L’évolution des pangénomes de procaryotes sur des échelles de temps humaines
The pangenome is the collection of unique genes found in a species. For prokaryotes, especially those present in the human gut microbiota, variation in gene content is characterized by gene gain through horizontal gene transfer (HGT) and gene loss. In human gut, gene content variations can occur at faster rates than mutation, which allow microbes to adapt rapidly to environmental changes. This justifies the study of the prokaryotes pangenome evolution on human time scales which are considered evolutionarily short, e.g. in the order of few years. Most studies about the evolution of prokaryotic pangenomes involve relatively distant species that have diverged since millions of years. In addition, the balance of major evolutionary forces involved, such as horizontal transfer, selection, genetic drift, and mutations, is not clearly defined and is debated in literature. This master's project therefore aims to broaden the evolutionary portrait of prokaryotic pangenome evolution by focusing on near-term evolution. To do this, we will first review the relevant literature related to this topic, including the methods used to detect mobile genes and the pangenome evolution models. We will then analyze the evolution of a pre-existing collection of 37 853 mobile genes involved in recent HGT events detected in the gut microbiota of individuals from North America and Fiji Islands. To detect evolutionary signatures of the forces in action, we will estimate various population genetics parameters from the alignment between metagenomic sequencing reads of 176 Fijian microbiomes and this collection of mobile genes. We will also explain the evolutionary simulation tool that we have developed in order to validate and explain some of our observations. While we don’t exclude the importance of selection for specific cellular functions for pangenome evolution, we found that the near-term evolution of mobile genes can be explained by a model in which mobile genes can spread selfishly without being largely adaptive to their human or microbial hosts, contrarily to what is often observed over longer evolutionary time scales.
Pangenome Evolution Mobile genes Horizontal Gene Transfer Human gut microbiome Simulation