Folyt1, a new member of the hAT family, is active in the genome of the plant pathogen Fusarium oxysporum

Comparative genomics and prediction of conditionally dispensable sequences in legume-infecting Fusarium oxysporum formae speciales facilitates identification of candidate effectors

BACKGROUND

Soil-borne fungi of the Fusarium oxysporum species complex cause devastating wilt disease on many crops including legumes that supply human dietary protein needs across many parts of the globe. We present and compare draft genome assemblies for three legume-infecting formae speciales (ff. spp.): F. oxysporum f. sp. ciceris (Foc-38-1) and f. sp. pisi (Fop-37622), significant pathogens of chickpea and pea respectively, the world's second and third most important grain legumes, and lastly f. sp. medicaginis (Fom-5190a) for which we developed a model legume pathosystem utilising Medicago truncatula.

RESULTS

Focusing on the identification of pathogenicity gene content, we leveraged the reference genomes of Fusarium pathogens F. oxysporum f. sp. lycopersici (tomato-infecting) and F. solani (pea-infecting) and their well-characterised core and dispensable chromosomes to predict genomic organisation in the newly sequenced legume-infecting isolates. Dispensable chromosomes are not essential for growth and in Fusarium species are known to be enriched in host-specificity and pathogenicity-associated genes. Comparative genomics of the publicly available Fusarium species revealed differential patterns of sequence conservation across F. oxysporum formae speciales, with legume-pathogenic formae speciales not exhibiting greater sequence conservation between them relative to non-legume-infecting formae speciales, possibly indicating the lack of a common ancestral source for legume pathogenicity. Combining predicted dispensable gene content with in planta expression in the model legume-infecting isolate, we identified small conserved regions and candidate effectors, four of which shared greatest similarity to proteins from another legume-infecting ff. spp.

CONCLUSIONS

We demonstrate that distinction of core and potential dispensable genomic regions of novel F. oxysporum genomes is an effective tool to facilitate effector discovery and the identification of gene content possibly linked to host specificity. While the legume-infecting isolates didn't share large genomic regions of pathogenicity-related content, smaller regions and candidate effector proteins were highly conserved, suggesting that they may play specific roles in inducing disease on legume hosts.

Multilocus analysis using putative fungal effectors to describe a population of Fusarium oxysporum from sugar beet

Sugar beet (Beta vulgaris) Fusarium yellows is caused by Fusarium oxysporum f. sp. betae and can lead to significant reductions in root yield, sucrose percentage, juice purity, and storability. F. oxysporum f. sp. betae can be highly variable and many F. oxysporum strains isolated from symptomatic sugar beet are nonpathogenic. Identifying pathogenicity factors and their diversity in the F. oxysporum f. sp. betae population could further understanding of how this pathogen causes disease and potentially provide molecular markers to rapidly identify pathogenic isolates. This study used several previously described fungal effector genes (Fmk1, Fow1, Pda1, PelA, PelD, Pep1, Prt1, Rho1, Sge1, Six1, Six6, Snf1, and Ste12) as genetic markers, in a population of 26 pathogenic and nonpathogenic isolates of F. oxysporum originally isolated from symptomatic sugar beet. Of the genes investigated, six were present in all F. oxysporum isolates from sugar beet (Fmk1, Fow1, PelA, Rho1, Snf1, and Ste12), and seven were found to be dispersed within the population (Pda1, PelD, Pep1, Prt1, Sge1, Six1, and Six6). Of these, Fmk1, Fow1, PelA, Rho1, Sge1, Snf1, and Ste12 were significant in relating clade designations and PelD, and Prt1 were significant for correlating with pathogenicity in F. oxysporum f. sp. betae.

MITEs in the promoters of effector genes allow prediction of novel virulence genes in Fusarium oxysporum

BACKGROUND

The plant-pathogenic fungus Fusarium oxysporum f.sp.lycopersici (Fol) has accessory, lineage-specific (LS) chromosomes that can be transferred horizontally between strains. A single LS chromosome in the Fol4287 reference strain harbors all known Fol effector genes. Transfer of this pathogenicity chromosome confers virulence to a previously non-pathogenic recipient strain. We hypothesize that expression and evolution of effector genes is influenced by their genomic context.

RESULTS

To gain a better understanding of the genomic context of the effector genes, we manually curated the annotated genes on the pathogenicity chromosome and identified and classified transposable elements. Both retro- and DNA transposons are present with no particular overrepresented class. Retrotransposons appear evenly distributed over the chromosome, while DNA transposons tend to concentrate in large chromosomal subregions. In general, genes on the pathogenicity chromosome are dispersed within the repeat landscape. Effector genes are present within subregions enriched for DNA transposons. A miniature Impala (mimp) is always present in their promoters. Although promoter deletion studies of two effector gene loci did not reveal a direct function of the mimp for gene expression, we were able to use proximity to a mimp as a criterion to identify new effector gene candidates. Through xylem sap proteomics we confirmed that several of these candidates encode proteins secreted during plant infection.

