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

Elfstrand, Malin and Chen, Jun and Cleary, Michelle and Halecker, Sandra and Ihrmark, Katarina and Karlsson, Magnus and Davydenko, Kateryna and Stenlid, Jan and Stadler, Marc and Brandström Durling, Mikael (2021). Comparative analyses of the Hymenoscyphus fraxineus and Hymenoscyphus albidus genomes reveals potentially adaptive differences in secondary metabolite and transposable element repertoires. BMC Genomics. 22 , 503
[Research article]

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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.

Authors/Creators:Elfstrand, Malin and Chen, Jun and Cleary, Michelle and Halecker, Sandra and Ihrmark, Katarina and Karlsson, Magnus and Davydenko, Kateryna and Stenlid, Jan and Stadler, Marc and Brandström Durling, Mikael
Title:Comparative analyses of the Hymenoscyphus fraxineus and Hymenoscyphus albidus genomes reveals potentially adaptive differences in secondary metabolite and transposable element repertoires
Series Name/Journal:BMC Genomics
Year of publishing :2021
Volume:22
Article number:503
Number of Pages:15
Publisher:BMC
ISSN:1471-2164
Language:English
Publication Type:Research article
Article category:Scientific peer reviewed
Version:Published version
Copyright:Creative Commons: Attribution 4.0
Full Text Status:Public
Subjects:(A) Swedish standard research categories 2011 > 1 Natural sciences > 106 Biological Sciences (Medical to be 3 and Agricultural to be 4) > Genetics (medical genetics to be 30107 and agricultural genetics to be 40402)
Keywords:Ash dieback, Viridiol, Fraxinus excelsior, Transposable elements, Secondary metabolites, invasive species
URN:NBN:urn:nbn:se:slu:epsilon-p-113097
Permanent URL:
http://urn.kb.se/resolve?urn=urn:nbn:se:slu:epsilon-p-113097
Additional ID:
Type of IDID
DOI10.1186/s12864-021-07837-2
Web of Science (WoS)000669296100001
ID Code:25524
Faculty:S - Faculty of Forest Sciences
Department:(NL, NJ) > Dept. of Forest Mycology and Plant Pathology
(S) > Dept. of Forest Mycology and Plant Pathology

(S) > Southern Swedish Forest Research Centre
Deposited By: SLUpub Connector
Deposited On:28 Sep 2021 04:25
Metadata Last Modified:28 Sep 2021 05:01

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