Genome-assembly-T_gamsii_T035 Pipeline to assemble and annotate the genome of Trichoderma gamsii strain T035 from Oxford Nanopore Technologies (ONT) reads. Overview This repository contains all data, scripts, and results used in the assembly, annotation, and validation of the T035 genome. It also includes data and scripts used to evaluate the biocontrol capacity of T. gamsii T035 and perform comparative genomics. Repository Structure data/ Contains strain information, transcriptomic data, and supplementary tables. "List_of_transcriptomic_data.xlsx": Origin of transcriptomic data used to confirm the quality of the genome structural annotation. "Strains_for_MashTree.xlsx": Names and origins of all strains used to generate the MashTree presented in Figure 2. "Table pathogens.xlsx": Names and origins of plant pathogens used to evaluate the biocontrol capacity of T. gamsii T035. "Supplementary_tables.xlsx": All supplementary tables relevant to the study. results/ Contains supplementary figures and genome annotations. "Supplementary_Figure_S1.png": Scale used to evaluate T. gamsii overgrowth on several plant pathogens (Figure 4A). "T_gamsii_T035.gff": Structural genome annotation obtained with Helixer. "T_gamsii_T035_anno.gff": Structural annotation supplemented with functional annotation from Eggnog. scripts/ All scripts used in the study, organized by analysis type. Annotation/ "EDTA": SLURM script to detect transposable elements. Outputs summarized in Supplementary Table S4 ("Supplementary_tables.xlsx"). "GFFread.txt": SLURM script to extract CDS, transcript, and protein files from the genome and its GFF annotation. Genome_assembly/ "Genome_assembly_contigs.txt": SLURM script to assemble T035 genome de novo using sequencing reads from BioProject PRJNA1327094. "Contigs_to_scaffolds_Ragtag": SLURM script to scaffold contigs using the T. atroviride reference genome (GCF_020647795.1). The resulting assembly has been submitted to the same BioProject (PRJNA1327094) but is not yet publicly available (as of 07/10/2025). In_vitro_tests/ "Antibiosis_script": Script to generate Figure 4B’s boxplot from "test.xlsx". "Parasitism_script.txt": Script to generate Figure 4A’s radar plot from "df.xlsx". "df.xlsx": Data for the radar plot (Figure 4A). Column A: tested pathogens; Column B: antagonist strain (I1237 or T035); Columns C & D: technical and biological replicates; Column E: parasitic graduation (see "Supplementary_Figure_S1.png"). "test.xlsx": Data for the boxplot (Figure 4B). Column A: bacterial pathogens; Column B: antagonist strain (I1237, T035, or control); Columns C & D: technical and biological replicates; Column E: area under the curve (AUC) of bacterial growth, measured by spectrophotometry. Mash_comparison/ "MashTree": SLURM script to generate the Newick tree for Figure 2. Genomes used are listed in "Strains_for_MashTree.xlsx". Validation_with_STAR/ "STAR": SLURM script to validate the structural genome annotation ("T_gamsii_T035.gff") using public transcriptomic data ("List_of_transcriptomic_data.xlsx"). Usage Scripts are designed for SLURM-based clusters with Conda environments. Genome Data Availability BioProject: PRJNA1327094 (Trichoderma gamsii strain T035 genome sequencing) BioSample: SAMN51264459 SRA: SRR35336635 TaxID: 398673 Citation If you use this dataset or pipeline, please cite: Draft genome of Trichoderma gamsii strain T035 a promising beneficial fungus in agriculture (https://doi.org/10.1101/2025.09.22.677720). GitHub Repository The scripts and pipeline are also available on GitHub: https://github.com/JustiCol/Genome-assembly-T_gamsii_T035/tree/main.

Addition of a more detailed README.