Biology subjects

Doddi, A.

Publications and source records attributed to Doddi, A..

6 recordsLinked to original sources

bioRxiv2026

Killer meiotic driver prevents chromosome loss and enhances fitness in a fungal pathogen

Fungal pathogens often carry dispensable chromosomes (DCs) that confer a selective advantage in adverse environments or during host infection but can be spontaneously lost under non-selective conditions. How DCs are maintained in evolving populations remains poorly understood. Here we show that a meiotic driver known as Spore Killer (spok), located on a giant Starship transposon, limits spontaneous loss of a conserved DC in the cross-kingdom pathogen Fusarium oxysporum. Transfer of a functional spok gene, but not of a killing-deficient mutant allele, to a mitotically unstable DC significantly reduced its loss rate, while spok deletion from a stably maintained DC increased loss frequency. Competition experiments between isogenic strains carrying a functional or a killing-deficient spok allele revealed a dramatic fitness gain conferred by Spok killing activity, which required transmission by hyphal fusion. Thus, spoks and their Starship carriers benefit fungal hosts by preventing DC loss and preserving long-term metabolic and pathogenic plasticity.

microbiology↗

bioRxiv2026

A near-complete genome assembly of the Fusarium oxysporum keratitis isolate MRL8996

Fusarium oxysporum MRL8996 is a fungal strain isolated from a severe case of contact lens-associated keratitis. Here we report a near-complete genome assembly of this isolate using a hybrid Nanopore and Hi-C scaffolding approach. The assembly resolves the genome into 16 distinct chromosomes, including 11 core and 5 lineage-specific chromosomes. This high-quality reference genome provides an unprecedented tool for investigating the large-scale structural variations and evolutionary mechanisms driving adaptation in this highly versatile fungal lineage.

genomics↗

bioRxiv2026

A chromosome-level assembly of the Fusarium oxysporum biocontrol strain FO12

Fusarium oxysporum FO12 was originally isolated from cork oak (Quercus suber L.) and has been characterised as a highly effective biological control agent of wilt diseases on different crops. FO12 endophytically colonises roots and basal stems of plants, reducing the establishment of the soil-borne pathogen Verticillium dahliae and triggering plant defence-related genes. Here, we report a chromosome-level genome assembly of FO12 using Nanopore and Hi-C data. The 57.60 Mb assembly comprises 14 chromosome-scale scaffolds with centromeres resolved and telomeric repeats detected at 4 of 28 chromosome ends. This high-quality reference genome provides a valuable resource for further research into the use of FO12 in agriculture as a biocontrol agent.

genomics↗

bioRxiv2026

A structurally unique effector shared between Verticillium dahliae and Fusarium oxysporum is involved in cotton defoliation and virulence on other hosts

Defoliating (D) strains of the vascular wilt fungus Verticillium dahliae cause severe yield losses in cotton and olive worldwide, yet the genetic basis underlying this pathotype has remained unknown. Here, we combined comparative genomics, functional genetics, structural analysis, and phylogenomics to uncover the molecular determinant of defoliation. We identified a small, D pathotype-specific genomic region encoding two duplicated secreted effector genes. Simultaneous deletion of both gene copies abolished pathogenicity and defoliation in cotton, olive, Nicotiana benthamiana, and Arabidopsis thaliana, whereas single deletions reduced virulence and genetic complementation restored disease symptoms. Conversely, expression of the D effector in non-defoliating strains was sufficient to induce defoliation. Moreover, or exogenous application of the purified protein, induced wilting and defoliation as well. Structural analyses revealed that D homologs share a conserved but previously uncharacterized protein fold and are distributed across Verticillium and Fusarium species, exhibiting functional diversification and host-specific activity. Phylogenomic and genomic context analyses indicate repeated horizontal transfer events mediated by giant transposable elements known as Starships. Together, our findings identify the D effector as a central pathogenicity factor that drives defoliation and virulence, and demonstrate how Starship-mediated horizontal gene transfer shapes the emergence and dissemination of an agriculturally devastating fungal trait.

plant biology↗

bioRxiv2025

Undermining the cry for help: The phytopathogenic fungus Verticillium dahliae secretes an antimicrobial effector protein to undermine host recruitment of antagonistic Pseudomonas bacteria

During pathogen attack, plants recruit beneficial microbes in a "cry for help" to mitigate disease development. Simultaneously, pathogens secrete effectors to promote host colonization through various mechanisms, including targeted host microbiota manipulation. Here, we characterize the Av2 effector of the vascular wilt fungus Verticillium dahliae as a suppressor of the cry for help. Inspired by in silico antimicrobial activity prediction, we investigated the antimicrobial activity of Av2 in vitro. Furthermore, its role in V. dahliae virulence was assessed through microbiota sequencing of inoculated plants, microbial co-cultivation assays, and inoculations in a gnotobiotic plant cultivation system. We show that Av2 inhibits bacterial growth, and acts as a virulence factor during host colonization. Microbiota sequencing revealed involvement of Av2 in suppression of Pseudomonas spp. recruitment upon plant inoculation with V. dahliae, suggesting that Av2 suppresses the cry for help. We show that several Pseudomonas spp. are antagonistic to V. dahliae and sensitive to Av2 treatment. We conclude that V. dahliae secretes Av2 to supress the cry for help by inhibiting the recruitment of antagonistic Pseudomonas spp. to pave the way for successful plant invasion.

plant biology↗

bioRxiv2018

Deep Learning Predicts Tuberculosis Drug Resistance Status from Whole-Genome Sequencing Data

BackgroundThe diagnosis of multidrug resistant and extensively drug resistant tuberculosis is a global health priority. Whole genome sequencing of clinical Mycobacterium tuberculosis isolates promises to circumvent the long wait times and limited scope of conventional phenotypic antimicrobial susceptibility, but gaps remain for predicting phenotype accurately from genotypic data.\n\nMethods and FindingsUsing targeted or whole genome sequencing and conventional drug resistance phenotyping data from 3,601 Mycobacterium tuberculosis strains, 1,228 of which were multidrug resistant, we investigated the use of machine learning to predict phenotypic drug resistance to 10 anti-tuberculosis drugs. The final model, a multitask wide and deep neural network (MD-WDNN), achieved improved high predictive performance: the average AUCs were 0.979 for first-line drugs and 0.936 for second-line drugs during repeated cross-validation. On an independent validation set, the MD-WDNN showed average AUCs, sensitivities, and specificities, respectively, of 0.937, 87.9%, and 92.7% for first-line drugs and 0.891, 82.0% and 90.1% for second-line drugs. In addition to being able to learn from samples that have only been partially phenotyped, our proposed multidrug architecture shares information across different anti-tuberculosis drugs and genes to provide a more accurate phenotypic prediction. We use t-distributed Stochastic Neighbor Embedding (t-SNE) visualization and feature importance analyses to examine inter-drug similarities.\n\nConclusionsMachine learning is capable of accurately predicting resistant status using genomic information and holds promise in bringing sequencing technologies closer to the bedside.

bioinformatics↗