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1. Kinome Expansion in the Fusarium oxysporum Species Complex Driven by Accessory Chromosomes

   https://doi.org/10.1128/mSphere.00231-18  

   DeIulio, Gregory A. ; Guo, Li ; Zhang, Yong ; Goldberg, Jonathan M. ; Kistler, H. Corby ; Ma, Li-Jun ; Mitchell, Aaron P. ( June 2018 , mSphere)

   ABSTRACT The Fusarium oxysporum species complex (FOSC) is a group of soilborne pathogens causing severe disease in more than 100 plant hosts, while individual strains exhibit strong host specificity. Both chromosome transfer and comparative genomics experiments have demonstrated that lineage-specific (LS) chromosomes contribute to the host-specific pathogenicity. However, little is known about the functional importance of genes encoded in these LS chromosomes. Focusing on signaling transduction, this study compared the kinomes of 12 F. oxysporum isolates, including both plant and human pathogens and 1 nonpathogenic biocontrol strain, with 7 additional publicly available ascomycete genomes. Overall, F. oxysporum kinomes are the largest, facilitated in part by the acquisitions of the LS chromosomes. The comparative study identified 99 kinases that are present in almost all examined fungal genomes, forming the core signaling network of ascomycete fungi. Compared to the conserved ascomycete kinome, the expansion of the F. oxysporum kinome occurs in several kinase families such as histidine kinases that are involved in environmental signal sensing and target of rapamycin (TOR) kinase that mediates cellular responses. Comparative kinome analysis suggests a convergent evolution that shapes individual F. oxysporum isolates with an enhanced and unique capacity for environmental perception and associated downstream responses. IMPORTANCE Isolates of Fusarium oxysporum are adapted to survive a wide range of host and nonhost conditions. In addition, F. oxysporum was recently recognized as the top emerging opportunistic fungal pathogen infecting immunocompromised humans. The sensory and response networks of these fungi undoubtedly play a fundamental role in establishing the adaptability of this group. We have examined the kinomes of 12 F. oxysporum isolates and highlighted kinase families that distinguish F. oxysporum from other fungi, as well as different isolates from one another. The amplification of kinases involved in environmental signal relay and regulating downstream cellular responses clearly sets Fusarium apart from other Ascomycetes . Although the functions of many of these kinases are still unclear, their specific proliferation highlights them as a result of the evolutionary forces that have shaped this species complex and clearly marks them as targets for exploitation in order to combat disease. 

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2. Paralogous Cyp51s mediate the differential sensitivity of Fusarium oxysporum to sterol demethylation inhibitors

   https://doi.org/10.1002/ps.5127  

   Zheng, Bangxian ; Yan, Leiyan ; Liang, Wenxing ; Yang, Qianqian ( August 2018 , Pest Management Science)

   As a soilborne fungus,Fusarium oxysporumcan cause vascular wilt in numerous economically important crops. Application of antifungal drugs is the primary method for the control ofF. oxysporum. Cyp51, a key enzyme of sterol biosynthesis is the main target of sterol demethylation inhibitors.

   TheF. oxysporumgenome contains three paralogousCYP51genes (namedFoCYP51A,FoCYP51BandFoCYP51C) that putatively encode sterol 14α‐demethylase enzymes. Each of the three genes was able to partially complement theSaccharomyces cerevisiaeERG11mutant. Growth assays demonstrated that deletion mutants ofFoCYP51B, but notFoCYP51AandFoCYP51Cwere significantly retarded in hyphal growth. Deletion ofFoCYP51A(ΔFoCyp51A and ΔFoCyp51AC) led to increased sensitivity to 11 sterol demethylation inhibitors (DMIs). Interestingly,FoCYP51Bdeletion mutants (ΔFoCyp51B and ΔFoCyp51BC) exhibited significantly increased sensitivity to only four DMIs (two of which are in common with the 11 DMIs mentioned earlier). Deletion ofFoCYP51Cdid not change DMI sensitivity ofF. oxysporum. None of the threeFoCYP51s are involved inF. oxysporumvirulence. The sensitivity ofF. oxysporumisolates increased significantly when subjected to a mixture of different subgroups of DMIs classified based on the different sensitivities ofFoCYP51mutants to DMIs compared to the individual components.

