Study On Adaptive Evolution Of S.cerevisiae And E. Coli By Population Genomics

With the rapid development and widespread use of sequencing technology,huge volumes of data from different organisms has now been accumulated.How to accurately mine valuable information from these data has become an issue worth considering deeply.In natural environments,selective pressure constantly acts on genomes which serve as the carrier of genetic information,causing organisms to undergo adaptive evolution to survive and multiply in diverse ecological environments.In this thesis,we focus on the adaptive evolution of classical model organism S.cerevisiae and E.coli,gather all available genomic data from public database,and study the adaptive evolution at population level from multiple perspectives for new findings.The first part of this thesis mainly revolves around the population genomes of S.cerevisiae to conduct the research.Firstly,we accurately identify the ultra-conserved genomic regions of S.cerevisiae by comparative genomics and logistic regression analysis,find that ultra-conserved sequences participate in these biological pathways such as acid secretion,sensing and transport of nutrients,indicating S.cerevisiae maintains a strong adaptability to acid stress and an excellent ability of sensing and transporting nutrients by highly conserved molecular mechanisms.Then,we carry out the recombination analysis from population level,find that homologous recombination(HR)may play a important role in environmental adaptability,these genes more frequently(? 0.9)repaired by HR are evolutionarily more conservative,and they significantly enrich in these pathways related to specific diseases,indicating that HR repair may be of great importance for resisting specific diseases.Finally,we analyze its pan-genome and replication origins,find that strain-specific genes are significantly different from core genes and dispensable genes in gene length and GC content,and find that core genes mainly enrich in the essential biological process,but strain-specific genes mainly enrich in biological processes related to environmental adaptability,indicating that S.cerevisiae adapts to specific environments possibly by obtaining and integrating foreign genetic materials,we also find that certain biological functions are significantly enriched in genes adjacent to replication origins.The second part of this thesis carry out the pan-genomic analysis based on hundreds of complete E.coli genomes,based on which the association analysis of dispensable genes with host sources and the exploration of genome reduction are further done.By pan-genomic analysis,we more accurately identify its core genes and dispensable genes,which would provide theoretical guidance for further reduction of E.coli genome.By association analysis,we find that quorum sensing system may play an important role in the harmony of E.coli with human host,also find the nonhuman strains may have an excellent ability of integrating exogenous genes.This part would provide a useful reference for further reducing the genome of E.coli,and also point out a direction for studying the intrinsic mechanism of harmony between human host and E.coli population.