title: Density peaks of paralog pairs in human and mouse genomes.
abstract: Paralog gene trees, which reflect the increase of genomic complexity in the evolution, can be complicated and ambiguous. A simpler complementary approach is analysis of density distribution of paralog pairs. It can reveal general features of genome evolution, which may be hidden in the forest of gene trees. It is known that distribution of human paralog pairs along the axis of protein divergence between pair members forms two main peaks. Here I show that there are three main peaks in the mouse genome. Thus, the multimodality of paralog pair distribution seems to be a fundamental feature of mammalian genomes. Despite the great diversity of domains presented in small amounts or in multidomain architectures with a few predominant domains, both in human and mouse the first peak consists mostly of gene pairs with zinc finger domains or olfactory receptor domain. In the mouse the olfactory receptor predominates, which stipulates the three-peak distribution (since in the olfactory receptors the second peak is closer to the first peak than in other genes). The mammalian-wide zinc finger orthologs are biased towards the second peak. Thus, the marsupial orthologs are nearly absent in the first peak of human and mouse. The gene pairs in the first peak show a lower ratio of nonsynonymous to synonymous substitutions, which suggests that their evolution is more constrained. The plausible explanation is that they are in subfunctionalization state (partition of initial function of ancestral gene), whereas the second peak contains gene pairs that are already in neofunctionalization state (acquiring of novel functions). These data suggest that the adaptive radiation of mammals was accompanied by a burst of duplication of zinc finger genes, which are located in the first (most recent) peak of paralog pairs.
authors.affiliation: Institute of Cytology, Russian Academy of Sciences, St. Petersburg 194064, Russia. aevin@mail.cytspb.rssi.ru
authors.forename: Alexander E
authors.initials: AE
authors.lastname: Vinogradov
mesh_terms: D000483:Alleles; D000818:Animals; D019143:Evolution, Molecular; D020440:Gene Duplication; D015894:Genome, Human; D006801:Humans; D051379:Mice; D008957:Models, Genetic; D018035:Receptors, Odorant / Q000235:genetics; D012689:Sequence Homology, Nucleic Acid; D016335:Zinc Fingers / Q000235:genetics
chemical_list: D018035:Receptors, Odorant
keywords: Blosum; C2H2; C2H2 zinc finger; C2H2-zf; Complexity; G protein coupled receptor A; GPCR_A; Gene duplication; KRAB; Krueppel-associated box domain; Olfactory receptors; Orthologs; PAML; Paralogs; Pfam; Protein Families (the database of protein domains); RefSeq; Reference Sequence (the database of non-redundant sequences); RevTrans; Zinc fingers; blocks of amino acid substitution matrix; cysteine(2)histidine(2); dN; dS; distance of nonsynonymous substitutions; distance of synonymous substitutions; phylogenetic analysis by maximum likelihood; reverse translation alignment program