## 3 Results  
The newly assembled genome of _Neonectria lugdunensis_ has 44.78 Mbp and 97.6% genome completeness with N50 of 44.7 Mbp, showing similar characteristics to many genomes available in NCBI from _Nectriaceae_, as shown in this study (Table 1). We detected 4.38% of repetitive elements in _N. lugdunensis_, where 2.04% were retroelements and 0.33% were DNA transposons. Only 207 sequences of tRNA were identified in _N. lugdunensis_, which is the smallest amount in comparison with the freshwater saprobe fungus _Aquancetria pencillioides_ (222) and the soil saprobe _Thelonectria discophora_ (225). _N. lugdunensis_ has fewer predicted genes (11,480) than the freshwater saprobe _Aquancetria pencillioides_ with 12,575, although this is higher than the soil saprobe _Thelonectria discophora_ with 10,364 genes. This result is also reflected in the number of secreted proteins of _N. lugdunensis_ being smaller (797) than that of freshwater _A. pencillioides_ (820) and higher than that of the soil saprobe _Thelonectria discophora_ (655). It is also reflected in the number of effector genes (229 in _N. lugdunensis_, 254 in _A. pencillioides_, and 191 in soil saprobe _T. discophora_) (Table S1). Regarding BGCs, _N. lugdunensis_ had higher amounts among saprobe fungi with 48 predicted clusters, followed by the other freshwater fungus _A. pencillioides_ with 40 and the soil saprobe _T. discophora_ with 33 (Table S2). _N. lugdunensis_ was the only freshwater fungus in this study to have a BGC for NRP metallophore. The species _Ilyonectria robusta_ (current name according to Mycobank: _Ramularia robusta_) is known to be a plant pathogen and endophyte. However, the genome strain was isolated as an endophyte ([[https://mycocosm.jgi.doe.gov/Ilyrob1/Ilyrob1.home.html](https://mycocosm.jgi.doe.gov/Ilyrob1/Ilyrob1.home.html)]([https://mycocosm.jgi.doe.gov/Ilyrob1/Ilyrob1.home.html](https://mycocosm.jgi.doe.gov/Ilyrob1/Ilyrob1.home.html)), accessed on 20 November 2023) and it is therefore presented in this study as such (Table S1). We obtained 2684 single-copy ortholog genes, which yielded a robust, well-resolved, and comprehensive phylogeny for the _Nectriaceae_ family (Figure 1). The internodes in the tree received a strong bootstrap value higher than 95%, indicating a strongly supported tree that was not particularly associated with the lifestyle of the fungi. _Neonectria galligena_ is nowadays a known synonym for _Neonectria ditissima_ and they have been described as being the same species since 1995 [8], although, in the NCBI database, both names are represented with different genomes. The genome-to-genome analysis through ANI confirmed that they are the same species (ANI value of 98.91%), but the enzymatic profile suggests that they are from different strains, presenting different phenotypes, and therefore the synonymy is kept in this study. All other genome comparisons using ANI showed values smaller than 95% between the species' genomes. Our results show that the genome length of endophyte organisms was, on average, larger (49.24 Mbp) than that of plant pathogens (48.04 Mbp) and saprobes (46.71 Mbp), despite the largest genome in the study being that of _Dactylonectria alacerensis_, which is a plant pathogen, with 61.76 Mbp (Figure S1). This value was also reflected in the average number of amino acid sequences predicted, where endophytes (12,971) had the highest, followed by plant pathogens (12,798) and saprobes (11,473) (Figure S2). However, we observed a change in the GC content, where the highest average was found in the plant pathogens compared to saprobe fungi and endophytes (51.54, 51.42, and 51.07, respectively) (Figure S3). The plant-pathogenic fungi in this study presented more tRNA on average than saprobes and endophytes (218.42, 218.00, and 212.67 respectively). We observed a large variation in the repetitive elements according to the fungi' lifestyles (Figure S5), where, on average, the saprobes (7.35) had more repetitive elements than plant pathogens (5.28) and endophytes (3.13).