Comparative Genomics of Microbial Eukaryotes

Sandra L. Baldauf

Uppsala University, Sweden

Abstract

We now have 1000s of bacterial genome sequences, and we will soon have 1000s of genome sequences from humans. However, there is still very little genomic data from microbial eukaryotes. These species represent most of the history of eukaryotes, as well as most of their biomass and most of their diversity. They include some of the most ecologically important eukaryotic species and some of the most bizarre. With the rapidly decreasing cost and increasing efficiency of genome sequencing and post-genomic technologies, we are beginning to fill this gap, albeit slowly. We should expect that one of the next major frontiers in bioinformatics will be the comparative genomics of eukaryotic microbes.

Most of eukaryotic diversity is unicellular organisms - eukaryotic microbes or "protists". These include ecologically important species such as microalgae and their parasites, soil microbes such as diverse amoebae and single-celled flagellates, and major human pathogens. We have very little molecular data from the vast majority of these species, including whole major groups that have been evolving independently for over a billion years. These organisms are adapted to a wide range of environments and life styles, and it is largely through analysis of their genomes that we can begin to understand the unusual ways in which they do this. Thus, as we begin to explore these genomes, we should expect to find novel genes, unexpected molecular mechanisms and new metabolic pathways. By comparing these genomes we will learn fundamental principles of biology, as well as variations upon these basic principles that we cannot yet imagine.

I will give an overview of our current understanding of eukaryotic diversity, and some examples of novel recent discoveries in comparative eukaryote genomics. I will also discuss what some of the important future challenges in eukaryotic genomics are, and where some of the most interesting potential discoveries might lie.