PhylomeDB v3.0: an expanding repository of genome-wide collections of trees, alignments and phylogeny-based orthology and paralogy predictions

Abstract

The growing availability of complete genomic sequences from diverse species has brought about the need to scale up phylogenomic analyses, including the reconstruction of large collections of phylogenetic trees. Here, we present the third version of PhylomeDB (http://phylomeDB.org), a public database for genome-wide collections of gene phylogenies (phylomes). Currently, PhylomeDB is the largest phylogenetic repository and hosts 17 phylomes, comprising 416,093 trees and 165,840 alignments. It is also a major source for phylogeny-based orthology and paralogy predictions, covering about 5 million proteins in 717 fully-sequenced genomes. For each protein-coding gene in a seed genome, the database provides original and processed alignments, phylogenetic trees derived from various methods and phylogeny-based predictions of orthology and paralogy relationships. The new version of phylomeDB has been extended with novel data access and visualization features, including the possibility of programmatic access. Available seed species include model organisms such as human, yeast, Escherichia coli or Arabidopsis thaliana, but also alternative model species such as the human pathogen Candida albicans, or the pea aphid Acyrtosiphon pisum. Finally, PhylomeDB is currently being used by several genome sequencing projects that couple the genome annotation process with the reconstruction of the corresponding phylome, a strategy that provides relevant evolutionary insights.

Figure 1.

PhylomeDB web interface. (A) Entry page of phylomeDB, containing latest news, PhylomeDB statistics, login options and the main search panel. (B) Phylome description page. In the example, the phylogenetic pipeline and proteomes used to reconstruct the A. pisum phylome are shown. A Link is provided to browse all phylome resources (C) A multiple sequence alignment visualized through the integrated Jalview plugin. (D) Interactive tree visualization panel showing a particular tree from the human phylome. This panel allows online manipulation of tree topology and provides links to other related phylogenies in phylomeDB. Each sequence in the tree is also linked to external databases such as Ensembl, UniProtUniProt or MetaPhors. (E) Orthology prediction panel associated to each active tree. Phylogeny-based orthologs and paralogs of the seed sequence are shown sorted by species.