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Key Words
homolog, ortholog, paralog, pseudoortholog, pseudoparalog, xenolog
Abstract
Orthologs and paralogs are two fundamentally different types of homologous genes that evolved, respectively, by vertical descent from a single ancestral gene and by duplication. Orthology and paralogy are key concepts of evolutionary genomics. A clear distinction between orthologs and paralogs is critical for the construction of a robust evolutionary classification of genes and reliable functional annotation of newly sequenced genomes. Genome comparisons show that orthologous relationships with genes from taxonomically distant species can be established for the majority of the genes from each sequenced genome. This review examines in depth the definitions and subtypes of orthologs and paralogs, outlines the principal methodological approaches employed for identification of orthology and paralogy, and considers evolutionary and functional implications of these concepts.
INTRODUCTION
One of the most fascinating aspects of modern genomics is the radical change it brings to evolutionary biology. The availability of multiple, complete genomes of diverse life forms for comparative analysis provides a qualitatively new perspective on homologous relationships between genes. By comparing the sequences of all genes between genomes from different taxa and within each genome, it is, in principle, possible to reconstruct the evolutionary history of each gene in its entirety (within the set of sequenced genomes). This, in turn, will allow a deeper understanding of the general trends in the evolution of genomic complexity and lineage-specific adaptations. Gene histories must be presented in the form of scenarios that comprise several types of elementary events (55, 64, 84). The elementary events of gene evolution can be classified as follows, roughly in the order of relative contribution to the evolutionary process: (i) vertical descent (speciation) with modification; (ii) gene duplication, also followed by descent with modification; (iii) gene loss; (iv) horizontal gene transfer (HGT); and (v) fusion, fission, and other rearrangements of genes. Vertical descent and duplication might be considered the primary events of genome evolution and have been well recognized in the pregenomic era. In contrast, the crucial evolutionary importance of gene loss, HGT, and gene rearrangements was among the major, fundamental generalizations of the emerging evolutionary genomics (13, 14, 16, 50, 51, 57, 77, 78).
Along with the notion of elementary evolutionary events, all descriptions of evolution of genes, gene ensembles,...