Ancestral Genomes: a resource for reconstructed ancestral genes and genomes across the tree of life

Abstract

A growing number of whole genome sequencing projects, in combination with development of phylogenetic methods for reconstructing gene evolution, have provided us with a window into genomes that existed millions, and even billions, of years ago. Ancestral Genomes (http://ancestralgenomes.org) is a resource for comprehensive reconstructions of these 'fossil genomes'. Comprehensive sets of protein-coding genes have been reconstructed for 78 genomes of now-extinct species that were the common ancestors of extant species from across the tree of life. The reconstructed genes are based on the extensive library of over 15 000 gene family trees from the PANTHER database, and are updated on a yearly basis. For each ancestral gene, we assign a stable identifier, and provide additional information designed to facilitate analysis: an inferred name, a reconstructed protein sequence, a set of inferred Gene Ontology (GO) annotations, and a 'proxy gene' for each ancestral gene, defined as the least-diverged descendant of the ancestral gene in a given extant genome. On the Ancestral Genomes website, users can browse the Ancestral Genomes by selecting nodes in a species tree, and can compare an extant genome with any of its reconstructed ancestors to understand how the genome evolved.

Figure 1.

Browsing and selecting an ancestral genome. (A) Users can browse the available genomes on the left panel. Clicking on a genome (e.g. Opisthokonts) brings up the list of genes in the right panel. (B) Clicking on the ‘…’ (info) button in the left panel in (A) brings up more information about that ancestral organism, including links to information in other resources, and the estimated age of that ancestor (in millions of years ago) as reported in the TimeTree (30) resource.

Figure 2.

Species Tree Browser. We also provide a species tree view of the genomes in Ancestral Genomes. This view is much less compact than the default nested hierarchical view, but it is a more standard view in phylogenetics. Right-clicking on a node will bring up the ancestral genome overview page (Figure 1B) for that genome, from which users can bring up the list of genes inferred for that genome.

Figure 3.

Ancestral gene information page. This page has information about the ancestral gene, including stable identifier, protein name, reconstructed sequence, inferred GO functions and proxy genes.

Figure 4.

Extant species information page. This page has information about the extant species, including species name, total number of protein coding genes, its ancestral species and their speciation times. Each ancestral species is followed by a link to the genome comparison page.

Figure 5.

Extant and Ancestral Genomes comparison page. There are four collapsible sections on the page, each with a header displaying summarizing information about the changes in gene content from the ancestral genome to the extant genome. Each section can be expanded to list the genes in that category.

Figure 6.

Gene Tree Viewer. Gene loss is shown explicitly in red, with text indicating the ancestral species prior to which the gene was lost.