asexual isolates, in which were identified and sequenced alleles of genes for beta-tubulin (tub2) and translation elongation factor 1-alpha (tef1), and microsatellite alleles were identified by length polymorphisms. The majority of asexual isolates had two or three alleles of most loci, but every sexual isolate had only single alleles for each locus. Phylogenetic analysis of tub2 and tef1 indicated that in all instances of multiple alleles in an isolate, the alleles were derived from different sexual species. It is concluded that, whereas horizontally transmissible species had haploid genomes and speciation occurred cladistically, most of the strictly seedborne mutualists were interspecific hybrids with heteroploid (aneuploid or polyploid) genomes. Furthermore, the phylogenetic evidence indicated that, in at least some instances, hybridization followed rather than caused evolution of the strictly seedborne habit. Therefore, the abundance of hybrid species among grass endophytes, and their prevalence in many host populations suggests a selective advantage of hybridization for the mutualistic endophytes.

Necrotic Lesion Resistance Induced by Peronospora tabacina on Leaves of Nicotiana obtusifolia.

ABSTRACT Infection of Nicotiana obtusifolia plant introduction (PI) #555573 by the downy mildew pathogen Peronospora tabacina resulted in a compatible interaction, in which P. tabacina penetrated and freely colonized host leaf tissue. This interaction became incompatible 5 to 6 days later, with the appearance of necrotic lesions (NLs) and inhibition of pathogen growth and subsequent sporulation. NL development depended upon the presence of P. tabacina in host tissue, was not due to the effects of other microbes, and occurred co-incident in time with the pathogen's ability to produce asexual sporangia on a susceptible N. obtusifolia genotype. Inhibition of the necrotic response by CoCl(2) (a calcium channel blocker) and pathogen-induced transcription of a defense-related gene (PR-1a) suggested that necrosis was due to hypersensitive cell death in the host. In contrast, N. obtusifolia PI#555543 did not exhibit hypersensitivity upon infection by P. tabacina, but rather developed characteristic symptoms of tobacco blue mold disease: chlorotic lesions accompanied by abundant pathogen sporulation. Disease reactions scored on PI#555573 x PI#555543 F(2) progeny inoculated with P. tabacina sporangia indicated that the resistance phenotype was due to the action of a single gene from N. obtusifolia PI#555573, which we have named Rpt1. To date, Rpt1 is the only gene known to confer a hypersensitive response (HR) to P. tabacina infection in any species of Nicotiana. A survey of wild N. obtusifolia revealed that the HR to P. tabacina was expressed in the progeny of 7 of 21 (33%) plants collected in southern Arizona, but not in the progeny of plants originating from Death Valley National Park in California and the Big Bend National Park in west Texas.

Interspecific hybridization in plant-associated fungi and oomycetes: a review.

Fungi (kingdom Mycota) and oomycetes (kingdom Stramenopila, phylum Oomycota) are crucially important in the nutrient cycles of the world. Their interactions with plants sometimes benefit and sometimes act to the detriment of humans. Many fungi establish ecologically vital mutualisms, such as in mycorrhizal fungi that enhance nutrient acquisition, and endophytes that combat insects and other herbivores. Other fungi and many oomycetes are plant pathogens that devastate natural and agricultural populations of plant species. Studies of fungal and oomycete evolution were extraordinarily difficult until the advent of molecular phylogenetics. Over the past decade, researchers applying these new tools to fungi and oomycetes have made astounding new discoveries, among which is the potential for interspecific hybridization. Consequences of hybridization among pathogens include adaptation to new niches such as new host species, and increased or decreased virulence. Hybrid mutualists may also be better adapted to new hosts and can provide greater or more diverse benefits to host plants.

Interactions of Peronospora tabacina with Roots of Nicotiana spp. in Gnotobiotic Associations.

