Isolation, Biocontrol Efficacy and Genomic Analysis of Trichoderma harzianum Snef3255 Against Peanut Root-Knot Nematode Disease

Peanut root-knot nematode (RKN) disease caused by Meloidogyne hapla is among the most destructive soil-borne diseases threatening peanut production worldwide. We isolated Trichoderma harzianum strain Snef3255 from peanut rhizosphere soil, which exhibited high virulence against second-stage juveniles, with a mortality rate of 86.08%. Field trials demonstrated that TC and TS provided control efficacies of 70.85% and 61.88%, respectively, while boosting peanut yields by 18.15% and 13.61%. We report a high-quality chromosome-level genome assembly of T. harzianum Snef3255 using Oxford Nanopore, Illumina and high-throughput chromatin conformation capture (Hi-C) sequencing data. This assembly comprised seven chromosomes (40,811,729 bp) with a BUSCO completeness of 99.31%. A total of 13,611 protein-coding genes were predicted. Systematic comparative genomic analysis of T. harzianum Snef3255 with other Trichoderma species was performed, and putative functional gene clusters were investigated. Furthermore, we identified two candidate secreted proteins, ThCP1 and ThLysM1, and screened their interacting proteins in peanut, respectively. This study demonstrated the potential of Snef3255 as a biocontrol agent for peanut RKN disease and provided a genomic basis for understanding Trichoderma–peanut interactions.