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. 2021 Jul 4;22(1):503.
doi: 10.1186/s12864-021-07837-2.

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

Malin Elfstrand  1 , Jun Chen  2   3 , Michelle Cleary  4 , Sandra Halecker  5 , Katarina Ihrmark  2 , Magnus Karlsson  2 , Kateryna Davydenko  2   6 , Jan Stenlid  2 , Marc Stadler  5 , Mikael Brandström Durling  2
Affiliations

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

Malin Elfstrand et al. BMC Genomics. .

Abstract

Background: The dieback epidemic decimating common ash (Fraxinus excelsior) in Europe is caused by the invasive fungus Hymenoscyphus fraxineus. In this study we analyzed the genomes of H. fraxineus and H. albidus, its native but, now essentially displaced, non-pathogenic sister species, and compared them with several other members of Helotiales. The focus of the analyses was to identify signals in the genome that may explain the rapid establishment of H. fraxineus and displacement of H. albidus.

Results: The genomes of H. fraxineus and H. albidus showed a high level of synteny and identity. The assembly of H. fraxineus is 13 Mb longer than that of H. albidus', most of this difference can be attributed to higher dispersed repeat content (i.e. transposable elements [TEs]) in H. fraxineus. In general, TE families in H. fraxineus showed more signals of repeat-induced point mutations (RIP) than in H. albidus, 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 did appeared to be associated with secondary metabolite genes families, including gene families containing two of the genes in the H. fraxineus-specific, hymenosetin biosynthetic gene cluster (BGC).

Conclusion: The genomes of H. fraxineus and H. albidus show a high degree of synteny, and are rich in both TEs and BGCs, but the genomic signatures also indicated that H. albidus may be less well equipped to adapt and maintain its ecological niche in a rapidly changing environment.

Keywords: Ash dieback; Fraxinus excelsior; Secondary metabolites; Transposable elements; Viridiol; invasive species.

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Conflict of interest statement

The authors declare that they have no competing interests.

Figures

Fig. 1
Fig. 1
Genome composition of H. fraxineus, H. albidus and seven other Helotialean species. Gene models and repeats were predicted using the same MAKER and RepeatMasker pipelines, for all eight fungal genomes in the Helotiales (Hymenoscyphus fraxineus, Hymenoscypus albidus, Glarea lozoyensis, Ascocoryne sarcoides, Marssonina brunnea, Sclerotinia borealis, Sclerotinia sclerotiorum and Botrytis cinerea) and the outgroup Blumeria graminis
Fig. 2
Fig. 2
Plot of ω values in genes differently evolving in H. fraxineus (outcrossing) and H. albidus (selfing). In this case differently evolving means better fit of our data to a two-ratio model allowing for a difference in ω between H. fraxineus and H. albidus branches in the tree. For clarity only the differentially evolving genes are plotted
Fig. 3
Fig. 3
Biosynthetic gene cluster (BGC) comparison of H. fraxineus and H. albidus BGCs associated with the production of viridiol and hymenosetin. The clusters were identified using TBLASTX visualized by clinker: (a) Gene map of the known demethoxyviridin (vid) BGC from Nodulisporium sp. (Nsp) and the identified homologous viridiol (vir) BGC from H. fraxineus nf4 (Hf) and H. albidus 111/1/4 (Ha). The structures of the respective pathway products are shown; (b) Gene map of the known equisetin (eqx) BGC from Fusarium heterosporum (Fh) and the respective homologous hym BGC from H. fraxineus nf4 (Hf) putatively responsible for hymenosetin production. In H. albidus, most likely a deletion event of a 10 kb fragment of genomic DNA took place within the hym cluster and lead to the absence of essential members of the hym cluster. The structures of the respective pathway products are shown below
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