## 4 Discussion  
Endophytes exist within plant tissue without causing apparent harm to the host, whereas plant pathogens infect and cause illness in plants. Both of these groups work closely with living plant cells, overcoming the plant's immunological defenses and adapting to its metabolic environment [80; 81; 82; 83]. These interactions need a complex set of genes that create enzymes, toxins, and other compounds that aid the invasion of plant cells, suppressing the plant immune system's responses, and manipulating the plant's metabolism. As a result, their genomes frequently contain genes for complicated secondary metabolite production, a variety of transporters, and genes that confer resistance to plant defense mechanisms [84; 85]. On the other hand, saprobe fungi, as decomposers of organic material, require a different set of enzymatic tools focused primarily on breaking down cellulose, lignin, and other plant structural components. While this still requires a diverse set of enzymes, the interaction with non-living material is less complex than manipulating and responding to living cells; therefore, it is expected that saprobes have fewer genes than endophytes and plant pathogens [86; 87; 88]. The repetitive elements are microsatellite regions or, more often, transposable elements (transposons), which increase their number in the genome, mainly due to cellular stress, which is not a characteristic of endophyte environments [89; 90; 91]. This corroborates our findings of fewer repetitive elements in endophyte genomes, which is likely influenced by their lifestyle, since being endophytic is a very cost-effective strategy. When establishing themselves within plants, they are shielded from abiotic and biotic challenges, being less subjected to stress, which is a factor involved in the multiplication of transposable elements [92]. Our study confirms the results of [PERSON], 2020 [93], where the number of repetitive elements was a key factor in distinguishing between pathogenic and endophytic fungi, despite its lack of statistical significance. Several studies have found transposable elements to be abundant in plant-pathogenic fungi [94; 95; 96]. In our study, this case was even better observed with retrotransposons, where the difference in occurrence between endophytes and plant pathogens was statistically significant. The amount of retroelements  
Figure 6: Principal component analysis (PCA) of fungal species based on lifestyle considering secreted genes, effector proteins, and total biosynthetic gene clusters. identified in endophytes is smaller than in sap probe and statistically significantly smaller than in plant pathogens. Transposable elements contribute significantly to genomic plasticity, which is crucial in adapting to host defenses. For instance, in the case of the plant pathogen _Verticillium dahliae_, TEs exert an influence on gene expression variations that are essential for pathogenicity, enabling the fungus to adapt rapidly to host-induced stresses or resistance [97]. Meanwhile, saprobe fungi are not known for presenting large amounts of TEs [98; 99; 95], since they have a lesser requirement for adaptation to host living cells and may reside in less stressful environments [100; 101; 102], although the higher number of TEs found for saprobes in our study could indicate potential adaptation to more dynamic or challenging environmental conditions [95]. The secretome of fungi, which includes CAZy enzymes, plays a pivotal role in the interaction between fungi and plants. These enzymes are crucial not only in breaking down the complex polysaccharides found in plant cell walls, which aids in nutrient acquisition and infection processes, but also in helping fungi to evade plant immune responses, facilitating their survival and propagation in various environments [103; 104; 105]. The CAZymes of classes CE, GH, and PL are often referred to as plant-litter-degrading enzymes because they play crucial roles in the degradation of plant biomass by fungi and bacteria [106].