Comparative genomics and early cell evolution

Abstract

The awareness that genes and genomes are extraordinarily rich historical documents from which a wealth of evolutionary information can be retrieved has widened the range of phylogenetic studies to previously unsuspected heights. The development of ef! cient sequencing techniques, which now allows the rapid sequencing of complete cellular genomes, combined with the simultaneous and independent blossoming of computer science, has led not only to an explosive growth of databases and new sophisticated tools for their exploitation, but also to the recognition that, in spite of many lateral gene-transfer events (LGT), different macromolecules are uniquely suited as molecular chronometers in the construction of nearly universal phylogenies. Cladistic analysis of rRNA sequences is acknowledged as a prime force in systematics and from its very inception had a major impact to our understanding of early cellular evolution. The comparison of small-subunit ribosomal-RNA (16/18S rRNA) sequences led to the construction of a trifurcated unrooted tree in which all known organisms can be grouped in one of three major monophyletic cell lineages, i.e. the domains bacteria (eubacteria), Archaea (Archaeabacteria) and eucarya (eukaryotes) (Woese et al ., 1990 ), which are all derived from an ancestral form, known as the last common ancestor (LCA). From a cladistic viewpoint, the LCA is merely an inferred inventory of features shared among extant organisms, all of which are located at the tip of the branches of molecular phylogenies. Some time ago it was surmized that the sketchy picture developed with the limited databases would be con! rmed by completely sequenced cell genomes from the three primary domains. This has not been the case: the availability of an increasingly large number of completely sequenced cellular genomes has sparked new debates, rekindling the discussion on the nature of the ancestral entity and its predecessors. As reviewed by Becerra et al . ( 2007 ), this is shown in the diversity of names that have been coined to describe it, which include, among others, progenote (Woese and Fox, 1977 ), cenancestor (Fitch and Upper, 1987 ), LUCA, last universal common ancestor (Kyrpides et al ., 1999 ) or, later on, last universal cellular ancestor (Philippe and Forterre, 1999 ), universal ancestor (Doolittle, 2000), LCC, last common community (Line, 2002 ), and MRCA, most recent common ancestor (Zhaxybayeva and Gogarten, 2004 ). Close analysis shows that these