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1. Improved Assembly of Reference Genome Fusarium oxysporum f. sp. lycopersici Strain Fol4287

   https://doi.org/10.1128/MRA.00910-18  

   Ayhan, Dilay Hazal; López-Díaz, Cristina; Di Pietro, Antonio; Ma, Li-Jun; Rokas, Antonis (September 2018, Microbiology Resource Announcements)

   ABSTRACT Fusarium oxysporum is a pathogenic fungus that infects hundreds of plant species. This paper reports the improved genome assembly of a reference strain, F. oxysporum f. sp. lycopersici Fol4287, a tomato pathogen. 

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

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

   Li Guo, 1 Houlin (November 2021, Molecular plantmicrobe interactions)

   Plants are continuously exposed to beneficial and pathogenic microbes, but how plants recognize and respond to friends ver- sus foes remains poorly understood. Here, we compared the molecular response of Arabidopsis thaliana independently chal- lenged 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 path- ogenic interaction activates plant stress responses and sup- presses 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 interac- tion 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. 

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4. Differential Colonization of the Plant Vasculature Between Endophytic Versus Pathogenic Fusarium oxysporum Strains

   https://doi.org/10.1094/MPMI-08-22-0166-SC  

   Martínez-Soto, Domingo; Yu, Houlin; Allen, Kelly S.; Ma, Li-Jun (January 2023, Molecular Plant-Microbe Interactions®)

   Plant xylem colonization is the hallmark of vascular wilt diseases caused by phytopathogens within the Fusarium oxysporum species complex. Recently, xylem colonization has also been reported among endophytic F. oxysporum strains, resulting in some uncertainty. This study compares xylem colonization processes by pathogenic versus endophytic strains in Arabidopsis thaliana and Solanum lycopersicum, using Arabidopsis pathogen Fo5176, tomato pathogen Fol4287, and the endophyte Fo47, which can colonize both plant hosts. We observed that all strains were able to advance from epidermis to endodermis within 3 days postinoculation (dpi) and reached the root xylem at 4 dpi. However, this shared progression was restricted to lateral roots and the elongation zone of the primary root. Only pathogens reached the xylem above the primary-root maturation zone (PMZ). Related to the distinct colonization patterns, we also observed stronger induction of callose at the PMZ and lignin deposition at primary-lateral root junctions by the endophyte in both plants. This observation was further supported by stronger induction of Arabidopsis genes involved in callose and lignin biosynthesis during the endophytic colonization (Fo47) compared with the pathogenic interaction (Fo5176). Moreover, both pathogens encode more plant cell wall–degrading enzymes than the endophyte Fo47. Therefore, observed differences in callose and lignin deposition could be the combination of host production and the subsequent fungal degradation. In summary, this study demonstrates spatial differences between endophytic and pathogenic colonization, strongly suggesting that further investigations of molecular arm-races are needed to understand how plants differentiate friend from foe. [Formula: see text] Copyright © 2023 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. Genome Sequence Resource of Fusarium graminearum TaB10 and Fusarium avenaceum KA13, Causal Agents of Stored Apple Rot

   https://doi.org/10.1094/MPMI-03-22-0069-A  

   Petreš, Mladen; Hrustić, Jovana; Vučinić, Nataša; Ma, Li-Jun; Ayhan, Dilay Hazal; Grahovac, Mila (January 2023, Molecular Plant-Microbe Interactions®)

   The filamentous fungus Fusarium graminearum is a well-known cereal pathogen and F. avenaceum is a pathogen with a wide host range. Recently, both species were reported as causal agents of apple rot, raising concerns about postharvest yield losses and mycotoxin contamination. Here, we report genome assemblies of F. avenaceum KA13 and F. graminearum TaB10, both isolated from fruits with symptoms of apple rot. The final F. avenaceum KA13 genome sequence assembly of 41.7 Mb consists of 34 scaffolds, with an N 50 value of 2.2 Mb and 15,886 predicted genes. The total size of the final F. graminearum TaB10 assembly is 36.76 Mb, consisting of 54 scaffolds with an N 50 value of 1.7 Mb, and it consists of 14,132 predicted genes. These new genomes provide valuable resources to better understand plant-microbe interaction in stored apple rot disease. [Formula: see text] Copyright © 2022 The Author(s). This is an open access article distributed under the CC BY 4.0 International license . 

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