## 2 Materials and Methods
The soft-masked genomes from NCBI (17 _Nectriaceae_ and 2 outgroup taxa), together with the newly assembled genome of _Neonectria lugdunensis_, were then submitted to the Braker3 v3.0.3 [64] pipeline to perform ab initio gene prediction with the parameters \"--esmode\" and \"--fungus\", using, therefore, the software GeneMarker-ES v4.71_lic [65], to produce de novo hints to train Augustus v3.5.0 [66], which then predicted the amino acid sequences of each genome. The produced amino acid sequences were used in Orthofinder v3.0.0 [67] with the \"-og\" option to predict only the single orthologs common to all species in this study, followed by generating sequence clusters. Each cluster was aligned using MAFFT v7.520 [68] with the option \"--auto\" and trimmed using Trimal v1.4.rev15 [69] with the option \"-automated1\" to remove poor alignment regions. The phylogenetic clusters were than merged into a unique phylogenetic tree using IQTREE2 v2.2.2.7 [70] with the options -bb 1000 -m TEST. The -m TEST parameter stands for ModelFinder [71], which searches for the best evolutive model for each gene cluster, considering the evolutionary specificity of each gene. To investigate the genetic potential of the _Nectriaceae_ fungi for secondary metabolite production, the AntiSMASH fungal cluster predictor (v7.0.1) [72] was implemented. The presence of genes and clusters associated with the biosynthesis of secondary metabolites was assessed in every genome. Fasta files containing genome sequences were utilized as inputs, with the default search parameter set to \"relaxed\". Every additional feature was enabled, including cluster border prediction by utilizing transcription factor binding sites (CASSIS). The predicted amino acid sequences from the Braker3 pipeline were used for secretome prediction using a combination of tools. To predict where the provided protein \begin{table}
\begin{tabular}{c c c c c c} \hline \hline
**Species** & \begin{tabular}{c} **Genome Length** \\ **(Mbp)** \\ \end{tabular} & \begin{tabular}{c} **Genome Compl.** \\ **(\%)** \\ \end{tabular} & \
\begin{tabular}{c} **GC Content** \\ **(\%)** \\ \end{tabular} &
\begin{tabular}{c} **N50** \\ **Accession** \\ \end{tabular} \\ \hline _Aquanectria pencillioides_ & 53.76 & 95.0\% & 47.94 & 4.93 Mbp & GCA\_003415625.1 \\ \hline _Calonectria pteridis_ & 58.37 & 97.7\% & 50.21 & 3.2 Mb & GCA\_022837005.1 \\ \hline _Cylindricalrudendrum hubetiene_ & 48.81 & 96.5\% & 51.81 & 85.2 Kb & GCA\_014621425.1 \\ \hline _Dactyloncteris alaccerensis_ & 61.76 & 97.9\% & 49.86 & 4.3 Mb & GCA\_029931735.1 \\ \hline _Fusarium nematophilum_ & 50.82 & 96.4\% & 53.92 & 148.30 Kb & GCA\_033030565.1 \\ \hline _Fusarium parananese_ & 53.40 & 98.2\% & 49.21 & 859.2 Kb & GCA\_027886155.1 \\ \hline _Ilyonectria robusta_ & 59.64 & 97.5\% & 51.68 & 1.2 Mb & GCF\_021365365.1 \\ \hline _Marianmaea_ sp. PMI 226 & 42.25 & 97.7\% & 48.55 & 2.9 Mb & GCA\_024336345.1 \\ \hline _Neonectria coccinea_ & 42.74 & 97.3\% & 51.65 & 178.8 Kb & GCA\_019137265.1 \\ \hline _Noncteria ditissima_ & 44.95 & 97.5\% & 51.83 & 1.8 Mb & GCA\_001305505.1 \\ \hline _Noncteria fagimata_ & 42.94 & 97.4\% & 52.48 & 4.4 Mb & GCA\_030864175.1 \\ \hline _Noncteria galligena_ & 41.00 & 96.7\% & 53.9 & 31.3 Kb & GCA\_013759035.1 \\ \hline _Neonectria lederae_ & 43.28 & 97.5\% & 49.43 & 248.9 Kb & GCA\_003385265.1 \\ \hline _Neonectria lugdunensis_ & 44.78 & 97.6\% & 52.17 & 44.7 Mb & GCA\_041721585.1 \\ \hline _Neonectria punicea_ & 41.47 & 96.8\% & 52.72 & 41.4 Mb & GCA\_003385315.1 \\ \hline _Neonectria sp. DH2 & 45.82 & 94.8\% & 52.99 & 45.8 Mb & GCA\_003934905.1 \\ \hline _Rugonectria rugulosa_ & 46.95 & 97.6\% & 51.43 & 56.0 Kb & GCA\_023509875.1 \\ \hline _Thelonectria discophora_ & 41.60 & 97.8\% & 54.16 & 41.6 Mb & GCA\_911649645.1 \\ \hline \hline \end{tabular}
\end{table} 
Table 1: Basal genome information of the _Nectriaceae_ family in this study. The plant pathogen fungus _N. galligent_’s current name is _N. ditissima_.