Available online 30 September 2025

Root nodule symbiosis (RNS) is a mutualistic association formed between nitrogen-fixing rhizobia or Frankia and host plants limited to four orders within Rosid I—Fabales, Fagales, Cucurbitales and Rosales—which comprise the so-called ‘Nitrogen Fixing Nodulation Clade’ (NFNC). The majority of nodulation studies have focused on Leguminosae, given their agricultural and environmental importance, as well as the widespread occurrence of nodulation among members of this family. Endowing cereal crops with nitrogen fixation, like Leguminosae, presents a strategy to reduce the detrimental effects of synthetic fertilizer overuse. Different hypotheses on the origin of RNS have been proposed, however key genetic innovations underlying the evolution of RNS, even in Leguminsoae, have been rarely reported. In this review, we begin by examining current knowledge of genetic innovations—including gene gain, gene loss, and the acquisition or loss of conserved noncoding sequences (CNS) in preexisting genes. We explore the available evidence supporting these genetic innovations underlying the evolution of RNS in Leguminosae and offer the phylogenomics approach that could be applied to uncover these genetic innovations. Finally, we conclude by proposing a model of genetic innovations underlying the evolution of RNS in Leguminsoae and consider the potential implications for the development of nitrogen-fixing crops.

Root nodule symbiosis

Leguminosae

Genetic innovations

Gene gain

Gene loss

Conserved noncoding sequences

Phylogenomics

© 2025 Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, and Genetics Society of China. Published by Elsevier Limited and Science Press.