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PubMed1983

Rapid evolution of goat and sheep globin genes following gene duplication.

Statistical analyses of DNA sequences of globin genes (beta A, beta C, and gamma) from goat and sheep (including new sequence information for the second intron of sheep beta A and gamma, kindly provided by A. Davis and A. W. Nienhuis) indicate that the rates of nonsynonymous substitution in these genes have been greatly accelerated following the gene duplication separating gamma and the ancestor of beta A and beta C and the gene duplication separating beta A and beta C. In both cases the acceleration was apparently due to relaxation of purifying selection (functional constraints) rather than advantageous mutations because acceleration occurred only in less important parts of the beta globin chain. The rates of nonsynonymous substitution in these genes are estimated to be about 2.3 x 10(-9) per site per year, which is three times higher than that for the divergence between human beta and mouse beta major globin genes. Our analyses further suggest that the rate of synonymous substitution in functional genes and the rate of substitution in pseudogenes are approximately equal and are between 2.8 x 10(-9) and 5.0 x 10(-9) and that the rate of substitution in introns is about 3.0 x 10(-9). The divergence time between beta A and beta C and that between gamma and the beta A-beta C pair are about 12 and 30 million years, respectively. The proportion of transition mutations is estimated to be 64%, two times higher than expected under random mutation but considerably lower than the 96% estimated for animal mitochondrial DNA.

Animals↗

PubMed2004

Duplicate genes increase gene expression diversity within and between species.

Using microarray gene expression data from several Drosophila species and strains, we show that duplicated genes, compared with single-copy genes, significantly increase gene expression diversity during development. We show further that duplicate genes tend to cause expression divergences between Drosophila species (or strains) to evolve faster than do single-copy genes. This conclusion is also supported by data from different yeast strains.

Animals↗

PubMed2003

Parallel evolution by gene duplication in the genomes of two unicellular fungi.

Phylogenetic analysis of conserved gene families in fission yeast Schizosaccharomyces pombe and brewer's yeast Saccharomyces cerevisiae showed that gene duplications have occurred independently in the same families in each of these two lineages to a far greater extent than expected by chance. These species represent distinct lineages of the phylum Ascomycota that independently evolved a "yeast" life cycle with a unicellular thallus that reproduces by budding, and many of the genes that have duplicated independently in the two lineages are known to be involved in crucial aspects of this life cycle. Parallel gene duplication thus appears to have played a role in the independent origin of similar adaptations in the two species. The results indicate that using phylogenetic analysis to test for parallel gene duplication in different species may help in identifying genes responsible for similar but independently evolved adaptations.

Evolution, Molecular↗

PubMed2003

Parallel evolution by gene duplication in the genomes of two unicellular fungi.

Evolution, Molecular↗

PubMed2005

Alternative splicing and gene duplication are inversely correlated evolutionary mechanisms.

Gene duplication and alternative splicing are distinct evolutionary mechanisms that provide the raw material for new biological functions. We explored their relationships in human and mouse and found an inverse correlation between the size of a gene's family and its use of alternatively spliced isoforms. A cross-organism analysis suggests that selection for genome-wide genic proliferation might be interchangeably met by either evolutionary mechanism.

Alternative Splicing↗

PubMed2003

Distribution and evolution of chitinase genes in Streptomyces species: involvement of gene-duplication and domain-deletion.

Streptomyces coelicolor A3(2) possesses nine genes for family 18 chitinases and two for family 19, showing high multiplicity. By hybridization analyses, distribution of those chitinase genes was investigated in six other Streptomyces species covering the whole phylogenetic range based on 16S rDNA sequences. All strains showed high-multiplicity of chitinase genes, like S. coelicolor A3(2). The phylogeny and gene organization of the family 18 chitinase genes cloned from Streptomyces species so far were then analyzed to investigate the gene evolution. It was concluded that Streptomyces already possessed a variety of chitinase genes prior to branching into many species, and that the ancestral genes of chiA and chiB have been generated by gene-duplication. In the course of the analyses, evidence that the chi30 and chi40 genes of S. thermoviolaceus were derived from their corresponding original chitinase genes by losing gene parts for substrate-binding domains and fibronectin type III-like domains was obtained. It was thus shown that gene-duplication and domain-deletion were implicated in generating the high diversity and multiplicity of chitinase genes in Streptomyces species.

Bacterial Proteins↗

PubMed2005

The evolution of introns in human duplicated genes.

In previous work [Jabbari, K., Rayko, E., Bernardi, G., 2003. The major shifts of human duplicated genes. Gene 317, 203-208], we investigated the fate of ancient duplicated genes after the compositional transitions that occurred between the genomes of cold- and warm-blooded vertebrates. We found that the majority of duplicated copies were transposed to the "ancestral genome core", the gene-dense genome compartment that underwent a GC enrichment at the compositional transitions. Here, we studied the consequences of the events just outlined on the introns of duplicated genes. We found that, while intron number was highly conserved, total intron size (the sum of intron sizes within any given gene) was smaller in the GC-rich copies compared to the GC-poor copies, especially in dispersed copies (i.e., copies located on different chromosomes or chromosome arms). GC-rich copies also showed higher densities of CpG islands and Alus, whereas GC-poor copies were characterized by higher densities of LINEs. The features of the copies that underwent the compositional transition and became GC-richer are suggestive of, or related to, functional changes.

