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Data from: Impacts of gene duplication in the evolution of symbiotic root nodule symbiosis

Published by Agricultural Research Service | Department of Agriculture | Catalog Last Checked: May 05, 2026 at 11:39 PM | Dataset Last Updated: September 29, 2025
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. The data in this repository includes gene families for the legumes and allied species (some with RNS, some without), that has been used in associated manuscript to trace the origin of a collection of genes involved in RNS.

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Complete Metadata
@type dcat:Dataset
accessLevel public
bureauCode 
                                            [
  "005:18"
]
contactPoint 
                                            {
  "fn": "Cannon, Steven B.",
  "hasEmail": "mailto:steven.cannon@usda.gov"
}
description <p dir="ltr">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. The data in this repository includes gene families for the legumes and allied species (some with RNS, some without), that has been used in associated manuscript to trace the origin of a collection of genes involved in RNS.</p>
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identifier 10.15482/USDA.ADC/30142387.v1
keyword 
                                            [
  "Evolution",
  "Gene expression",
  "Gene families",
  "Root Nodule Symbiosis",
  "symbiotic nitrogen fixation (SNF)"
]
license https://creativecommons.org/publicdomain/zero/1.0/
modified 2025-09-29
programCode 
                                            [
  "005:040"
]
publisher 
                                            {
  "name": "Agricultural Research Service",
  "@type": "org:Organization"
}
temporal 2025-09-23/2025-09-23
title Data from: Impacts of gene duplication in the evolution of symbiotic root nodule symbiosis

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