Genomes, phylogeny, and evolutionary systems biology

Abstract

With the completion of the human genome and the growing number of diverse genomes being sequenced, a new age of evolutionary research is currently taking shape. The myriad of technological breakthroughs in biology that are leading to the unification of broad scientific fields such as molecular biology, biochemistry, physics, mathematics, and computer science are now known as systems biology. Here, I present an overview, with an emphasis on eukaryotes, of how the postgenomics era is adopting comparative approaches that go beyond comparisons among model organisms to shape the nascent field of evolutionary systems biology.postgenomics ͉ eukaryotic genomics ͉ network evolution Systems biology is in the eye of the beholder.Leroy Hood O nly in the last decade have we had access to nearly complete genomes of a diversity of organisms allowing for large-scale comparative analysis. The access to this immense amount of data is providing profound insight into the tree of life at all levels of divergence ( Fig. 1 A). It is thus not surprising that understanding phylogenetic relationships is a prevalent research goal among not only evolutionary biologists but also all scientists interested in the organization and function of the genome. New genome sequences and analysis methods are helping improve our understanding of phylogeny, and at the same time improved phylogenies and phylogenetic theory are generating a better understanding of genome evolution. Currently however, the level of genome sequencing for different branches of the tree of life is far from equivalent. Prokaryotic genome projects are abundant, mainly due to their small genome sizes, with Ͼ200 genomes already published and at least 500 currently in progress (www. genomesonline.org). In contrast, Ͻ300 eukaryotic genomes are either finished or in progress (www.genomesonline.org). Nevertheless, these data are starting to have a major impact on our understanding of eukaryotic evolution.These new genomic data have informed our understanding of phylogenetic relationships, and the emerging consensus topologies are adding new insight to the small subunit ribosomal RNA phylogenies. For example, the topology of the ribosomal eukaryotic tree has been recently redrawn with the use of genomic signatures that place the root of all eukaryotic life between two newly uncovered major clades, Unikonts and Bikonts (Fig. 1 A). Unikonts, which contain the heterotrophic groups Opisthokonta and the Amebozoa, share a derived three-gene fusion of enzymeencoding genes in the pyrimidine synthesis pathway (1), whereas Bikonts, which contain the remaining eukaryotic clades, share another derived gene fusion between dihydrofolate reductase and thymidine synthase (2). All photosynthetic groups of primary and secondary plastid symbiotic origins are now thought to be within the Bikonts. Although the animal, fungal, and plant lineages are the most widely represented in terms of genome initiatives (Fig. 1 B-D), it is significant that multiple protistan genome projects have also been initiated by th...

Primitive Defence: The MiAMP1 Antimicrobial Peptide Family

“…These sequence similarities are consistent with a distribution amongst more primitive plant species according to current models for phylogenetic relations in the plant kingdom (Jansen et al 2007;Medina 2005;Soltis et al 2008). For example, the sequences of the more primitive lycophyte Selaginella and the gymnosperms share substantial aa identity (65%) and cluster together away from the angiosperms.…”

Origin of the polycomb repressive complex 2 and gene silencing by an E(z) homolog in the unicellular alga Chlamydomonas

“…1A). Moreover, none of the best phylogenetic trees for E(z), ESC or Su(z)12 polypeptides (see below) strictly coincided with the consensus tree of Eukaryota 44 nor could reconstruct the monophyly of some higher-order eukaryotic groups, as previously reported for individual gene or protein trees. 43,45 Besides the usual problems of weakness of phylogenetic signal, lateral gene transfers, hidden paralogy and tree reconstruction artifacts, 45 incorrectly predicted protein models (since some sequences were extracted from draft genomes) may have contributed to greater than usual divergences making the relationship among deep branches difficult to resolve.…”

On the origin and functions of RNA-mediated silencing: from protists to man

“…This conclusion is reinforced when the phylogenetic tree for the family in question conforms to the topology of the eukaryotic tree. However, none of the best phylogenetic trees for Ago-Piwi, Dicer-like, or RdRP polypeptides strictly coincided with the consensus tree of Eukaryota (Medina 2005) nor could reconstruct the monophyly of some higher-order eukaryotic groups, as previously reported for individual gene/protein trees (Arisue et al 2004;Philippe et al 2004). Besides the usual problems of weakness of phylogenetic signal, lateral gene transfers, hidden paralogy, and tree reconstruction artefacts (Philippe et al 2004), incorrectly predicted protein models (since some sequences were extracted from draft genomes) may have contributed to greater than usual divergences making the relationship among deep branches difficult to resolve.…”

“…Based on morphological, biochemical, and molecular phylogenetic approaches, eukaryotes have recently been classified into six supergroups: the Opisthokonta, including animals and fungi; the Amoebozoa, including most traditional amoebae and slime moulds; the Excavata, grouping diplomonads, several genera of heterotrophic flagellates, and possibly the Euglenozoa; the Rhizaria, including the Foraminifera and the Cercozoa; the Archaeplastida, grouping red algae, green algae, and plants; and the Chromalveolata, including dinoflagellates, apicomplexan parasites, and the Stramenopiles (brown algae, diatoms, and many zoosporic fungi) (Adl et al 2005;Medina 2005). In order to evaluate the phyletic distribution of the RNAi machinery components, we have surveyed 25 complete or near-complete genomes that belong to five eukaryotic supergroups (with only Rhizaria remaining unsampled).…”