Comparative Genomics of Ascomycete Fungi

The genome reference sequences of the other 14 Ascomycetes species (see Supplementary Tables S1, S2 in the supplemental materials) were downloaded from the NCBI database and were used to construct gene families. Sequence alignment was done with MUSCLE (Edgar, 2004 (link)), and positions containing gaps of ≥80% in multiple sequence alignment were trimmed using TrimaAI v1.4. rev22 (Capella-Gutiérrez et al., 2009 (link)). The comparison and annotation of orthologous gene clusters were carried out using OrthoFinder 2.2.7 (Emms and Kelly, 2019 (link)). Phylogenetic trees were constructed using the maximum-likelihood approach implemented in RAxML v8.0 (Stamatakis, 2014 (link)), the sequence of Coccidioides immitis (Stiles) (GenBank accession number GCA_000146045.2) was used as an outgroup. Gene family expansion and contraction were identified using CAFE v4.2 (De Bie et al., 2006 (link)). A time-calibrated phylogeny was inferred under the Bayesian framework employing fossil information (Drummond and Rambaut, 2007 (link)). The chronograms shown were calculated using the median clade credibility tree and 95% confidence intervals. The PAML mcmctree v4.5 program (Yang and Rannala, 2006 (link)) was used to compute split times using the approximate likelihood calculation algorithm. The model of sequence evolution was determined using Modeltest 3.7⁵. Tracer v1.5.0⁶ was applied to examine convergence, and two independent runs were performed for confirmation.