ABSTRACT Peronospora tabacina is an obligate plant pathogen that causes downy mildew disease on several species of Nicotiana, including N. tabacum (tobacco). The primary objective of this study was to use gnotobiotic associations to describe interactions between the pathogen and roots of either N. tabacum (cv. KY14) or N. repanda. We found that the pathogen was capable of moving systemically from shoots to roots of both host species and emerged from the root tissues as hyphae. We also demonstrated that root-associated hyphae were infectious on roots of nearby plants and resulted in new systemic infections. Following overnight darkness, sporulation of the pathogen was observed on infected roots exposed to air on both host species. We also found that within 2 months in culture, structures resembling resting stages of Peronospora tabacina were produced on hyphae emerging from roots of N. repanda but not N. tabacum. These findings appear relevant to both the epidemiology of the disease and to future studies of this and other downy mildew pathosystems.

Elimination of ergovaline from a grass-Neotyphodium endophyte symbiosis by genetic modification of the endophyte.

The fungal endophytes Neotyphodium lolii and Neotyphodium sp. Lp1 from perennial ryegrass (Lolium perenne), and related endophytes in other grasses, produce the ergopeptine toxin ergovaline, among other alkaloids, while also increasing plant fitness and resistance to biotic and abiotic stress. In the related fungus, Claviceps purpurea, the biosynthesis of ergopeptines requires the activities of two peptide synthetases, LPS1 and LPS2. A peptide synthetase gene hypothesized to be important for ergopeptine biosynthesis was identified in C. purpurea by its clustering with another ergot alkaloid biosynthetic gene, dmaW. Sequence analysis conducted independently of the research presented here indicates that this gene encodes LPS1 [Tudzynski, P., Holter, K., Correia, T., Arntz, C., Grammel, N. & Keller, U. (1999) Mol. Gen. Genet. 261, 133-141]. We have cloned a similar peptide synthetase gene from Neotyphodium lolii and inactivated it by gene knockout in Neotyphodium sp. Lp1. The resulting strain retained full compatibility with its perennial ryegrass host plant as assessed by immunoblotting of tillers and quantitative PCR. However, grass-endophyte associations containing the knockout strain did not produce detectable quantities of ergovaline as analyzed by HPLC with fluorescence detection. Disruption of this gene provides a means to manipulate the accumulation of ergovaline in endophyte-infected grasses for the purpose of determining the roles of ergovaline in endophyte-associated traits and, potentially, for ameliorating toxicoses in livestock.

Production of loline alkaloids by the grass endophyte, Neotyphodium uncinatum, in defined media.

Lolines (saturated 1-aminopyrrolizidines with an oxygen bridge) are insecticidal alkaloids produced in symbioses of certain Epichloë (anamorph-Neotyphodium) species (fungal endophytes) with grasses, particularly of the genera Lolium and Festuca. Prior to the present study, it was unknown whether lolines were of plant or fungal origin. Neotyphodium uncinatum, the common endophyte of meadow fescue (Lolium pratense=Festuca pratensis) produced loline, N-acetylnorloline, and N-formylloline when grown in the defined minimal media at pH 5.0-7.5, with both organic and inorganic nitrogen sources and sugars as carbon sources. In contrast, lolines were not detected in complex medium cultures. GC-MS and 13C NMR spectroscopic analyses confirmed the identity of the alkaloids isolated from the defined medium cultures. Lolines accumulated to ca. 700 mg/l (4 mM) in cultures with 16.7 mM sucrose and 15-30 mM asparagine, ornithine or urea. Kinetics of loline production and fungal growth were assessed in defined medium with 16.7 mM sucrose and 30 mM ornithine. The alkaloid production rate peaked after the onset of stationary phase, as is common for secondary metabolism in other microbes.

Epichloë festucae and related mutualistic symbionts of grasses.

