Pangenomics of the Symbiotic Rhizobiales. Core and Accessory Functions Across a Group Endowed with High Levels of Genomic Plasticity

Rosselli, Riccardo; La Porta, Nicola; Muresu, Rosella; Stevanato, Piergiorgio; Concheri, Giuseppe; Squartini, Andrea

doi:10.3390/microorganisms9020407

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Pangenomics of the Symbiotic Rhizobiales. Core and Accessory Functions Across a Group Endowed with High Levels of Genomic Plasticity

Riccardo Rosselli

^1,2

Nicola La Porta

^3,4

Rosella Muresu

⁵,

Piergiorgio Stevanato

⁶

Giuseppe Concheri

⁶

and

Andrea Squartini

^6,*

Department of Marine Microbiology and Biogeochemistry, NIOZ Royal Netherlands Institute of Sea Research, NL-1790 AB Den Burg, The Netherlands

Departamento de Fisiología, Genética y Microbiología, Universidad de Alicante, 03690 Alicante, Spain

Department of Sustainable Agrobiosystems and Bioresources, Research and Innovation Centre, Fondazione Edmund Mach, 38098 San Michele all’Adige, Italy

⁴

MOUNTFOR Project Centre, European Forest Institute, 38098 San Michele all’Adige, Italy

⁵

Institute of Animal Production Systems in Mediterranean Environments-National Research Council, 07040 Sassari, Italy

⁶

Department of Agronomy, Food, Natural Resources, Animals and Environment, University of Padova, 35020 Legnaro, Italy

Author to whom correspondence should be addressed.

Academic Editor: Alessio Mengoni

Microorganisms 2021, 9(2), 407; https://doi.org/10.3390/microorganisms9020407

Received: 4 November 2020 / Revised: 10 February 2021 / Accepted: 11 February 2021 / Published: 16 February 2021

(This article belongs to the Special Issue Genomics of Nitrogen-Fixing Plant Symbiotic Bacteria)

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Abstract

Pangenome analyses reveal major clues on evolutionary instances and critical genome core conservation. The order Rhizobiales encompasses several families with rather disparate ecological attitudes. Among them, Rhizobiaceae, Bradyrhizobiaceae, Phyllobacteriacreae and Xanthobacteriaceae, include members proficient in mutualistic symbioses with plants based on the bacterial conversion of N₂ into ammonia (nitrogen-fixation). The pangenome of 12 nitrogen-fixing plant symbionts of the Rhizobiales was analyzed yielding total 37,364 loci, with a core genome constituting 700 genes. The percentage of core genes averaged 10.2% over single genomes, and between 5% to 7% were found to be plasmid-associated. The comparison between a representative reference genome and the core genome subset, showed the core genome highly enriched in genes for macromolecule metabolism, ribosomal constituents and overall translation machinery, while membrane/periplasm-associated genes, and transport domains resulted under-represented. The analysis of protein functions revealed that between 1.7% and 4.9% of core proteins could putatively have different functions. View Full-Text

Keywords: pangenome; core genome; rhizobiales; nitrogen-fixing symbiosis; nodulation genes; functional divergence; Rhizobium sullae

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Rosselli, R.; La Porta, N.; Muresu, R.; Stevanato, P.; Concheri, G.; Squartini, A. Pangenomics of the Symbiotic Rhizobiales. Core and Accessory Functions Across a Group Endowed with High Levels of Genomic Plasticity. Microorganisms 2021, 9, 407. https://doi.org/10.3390/microorganisms9020407

AMA Style

Rosselli R, La Porta N, Muresu R, Stevanato P, Concheri G, Squartini A. Pangenomics of the Symbiotic Rhizobiales. Core and Accessory Functions Across a Group Endowed with High Levels of Genomic Plasticity. Microorganisms. 2021; 9(2):407. https://doi.org/10.3390/microorganisms9020407

Chicago/Turabian Style

Rosselli, Riccardo, Nicola La Porta, Rosella Muresu, Piergiorgio Stevanato, Giuseppe Concheri, and Andrea Squartini. 2021. "Pangenomics of the Symbiotic Rhizobiales. Core and Accessory Functions Across a Group Endowed with High Levels of Genomic Plasticity" Microorganisms 9, no. 2: 407. https://doi.org/10.3390/microorganisms9020407

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Pangenomics of the Symbiotic Rhizobiales. Core and Accessory Functions Across a Group Endowed with High Levels of Genomic Plasticity

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