ArticlePlant communications2024
Comparative phylogenomics and phylotranscriptomics provide insights into the genetic complexity of nitrogen-fixing root-nodule symbiosis.
Article in Plant communications, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers.
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21 citing papers in PubMed, 31 citations in OpenAlex.
- Nissolia brasiliensis as a nonnodulating model legume.Plant physiology · 2026Article
- Integrated multi-omics decipher the complex nodule microbiota and distinct Frankiaceae symbiotic traits in wild actinorhizal plants.The New phytologist · 2026Article
- Nonnodulating Fagales retain the functional NODULE INCEPTION gene.The New phytologist · 2026Article
- Toward telomere-to-telomere genomics in Fabaceae: Unlocking comparative and functional insights into symbiotic nitrogen fixation.Cell genomics · 2026Review
- Chromosome-Level Genome and Organ-Specific Transcriptome of Alnus glutinosa Uncover Lineage-Specific Innovations in Root Nodule Symbiosis.Plant, cell & environment · 2026Article
- Ancestral functionality and symbiotic refinement of NIN in root nodule symbiosis.Nature communications · 2026Article
- Advances in single-cell and spatial omics for studying symbiotic nitrogen fixation: comparative cellular and evolutionary perspectives.Genome biology · 2026Review
- The root nodule symbiosis regulator NIN exhibits broad DNA binding specificity conferred by an NLP-inherited motif.Science advances · 2026Article
- Impacts of gene duplication in the evolution of symbiotic root nodule symbiosis in legumes.Frontiers in plant science · 2026Article
- From assemblies to ancestry: Genomic advances illuminates legume evolution.Genetics and molecular biology · 2026Article
- Hormone-modulated transcription factors orchestrating the root nodule symbiosis.Frontiers in plant science · 2026Review
- Review
- One versus many independent assemblies of symbiotic nitrogen fixation in flowering plants.Nature communications · 2025Review
- Article
- Article
- Unveiling root nodulation in Tribulus terrestris and Roystonea regia via metagenomics analysis.Molecular genetics and genomics : MGG · 2024Article
- The secret of self-fertilizing plants: NIN-NAD1's role in symbiotic nitrogen fixation.The Plant cell · 2024Article
- Conserved cis-elements enable NODULES WITH ACTIVATED DEFENSE1 regulation by NODULE INCEPTION during nodulation.The Plant cell · 2024Article
- Loss of Lateral suppressor gene is associated with evolution of root nodule symbiosis in Leguminosae.Genome biology · 2024Article
- The symbiosome-a transient organelle in evolution.Journal of experimental botany · 2024Article
Corrections and comments
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Authors and funding
32 authors at 13 institutions in 9 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Plant root-nodule symbiosis (RNS) with mutualistic nitrogen-fixing bacteria is restricted to a single clade of angiosperms, the Nitrogen-Fixing Nodulation Clade (NFNC), and is best understood in the legume family. Nodulating species share many commonalities, explained either by divergence from a common ancestor over 100 million years ago or by convergence following independent origins over that same time period. Regardless, comparative analyses of diverse nodulation syndromes can provide insights into constraints on nodulation-what must be acquired or cannot be lost for a functional symbiosis-and the latitude for variation in the symbiosis. However, much remains to be learned about nodulation, especially outside of legumes. Here, we employed a large-scale phylogenomic analysis across 88 species, complemented by 151 RNA-seq libraries, to elucidate the evolution of RNS. Our phylogenomic analyses further emphasize the uniqueness of the transcription factor NIN as a master regulator of nodulation and identify key mutations that affect its function across the NFNC. Comparative transcriptomic assessment revealed nodule-specific upregulated genes across diverse nodulating plants, while also identifying nodule-specific and nitrogen-response genes. Approximately 70% of symbiosis-related genes are highly conserved in the four representative species, whereas defense-related and host-range restriction genes tend to be lineage specific. Our study also identified over 900 000 conserved non-coding elements (CNEs), over 300 000 of which are unique to sampled NFNC species. NFNC-specific CNEs are enriched with the active H3K9ac mark and are correlated with accessible chromatin regions, thus representing a pool of candidate regulatory elements for genes involved in RNS. Collectively, our results provide novel insights into the evolution of nodulation and lay a foundation for engineering of RNS traits in agriculturally important crops.
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