Epichloë and Neotyphodium species (Ascomycota) are mutualistic symbionts (endophytes) of temperate grasses, to which they impart numerous and profound fitness benefits. Epichloë festucae, a common symbiont of Festuca, Lolium,and Koeleria spp., is a model for endophyte research that is amenable to Mendelian and molecular genetic analysis. Characteristics of E. festucae include: (i) production of the anti-insect alkaloids peramine and lolines, (ii) production of the anti-vertebrate alkaloids lolitrem B and ergovaline, (iii) efficient vertical transmission via host seeds, (iv) a mildly pathogenic state associated with the E. festucae sexual cycle, and (v) a clear role in enhancing survival of host plants. Genetic analysis of alkaloid production has recently begun. Also, physiological and ultrastructural studies suggest that signals communicated between E. festucae and host plants ensure an exquisitely balanced interaction to the mutual benefit of both partners. Several mutualistic Neotyphodium species are hybrids between E. festucae and other endophyte species.

Cocultures of Peronospora tabacina and Nicotiana Species to Study Host-Pathogen Interactions.

ABSTRACT Long-term cocultures of the tobacco blue mold pathogen, Peronospora tabacina, with Nicotiana tabacum and N. repanda callus were derived from infected host plant tissue. In this apparently contaminant-free system, sporulation occurred under similar conditions as in intact plants. Sporangia were collected from cocultures and used to complete Koch's postulates. The cocultures were grown under two light regimes. One consisted of 23 h of light followed by 1 h of darkness and the second comprised total darkness. Sporulation occurred frequently in the 23 h light-grown cocultures but resulted in production of abnormal sporangiophores and sporangia. Production of normal sporangiophores and sporangia was achieved by transferring light-grown cocultures to overnight darkness and resulted in necrosis of the callus. Cocultures of Peronospora tabacina with either host species, grown in total darkness, frequently sporulated with minimal necrosis over the course of 1 year. Thus, cocultures should prove useful as a source of Peronospora tabacina over extended periods of time at low risk of pathogen release, for studying the physiology of Peronospora tabacina- Nicotiana interactions, maintaining Peronospora tabacina lines for genetic studies, and providing a reliable source of axenic inoculum for research.

Contribution of fungal loline alkaloids to protection from aphids in a grass-endophyte mutualism.

Fungal endophytes provide grasses with enhanced protection from herbivory, drought, and pathogens. The loline alkaloids (saturated 1-aminopyrrolizidines with an oxygen bridge) are fungal metabolites often present in grasses with fungal endophytes of the genera Epichloë or Neotyphodium. We conducted a Mendelian genetic analysis to test for activity of lolines produced in plants against aphids feeding on those plants. Though most loline-producing endophytes are asexual, we found that a recently described sexual endophyte, Epichloë festucae, had heritable variation for loline alkaloid expression (Lol+) or nonexpression (Lol-). By analyzing segregation of these phenotypes and of linked DNA polymorphisms in crosses, we identified a single genetic locus controlling loline alkaloid expression in those E. festucae parents. We then tested segregating Lol+ and Lol- full-sibling fungal progeny for their ability to protect host plants from two aphid species, and observed that alkaloid expression cosegregated with activity against these insects. The in planta loline alkaloid levels correlated with levels of anti-aphid activity. These results suggested a key role of the loline alkaloids in protection of host plants from certain aphids, and represent, to our knowledge, the first Mendelian analysis demonstrating how a fungal factor contributes protection to plant-fungus mutualism.

Endophytic fungi in indigenous Australasian grasses associated with toxicity to livestock.

Grazing of Echinopogon spp. by livestock in Australia has caused symptoms similar to those of perennial ryegrass staggers. We observed an endophytic fungus in the intercellular spaces of the leaves and seeds of New Zealand and Australian specimens of Echinopogon ovatus. Culture of surface-sterilized seeds from New Zealand specimens yielded a slow-growing fungus. An examination in which immunoblotting and an enzyme-linked immunosorbent assay (ELISA) were used indicated that E. ovatus plants from Australia and New Zealand were infected with fungi serologically related to Neotyphodium lolii (the endophyte of perennial ryegrass) and other Epichloe and Neotyphodium spp. endophytic in pooid grasses. No lolitrems (the indole-diterpenoids implicated as the causative agents of perennial ryegrass staggers), peramine analogs, or ergot alkaloids were detected in the infected specimens by high-performance liquid chromatography or ELISA. However, in endophyte-infected E. ovatus plants from New Zealand, analogs of the indole-diterpenoid paxilline (thought to be a biosynthetic precursor of the lolitrems and related tremorgens) were detected by ELISA, and N-formylloline was detected by gas chromatography. Endophyte-free specimens of New Zealand E. ovatus did not contain detectable paxilline analogs or lolines and were more palatable than infected specimens to adults of the pasture pest Listronotus bonariensis (Argentine stem weevil). Hyphae similar to those of the E. ovatus endophyte were also found in herbarium specimens of Echinopogon nutans var. major, Echinopogon intermedius, Echinopogon caespitosus, and Echinopogon cheeli. This appears to be the first time that an endophytic Neotyphodium species has been identified in grasses endemic to New Zealand or Australia.

