Department of Biology, University of Florence, Via Madonna del Piano 6, 50019, Sesto Fiorentino (FI), Italy.
Department of Genetics and Microbiology, Maria Curie-Skłodowska University, Akademicka 19, 20-033, Lublin, Poland.
Microb Genom. 2023 May;9(5). doi: 10.1099/mgen.0.001025.
Multipartite genomes, consisting of more than one replicon, have been found in approximately 10 % of bacteria, many of which belong to the phylum Proteobacteria. Many aspects of their origin and evolution, and the possible advantages related to this type of genome structure, remain to be elucidated. Here, we performed a systematic analysis of the presence and distribution of multipartite genomes in the class Gammaproteobacteria, which includes several genera with diverse lifestyles. Within this class, multipartite genomes are mainly found in the order Alteromonadales (mostly in the genus ) and in the family . Our data suggest that the emergence of secondary replicons in Gammaproteobacteria is rare and that they derive from plasmids. Despite their multiple origins, we highlighted the presence of evolutionary trends such as the inverse proportionality of the genome to chromosome size ratio, which appears to be a general feature of bacteria with multipartite genomes irrespective of taxonomic group. We also highlighted some functional trends. The core gene set of the secondary replicons is extremely small, probably limited to essential genes or genes that favour their maintenance in the genome, while the other genes are less conserved. This hypothesis agrees with the idea that the primary advantage of secondary replicons could be to facilitate gene acquisition through horizontal gene transfer, resulting in replicons enriched in genes associated with adaptation to different ecological niches. Indeed, secondary replicons are enriched both in genes that could promote adaptation to harsh environments, such as those involved in antibiotic, biocide and metal resistance, and in functional categories related to the exploitation of environmental resources (e.g. carbohydrates), which can complement chromosomal functions.
多聚体基因组由一个以上的复制子组成，在大约 10%的细菌中被发现，其中许多属于变形菌门。它们的起源和进化的许多方面，以及与这种基因组结构相关的可能优势，仍有待阐明。在这里，我们对包括具有不同生活方式的属在内的γ变形菌纲中的多聚体基因组的存在和分布进行了系统分析。在该纲中，多聚体基因组主要存在于交替单胞菌目（主要在属中）和海洋螺菌科中。我们的数据表明，γ变形菌中次级复制子的出现是罕见的，它们来源于质粒。尽管它们有多种起源，但我们强调了进化趋势的存在，例如基因组与染色体大小的比例呈反比，这似乎是具有多聚体基因组的细菌的一般特征，与分类群无关。我们还强调了一些功能趋势。次级复制子的核心基因集非常小，可能仅限于必需基因或有利于其在基因组中维持的基因，而其他基因则不太保守。这个假设与次级复制子的主要优势可能是通过水平基因转移促进基因获取的观点是一致的，这导致了复制子富含与适应不同生态位相关的基因。事实上，次级复制子富含促进适应恶劣环境的基因，如抗生素、杀菌剂和金属抗性基因，以及与利用环境资源（如碳水化合物）相关的功能类别，这些基因可以补充染色体的功能。
