Rosselli Riccardo, La Porta Nicola, Muresu Rosella, Stevanato Piergiorgio, Concheri Giuseppe, Squartini Andrea
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.
Microorganisms. 2021 Feb 16;9(2):407. doi: 10.3390/microorganisms9020407.
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 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.
泛基因组分析揭示了进化实例和关键基因组核心保守性的主要线索。根瘤菌目包含几个生态习性差异较大的科。其中，根瘤菌科、慢生根瘤菌科、叶杆菌科和黄色杆菌科，包括一些能够基于细菌将氮转化为氨（固氮作用）与植物进行互利共生的成员。对根瘤菌目的12种固氮植物共生体的泛基因组进行了分析，共产生了37364个基因座，核心基因组由700个基因组成。核心基因在单个基因组中的平均比例为10.2%，发现5%至7%的核心基因与质粒相关。代表性参考基因组与核心基因组子集之间的比较表明，核心基因组在大分子代谢、核糖体成分和整体翻译机制的基因中高度富集，而与膜/周质相关的基因和转运结构域则代表性不足。蛋白质功能分析表明，1.7%至4.9%的核心蛋白质可能具有不同的功能。
