EnsemblCompara GeneTrees: Complete, duplication-aware phylogenetic trees in vertebrates

Abstract

We have developed a comprehensive gene orientated phylogenetic resource, EnsemblCompara GeneTrees, based on a computational pipeline to handle clustering, multiple alignment, and tree generation, including the handling of large gene families. We developed two novel non-sequence-based metrics of gene tree correctness and benchmarked a number of tree methods. The TreeBeST method from TreeFam shows the best performance in our hands. We also compared this phylogenetic approach to clustering approaches for ortholog prediction, showing a large increase in coverage using the phylogenetic approach. All data are made available in a number of formats and will be kept up to date with the Ensembl project.[Supplemental material is available online at www.genome.org.]The use of phylogenetic trees to describe the evolution of biological processes was established in the 1950s (Hennig 1952) and remains a fundamental approach to understanding the evolution of individual genes through to complete genomes; for example, in the mouse (Mouse Genome Sequencing Consortium 2002), rat (Gibbs et al. 2004), chicken (International Chicken Genome Sequencing Consortium 2004), and monodelphis (Mikkelsen et al. 2007) genome papers, and numerous papers on individual sequences. Now routine, the determination of vertebrate genome sequences provides a rich data source to understand evolution, and using phylogenetic trees of the genes is one of the best ways to organize these data. However, the increased set of genomes makes the compute and engineering tasks to form all the gene trees , we replaced this system with a phylogenetically sound, gene tree-based approach, providing a complete set of phylogenetic trees spanning 91% of genes across vertebrates. In addition to the vertebrates we have included a few important non-vertebrate species (fly, worm, and yeast) to act both as out groups and provide links to these model organisms. In this paper we provide the motivation, implementation, and benchmarking of this method and document the display and access methods for these trees.There have been a number of methods proposed for routine generation of genomewide orthology descriptions, including ) uses a tree-based method, but between pairs of closely related species, resolving paralogs accurately by using neutral substitution (as measured by d S , the synonymous substitution rate). TreeFam provides an explicit gene tree across multiple species, using both d S , d N (nonsynonymous substitution rate), nucleotide and protein distance measures, and the standard species tree to balance duplications vs. deletions to inform the tree construction, using the program TreeBeST (http:// treesoft.sourceforge.net/treebest.shtml; L. Heng, A.J. Vilella, E. Birney, and R. Durbin, in prep.).The PhiGs method (Dehal and Boore 2006) is a leading phylogenetic-based method that produced a comprehensive phylogenetic resource for the genomes at the time it was run, and the basic outline of its analysis, which was clustering of protein sequences, followed by phylogenetic trees, is...

Introgression and repeated co-option facilitated the recurrent emergence of C4photosynthesis among close relatives

“…Our automated pipeline started with gene families previously inferred for eight plant genomes (homologs: i.e., all the paralogs and orthologs; Vilella et al. 2009), including two Panicoideae grasses ( Setaria italica and Sorghum bicolor ), two non‐Panicoideae grasses ( Brachypodium distachyon and Oryza sativa ), and four nongrass species ( Amborella trichopoda, A. thaliana , Populus trichocarpa , and Selaginella moellendorffii ). To ensure accurate annotation, we restricted the analysis to gene families that included at least one A. thaliana sequence.…”

Evidence for widespread subfunctionalization of splice forms in vertebrate genomes

“…This means that if exon divergent paralogs are enriched in young duplicates, the influence of duplication age may make it appear as though exon structure divergence between paralogs results in lower levels of alternative splicing. Figure 3B plots the proportions of exon divergent and nondivergent paralogs created during a variety of evolutionary epochs as indicated by Ensembl Compara (Vilella et al 2009). Within each plot, the proportions of divergent and nondivergent paralogs produced at each epoch are strikingly similar.…”

Inferring evolution of gene duplicates using probabilistic models and nonparametric belief propagation

“…We constructed phylogenetic trees based on 3679 human paralogous families extracted from the Ensembl database [21]. We used the multiple sequence alignment (MSA) algorithm ClustalW2 [22] to align the nucleotide sequences.…”