Christoph Bleidorn - Phylogenomics

Museo Nacional de Ciencias Naturales, Spanish National Research Council (CSIC), Madrid, Spain

Life on earth was for a long time classified into two major groups, prokaryotes and eukaryotes (Stanier and van Niel ).

Distinguishing life into two major groups was challenged by a series of publications from the group of the American evolutionary microbiologist Carl Woese. Investigating ribosomal sequence data, they found profound distances between two prokaryote groups, now usually referred to as Bacteria and Archaea (Woese and Fox ).

One of the defining features of eukaryotes is the possession of mitochondria. The primary function of these organelles is ATP synthesis through the oxidative electron transport chain, but also other functions are described (e.g. intracellular signalling). Similarities in the physiology and biochemistry of mitochondria with bacterial cells led to the endosymbiotic theory. According to this theory, mitochondria are of bacterial origin, an idea that dates back to a proposal from Ivan E. Wallin ().

The three-domain hypothesis suggests the respective monophyly of Bacteria, Archaea and Eukaryota. In this case, these groups should include all descendent lineages of a common ancestor and only these. Phylogenomic analyses were used to investigate this question, and analyses based on a small set of core genes, which are present in all three groups and which are regarded as not been transferred horizontally between groups, recovered the three-domain tree (Ciccarelli et al. ).

Sequencing of bacterial, archaeal and eukaryote genomes enabled the discovery of many important insights into the evolution, ecology and physiology of these organisms (Fraser et al. ).

There are profound differences between prokaryotes and eukaryotes in the structure and organization of their genomes, which in turn strongly influence the way to work with them in phylogenomic studies. Generally, prokaryote genomes are smaller and more compact than those of eukaryotes, clearly reducing the effort of sequencing and assembling them. However, due to the endosymbiotic origin of eukaryotes, it is obvious that a mosaic-like distribution for many of the features discussed below is found. Most genomes of bacteria and archaeans are contained by a single, circular DNA molecule, located in the nucleoid. For packaging, the double-stranded DNA molecule is supercoiled, which is facilitated by DNA-binding proteins. Whereas in bacteria the supercoiling is achieved by proteins like DNA gyrase, DNA topoisomerase I and HU proteins, archaeans have proteins for packaging that are similar to the histones of eukaryotes (White and Bell ).

Prokaryotes often have a high potential for horizontal gene transfer (HGT) by mobile genetic elements. Movement of DNA can be facilitated by transformation, conjugation or transduction. In the case of transformation, cellular DNA is taken up by the recipient due to the presence of special proteins. Conjugation is gene transfer mediated by plasmids or so-called integrative conjugative elements (ICEs) via contact between donor recipient cells. Finally, transduction is gene transfer by bacteriophages (Frost et al. ).

Prokaryotic genomes are usually compactly organized, with a small proportion of non-coding intragenic DNA. Consequently, prokaryotic genomes are relatively small, rarely exceeding sizes of 10 Mb. The smallest known genomes are reported for endosymbiotic bacteria, with the betaproteobacterium Candidatus Tremblaya princeps as record holder with its only 139 Kb genome. Bacteria with extremely reduced genomes are dependent on genes from their host or from other co-occurring endosymbionts (Husnik et al. ).

Eukaryote genomes often carry a huge proportion of interspersed elements and tandem repeats. Both types are usually rare or completely absent in prokaryotic genomes. Tandemly repeated DNA, which is sometimes called satellite DNA, can be found around centromeres or randomly scattered across chromosomes. Tandem repeats with short repetitive motifs are known as mini- and microsatellites (Brown ).

The genome size of an organism can be measured by the c-value, which describes the mass of DNA content of a haploid cell in picogram (pg). A c-value of 1 pg equals ~978 Mb (Dolezel et al. ).

Several evolutionary hypotheses have been formulated to explain the huge differences in genome size between organisms. The selfish DNA hypothesis states that non-coding DNA is a by-product of selfish transposable elements (Orgel and Crick ).

Besides a lack of correlation between genome size and complexity, there seems also to be no relationship between complexity and gene number, sometimes termed g-value paradox (Hahn and Wray ).