Maria C. Rivera

The ring of life provides evidence for a genome fusion origin of eukaryotes

Genomes hold within them the record of the evolution of life on Earth. But genome fusions and horizontal gene transfer seem to have obscured sufficiently the gene sequence record such that it is difficult to reconstruct the phylogenetic tree of life. Here we determine the general outline of the tree using complete genome data from representative prokaryotes and eukaryotes and a new genome analysis method that makes it possible to reconstruct ancient genome fusions and phylogenetic trees. Our analyses indicate that the eukaryotic genome resulted from a fusion of two diverse prokaryotic genomes, and therefore at the deepest levels linking prokaryotes and eukaryotes, the tree of life is actually a ring of life. One fusion partner branches from deep within an ancient photosynthetic clade, and the other is related to the archaeal prokaryotes. The eubacterial organism is either a proteobacterium, or a member of a larger photosynthetic clade that includes the Cyanobacteria and the Proteobacteria.

The phylogeny of Methanopyrus kandleri

The phylogenetic position of Methanopyrus kandleri has been difficult to determine because reconstructions of phylogenetic trees based on rRNA sequences have been ambiguous. The most probable trees determined by most algorithms place the genus Methanopyrus at the base of a group that includes the halobacteria and the methanogens and their relatives, although occasionally some algorithms place this genus near the eocytes (the hyperthermophilic, sulfur-metabolizing prokaryotes), suggesting that it may belong to this lineage. In order to resolve the phylogeny of the genus Methanopyrus, we determined the sequence of an informative region of elongation factor 1-alpha that contains an 11-amino-acid insertion in eocytes and eukaryotes which is replaced by a 4-amino-acid insertion in methanogens, halobacteria, and eubacteria. On the basis of the results of our elongation factor 1-alpha gene analysis, we concluded that the genus Methanopyrus diverged from the eocyte branch before the eukaryotic and eocyte lineages separated and therefore is not an eocyte.

Genome evolution and the impact of the physical environment

Publisher Summary This chapter provides an overview of the latest findings in gene evolution and the role of horizontal gene transfer in genome evolution. Whole genome studies and increased knowledge of extreme environments are providing a window into genome evolution and their interactions with the physical environment. The extensive amount of horizontal transfer among prokaryotes observed in genome studies was unthinkable in the pregenome era. Horizontal gene transfer has contributed significantly to the evolution of genomes in both eukaryotes and prokaryotes, although possibly by very different mechanisms. The taxonomic breadth and extent of transfer has been so vast that in prokaryotes operational gene component can be considered as a single global organism. Thus although prokaryotes have separate identities through their informational genes, they have global commonalities through their operational genes. The effective population size for the worldwide collection of operational genes is enormous and the potential for the creation of innovations is great.