Fusarium species are among the most important phytopathogenic fungi and have significant impact on crop production and animal health. Distinctively, strains of F. oxysporum exhibit wide host range, reflecting remarkable genetic adaptability. The advent of genome sequencing and comparative genomics had accelerated the discovery of the molecular basis and genomic processes that underlie the evolution of plant pathogenicity in this group of organisms. Specifically, comparative genomes revealed greatly expanded lineage-specific (LS) genomic regions in F. oxysporum that include four entire chromosomes and account for more than one-quarter of the genome. The transfer of the LS chromosomes between strains of F. oxysporum was demonstrated experimentally and resulted in the conversion of a non-pathogenic strain into a pathogen. Read more
• Ecological adaptation and genomic dynamics.
• Structural and functional flexibility and organism adaptation.
• Regulatory circuitries that control the core genome and the LS regions.
Niche adaptation of plant vascular wilt pathogens
The vascular wilt fungi Verticillium dahliae and V. albo-atrum infect over 200 plant species, causing billions of dollars in annual crop losses. The characteristic wilt symptoms are a result of colonization and proliferation of the pathogens in the xylem vessels, which undergo fluctuations in osmolarity. To gain insights into the mechanisms that confer the organisms’ pathogenicity and enable them to proliferate in the unique ecological niche of the plant vascular system, we sequenced the genomes of V. dahliae and V. albo-atrum and compared them to each other, and to the genome of Fusarium oxysporum, another fungal wilt pathogen.
Our analyses identified a set of proteins that are shared among all three wilt pathogens, and present in few other fungal species. One of these is a homolog of a bacterial glucosyltransferase that synthesizes virulence-related osmoregulated periplasmic glucans in bacteria. Pathogenicity tests of the corresponding V. dahliae glucosyltransferase gene deletion mutants indicate that the gene is required for full virulence in the Australian tobacco species Nicotiana benthamiana. Compared to other fungi, the two sequenced Verticillium genomes encode more pectin-degrading enzymes and other carbohydrate-active enzymes, suggesting an extraordinary capacity to degrade plant pectin barricades. The high level of synteny between the two Verticillium assemblies highlighted four flexible genomic islands in V. dahliae that are enriched for transposable elements, and contain duplicated genes and genes that are important in signaling/transcriptional regulation and iron/lipid metabolism. Coupled with an enhanced capacity to degrade plant materials, these genomic islands may contribute to the expanded genetic diversity and virulence of V. dahliae, the primary causal agent of Verticillium wilts. Significantly, our study reveals insights into the genetic mechanisms of niche adaptation of fungal wilt pathogens, advances our understanding of the evolution and development of their pathogenesis, and sheds light on potential avenues for the development of novel disease management strategies to combat destructive wilt diseases.
Strategies for Improving Disease Management of Sweet Basil
Sweet basil (Ocimum basilicum L.), a frequent visitor of our dining tables, is commercially the most important annual culinary herb crop in the United States. However, 100% of the US production acreage (~11,000) is at-risk to two economically-important diseases, Downy mildew and Fusarium wilt. Since 2007, entire fields and greenhouse stocks have been lost due to inadequate control options of these two diseases.
A team from PSIS has joined a multistate research team that includes Rutgers University, University of Florida, University of and Cornell University to tackle this specific problem. A research project proposed by this collaborative effort: “Strategies for Improving the U.S. Responses to Fusarium, Downy Mildew and Chilling Injury in Production of Sweet Basil (Ocimum basilicum L.)” was recently awarded a $ 1.8 million in funds from USDA. The project runs over a four year period, with the objectives to i) develop improved varieties with tolerance to Downy mildew, Fusarium wilt and chilling-injury, ii) to develop the standard laboratory techniques that will be used for the detection of Fusarium wilt and Downy mildew infested seed before distribution, iii) develop improved management strategies to effectively control Downy mildew based on a disease forecasting and monitoring system and through the identification of effective organic and conventional fungicides, and (iv) develop cost: benefit considerations for each strategy. The PIs of this lab will combine the strengths in plant pathology and genomics to survey basil seed for the pathogens, investigate the population structure of the downy mildew organism Peronospora belbahrii and study the relationship of the yeast Pseudozyma which colonizes P. belbaharii.
Transcriptional & Regulatory Networks
Regulatory networks control gene expression and serve as decision-making circuits within an organism. As functional elements, transcription factor binding sites often evolve at a much slower rate than neutral sequences, and therefore they often stand out from the surrounding sequences by virtue of their greater levels of conservation. This property enables the recognition of these conserved elements through comparative genomics. In addition empirical data generated through functional genomics such RNA-seq, chip-seq will be used to validate the co-expression of gene sets, the specific binding properties of these potential TF bonding sites, and therefore could be used to infer the regulatory networks.