Whole-genome assembly and comparative genomic analyses provide insight into the endophytic lifestyle of Trichoderma lixii.

Trichoderma species exhibit remarkable versatility in adaptability and in occupying habitats with lifestyles ranging from mycoparasitism and saprotrophy to endophytism. In this study, we present the first high-quality whole-genome assembly and annotation of T. lixii using Illumina HiSeq technology to explore the mechanisms of endophytic lifestyle and plant colonization. The genome size was 41.1 Mbp, comprising 15,430 predicted genes, of which 7,918 were functionally annotated. Comparative analysis identified 82 CAZyme families involved in cellulose and hemicellulose degradation, notably Glycoside Hydrolases (GHs) (43) [e.g., GH3 (14), GH5 (10), GH7 (4) ], Carbohydrate Esterases (CEs) (10), and Auxiliary Activities (AAs) (29) [e.g., AA3 (20), AA9 ]. GHs primarily degrade cellulose, while Polysaccharide Lyases (PLs), along with other CAZymes like CEs and Lytic Polysaccharide Monooxygenases (LPMOs), assist in modifying substrates or targeting specific bonds. These enzymes facilitate substrate breakdown, host tissue penetration, and nutrient acquisition, supporting a non-pathogenic, endophytic lifestyle. The presence of 53 secondary metabolite biosynthetic gene clusters indicates a strong biosynthetic potential. KEGG analysis assigned 2,469 genes to multiple metabolic and signaling pathways, highlighting an enriched profile for carbohydrate metabolism, signal transduction, and antibiotic biosynthesis. Comparative genomics also revealed both preserved and distinctive traits of T. lixii, confirming its ecological flexibility and promise as a source of new bioactive molecules. These findings reveal genetic diversity among the species, providing a foundation for future studies on biocontrol and endophytic functions. The growing availability of Trichoderma genomes deepens understanding of their unique features and offers new prospects for agricultural and biotechnological applications.