CONCLUSIONS

Effector genes in Fol reside in characteristic subregions on a pathogenicity chromosome. Their genomic context allowed us to develop a method for the successful identification of novel effector genes. Since our approach is not based on effector gene similarity, but on unique genomic features, it can easily be extended to identify effector genes in Fo strains with different host specificities.

Recent developments in the molecular discrimination of formae speciales of Fusarium oxysporum

Rapid and reliable detection and identification of potential plant pathogens is required for taking appropriate and timely disease management measures. For many microbial species of which all strains generally are plant pathogens on a known host range, this has become quite straightforward. However, for some fungal species this is quite a challenge. One of these is Fusarium oxysporum Schlechtend:Fr., which, as a species, has a very broad host range, while individual strains are usually highly host-specific. Moreover, many strains of this fungus are non-pathogenic soil inhabitants. Thus, with regard to effective disease management, identification below the species level is highly desirable. So far, the genetic basis of host specificity in F. oxysporum is poorly understood. Furthermore, strains that infect a particular plant species are not necessarily more closely related to each other than to strains that infect other hosts. Despite these difficulties, recently an increasing number of studies have reported the successful development of molecular markers to discriminate F. oxysporum strains below the species level.

Evolution of virulence in Fusarium oxysporum f. sp. vasinfectum using serial passage assays through susceptible cotton

Fifty strains of Fusarium oxysporum, recovered from rhizosphere soil around native Gossypium species and found to be mildly virulent on cotton (Gossypium hirsutum), were used to assay the propensity for evolution of virulence using serial passage assays through cotton. Only one lineage A strain, 2613, successfully completed 10 successive passages, while all others lost the ability to cause foliar disease symptoms at various stages during this process. Based on 46 amplified fragment length polymorphism (AFLP) markers generated with four EcoRI x MseI primer combinations, mutants were identified in offspring isolates from strain 2613 regardless of whether serial passages occurred in cotton or on water agar, suggesting the occurrence of spontaneous mutations. Significantly increased virulence was observed in the offspring isolates generated on cotton, while no increasing virulence was found in those obtained on water agar, suggesting that the evolution of virulence in F. oxysporum f. sp. vasinfectum is associated with the presence of cotton. No clear correlation was observed between the AFLP mutations and increased virulence in this study.

A robust identification and detection assay to discriminate the cucumber pathogens Fusarium oxysporum f. sp. cucumerinum and f. sp. radicis-cucumerinum

The fungal species Fusarium oxysporum is a ubiquitous inhabitant of soils worldwide that includes pathogenic as well as non-pathogenic or even beneficial strains. Pathogenic strains are characterized by a high degree of host specificity and strains that infect the same host range are organized in so-called formae speciales. Strains for which no host plant has been identified are believed to be non-pathogenic strains. Therefore, identification below the species level is highly desired. However, the genetic basis of host specificity and virulence in F. oxysporum is so far unknown. In this study, a robust random-amplified polymorphic DNA (RAPD) marker-based assay was developed to specifically detect and identify the economically important cucumber pathogens F. oxysporum f. sp. cucumerinum and F. oxysporum f. sp. radicis-cucumerinum. While the F. oxysporum radicis-cucumerinum strains were found to cluster in a separate clade based on elongation factor-1alpha phylogeny, strains belonging to F. oxysporum f. sp. cucumerinum were found to be genetically more diverse. This is reflected in the observation that specificity testing of the identified markers using a broad collection of F. oxysporum strains with all known vegetative compatibility groups of the target formae speciales, as well as representative strains belonging to other formae speciales, resulted in two cross-reactions for the F. oxysporum f. sp. cucumerimum marker. However, no cross-reactions were observed for the F. oxysporum f. sp. radicis-cucumerimum marker. This F. oxysporum f. sp. radicis-cucumerimum marker shows homology to Folyt1, a transposable element identified in the tomato pathogen F. oxysporum f. sp. lycopersici and may possibly play a role in host-range specificity in the target forma specialis. The markers were implemented in a DNA array that enabled parallel and sensitive detection and identification of the pathogens in complex samples from diverse origins.

