Convergent losses of decay mechanisms and rapid turnover of symbiosis genes in mycorrhizal mutualists

@article{Kohler2015ConvergentLO,
  title={Convergent losses of decay mechanisms and rapid turnover of symbiosis genes in mycorrhizal mutualists},
  author={Annegret Kohler and Alan Kuo and L{\'a}szl{\'o} G. Nagy and Emmanuelle Morin and Kerrie W. Barry and François Buscot and Bj{\"o}rn Canb{\"a}ck and Cindy Miok Choi and Nicolas Cichocki and Alicia Clum and Jan Colpaert and Alex Copeland and Maur{\'i}cio Dutra Costa and Jeanne Dor{\'e} and Dimitrios Floudas and Gilles Gay and Mariangela Girlanda and Bernard Henrissat and Sylvie Herrmann and Jaqueline Hess and Nils O. S. H{\"o}gberg and Tomas Johansson and Hassine Radhouane Khouja and Kurt LaButti and Urs Lahrmann and Anthony Levasseur and Erika A. Lindquist and Anna Lipzen and Roland Marmeisse and Elena Martino and Claude Murat and Chew Yee Ngan and Uwe Nehls and Jonathan M. Plett and Anne Pringle and Robin A. Ohm and Silvia Perotto and Martina Peter and Robert Riley and Francois Rineau and Joske Ruytinx and Asaf A. Salamov and Firoz Shah and Hui Sun and Mika Tapio Tarkka and Andrew J. Tritt and Claire Veneault-Fourrey and Alga Zuccaro and Anders Tunlid and Igor V. Grigoriev and David S. Hibbett and Francis M. Martin},
  journal={Nature Genetics},
  year={2015},
  volume={47},
  pages={410-415}
}
To elucidate the genetic bases of mycorrhizal lifestyle evolution, we sequenced new fungal genomes, including 13 ectomycorrhizal (ECM), orchid (ORM) and ericoid (ERM) species, and five saprotrophs, which we analyzed along with other fungal genomes. Ectomycorrhizal fungi have a reduced complement of genes encoding plant cell wall–degrading enzymes (PCWDEs), as compared to their ancestral wood decayers. Nevertheless, they have retained a unique array of PCWDEs, thus suggesting that they possess… 
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References

SHOWING 1-10 OF 26 REFERENCES
The genome of Laccaria bicolor provides insights into mycorrhizal symbiosis
TLDR
The predicted gene inventory of the L. bicolor genome points to previously unknown mechanisms of symbiosis operating in biotrophic mycorrhizal fungi, providing an unparalleled opportunity to develop a deeper understanding of the processes by which symbionts interact with plants within their ecosystem to perform vital functions in the carbon and nitrogen cycles that are fundamental to sustainable plant productivity.
Genome of an arbuscular mycorrhizal fungus provides insight into the oldest plant symbiosis
TLDR
The genome of Rhizophagus irregularis provides insight into genes involved in obligate biotrophy and mycorrhizal symbioses and the evolution of an ancient asexual organism, and is of fundamental importance to the field of genome evolution.
A Secreted Effector Protein of Laccaria bicolor Is Required for Symbiosis Development
TLDR
It is demonstrated that MYCORRHIZAL iNDUCED SMALL SECRETED PROTEin 7 (MiSSP7), the most highly symbiosis-upregulated gene from the ectomycorrhizal fungus Laccaria bicolor, encodes an effector protein indispensible for the establishment of mutualism.
Genomic and transcriptomic analysis of Laccaria bicolor CAZome reveals insights into polysaccharides remodelling during symbiosis establishment.
TLDR
Data suggest an active remodelling of fungal cell wall with a possible involvement of expansin during ECM development, and it is demonstrated that one expansin-like protein, whose expression is specific to symbiotic tissues, localizes within fungalcell wall.
The Plant Cell Wall–Decomposing Machinery Underlies the Functional Diversity of Forest Fungi
TLDR
Fungal nutritional mode diversification suggests that the boreal forest biome originated via genetic coevolution of above- and below-ground biota through convergent evolution and divergence among fungal decomposers.
Ectomycorrhizal lifestyle in fungi: global diversity, distribution, and evolution of phylogenetic lineages
TLDR
In conclusion, EcM fungi are phylogenetically highly diverse, and molecular surveys particularly in tropical and south temperate habitats are likely to supplement to the present figures.
Effector MiSSP7 of the mutualistic fungus Laccaria bicolor stabilizes the Populus JAZ6 protein and represses jasmonic acid (JA) responsive genes
TLDR
It is demonstrated that the MiSSP7 (Mycorrhiza-induced small secreted protein-7) protein of the beneficial fungus Laccaria bicolor interacts with host plant JA signaling repressors and, in contrast to biotrophic pathogens, promotes symbiosis by blocking JA action.
Asynchronous origins of ectomycorrhizal clades of Agaricales
TLDR
While it is demonstrated support for asynchronous origins of ECM Agaricales, the timing of such events appears to have occurred more recently than suggested by the first hypothesis, first during the Cretaceous and later during the Palaeogene.
Mycorrhizal fungi as drivers of ecosystem processes in heathland and boreal forest biomes
TLDR
What unites mycorrhizas in heathland and boreal forest biomes is their apparent affinity for acidic organic soils of inherently low accessibility of the major nutrients nitrogen (N) and phosphorus (P).
Carbon availability triggers the decomposition of plant litter and assimilation of nitrogen by an ectomycorrhizal fungus
TLDR
The data suggest that the expression of the decomposition and nitrogen assimilation processes of EMF can be tightly regulated by the host carbon supply and that the availability of inorganic nitrogen as such has limited effects on saprotrophic activities.
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1
2
3
...