   FoCYP51AandFoCYP51Bare responsible for sensitivity to different azoles. These findings have direct implications for fungicide application strategies of plant and human diseases caused byF. oxysporum. © 2018 Society of Chemical Industry

    

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3. Genome Sequence of Fusarium oxysporum f. sp. matthiolae , a Brassicaceae Pathogen

   https://doi.org/10.1094/MPMI-11-19-0324-A  

   Yu, Houlin ; Ayhan, Dilay Hazal ; Diener, Andrew C. ; Ma, Li-Jun ( April 2020 , Molecular Plant-Microbe Interactions®)

   null (Ed.)

   The filamentous fungus Fusarium oxysporum is a soilborne pathogen of many cultivated species and an opportunistic pathogen of humans. F. oxysporum f. sp. matthiolae is one of three formae speciales that are pathogenic to crucifers, including Arabidopsis thaliana, a premier model for plant molecular biology and genetics. Here, we report a genome assembly of F. oxysporum f. sp. matthiolae strain PHW726, generated using a combination of PacBio and Illumina sequencing technologies. The genome assembly presented here should facilitate in-depth investigation of F. oxysporum–Arabidopsis interactions and shed light on the genetics of fungal pathogenesis and plant immunity. 

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4. Metatranscriptomic Comparison of Endophytic and Pathogenic Fusarium –Arabidopsis Interactions Reveals Plant Transcriptional Plasticity

   https://doi.org/10.1094/MPMI-03-21-0063-R  

   Guo, Li ; Yu, Houlin ; Wang, Bo ; Vescio, Kathryn ; DeIulio, Gregory A. ; Yang, He ; Berg, Andrew ; Zhang, Lili ; Edel-Hermann, Véronique ; Steinberg, Christian ; et al ( September 2021 , Molecular Plant-Microbe Interactions®)

   Plants are continuously exposed to beneficial and pathogenic microbes, but how plants recognize and respond to friends versus foes remains poorly understood. Here, we compared the molecular response of Arabidopsis thaliana independently challenged with a Fusarium oxysporum endophyte Fo47 versus a pathogen Fo5176. These two F. oxysporum strains share a core genome of about 46 Mb, in addition to 1,229 and 5,415 unique accessory genes. Metatranscriptomic data reveal a shared pattern of expression for most plant genes (about 80%) in responding to both fungal inoculums at all timepoints from 12 to 96 h postinoculation (HPI). However, the distinct responding genes depict transcriptional plasticity, as the pathogenic interaction activates plant stress responses and suppresses functions related to plant growth and development, while the endophytic interaction attenuates host immunity but activates plant nitrogen assimilation. The differences in reprogramming of the plant transcriptome are most obvious in 12 HPI, the earliest timepoint sampled, and are linked to accessory genes in both fungal genomes. Collectively, our results indicate that the A. thaliana and F. oxysporum interaction displays both transcriptome conservation and plasticity in the early stages of infection, providing insights into the fine-tuning of gene regulation underlying plant differential responses to fungal endophytes and pathogens. [Formula: see text] Copyright © 2021 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license . 

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5. Accessory Chromosomes in Fusarium oxysporum

   https://doi.org/10.1094/PHYTO-03-20-0069-IA  

   Yang, He ; Yu, Houlin ; Ma, Li-Jun ( September 2020 , Phytopathology®)

   null (Ed.)

   Most genomes within the species complex of Fusarium oxysporum are organized into two compartments: the core chromosomes (CCs) and accessory chromosomes (ACs). As opposed to CCs, which are conserved and vertically transmitted to carry out essential housekeeping functions, lineage- or strain-specific ACs are believed to be initially horizontally acquired through unclear mechanisms. These two genomic compartments are different in terms of gene density, the distribution of transposable elements, and epigenetic markers. Although common in eukaryotes, the functional importance of ACs is uniquely emphasized among fungal species, specifically in relationship to fungal pathogenicity and their adaptation to diverse hosts. With a focus on the cross-kingdom fungal pathogen F. oxysporum, this review provides a summary of the differences between CCs and ACs based on current knowledge of gene functions, genome structures, and epigenetic signatures, and explores the transcriptional crosstalk between the core and accessory genomes. 

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