The multiple facets of homology and their use in comparative genomics to study the evolution of genes, genomes, and species

Descorps-Declère, Stéphane; Lemoine, Frédéric; Sculo, Quentin; Lespinet, Olivier; Labedan, Bernard

doi:10.1016/j.biochi.2007.09.010

Cited by 13 publications

(10 citation statements)

References 60 publications

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“…This definition is simple in principle, but complex combinations of lineage-specific gene duplications, losses and horizontal gene transfer events often give rise to intricate evolutionary scenarios and complicated relationships when considering more than a pair of genes (that is, when multiple paralogues and/or multiple species are involved) 6,14,17–19 (BOX 1). This inherent complexity of the evolutionary scenarios drove the adoption of additional definitions to account for particular situations when comparing two or more genomes (BOX 1).…”

Section: Gene Homology Relationshipsmentioning

confidence: 99%

“…Despite efforts to capture the complexity of the evolutionary process, the characteristic penchant for simplicity in the descriptions of evolutionary scenarios in non-specialist scientific literature has given rise to widespread misuse and abuse of the orthology concept 17,19,28,29 . It remains rather common to equate orthology to functional equivalence and thus seek ‘functional orthologues’ 30,31 or to imply the necessary existence of a single ‘true orthologue’ of a given gene in any species.…”

Section: Gene Homology Relationshipsmentioning

confidence: 99%

“…This orthology–function conjecture (which is a key facet of the generalized orthology conjecture discussed above) constitutes the conceptual basis of functional annotation of sequenced genomes that is essential for experimental biology in the post-genomic era 6,17 . The strongest form of the orthology conjecture would also encompass the converse hypothesis: namely, that functionally equivalent genes in organisms are orthologous.…”

Section: Orthology–function Conjecturementioning

confidence: 99%

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Functional and evolutionary implications of gene orthology

2013

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Orthologues and paralogues are types of homologous genes that are related by speciation or duplication, respectively. Orthologous genes are generally assumed to retain equivalent functions in different organisms and to share other key properties. Several recent comparative genomic studies have focused on testing these expectations. Here we discuss the complexity of the evolution of gene–phenotype relationships and assess the validity of the key implications of orthology and paralogy relationships as general statistical trends and guiding principles.

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Section: Gene Homology Relationshipsmentioning

confidence: 99%

Section: Gene Homology Relationshipsmentioning

confidence: 99%

Section: Orthology–function Conjecturementioning

confidence: 99%

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Functional and evolutionary implications of gene orthology

2013

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“…Some work has already been performed in this area, both for prokaryotic genomes (e.g. Mirkin et al 2003; Descorps-Declère et al 2007) and for eukaryotic genomes (e.g. Koonin et al 2004).…”

Section: Perspectivesmentioning

confidence: 99%

Strategies for Reliable Exploitation of Evolutionary Concepts in High Throughput Biology

Levasseur¹,

Pontarotti²,

Poch

et al. 2008

Evol Bioinform Online

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The recent availability of the complete genome sequences of a large number of model organisms, together with the immense amount of data being produced by the new high-throughput technologies, means that we can now begin comparative analyses to understand the mechanisms involved in the evolution of the genome and their consequences in the study of biological systems. Phylogenetic approaches provide a unique conceptual framework for performing comparative analyses of all this data, for propagating information between different systems and for predicting or inferring new knowledge. As a result, phylogeny-based inference systems are now playing an increasingly important role in most areas of high throughput genomics, including studies of promoters (phylogenetic footprinting), interactomes (based on the presence and degree of conservation of interacting proteins), and in comparisons of transcriptomes or proteomes (phylogenetic proximity and co-regulation/co-expression). Here we review the recent developments aimed at making automatic, reliable phylogeny-based inference feasible in large-scale projects. We also discuss how evolutionary concepts and phylogeny-based inference strategies are now being exploited in order to understand the evolution and function of biological systems. Such advances will be fundamental for the success of the emerging disciplines of systems biology and synthetic biology, and will have wide-reaching effects in applied fields such as biotechnology, medicine and pharmacology.

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“…The identification of homologous genes is a critical step to understand the evolutionary history of an organism. Homologs can be divided into two types: orthologs, which originated through a speciation event from a common ancestor and paralogs, which resulted from a duplication event [ 19 – 21 ]. This classification is critical to understanding the diversification processes because duplication events are often related to a posterior functional divergence [ 22 , 23 ].…”

Section: Introductionmentioning

confidence: 99%

The Leishmania metaphylome: a comprehensive survey of Leishmania protein phylogenetic relationships

Valdivia

Scholte²,

Oliveira

et al. 2015

BMC Genomics

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BackgroundLeishmaniasis is a neglected parasitic disease with diverse clinical manifestations and a complex epidemiology. It has been shown that its parasite-related traits vary between species and that they modulate infectivity, pathogenicity, and virulence. However, understanding of the species-specific adaptations responsible for these features and their evolutionary background is limited. To improve our knowledge regarding the parasite biology and adaptation mechanisms of different Leishmania species, we conducted a proteome-wide phylogenomic analysis to gain insights into Leishmania evolution.ResultsThe analysis of the reconstructed phylomes (totaling 45,918 phylogenies) allowed us to detect genes that are shared in pathogenic Leishmania species, such as calpain-like cysteine peptidases and 3'a2rel-related proteins, or genes that could be associated with visceral or cutaneous development. This analysis also established the phylogenetic relationship of several hypothetical proteins whose roles remain to be characterized. Our findings demonstrated that gene duplication constitutes an important evolutionary force in Leishmania, acting on protein families that mediate host-parasite interactions, such as amastins, GP63 metallopeptidases, cathepsin L-like proteases, and our methods permitted a deeper analysis of their phylogenetic relationships.ConclusionsOur results highlight the importance of proteome wide phylogenetic analyses to detect adaptation and evolutionary processes in different organisms and underscore the need to characterize the role of expanded and species-specific proteins in the context of Leishmania evolution by providing a framework for the phylogenetic relationships of Leishmania proteins.Phylogenomic data are publicly available for use through PhylomeDB (http://www.phylomedb.org).Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-015-2091-2) contains supplementary material, which is available to authorized users.

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The multiple facets of homology and their use in comparative genomics to study the evolution of genes, genomes, and species

Cited by 13 publications

References 60 publications

Functional and evolutionary implications of gene orthology

Functional and evolutionary implications of gene orthology

Strategies for Reliable Exploitation of Evolutionary Concepts in High Throughput Biology

The Leishmania metaphylome: a comprehensive survey of Leishmania protein phylogenetic relationships

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