The genomes of rhizobia

Abstract The genomes of α- and β-rhizobia belonging to the α- and β-proteobacteria respectively contain genes for nitrogen fixation in symbiosis with host plants (encoded by nif and fix genes) and nodulation of their host plants, most often using Nod Factor (synthesized by nod, noe, nol gene products). In α-rhizobia symbiotic genes are often organized on plasmids of the repABC family, and symbiotic genes for the β-rhizobia are also plasmid borne. In some α-rhizobia, symbiotic genes are encoded on the chromosome within symbiotic islands that are integrative conjugal elements. In this chapter we give an overview of general features of rhizobial genomes including the symbiotic genes they contain and their organization. We review the current understanding of common features of rhizobial genomes and genomic backgrounds that support nodulation and nitrogen fixation and discuss genome deconstruction as a tool for uncovering new genes involved in symbiosis with legume plants.

• Publication year

  2020

• Venue

  Advances in Botanical Research

• Publication date

  Unknown publication date

• Fields of study

  Biology, Environmental Science

• Identifiers
  DOI 10.1016/bs.abr.2019.09.014
• External record

  Open on Semantic Scholar

• Source metadata

  Semantic Scholar

• No claims are published for this paper.

• No concepts are published for this paper.

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• Multidisciplinary approaches for studying rhizobium-legume symbioses.

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• Evolution of fixNOQP genes encoding cytochrome oxidase with high affinity to oxygen in rhizobia and related bacteria

  2017cited by this paper
• Evolutionary persistence of tripartite integrative and conjugative elements.

  2017influential reference
• How effectors promote beneficial interactions.

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• Legume LysM receptors mediate symbiotic and pathogenic signalling.

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• Transcriptomic Studies of the Effect of nod Gene-Inducing Molecules in Rhizobia: Different Weapons, One Purpose

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