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

By Albert J. Vilella, Jessica Severin, Abel Ureta-Vidal, L. Heng, Richard Durbin, Ewan Birney. Genome Research, 2009

1,246 citations recorded by the source corpus.

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.

Subfields: Genetics, Molecular Biology, Plant Science

View Paper: https://www.semanticscholar.org/paper/36fa41f244561c759cff6b7f556e385e5fcb20c5

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Citations in the corpus

Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium (2011, background): “Compara does not annotate PGM1, but anno-tates PGM5 with three CC terms.”
expVIP: a Customizable RNA-seq Data Analysis and Visualization Platform1[OPEN] (2016, methodology): “The homeologues of each gene were extracted from EnsemblCompara release 26 (Vilella et al., 2009) and added as metadata to the genes.”
WormBase 2016: expanding to enable helminth genomic research (2015, methodology): “We have used the Ensembl Compara system (17) to infer evolutionary histories for all helminth genes, supplemented by gene sets from 9 free-living species (including C.”
Universal Patterns of Selection in Cancer and Somatic Tissues (2018, positive): “( A ) Species evolution: median dN/dS ratios across genes for missense mutations (data from (Martincorena et al., 2012), Ensembl (Vilella et al., 2009)).”
Expanded identification and characterization of mammalian circular RNAs (2014, methodology): “One-to-one gene ortholog tables for gene-level analysis were downloaded from Ensembl [32].”
Polyploidy in Fish and the Teleost Genome Duplication (2012, methodology): “Chromosomal location of paralogs determined by EnsemblCompara GeneTrees (Vilella et al. 2009) to be generated at the ‘Clupeocephala’ node.”
Maize Metabolic Network Construction and Transcriptome Analysis (2013, methodology): “EC numbers were assigned based on the annotations extracted from (1) mapped UniProt entries, (2) MaizeGDB curated pathways, and (3) orthologous gene annotation projections from RiceCyc, AraCyc, and PlantCyc, but supported by the phylogeny-based gene orthology tree clustering methods (Vilella et al.,”
UniProt Knowledgebase: a hub of integrated protein data (2011, background): “Reciprocal BLAST searches and phylogenetic resources such as Ensembl Compara (20) are used to identify putative homologs which are evaluated and curated.”
The iPlant Collaborative: Cyberinfrastructure for Plant Biology (2011, methodology): “The current implementation of the analysis pipeline is based on MUSCLE (Edgar, 2004) to align sequences, and TreeBeST (Vilella et al., 2009), a Maximum Likelihood method.”
Ensembl comparative genomics resources (2016, methodology): “As with the GeneTrees, protein similarities are detected using BLASTP (36).”
MobiDB 3.0: more annotations for intrinsic disorder, conformational diversity and interactions in proteins (2017, positive): “Regions homologous to experimentally characterized IDRs are mapped across homologs obtained from GeneTree alignments (37).”
The R-spondin/Lgr5/Rnf43 module: regulator of Wnt signal strength (2014, positive): “Evolutionary history as reconstructed in the Ensembl Compara database (Vilella et al. 2009) detects an ancient protein with the same domain architecture in plants, fungi, and diverse protists.”
Homoeologs: What Are They and How Do We Infer Them? (2016, methodology): “To our knowledge, the only phylogenetic tree-based homoeology inference approach taken so far is that of Ensembl Genomes, which has repurposed their Compara phylogenetic tree-based pipeline [73] to distinguish orthologs, paralogs, and homoeologs in wheat [74].”