Comparative analyses of the Hymenoscyphus fraxineus and Hymenoscyphus albidus genomes reveals potentially adaptive differences in secondary metabolite and transposable element repertoires

<strong>Background </strong>The dieback epidemic decimating common ash (<em>Fraxinus excelsior</em>) in Europe is caused by the invasive fungus <em>Hymenoscyphus fraxineus</em>. In this study we analyzed the genomes of <em>H. fraxineus</em> and <em>H. albidus</em>, its native but, now essentially displaced, non-pathogenic sister species, and compared them with several other members of <em>Helotiales</em>. The focus of the analyses was to identify signals in the genome that may explain the rapid establishment of <em>H. fraxineus</em> and displacement of <em>H. albidus</em>. <strong>Results</strong> The genomes of <em>H. fraxineus</em> and <em>H. albidus </em>showed a high level of synteny and identity. The assembly of <em>H. fraxineus </em>is 13 Mb longer than that of <em>H. albidus’, </em>most of this difference can be attributed to higher dispersed repeat content ((i.e transposable elements [TEs]) in <em>H. fraxineus</em>. In general, TE families in <em>H. fraxineus</em>showed more signals of repeat-induced point mutations (RIP) than in <em>H. albidus</em>, especially in Long-terminal repeat (LTR)/Copia and LTR/Gypsy elements. Comparing gene family expansions and 1:1 orthologs, relatively few genes show signs of positive selection between species. However, several of those that did appeared to be associated with secondary metabolite genes families, including gene families containing two of the genes in the <em>H. fraxineus-</em>specific, <em>hymenosetin </em>biosynthetic gene cluster (BGC). <strong>C</strong><strong>onclusion </strong>The genomes of <em>H. fraxineus</em> and <em>H. albidus</em> show a high degree of synteny, and are rich in both TEs and BGCs, but the genomic signatures also indicated that <em>H. albidus</em> may be less well equipped to adapt and maintain its ecological niche in a rapidly changing environment. <strong>Data included</strong> This post contains the alternate structural and functional annotations of the genomes of Helotealean fungi used in the study.