Impacts of gene duplication in the evolution of symbiotic root nodule symbiosis in legumes

Authors: LEE, HYUNOH - Oak Ridge Institute For Science And Education (ORISE); FARMER, ANDREW - National Center For Genome Resources; O'Rourke, Jamie; DOYLE, JEFFREY - Cornell University; Cannon, Steven

Submitted to: Frontiers in Plant Science
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 4/16/2026
Publication Date: 5/12/2026
Citation: Lee, H., Farmer, A.D., O'Rourke, J.A., Doyle, J.J., Cannon, S.B. 2026. Impacts of gene duplication in the evolution of symbiotic root nodule symbiosis in legumes. Frontiers in Plant Science. https://doi.org/10.3389/fpls.2026.1784647.
DOI: https://doi.org/10.3389/fpls.2026.1784647

Interpretive Summary: Many plants in the legume family, including important crops such as soybean, chickpea, alfalfa, and peanut, have a symbiotic relationship with soil bacteria that allows the plants to use atmospheric nitrogen directly as fertilizer. Some species in four related non-legume plant families also have this capacity for symbiotic nitrogen fixation. Previous studies have determined that this capacity was probably gained semi-independently several times over the course of evolution, and lost in several lineages as well. This research study traces the origin of key genes involved in symbiotic nitrogen fixation. This information will help researchers understand the origin of this important trait, and potentially to help develop crops with improved capacity for nitrogen fixation and utilization.

Technical Abstract: The emerging consensus regarding the origin of root nodule symbiosis (RNS), based on modeling of trait gain and loss across approximately 13,000 species within the "nitrogen-fixing clade" in the rosid group, is that the trait has arisen multiple times, probably semi-independently, and has also been lost repeatedly. Evolution of a new organ and functions involves many thousands of genes; but the evolutionary histories for many of these genes may be uninformative regarding RNS evolution. A portion of the genes, however, are likely to be derived from prior gene duplications and to have acquired new functions or to have come under new regulatory patterns. Whole genome duplications (WGDs) could conceivably enable the necessary neo- or sub-functionalization for new roles in the nodule. All species that exhibit RNS share a history of several ancient WGDs; but the last such common WGD for these species was the "gamma" paleohexaploidy that occurred early in the core eudicot lineage, ~120 million years ago (Mya). This presents a puzzle: if RNS didn't originate until ~60-80 Mya, within the respective families exhibiting RNS, what explains the long quiescent period (~40-60 million years) and the many eudicot lineages without RNS? This study focuses on a collection of gene families with additional independent WGDs that appear to have occurred in the interim period, after the gamma triplication and prior to the evolution of RNS, identifying several that are both essential for RNS and that show evidence of critical roles of both ancient WGDs and more recent local duplications.