Pangenomics of the Symbiotic Rhizobiales. Core and Accessory Functions Across a Group Endowed with High Levels of Genomic Plasticity
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 membe...
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| Format: | Article |
| Language: | English |
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MDPI AG
2021-02-01
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| Series: | Microorganisms |
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| Online Access: | https://www.mdpi.com/2076-2607/9/2/407 |
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| author | Riccardo Rosselli Nicola La Porta Rosella Muresu Piergiorgio Stevanato Giuseppe Concheri Andrea Squartini |
| author_facet | Riccardo Rosselli Nicola La Porta Rosella Muresu Piergiorgio Stevanato Giuseppe Concheri Andrea Squartini |
| author_sort | Riccardo Rosselli |
| collection | DOAJ |
| description | 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 N<sub>2</sub> 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. |
| first_indexed | 2024-03-09T00:49:46Z |
| format | Article |
| id | doaj.art-9ea8f29e58bc4f40a1f69e272f60bd56 |
| institution | Directory Open Access Journal |
| issn | 2076-2607 |
| language | English |
| last_indexed | 2024-03-09T00:49:46Z |
| publishDate | 2021-02-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Microorganisms |
| spelling | doaj.art-9ea8f29e58bc4f40a1f69e272f60bd562023-12-11T17:17:27ZengMDPI AGMicroorganisms2076-26072021-02-019240710.3390/microorganisms9020407Pangenomics of the Symbiotic Rhizobiales. Core and Accessory Functions Across a Group Endowed with High Levels of Genomic PlasticityRiccardo Rosselli0Nicola La Porta1Rosella Muresu2Piergiorgio Stevanato3Giuseppe Concheri4Andrea Squartini5Department of Marine Microbiology and Biogeochemistry, NIOZ Royal Netherlands Institute of Sea Research, NL-1790 AB Den Burg, The NetherlandsDepartment of Sustainable Agrobiosystems and Bioresources, Research and Innovation Centre, Fondazione Edmund Mach, 38098 San Michele all’Adige, ItalyInstitute of Animal Production Systems in Mediterranean Environments-National Research Council, 07040 Sassari, ItalyDepartment of Agronomy, Food, Natural Resources, Animals and Environment, University of Padova, 35020 Legnaro, ItalyDepartment of Agronomy, Food, Natural Resources, Animals and Environment, University of Padova, 35020 Legnaro, ItalyDepartment of Agronomy, Food, Natural Resources, Animals and Environment, University of Padova, 35020 Legnaro, ItalyPangenome 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 N<sub>2</sub> 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.https://www.mdpi.com/2076-2607/9/2/407pangenomecore genomerhizobialesnitrogen-fixing symbiosisnodulation genesfunctional divergence |
| spellingShingle | Riccardo Rosselli Nicola La Porta Rosella Muresu Piergiorgio Stevanato Giuseppe Concheri Andrea Squartini Pangenomics of the Symbiotic Rhizobiales. Core and Accessory Functions Across a Group Endowed with High Levels of Genomic Plasticity Microorganisms pangenome core genome rhizobiales nitrogen-fixing symbiosis nodulation genes functional divergence |
| title | Pangenomics of the Symbiotic Rhizobiales. Core and Accessory Functions Across a Group Endowed with High Levels of Genomic Plasticity |
| title_full | Pangenomics of the Symbiotic Rhizobiales. Core and Accessory Functions Across a Group Endowed with High Levels of Genomic Plasticity |
| title_fullStr | Pangenomics of the Symbiotic Rhizobiales. Core and Accessory Functions Across a Group Endowed with High Levels of Genomic Plasticity |
| title_full_unstemmed | Pangenomics of the Symbiotic Rhizobiales. Core and Accessory Functions Across a Group Endowed with High Levels of Genomic Plasticity |
| title_short | Pangenomics of the Symbiotic Rhizobiales. Core and Accessory Functions Across a Group Endowed with High Levels of Genomic Plasticity |
| title_sort | pangenomics of the symbiotic rhizobiales core and accessory functions across a group endowed with high levels of genomic plasticity |
| topic | pangenome core genome rhizobiales nitrogen-fixing symbiosis nodulation genes functional divergence |
| url | https://www.mdpi.com/2076-2607/9/2/407 |
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