Colletotrichum sublineolum genetic instability assessed by mutants resistant to chlorate

The fungus Colletotrichum sublineolum, causal agent of sorghum anthracnose, presents high variability, genetic instability and host specialization. The aims of the present work were to investigate the mechanisms involved in the genetic instability in this species. Mutants resistant to chlorate and unable to use nitrate (Nit mutants), were obtained spontaneously, isolated and characterized for complementation pattern, reversion frequency and RAPD profile. The results showed that chlorate-resistant mutants could be divided into six phenotypic classes that probably represented mutations in the structural nitrate reductase locus (nit1), in the structural nitrite reductase locus (nit6 and niiA of Neurospora and Aspergillus, respectively), in the specific regulator locus (nit3), in the main regulator locus (nit2), in loci that codified the cofactor containing molybdenum necessary for nitrate reductase activity (NitM), and one or more genes responsible for nitrate intake (crn). In addition, the genetic control of this metabolism in C. sublineolum seems to be similar to other fungi species such as Aspergillus, Neurospora and Fusarium. The high reversion frequency (10(-4) to 10(-5)) presented by nit1 mutants suggests that the instability in evaluated strains could be a result of transposable elements activity. The RAPD analysis enabled confirmation that the Nit mutants have a similar genetic background to original strain, and that polymorphism exists among wild-type strains, nit1 mutants and revertants of C. sublineolum. These are important aspects for the later direction of molecular analysis, where these mutants will be used as a tool to isolate the active transposable elements in the C. sublineolum genome.

Drifter, a novel, low copy hAT-like transposon in Fusarium oxysporum is activated during starvation

The facultative pathogenic fungus Fusarium oxysporum is known to harbour many different transposable and/or repetitive elements. We have identified Drifter, a novel DNA transposon of the hAT family in F. oxysporum. It was found adjoining SIX1-H, a truncated homolog of the SIX1 avirulence gene in F. oxysporum f. sp. lycopersici. Absence of a target site duplication as well as the 5' part of SIX1-H suggests that transposition of Drifter into the ancestor of SIX1-H was followed by loss of a chromosomal segment through recombination between Drifters. F. oxysporum isolates belonging to various formae speciales harbour between 0 and 5 full-length copies of Drifter and/or one or more copies with an internal deletion. Transcription of Drifter is activated during starvation for carbon or nitrogen.

The hAT -like DNA transposon DodoPi resides in a cluster of retro- and DNA transposons in the stramenopile Phytophthora infestans

A family of transposable elements belonging to the hAT group of DNA transposons is described from an oomycete, the plant pathogen Phytophthora infestans. The family, named DodoPi, was identified by studying a hotspot for retro- and DNA transposon insertions adjacent to the mating type locus. The DodoPi family comprises a small number of full-length copies, each of which is 2.7 kb long and predicted to encode a transposase-like protein consisting of 617 amino acids, and several truncated copies. Both types contain 12-bp terminal inverted repeats and are flanked by 8-bp target site duplications. Despite the detection of a DodoPi transcript and of many polymorphisms between isolates, conclusive evidence of recent transposition was not obtained. A phylogenetic analysis indicated that DodoPi was novel, with only modest similarity to some elements from plants and fungi. Relatives were detected in only some members of the genus. This is the first DNA transposon identified in the stramenopile group of eukaryotes.

Transposable elements in filamentous fungi

The past 10 years have been productive in the characterization of fungal transposable elements (TEs). All eukaryotic TEs described are found including an extraordinary prevalence of active members of the pogo family. The role of TEs in mutation and genome organization is well documented, leading to significant advances in our perception of the mechanisms underlying genetic changes in these organisms. TE-mediated changes, associated with transposition and recombination, provide a broad range of genetic variation, which is useful for natural populations in their adaptation to environmental constraints, especially for those lacking the sexual stage. Interestingly, some fungal species have evolved distinct silencing mechanisms that are regarded as host defense systems against TEs. The examination of forces acting on the evolutionary dynamics of TEs should provide important insights into the interactions between TEs and the fungal genome. Another issue of major significance is the practical applications of TEs in gene tagging and population analysis, which will undoubtedly facilitate research in systematic biology and functional genomics.

Heterologous transposition in Ustilago maydis

The phytopathogenic basidiomycete Ustilago maydis has become a model system for the analysis of plant-pathogen interactions. The genome sequence of this organism will soon be available, increasing the need for techniques to analyse gene function on a broad basis. We describe a heterologous transposition system for U. maydis that is based on the Caenorhabditis transposon Tc1, which is known to function independently of host factors and to be active in evolutionarily distant species. We have established a nitrate reductase based two-component counterselection system to screen for Tc1 transposition. The element was shown to be functional and transposed to several different locations in the genome of U. maydis. The insertion pattern observed was consistent with the proposed general mechanism of Tc1/mariner integration and constitutes a proof of principle for the first heterologous transposition system in a basidiomycete species. By mapping the insertion site context to known genomic sequences, Tc1 insertion events were shown to occur on different chromosomes, but exhibit a preference for non-coding regions. Only 20% of the insertions were found in putative open reading frames. The establishment of this system will permit efficient gene tagging in U. maydis and possibly also in other fungi.

