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Research article - Peer-reviewed, 2021

Genetic determinants of endophytism in the Arabidopsis root mycobiome

Mesny, Fantin; Miyauchi, Shingo; Thiergart, Thorsten; Pickel, Brigitte; Atanasova, Lea; Karlsson, Magnus; Huettel, Bruno; Barry, Kerrie W.; Haridas, Sajeet; Chen, Cindy; Bauer, Diane; Andreopoulos, William; Pangilinan, Jasmyn; LaButti, Kurt; Riley, Robert; Lipzen, Anna; Clum, Alicia; Drula, Elodie; Henrissat, Bernard; Kohler, Annegret;
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Abstract

Plant roots host diverse fungal communities that affect plant health. Here, Mesny et al. use comparative genomics and transcriptomics of fungal isolates from the Arabidopsis thaliana root mycobiota, together with root colonization assays, to identify genetic determinants of endophytism.The roots of Arabidopsis thaliana host diverse fungal communities that affect plant health and disease states. Here, we sequence the genomes of 41 fungal isolates representative of the A. thaliana root mycobiota for comparative analysis with other 79 plant-associated fungi. Our analyses indicate that root mycobiota members evolved from ancestors with diverse lifestyles and retain large repertoires of plant cell wall-degrading enzymes (PCWDEs) and effector-like small secreted proteins. We identify a set of 84 gene families associated with endophytism, including genes encoding PCWDEs acting on xylan (family GH10) and cellulose (family AA9). Transcripts encoding these enzymes are also part of a conserved transcriptional program activated by phylogenetically-distant mycobiota members upon host contact. Recolonization experiments with individual fungi indicate that strains with detrimental effects in mono-association with the host colonize roots more aggressively than those with beneficial activities, and dominate in natural root samples. Furthermore, we show that the pectin-degrading enzyme family PL1_7 links aggressiveness of endophytic colonization to plant health.

Published in

Nature Communications

2021, volume: 12, number: 1, article number: 7227
Publisher: NATURE PORTFOLIO

Authors' information

Mesny, Fantin
Max Planck Society
Miyauchi, Shingo
Max Planck Society
Miyauchi, Shingo
Universite de Lorraine
Thiergart, Thorsten
Max Planck Society
Pickel, Brigitte
Max Planck Society
Atanasova, Lea
University of Natural Resources and Life Sciences, Vienna
Atanasova, Lea
Technische Universitat Wien
Swedish University of Agricultural Sciences, Department of Forest Mycology and Plant Pathology
Huettel, Bruno
Max Planck Society
Barry, Kerrie W.
United States Department of Energy (DOE)
Haridas, Sajeet
United States Department of Energy (DOE)
Chen, Cindy
United States Department of Energy (DOE)
Bauer, Diane
United States Department of Energy (DOE)
Andreopoulos, William
United States Department of Energy (DOE)
Pangilinan, Jasmyn
United States Department of Energy (DOE)
LaButti, Kurt
United States Department of Energy (DOE)
Riley, Robert
United States Department of Energy (DOE)
Lipzen, Anna
United States Department of Energy (DOE)
Clum, Alicia
United States Department of Energy (DOE)
Drula, Elodie
Aix-Marseille Universite
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UKÄ Subject classification

Genetics
Botany

Publication Identifiers

DOI: https://doi.org/10.1038/s41467-021-27479-y

URI (permanent link to this page)

https://res.slu.se/id/publ/115068