Comparative Biocontrol Efficacy and Genomic Profiling of Indigenous Trichoderma virens against Ganoderma boninense

Abstract

Basal Stem Rot (BSR), caused by the fungus Ganoderma boninense, is a major disease in oil palm that leads to serious yield losses and threatens plantation sustainability. Since chemical control methods are often less effective and raise environmental concerns, biological control using beneficial fungi such as Trichoderma is considered a promising alternative. This study evaluated indigenous Trichoderma isolates for their ability to suppress G. boninense using DNA-based identification, molecular analysis, and dual culture assays to test antifungal activity. The most effective isolate (with 82.35% suppression efficiency) was further studied through Whole Genome Sequencing and was further characterized and identified as Trichoderma virens IPS5–T1 with genome size of 40.6 Mbp and GC content 47.35%, and a phylogenetic analysis was performed to understand genetic relationships. BUSCO analysis revealed 99.2% of the genome consisted of complete single-copy genes, 0.3% of them are complete but duplicated, only 0.1% and 0.3% of them are fragmented and missing. Microsatellite profiles of T. virens genomes were found to be highly conserved, serving as potential strong preliminary biomarker for Trichoderma species identification. Overall, the study highlights the potential of native T. virens in developing sustainable and eco-friendly strategies to manage BSR in oil palm plantations.