Comparative phylotranscriptomics reveals ancestral and derived root nodule symbiosis programmes

Area of Science:

• Evolutionary biology
• Plant science
• Microbiology

Background:

• Symbiotic interactions, like nitrogen-fixing root nodule symbiosis (RNS), are crucial for ecosystem structure and evolution.
• Understanding the evolutionary history of RNS in flowering plants is key to comprehending plant adaptation and nutrient cycling.

Purpose of the Study:

• To reconstruct the ancestral and intermediate evolutionary steps of RNS in flowering plants.
• To identify genes and pathways involved in the evolution of symbiotic interactions.

Main Methods:

• Comparative transcriptomics of nine host plants, including Mimosa pudica with a newly assembled chromosome-level genome.
• Reconstruction of the ancestral RNS transcriptome.
• Analysis of transcriptomic responses to experimentally evolved bacterial strains with varying symbiotic capabilities.

Main Results:

• The ancestral RNS transcriptome included known symbiotic genes and novel candidates.
• Core symbiotic responses—bacterial signaling, nodule infection, organogenesis, and nitrogen fixation—are ancestral.
• Symbiosome release is a more recently evolved trait, linked to novel small proteins.

Conclusions:

• The fundamental symbiotic machinery for RNS was established in the most recent common ancestor of RNS-forming species over 90 million years ago.
• Symbiosome release represents a later evolutionary innovation within different plant lineages.