PhylomeDB v4: zooming into the plurality of evolutionary histories of a genome

Abstract

Phylogenetic trees representing the evolutionary relationships of homologous genes are the entry point for many evolutionary analyses. For instance, the use of a phylogenetic tree can aid in the inference of orthology and paralogy relationships, and in the detection of relevant evolutionary events such as gene family expansions and contractions, horizontal gene transfer, recombination or incomplete lineage sorting. Similarly, given the plurality of evolutionary histories among genes encoded in a given genome, there is a need for the combined analysis of genome-wide collections of phylogenetic trees (phylomes). Here, we introduce a new release of PhylomeDB (http://phylomedb.org), a public repository of phylomes. Currently, PhylomeDB hosts 120 public phylomes, comprising >1.5 million maximum likelihood trees and multiple sequence alignments. In the current release, phylogenetic trees are annotated with taxonomic, protein-domain arrangement, functional and evolutionary information. PhylomeDB is also a major source for phylogeny-based predictions of orthology and paralogy, covering >10 million proteins across 1059 sequenced species. Here we describe newly implemented PhylomeDB features, and discuss a benchmark of the orthology predictions provided by the database, the impact of proteome updates and the use of the phylome approach in the analysis of newly sequenced genomes and transcriptomes.

Target selection by natural and redesigned PUF proteins

“…To identify distinctive features of the Puf2p-like family, we performed a phylogenetic analysis of PUF proteins from 60 fungal species using PhylomeDB (20). PUF2-like PUFs were identified in 42 species and possessed two characteristics: a conserved pattern of TRMs in the first four PUF repeats and an N-terminal RRM (Fig.…”

Mitochondrial Carriers Link the Catabolism of Hydroxyaromatic Compounds to the Central Metabolism in Candida parapsilosis

“…Phylogenetic histories of the relevant genes were first inspected using the Maximum Likelihood phylogenies available in PhylomeDB (Huerta-Cepas et al 2014), and reconstructing phylogenies of these proteins, and their closest 350 blast hits, in the NCBI nonredundant database searched as of January 2016. In brief, phylogenies were reconstructed as follows: protein sequences of the hits that passed a threshold of similarity ( E -value <10 −5 ) and coverage (>33% aligned over the query sequence), were aligned with MUSCLE (Edgar 2004) with default parameters, trimmed with trimAl v1.4 (Capella-Gutiérrez et al 2009) to eliminate alignment columns with > 50% gaps.…”

The Solanum commersonii Genome Sequence Provides Insights into Adaptation to Stress Conditions and Genome Evolution of Wild Potato Relatives

“…The resulting 35,182 phylogenetic trees, available through PhylomeDB (Huerta-Cepas et al, 2014), were scanned to predict phylogenybased orthology and paralogy relationships (Gabaldón, 2008), detect and date duplication events (Huerta-Cepas and Gabaldón, 2011), and transfer annotations to S. commersonii genes from their functionally characterized one-to-one orthologs (HuertaCepas and Gabaldón, 2011). Roughly 17,300 (44%) and 16,821 (42%) S. commersonii genes showed one-to-one orthology with genes from S. tuberosum and S. lycopersicum, respectively, but only 7058 (18%) with genes from the more distantly related asterid Mimulus guttatus (Supplemental Table 12).…”