## 3 Results
When observing the repetitive element sequences with origins in retroelements, we found statistically significant differences between endophytes (0.69) and plant pathogens (2.60) (Figure 2). The difference in retroelements between saprobes--the largest on average with 3.67--and plant pathogens was not significant; the same was true for saprobes and endophytes. Regarding the repetitive elements classified as DNA transposons (Figure S6), we observed a shift where saprobes had more repetitive DNA transposons on average (0.75) than endophytes (0.68) and plant pathogens (0.53) (Figure S6). Figure 1: Phylogenomic tree of _Nectriaceae_ genomes. Phylogenomic tree of _Nectriaceae_ family using 2684 single-copy orthologs genes. The plant pathogen fungus _N. galligena_’s current name is _N. ditissima_. The species in red represent plant pathogens, while those in green are endophytes and those in brown are saprobes. (*) indicates saprobe freshwater fungi. Log-likelihood of consensus tree \(-\)18,240,846.991. The number of genes present in endophytes was also higher than in plant pathogens and saprobes (Table S1). The number of secreted genes was higher in plant pathogens than in endophytes and saprobe fungi (953.33, 907, and 757.33, respectively) (Figure S7). The number of secreted genes with cold properties was higher in endophytes (382.67) than in plant pathogens (359.92) and saprobes (313.33) (Figure S8). On the other hand, the number of secreted genes with thermo-resistance was higher in plant pathogens (217.17) than endophytes (196.33) and the difference was statistically significant among plant pathogens and saprobes (146.00) (Figure 3). The average number of effector proteins secreted by endophytes (278.33) is higher than in plant pathogens (268.17) and saprobes (224.67) (Figure S9). The temperature adaptation for effector genes shows statistical significance between endophytes and saprobes for cold and thermal adaptation, where the number of effector genes adapted to cold was higher in endophytes (166.33), followed by plant pathogens (145.42) and saprobes (126.67) (Figure 4). The endophytes also showed higher potential in adapting to warmer temperatures than plant pathogens and saprobes (65.00, 59.08, and 44.67, respectively) (Figure 5). Endophytes have been shown to have more effector genes on average with apoplastic characteristics (237.00) than plant pathogens (223.92) and saprobes (190.67) (Figure S10). On the other hand, the difference in the number of effector genes with cytoplasmatic characteristics is shown to be statistically significant between endophytes (99.93 on average) and saprobes (71.00 on average); despite this, plant pathogens (101.58) had higher numbers than endophytes and saprobes (Figure S11). Figure 2: Comparative analysis of retroelement counts among different fungal lifestyles. Distribution of retroelements across three fungal lifestyles: endophytes, plant pathogens, and saprobes. Endophytes: represented in green, the retroelement counts for endophytes are low, with an average count of 0.69. The box plot shows minimal variation, with most values clustering around the average. Plant pathogens: represented in red, plant pathogens exhibit a higher average retroelement count of 2.60. The distribution shows greater variability compared to endophytes, with several outliers, indicating significantly higher counts. Saprobes: represented in brown, they have the highest average retroelement count of 3.67. This group shows larger variability in its retroelement counts. Figure 4: Comparative analysis of secreted cold effector counts among different fungal lifestyles. Differences in effector genes adapted to colder temperatures in endophytes, plant pathogens, and saprobe fungi. Endophytes: represented by green, the cold effector counts for endophytes have an average value of 166.33. The box plot shows moderate variation, with values clustering around the average. Plant pathogens: represented by red, plant pathogens exhibit a lower average cold effector count of 145.42 compared to endophytes.