Genetics of Host Specificity in Epichloë typhina.

ABSTRACT Epichloë typhina perennially and systemically infects grass plants, causing choke disease in which maturation of host inflorescences is suppressed. In seedling-inoculation tests, isolate E8 from perennial ryegrass established and maintained infection in this host but not in orchardgrass. In contrast, isolates E469, E2466, and E2467 from orchardgrass varied in infection frequency and stability in orchardgrass, but all were unable to establish stable infections in perennial ryegrass. To investigate the genetics of host specificity, isolate E8 was crossed with each of the isolates from orchardgrass. Seedlings of parental host species were inoculated with F(1) progeny, and the frequencies of seedling infection and stability in adult plants were assessed. In the E8 x E2466 cross, the F(1) progeny exhibited a wide range of infection frequency and stability in each parental host. In crosses E8 x E469 and E8 x E2467, where the orchardgrass-derived parents infected 5 to 13% of inoculated perennial ryegrass seedlings, the distributions of infection frequencies for the F(1) progeny wereskewed toward levels comparable to that of the parent from perennial ryegrass. In all crosses, most progeny had low frequencies of infection in orchardgrass. However, transgression was evident in a cross of E8 with E469, an isolate that infected orchardgrass seedlings at a low frequency (2 to 3%). The E8 x E469 cross had a few F(1) progeny that infected orchardgrass at high efficiency (up to 81%). A Spearman rank correlation applied to the E8 x E2466 progeny indicated a significant negative correlation between infection frequencies in perennial ryegrass and orchardgrass. Also, there was a significant correlation of infection frequency and stability in perennial ryegrass but not in orchardgrass. To test whether only a few genes governed infection frequency in perennial ryegrass, an E8 x E2466 F(1) progeny (designated E386.04), which had intermediate compatibility with this host, was backcrossed to E8. The progeny of this backcross exhibited a distribution of infection frequencies in perennial ryegrass between that of E386.04 and the backcross parent, suggesting that multiple genes may determine compatibility at the seedling infection stage. The results of these experiments indicated multiple genetic determinants of compatibility or incompatibility with each host, with intermediate or high heritability.

EPICHLOE SPECIES: fungal symbionts of grasses.

Epichloë species and their asexual descendants (Acremonium endophytes) are fungal symbionts of C3 grasses that span the symbiotic continuum from antagonism to mutualism depending on the relative importance, respectively, of horizontal transmission of sexual spores versus vertical clonal transmission in healthy grass seeds. At least seven sexual Epichloë species are identifiable by mating tests, and many asexual genotypes are interspecific hybrids. Benefits conferred by the symbionts on host plants include protection from biotic factors and abiotic stresses such as drought. Four classes of beneficial alkaloids are associated with the symbionts: ergot alkaloids, indolediterpenes (lolitrems), peramine, and saturated aminopyrrolizidines (lolines). These alkaloids protect host plants from insect and vertebrate herbivores, including livestock. Genetic engineering of the fungal symbionts as more suitable biological protectants for forage grasses requires identification of fungal genes for alkaloid biosynthesis, and DNA-mediated transformation of the fungi.

Inheritance of mitochondrial DNA and plasmids in the ascomycetous fungus, Epichloë typhina.

