Skip to main content

Lund University Publications

LUND UNIVERSITY LIBRARIES

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

Harder, Christoffer Bugge LU ; Miyauchi, Shingo ; Virágh, Máté ; Kuo, Alan ; Thoen, Ella ; Andreopoulos, Bill ; Lu, Dabao ; Skrede, Inger ; Drula, Elodie and Henrissat, Bernard , et al. (2024) In Cell Genomics 4(7).
Abstract

Mycena s.s. is a ubiquitous mushroom genus whose members degrade multiple dead plant substrates and opportunistically invade living plant roots. Having sequenced the nuclear genomes of 24 Mycena species, we find them to defy the expected patterns for fungi based on both their traditionally perceived saprotrophic ecology and substrate specializations. Mycena displayed massive genome expansions overall affecting all gene families, driven by novel gene family emergence, gene duplications, enlarged secretomes encoding polysaccharide degradation enzymes, transposable element (TE) proliferation, and horizontal gene transfers. Mainly due to TE proliferation, Arctic Mycena species display genomes of up to 502 Mbp (2–8× the temperate Mycena),... (More)

Mycena s.s. is a ubiquitous mushroom genus whose members degrade multiple dead plant substrates and opportunistically invade living plant roots. Having sequenced the nuclear genomes of 24 Mycena species, we find them to defy the expected patterns for fungi based on both their traditionally perceived saprotrophic ecology and substrate specializations. Mycena displayed massive genome expansions overall affecting all gene families, driven by novel gene family emergence, gene duplications, enlarged secretomes encoding polysaccharide degradation enzymes, transposable element (TE) proliferation, and horizontal gene transfers. Mainly due to TE proliferation, Arctic Mycena species display genomes of up to 502 Mbp (2–8× the temperate Mycena), the largest among mushroom-forming Agaricomycetes, indicating a possible evolutionary convergence to genomic expansions sometimes seen in Arctic plants. Overall, Mycena show highly unusual, varied mosaic-like genomic structures adaptable to multiple lifestyles, providing genomic illustration for the growing realization that fungal niche adaptations can be far more fluid than traditionally believed.

(Less)
Please use this url to cite or link to this publication:
author
; ; ; ; ; ; ; ; and , et al. (More)
; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; and (Less)
organization
publishing date
type
Contribution to journal
publication status
published
subject
keywords
Arctic biology, biotrophy–saprotrophy evolution, carbon degradation, fungal genomics, fungal guild, genome size diversity, plant-fungus interactions, root-associations, saprotrophs, TE proliferation
in
Cell Genomics
volume
4
issue
7
article number
100586
publisher
Cell Press
external identifiers
  • pmid:38942024
  • scopus:85198033926
ISSN
2666-979X
DOI
10.1016/j.xgen.2024.100586
language
English
LU publication?
yes
id
1d439e59-104f-46a9-8ca0-0d6946eb4904
date added to LUP
2024-09-24 15:36:27
date last changed
2024-10-08 19:29:44
@article{1d439e59-104f-46a9-8ca0-0d6946eb4904,
  abstract     = {{<p>Mycena s.s. is a ubiquitous mushroom genus whose members degrade multiple dead plant substrates and opportunistically invade living plant roots. Having sequenced the nuclear genomes of 24 Mycena species, we find them to defy the expected patterns for fungi based on both their traditionally perceived saprotrophic ecology and substrate specializations. Mycena displayed massive genome expansions overall affecting all gene families, driven by novel gene family emergence, gene duplications, enlarged secretomes encoding polysaccharide degradation enzymes, transposable element (TE) proliferation, and horizontal gene transfers. Mainly due to TE proliferation, Arctic Mycena species display genomes of up to 502 Mbp (2–8× the temperate Mycena), the largest among mushroom-forming Agaricomycetes, indicating a possible evolutionary convergence to genomic expansions sometimes seen in Arctic plants. Overall, Mycena show highly unusual, varied mosaic-like genomic structures adaptable to multiple lifestyles, providing genomic illustration for the growing realization that fungal niche adaptations can be far more fluid than traditionally believed.</p>}},
  author       = {{Harder, Christoffer Bugge and Miyauchi, Shingo and Virágh, Máté and Kuo, Alan and Thoen, Ella and Andreopoulos, Bill and Lu, Dabao and Skrede, Inger and Drula, Elodie and Henrissat, Bernard and Morin, Emmanuelle and Kohler, Annegret and Barry, Kerrie and LaButti, Kurt and Salamov, Asaf and Lipzen, Anna and Merényi, Zsolt and Hegedüs, Botond and Baldrian, Petr and Stursova, Martina and Weitz, Hedda and Taylor, Andy and Koriabine, Maxim and Savage, Emily and Grigoriev, Igor V. and Nagy, László G. and Martin, Francis and Kauserud, Håvard}},
  issn         = {{2666-979X}},
  keywords     = {{Arctic biology; biotrophy–saprotrophy evolution; carbon degradation; fungal genomics; fungal guild; genome size diversity; plant-fungus interactions; root-associations; saprotrophs; TE proliferation}},
  language     = {{eng}},
  number       = {{7}},
  publisher    = {{Cell Press}},
  series       = {{Cell Genomics}},
  title        = {{Extreme overall mushroom genome expansion in Mycena s.s. irrespective of plant hosts or substrate specializations}},
  url          = {{http://dx.doi.org/10.1016/j.xgen.2024.100586}},
  doi          = {{10.1016/j.xgen.2024.100586}},
  volume       = {{4}},
  year         = {{2024}},
}