The human phylome

By Jaime Huerta-Cepas, Hernán Dopazo, Joaquín Dopazo, Toni Gabaldón. 2007

208 citations recorded by the source corpus.

Background:Phylogenomics analyses serve to establish evolutionary relationships among organisms and their genes. A phylome, the complete collection of all gene phylogenies in a genome, constitutes a valuable source of information, but its use in large genomes still constitutes a technical challenge. The use of phylomes also requires the development of new methods that help us to interpret them.Results:We reconstruct here the human phylome, which includes the evolutionary relationships of all human proteins and their homologs among 39 fully sequenced eukaryotes. Phylogenetic techniques used include alignment trimming, branch length optimization, evolutionary model testing and maximum likelihood and Bayesian methods. Although differences with alternative topologies are minor, most of the trees support the Coelomata and Unikont hypotheses as well as the grouping of primates with laurasatheria to the exclusion of rodents. We assess the extent of gene duplication events and their relationship with the functional roles of the protein families involved. We find support for at least one, and probably two, rounds of whole genome duplications before vertebrate radiation. Using a novel algorithm that is independent from a species phylogeny, we derive orthology and paralogy relationships of human proteins among eukaryotic genomes.Conclusion:Topological variations among phylogenies for different genes are to be expected, highlighting the danger of gene-sampling effects in phylogenomic analyses. Several links can be established between the functions of gene families duplicated at certain phylogenetic splits and major evolutionary transitions in those lineages. The pipeline implemented here can be easily adapted for use in other organisms.

Subfields: Genetics, Molecular Biology

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Citations in the corpus

eggNOG 5.0: a hierarchical, functionally and phylogenetically annotated orthology resource based on 5090 organisms and 2502 viruses (2018, methodology): “in-paralogy relationships) using the species overlap algorithm described in (35), leading to pairwise orthology tables (differentiating one-to-one versus many-to-many relationships) for each OG.”
PhylomeDB v3.0: an expanding repository of genome-wide collections of trees, alignments and phylogeny-based orthology and paralogy predictions (2010, background): “The analysis of phylomes has proven to be very powerful in addressing a variety of questions, including the reconstruction of ancestral metabolisms (12), the evaluation of alternative species phylogenies (13,14), the identification of horizontal gene transfers (15), the inference of functional impli”
ETE: a python Environment for Tree Exploration (2010, methodology): “Currently, the ETE toolkit is used in diverse projects, including GEPAS [17], Phylemon [18] and PhylomeDB [15].”
Next-Generation Sequencing — An Overview of the History, Tools, and “Omic” Applications (2016, background): “Phylomes provide the combined analysis of genome-wide collections of phylogenetic trees to aid in the inference of orthological and paralogical relationships and the detection of evolu‐ tionary events such as whole-genome duplication (polyploidization), gene family expansion and contraction, horizon”
OrthoFinder: phylogenetic orthology inference for comparative genomics (2019, methodology): “A third approach, here referred to as the species-overlap method, is employed in a number of ortholog databases [20, 31] and was originally described in a method for determining orthologs of human genes [31].”
eggNOG 4.5: a hierarchical orthology framework with improved functional annotations for eukaryotic, prokaryotic and viral sequences (2015, methodology): “9 million phylogenetic trees were built using a slightly modified version of a previously described methodology (32,33).”
The genome of melon (Cucumis melo L.) (2012, unknown): “Duplication analysis on entire phylomes has been used to confirm ancient whole-genome duplication (WGD) events, which emerge as duplication peaks in the corresponding evolutionary periods (29).”
TreeFam: 2008 Update (2007, unknown): “These include HOGENOM (13) and PhylomeDB (14).”
Fast Genome-Wide Functional Annotation through Orthology Assignment by eggNOG-Mapper (2016, unknown): “excluding evident (in-)paralogs as described in (Huerta-Cepas et al. 2007)).”