Extreme overall mushroom genome expansion in Mycena s.s. irrespective of plant hosts or substrate specializations

• Published in: Cell Genomics
• Main Authors: Harder, Christoffer Bugge, Miyauchi, Shingo, Virágh, Máté, Kuo, Alan, Thoen, Ella, Andreopoulos, Bill, Lu, Dabao, Skrede, Inger, Drula, Elodie, Henrissat, Bernard, Morin, Emmanuelle, Kohler, Annegret, Barry, Kerrie, LaButti, Kurt, Salamov, Asaf, Lipzen, Anna, Merényi, Zsolt, Hegedüs, Botond, Baldrian, Petr, Stursova, Martina, Weitz, Hedda, Taylor, Andy, Koriabine, Maxim, Savage, Emily, Grigoriev, Igor V., Nagy, László G., Martin, Francis, Kauserud, Håvard
• Other Authors: University of Aberdeen.Biological Sciences
• Format: Article in Journal/Newspaper
• Language: English
• Published: 2024
• Subjects: Arctic biology; biotrophy–saprotrophy evolution; carbon degradation; fungal genomics; fungal guild; genome size diversity; plant-fungus interactions; root-associations; saprotrophs; TE proliferation; QH301 Biology; Biochemistry; Genetics and Molecular Biology (miscellaneous); Genetics; Supplementary Information; https://doi.org/10.1016/j.xgen.2024.100586; QH301; Arctic; Hess
• Online Access: https://hdl.handle.net/2164/24066; https://doi.org/10.1016/j.xgen.2024.100586; http://www.scopus.com/inward/record.url?scp=85198033926&partnerID=8YFLogxK

We are highly grateful to Thomas Kehlet, Arne Aronsen, and Thomas L\u00E6ss\u00F8e for very valuable help in locating several of the Mycena specimens for culturing. We furthermore wish to thank Cecilie Mathiesen, Jacqueline Hess, and Anna Sterngren for their laboratory assistance and very useful practical suggestions. C.B.H. H.K. I.S. A.T. F.M. and L.G.N. conceived and designed the study. F.M. is coordinating the JGI CSP \u201C1KFG: Deep sequencing of ecologically-relevant Dikarya.\u201D C.B.H. and H.K. conducted fieldwork and collected new Mycena cultures. C.B.H. isolated and grew Mycena cultures, and A.T. and H.W. provided additional cultures. C.B.H. E.T. and D.L. performed DNA/RNA extraction. P.B. and M.S. analyzed the enzyme cultures. A.L. K.B. N.B. K.L. A. Kuo, and I.V.G. handled nucleic acids and sequenced, assembled, and annotated the genomes. S.M. performed the comparative secretomic, TE, and genomic analyses. A. Kuo, V.M. Z.M. and L.G.N. analyzed the genome evolution and genomic stability genes. C.B.H. V.M. Z.M. and L.G.N. performed standard/multivariate statistical tests. E.M. and A. Kuo helped analyze the TE annotation. C.B.H. L.G.N. F.M. and S.M. wrote the first version of the manuscript and crafted the revision. All authors helped finalize the manuscript and read and approved it before submission. The authors declare no competing interests. Publisher Copyright: © 2024 The Authors Peer reviewed