In this study, we isolated 633 Trichoderma strains from 15 forest types across six climate zones. Our findings revealed that species diversity was highly underestimated, with 239 isolates identified as new species based on ITS, rpb2, and tef1 sequences. In tropical and subtropical regions, the mean values for the haplotype Chao1 richness index and the Shannon-Weiner diversity index are 73 and 3, respectively, significantly higher than those in temperate regions. Trichoderma cf. taiwanense was the most widely distributed, followed by T. asperellum, rather than widely reported T. harzianum. The maximum entropy model was used to analyse the effects of climatic factors on distribution of T. cf. taiwanense and T. asperellum, and showed that precipitation in the warmest quarter was the most important factor influencing their distribution. T. cf. taiwanense zj625y demonstrated significantly higher antagonistic ability, outperforming the other tested Trichoderma species. The genomic characteristics of T. cf. taiwanense were firstly revealed with 36.49 Mbp in size and contained 17 genes of β-1,3-glucanase and 24 genes of chitinase genes. Additionally, the activities of endochitinase, endo-1,3(4)-β-glucanase, and metallopeptidase were highly expressed in culture. Metabolomic analysis further identified specific substances produced by T. cf. taiwanense zj625y, such as ergothioneine, (3-carboxypropyl) trimethylammonium cation, NG-dimethyl-L-arginine (ADMA), N-acetyl-D-glucosamine, stearic acid, tyramine, citrate, L-leucine, and acetylcarnitine, which contribute to its potential antagonism and environmental adaptability.

Circular RNAs (circRNAs) are a group of widely discovered non-coding RNAs in different organisms, but their biological functions are largely unknown, especially in plant–microbial interactions. In this study, we identified an exonic circRNA (Che-circR2410) from the fungus Cochliobolus heterostrophus that, together with its corresponding linear RNA ChCYP51, synergistically regulates the virulence of C. heterostrophus to maize. Further in situ hybridization and dual-luciferase reporter assays revealed the interaction between pathogenic circRNA Che-circR2410 and its cross-kingdom host target, zma-miR399e-5p. Additionally, lesion areas caused by both the wild type C. heterostrophus and the circR2410 knock-out strain (ΔChcircR2410) showed no significant difference on the maize miR399e silencing mutant, providing support for the interaction between Che-circR2410 and zma-miR399e-5p. Moreover, we found that zma-miR399e affects the expression of autophagy-related genes, regulating maize immunity. Thus, our findings reveal a cross–kingdom interaction between the pathogenic exonic circRNA and host miRNA, modulating C. heterostrophus infection in maize. This study broadens our understanding of the C. heterostrophus-maize interaction at the level of non-coding RNA.