Genetics of nodulation in Aeschynomene evenia uncovers mechanisms of the rhizobium\u2013legume symbiosis

Johan Quilbé,Clémence Chaintreuil,Frédéric Gressent,Rémi Guyonnet,Bárbara Hufnagel,Joël Fardoux,Loïc Fontaine,Léo Lamy,Angélique D’Hont,Mickaël Bourge,Gaëtan Droc,Guillaume Martin,Djamel Gully,Marjorie Pervent,Cyril Libourel,Christophe Klopp,Nico Nouwen,Andrew Farmer,Amandine Delteil,Olivier Garsmeur,Irene Villar,Pierre Mournet,Thomas Benichou,Manuel Becana,Éric Giraud ,Nicolas Valentin,Alexis Dereeper,Philippe Leleux,Laurent Brottier,Fabienne Cartieaux,Ronan Rivallan,Jean‐François Arrighi

doi:10.1038/s41467-021-21094-7

Abstract

Among legumes (Fabaceae) capable of nitrogen-fixing nodulation, several Aeschynomene spp. use a unique symbiotic process that is independent of Nod factors and infection threads. They are also distinctive in developing root and stem nodules with photosynthetic bradyrhizobia. Despite the significance of these symbiotic features, their understanding remains limited. To overcome such limitations, we conduct genetic studies of nodulation in Aeschynomene evenia, supported by the development of a genome sequence for A. evenia and transcriptomic resources for 10 additional Aeschynomene spp. Comparative analysis of symbiotic genes substantiates singular mechanisms in the early and late nodulation steps. A forward genetic screen also shows that AeCRK, coding a receptor-like kinase, and the symbiotic signaling genes AePOLLUX, AeCCamK, AeCYCLOPS, AeNSP2, and AeNIN are required to trigger both root and stem nodulation. This work demonstrates the utility of the A. evenia model and provides a cornerstone to unravel mechanisms underlying the rhizobium–legume symbiosis.

Highlights

Among legumes (Fabaceae) capable of nitrogen-fixing nodulation, several Aeschynomene spp. use a unique symbiotic process that is independent of Nod factors and infection threads
A. evenia is a valuable legume species because: (i) it uses an alternative infection process mediated by intercellular penetration as is the case in 25% of legume species[14,15]; (ii) it is endowed with stem nodulation, a property shared with very few hydrophytic legume species[16,17]; and (iii) it groups with Arachis spp., including cultivated peanut (Arachis hypogaea) in the Dalbergioid clade, which is distantly related to L. japonicus and M. truncatula[11]
The resulting assembly was 376 Mb, representing 94–100% of the A. evenia genome, considering the estimated size of 400 Mb obtained by flow cytometry[12,16] or of 372 Mb derived from k-mer frequencies (Supplementary Fig. 1)

Summary

Introduction

Among legumes (Fabaceae) capable of nitrogen-fixing nodulation, several Aeschynomene spp. use a unique symbiotic process that is independent of Nod factors and infection threads They are distinctive in developing root and stem nodules with photosynthetic bradyrhizobia. Previous transcriptomic analysis from root and nodule tissues did not detect expression of several known genes involved in bacterial recognition (e.g., LYK3 and EPR3), infection (e.g., RPG and FLOT), and nodule functioning (e.g., SUNERGOS1 and VAG1)[12,18] Such data support the presence of distinct or divergent symbiotic mechanisms in A. evenia in comparison with other well-studied model legumes. They comfort A. evenia as a system of interest to study the evolution and diversity of the rhizobial symbiosis

Methods

Results

Conclusion