We analyzed the inheritance of mitochondrial DNA (mtDNA) species in matings of the grass symbiont Epichloë typhina. Eighty progeny were analyzed from a cross in which the maternal (stromal) parent possessed three linear plasmids, designated Callan-a (7.5 kb), Aubonne-a (2.1 kb) and Bergell (2.0 kb), and the paternal parent had one plasmid, Aubonne-b (2.1 kb). Maternal transmission of all plasmids was observed in 76 progeny; two progeny possessed Bergell and Callan-a, but had the maternal Aubonne-a replaced with the related paternal plasmid Aubonne-b; two progeny lacked Callan-a, but had the other two maternal plasmids. A total of 34 progeny were analyzed from four other matings, including a reciprocal pair, and in each progeny the plasmid transmission was maternal. The inheritance of mitochondrial genomes in all progeny was analyzed by profiles of restriction endonuclease-cleaved mtDNA. In most progeny the profiles closely resembled those of the maternal parents, but some progeny had nonparental mtDNA profiles that suggested recombination of mitochondrial genomes. These results indicate that the fertilized stroma of E. typhina is initially heteroplasmic, permitting parental mitochondria to fuse and their genomes to recombine.

The Claviceps purpurea gene encoding dimethylallyltryptophan synthase, the committed step for ergot alkaloid biosynthesis.

The first pathway-specific step of ergot alkaloid biosynthesis in the fungus, Claviceps purpurea, is catalyzed by the prenyltransferase, 4-(gamma,gamma-dimethylallyl)tryptophan synthase. Partial sequence information was obtained for the purified enzyme and a degenerate oligonucleotide mixture was used to identify and amplify segments of the gene, dmaW. The complete gene and near-full-length cDNA were cloned and sequenced. The cDNA was cloned in a yeast expression vector in sense and antisense orientations relative to the inducible GAL1 promoter. Extracts of yeast transformants with the sense constructs, but not antisense constructs or cloning vector, catalyzed production of 4-(gamma,gamma-dimethylallyl)tryptophan. The sequence of dmaW and its cDNA indicated that it encoded a 455 amino acid polypeptide with a predicted molecular mass of 51,824 Da and a putative prenyl diphosphate binding motif.

The Fusarium solani gene encoding kievitone hydratase, a secreted enzyme that catalyzes detoxification of a bean phytoalexin.

Among the antimicrobial phytoalexins produced by Phaseolus vulgaris (French bean) is the prenylated isoflavonoid, kievitone. The bean pathogen, Fusarium solani f. sp. phaseoli, secretes a glycoenzyme, kievitone hydratase (EC 4.2.1.95), which catalyzes conversion of kievitone to a less toxic metabolite. Among F. solani strains, those that are highly virulent to P. vulgaris also produce kievitone hydratase constitutively, suggesting that the enzyme is a virulence factor. Based on the N-terminal amino acid sequence of purified enzyme, the kievitone hydratase cDNA and gene (khs) were cloned. The identities of khs and the cDNA were confirmed by their expression in transgenic Neurospora crassa and Emericella nidulans. Based on the gene and cDNA sequences, khs is predicted to encode a preprotein of 350 amino acids, from which a 19 amino acid N-terminal transit peptide is removed during maturation and secretion. The predicted mass of the mature polypeptide, 37 kDa, contrasts with the 47 to 49 kDa size estimated by electrophoresis of purified enzyme, confirming that the enzyme is extensively glycosylated. The inferred polypeptide sequence has seven canonical sites for N-glycosylation. Southern blot-hybridization analysis of F. s. f. sp. phaseoli DNA indicates one khs locus and an additional locus with weak hybridization to the khs probe. Sequences related to khs were also detected in several isolates of F. solani and the related teleomorph, Nectria haematococca. However, strains of F. oxysporum known to exhibit inducible kievitone hydratase activity (but not pathogenic to bean) did not have detectable khs homology. Nevertheless, all isolates known to cause severe disease on bean possessed khs sequence.