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BMC Genomics. 2018 Jan 15;19(1):48. doi: 10.1186/s12864-017-4430-y.

The genome sequence of the commercially cultivated mushroom Agrocybe aegerita reveals a conserved repertoire of fruiting-related genes and a versatile suite of biopolymer-degrading enzymes.

Gupta DK1,2,3, Rühl M4,3,5, Mishra B1,2,3, Kleofas V4,3, Hofrichter M6, Herzog R7,2,3, Pecyna MJ8, Sharma R1,2,3, Kellner H6, Hennicke F9,10,11,12, Thines M13,14,15.

Author information

1
Senckenberg Biodiversity and Climate Research Centre (BiK-F), Frankfurt a. M., Germany.
2
Institute of Ecology, Evolution and Diversity, Goethe University Frankfurt, Frankfurt a. M., Germany.
3
LOEWE Cluster of Integrative Fungal Research (IPF), Frankfurt a. M., Germany.
4
Institute of Food Chemistry and Food Biotechnology, Justus Liebig University Giessen, Giessen, Germany.
5
Project Group "Bioresources", Fraunhofer IME, Giessen, Germany.
6
International Institute (IHI) Zittau, Technische Universität Dresden, Zittau, Germany.
7
Junior Research Group Genetics and Genomics of Fungi, Senckenberg Gesellschaft für Naturforschung, Frankfurt a. M., Germany.
8
University of Applied Sciences Zittau/Görlitz, Zittau, Germany.
9
Junior Research Group Genetics and Genomics of Fungi, Senckenberg Gesellschaft für Naturforschung, Frankfurt a. M., Germany. florian.hennicke@senckenberg.de.
10
Institute of Ecology, Evolution and Diversity, Goethe University Frankfurt, Frankfurt a. M., Germany. florian.hennicke@senckenberg.de.
11
LOEWE Cluster of Integrative Fungal Research (IPF), Frankfurt a. M., Germany. florian.hennicke@senckenberg.de.
12
Department of Biology, Microbiology, Utrecht University, Utrecht, The Netherlands. florian.hennicke@senckenberg.de.
13
Senckenberg Biodiversity and Climate Research Centre (BiK-F), Frankfurt a. M., Germany. m.thines@thines-lab.eu.
14
Institute of Ecology, Evolution and Diversity, Goethe University Frankfurt, Frankfurt a. M., Germany. m.thines@thines-lab.eu.
15
LOEWE Cluster of Integrative Fungal Research (IPF), Frankfurt a. M., Germany. m.thines@thines-lab.eu.

Abstract

BACKGROUND:

Agrocybe aegerita is an agaricomycete fungus with typical mushroom features, which is commercially cultivated for its culinary use. In nature, it is a saprotrophic or facultative pathogenic fungus causing a white-rot of hardwood in forests of warm and mild climate. The ease of cultivation and fructification on solidified media as well as its archetypal mushroom fruit body morphology render A. aegerita a well-suited model for investigating mushroom developmental biology.

RESULTS:

Here, the genome of the species is reported and analysed with respect to carbohydrate active genes and genes known to play a role during fruit body formation. In terms of fruit body development, our analyses revealed a conserved repertoire of fruiting-related genes, which corresponds well to the archetypal fruit body morphology of this mushroom. For some genes involved in fruit body formation, paralogisation was observed, but not all fruit body maturation-associated genes known from other agaricomycetes seem to be conserved in the genome sequence of A. aegerita. In terms of lytic enzymes, our analyses suggest a versatile arsenal of biopolymer-degrading enzymes that likely account for the flexible life style of this species. Regarding the amount of genes encoding CAZymes relevant for lignin degradation, A. aegerita shows more similarity to white-rot fungi than to litter decomposers, including 18 genes coding for unspecific peroxygenases and three dye-decolourising peroxidase genes expanding its lignocellulolytic machinery.

CONCLUSIONS:

The genome resource will be useful for developing strategies towards genetic manipulation of A. aegerita, which will subsequently allow functional genetics approaches to elucidate fundamentals of fruiting and vegetative growth including lignocellulolysis.

KEYWORDS:

Agaricales; Basidiomycetes; Carbohydrate active enzymes; Comparative genomics; Developmental biology; Fruit body; Mushroom; White-rot

PMID:
29334897
PMCID:
PMC5769442
DOI:
10.1186/s12864-017-4430-y
[Indexed for MEDLINE]
Free PMC Article

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