Fungal Comparative Genomics Lab

Fusarium Comparative Genomics to understand genome evolution

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

We are interested in using this group of organisms as a model system to study:
• Ecological adaptation and genomic dynamics.
• Structural and functional flexibility and organism adaptation.
• Regulatory circuitries that control the core genome and the LS regions.

Regulatory networks to study functional regulation

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, expression data (both microarray and RNA-seq data) can be used to infer co-expression of genes that are possibly co-regulated and protein-DNA interaction studies (such as ChIP-seq) can be used to identify specific binding of a transcription factor at the promoter regions of its target genes. Capitalizing on the availability of extensive knowledge on comparative and functional genomics, we are interested in employing a systems biology approach to reconstruct regulatory networks that identify the relationships between key transcription factors and their target genes. Our current method combines probabilistic Boolean networks and Bayesian network models that combine multivariate probability distributions and capture properties of conditional independence between variables.

Supplementary Tables for " Guo et al. Divergence of the conserved cAMP-PKA pathway contributes to organism niche adaptation: comparative transcriptomics of two filamentous fungi":
• GuoCPKA_Table S1_ArrayDescription.docx.
• GuoCPKA_Table S2_FgDEGs.xlsx.
• GuoCPKA_Table S3_FvDEGs.xlsx.
• GuoCPKA_Table S4_SharedDEGs.xlsx.
• GuoCPKA_Table S5_ROELs.xlsx.

Host-pathogen interactions-- host immunity and fungal pathogenicity

F. oxysporum is a eukaryotic pathogen that causes infections in both humans and plants, representing a multi-host model for the genetic dissection of fungal pathogenicity and to study host immunity. Both plant and animal models have been established to study F. oxysporum - host interactions. The established F. oxysporum - animal models include mouse, worm, and moth. Evolutionarily, F. oxysporum is a unique system where horizontally acquired chromosomes determine host-specific pathogenicity. Therefore its genome is divided into “core” and “accessory” regions. The vertically transmitted “core” is conserved and performs all essential functions. The horizontally transmitted “accessory” genome – in the form of lineage-specific (LS) chromosomes – only occurs in specific pathotypes and encodes host-specific virulence factors. Because of the unique structure and functional compartmentalization of this genome, future quests for host-specific effectors could focus on rather small “accessory” genomic regions. Dissecting host immunity against fungal infections has the potential to develop more effective anti-fungal drugs for the protection of both human and agricultural important crops.

Understand pathogenesis for the control of fungal diseases

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. Read more

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 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.

Summplementary for "L. Guo, et al. A De Novo-Assembly Based Data Analysis Pipeline for Plant Obligate Parasite Metatranscriptomic Studies. "
• fasta data for all assembled transcripts from sweet basil .

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