Exploring multipartite genomes using pangenome analysis

Bacteria are small single-celled organisms that are found in nearly every habitat on Earth. While bacterial genomes usually consist of one large circular replicon, about 10% of bacteria have organized their genes onto several large replicons. These multipartite bacteria are often found in symbiotic or pathogenic relationships with other higher organisms and are believed to have greater ability to adapt to new niches and to changing environments. However, much remains unknown about multipartite bacteria. In this study we aimed to gain a better understanding of why some bacteria have organized their genes on several large replicons. To do so, Vibrionacaeae and Pseudoalteromonas, which both consist of two large replicons, were used as model systems. In Paper 1, pangenome analysis and transcriptomic data of Vibrionaceae revealed a highly organized distribution pattern of different gene types on the chromosome, and a strong correlation between gene expression and distance to the origin of replication. In Paper 2, Pseudoalteromonas showed a similar distribution pattern and correlation with gene expression on the chromosome as in Vibrionaceae. In Paper 3, pangenome analysis showed that Vibrio and Pseudoalteromonas have a larger repertoire of genes than genomes with one chromosome. Furthermore, horizontally transferred genes are inserted into specific regions on the replicons. In Paper 4, seven new complete genomes of Vibrio anguillarum genomes were presented. Overall, results from these studies have increased our understanding of how multipartite genomes are organized with respect to their genes, how they are expressed and where newly acquired genes are retained on the replicons