Germline transformants spreading out to many insect species

The past 5 years have witnessed significant advances in our ability to introduce genes into the genomes of insects of medical and agricultural importance. A number of transposable elements now exist that are proving to be sufficiently robust to allow genetic transformation of species within three orders of insects. In particular all of these transposable elements can be used genetically to transform mosquitoes. These developments, together with the use of suitable genes as genetic markers, have enabled several genes and promoters to be transferred between insect species and their effects on the phenotype of the transgenic insect determined. Within a very short period of time, insights into the function of insect promoters in homologous and heterologous insect species are being gained. Furthermore, strategies aimed at ameliorating the harmful effects of pest insects, such as their ability to vector human pathogens, are now being tested in the pest insects themselves. We review the progress that has been made in the development of transgenic technology in pest insect species and conclude that the repertoire of transposable element-based genetic tools, long available to Drosophila geneticists, can now be applied to other insect species. In addition, it is likely that these developments will lead to the generation of pest insects that display a significantly reduced ability to transmit pathogens in the near future.

Ds-like restless deletion derivatives occur in Tolypocladium inflatum and two foreign hosts, Neurospora crassa and Penicillium chrysogenum

Single copies of the transposon Restless from Tolypocladium inflatum were introduced into Neurospora crassa and Penicillium chrysogenum. Excision of Restless from its donor site was investigated in N. crassa and in P. chrysogenum using direct selective conditions. In N. crassa, forward selection was also analyzed. Deleted Restless elements were frequently obtained in addition to the expected complete removal of Restless from its donor site. Similar deleted elements were also identified in T. inflatum employing a PCR amplification strategy. These deleted Restless copies strongly resemble maize Ds elements of various types, and direct repeated sequences of 3 to 16 bp were found to flank the truncated regions. In addition Ds1-like Restless elements were identified that carried foreign sequences between the inverted repeats. We discuss how Ds-like Restless elements might be generated by inaccurate excision from an active transposon copy.

Evolutionary history of the impala transposon in Fusarium oxysporum

Impala is an active DNA transposon family that was first identified in a strain of Fusarium oxysporum pathogenic to melon. The 10 copies present in this strain define three subfamilies that differ by about 20% at the nucleotide level. This high level of polymorphism suggests the existence of an ancestral polymorphism associated with vertical transmission and/or the introduction of some subfamilies by horizontal transfer from another species. To gain insights into the molecular evolution of this family, impala distribution was investigated in strains with various host specificities by Southern blot, PCR, and sequencing. Detection of impala elements in most of the F. oxysporum strains tested indicates that impala is an ancient component of the F. oxysporum genome. Subfamily-specific amplifications and sequence and phylogenetic analyses revealed five subfamilies, several of which can be found within the same genome. This supports the hypothesis of an ancestral polymorphism followed by vertical transmission and independent evolution in the host-specific forms. Highly similar elements showing unique features (internal deletions, high rates of CG-to-TA transitions) or being present at the same genomic location were identified in several strains with different host specificities, raising questions about the phylogenetic relationships of these strains. A phylogenetic analysis performed by sequencing a portion of the EF1alpha gene showed in most cases a correlation between the presence of a particular element and a close genetic relationship. All of these data provide important information on the evolutionary origin of this element and reveal its potential as a valuable tool for tracing populations.

Scooter, a new active transposon in Schizophyllum commune, has disrupted two genes regulating signal transduction

Two copies of scooter, a DNA-mediated transposon in the basidiomycetous fungus Schizophyllum commune, were characterized. Scooter is the first transposon isolated from S. commune. Scooter creates 8-bp target site duplications, comparable to members of the hAT superfamily, and has 32-bp terminal inverted repeats. Both copies of scooter are nonautonomous elements capable of movement. Southern blot hybridizations show that scooter-related sequences are present in all S. commune strains tested. Scooter-1 was identified initially as an insertion in the Bbeta2 pheromone receptor gene, bbr2, leading to a partial defect in mating. Scooter-2 spontaneously disrupted a gene to produce the frequently occurring morphological mutant phenotype known as thin. The scooter-2 insert permitted cloning of the disrupted gene, thn1, which encodes a putative regulator of G protein signaling (RGS) protein. Spontaneous insertion of scooter into genes with identifiable mutant phenotypes constitutes the first evidence of active transposition of a DNA-mediated transposon in a basidiomycete.