The origins and evolution of highly conserved gene families concerned with basic cellular and development processes

The mechanism of species evolution is one of the major goals of evolutionary biology and it was considered as a consequence of combination of various factors. Gene duplication and evolutionary changes of protein-coding sequences are considered as important contributors to the species evolution. Highly conserved gene families that are ubiquitous in living organisms can be used as a powerful tool to study the evolution of living organisms. Because DNA repair pathways are crucial for maintaining genome stability, the pathways together with the key genes involved are usually conserved between eukaryotes and prokaryotes. The evolutionary history of recombination repair genes recA/RAD51 family and mismatch repair genes MutS and MutL families were systematically examined in this study. Based on my results, I found that the origins of eukaryotic DNA repair genes are divergent. The eukaryotic RAD51-like genes were derived from the ancestral archaeal species. In contrast, the eukaryotic MutS and MutL genes likely originated from proteobacteria by endosymbiosis of mitochondria, indicating different origins of eukaryotic informational genes.;Although the two types of eukaryotic DNA repair genes have different origins, they also share some similar evolutionary patterns during early stage of eukaryote evolution. The numbers of these genes have expanded by multiple gene duplication events before the divergence of major eukaryotic lineages. Functional innovation and specialization have occurred on these duplicate genes, which might have considerably enhanced the efficiency of DNA repairs. Furthermore, the birth of meiosis-specific genes in both DNA repair genes might have promoted the evolution of sexual reproduction, which creates gene diversity and has contributed to the evolution of eukaryotic species.;In addition to gene duplication, the evolutionary changes on the coding regions also play an important role in species evolution, especially in these genes that are involved in the animal development. The bilaterian animals share a common set of fundamental genetic framework to control embryo development. The Hox genes, encoding transcription factors, determine the identities of embryo along the anterior-posterior axis by regulating their downstream genes. All Hox genes contain a highly conserved homeobox which encodes homeodomain. Although the functions of homeodomain have been well studied, the roles of the non-homeodomain regions remain largely unclear. In this study, I identified many ultraconserved coding regions (UCRs) in the mammalian Hox genes. Both synonymous and nonsynonymous sites are ultraconserved in UCRs and most of them are located outside the homeobox. These UCRs are unique to mammals and formed before the divergence of placental mammals. Our study indicates that the formation of UCRs is partially due to local variation of genomic DNA mutability, but mainly due to strong purifying selections. Potential factors that lead to the formation of UCRs are also discussed. We therefore postulate that these UCRs might have contributed to the evolution of placental mammals.