Alu Elements↗

PubMed2006

Divergence of duplicated genes in maize: evolution of contrasting targeting information for enzymes in the porphyrin pathway.

The divergence of sequence and expression pattern of duplicated genes provides a means for genetic innovation to occur without sacrificing an essential function. The cpx1 and cpx2 genes of maize are a singular example of duplicated genes that have diverged by deletion and creation of protein targeting information. The cpx genes encode coproporphyrinogen III oxidase ('coprogen oxidase'), which catalyzes a step in the synthesis of chlorophyll and heme. In plants, this enzyme has been found exclusively in the plastids. The cpx1 and cpx2 genes encode almost identical, catalytically active enzymes with distinctive N-terminal peptide sequences. The cpx1 gene encodes the expected plastid transit peptide, but this region is deleted from the cpx2 gene. While the 5' regions of both messenger RNAs are highly similar, the cpx2 gene has an open-reading frame that could encode a new targeting signal. GFP fused with CPX1 localized to the plastids. In contrast, the GFP fusion with CPX2 did not target plastids and appeared to localize to mitochondria. Both cpx genes are expressed ubiquitously but, based on mutant phenotype, they seem to have discrete biological roles. Seedlings homozygous for a null mutation in the cpx1 gene completely lack chlorophyll and develop necrotic lesions in the light. However, the mutant seedlings and callus cultures will grow in tissue culture in the dark, implying that they retain a capacity to produce heme. We discuss models for the evolution of the cpx genes and possible roles of mitochondrion-localized coprogen oxidase activity in maize.

Amino Acid Sequence↗

PubMed2003

Dopamine receptors for every species: gene duplications and functional diversification in Craniates.

The neuromodulatory effects of dopamine on the central nervous system of craniates are mediated by two classes of G protein-coupled receptors (D1 and D2), each comprising several subtypes. A systematic isolation and characterization of the D1 and D2-like receptors was carried out in most of the Craniate groups. It revealed that two events of gene duplications took place during vertebrate evolution, before or simultaneously to the emergence of Gnathostomes. It led to the conservation of two-to-four paralogous receptors (subtypes), depending on the species. Additional duplication of dopamine receptor gene occurred independently in the teleost fish lineage. Duplicated genes were maintained in most of the vertebrate groups, certainly by the acquisition of a few functional characters, specific of each subtypes, as well as by discrete changes in their expression territories in the brain. The evolutionary scenario elaborated from these data suggests that receptor gene duplications were the necessary conditions for the expansion of vertebrate forebrain to occur, allowing dopamine systems to exert their fundamental role as modulator of the adaptive capabilities acquired by vertebrate species.

Animals↗

PubMed1999

Extensive gene duplication in the early evolution of animals before the parazoan-eumetazoan split demonstrated by G proteins and protein tyrosine kinases from sponge and hydra.

To know whether genes involved in cell-cell communication typical of multicellular animals dramatically increased in concert with the Cambrian explosion, the rapid evolutionary burst in the major groups of animals, and whether these genes exist in the sponge lacking cell cohesiveness and coordination typical of eumetazoans, we have carried out cloning of the G-protein alpha subunit (Galpha) and the protein tyrosine kinase (PTK) cDNAs from Ephydatia fluviatilis (freshwater sponge) and Hydra magnipapillata strain 105 (hydra). We obtained 13 Galpha and 20 PTK cDNAs. Generally animal gene families diverged first by gene duplication (subtype duplication) that gave rise to diverse subtypes with different primary functions, followed by further gene duplication in the same subtype (isoform duplication) that gave rise to isoform genes with virtually identical function. Phylogenetic trees of Galpha and PTK families including cDNAs from sponge and hydra revealed that most of the present-day subtypes had been established in the very early evolution of animals before the parazoan-eumetazoan split, the earliest branching among the extant animal phyla, by extensive subtype duplication: for PTK and Galpha families, 23 and 9 subtype duplications were observed in the early stage before the parazoan-eumetazoan split, respectively, and after that split, only 2 and 1 subtype duplications were found, respectively. After the separation from arthropods, vertebrates underwent frequent isoform duplications before the fish-tetrapod split. Furthermore, rapid amino acid changes appear to have occurred in concert with the extensive subtype duplication and isoform duplication. Thus the pattern of gene diversification during animal evolution might be characterized by bursts of gene duplication interrupted by considerably long periods of silence, instead of proceeding gradually, and there might be no direct link between the Cambrian explosion and the extensive gene duplication that generated diverse functions (subtypes) of these families.

Amino Acid Substitution↗

PubMedDate not supplied

Evolution of a trypanosome surface antigen gene repertoire linked to non-duplicative gene activation.

African trypanosomes activate, one at a time, a large set of genes coding for different variant-specific surface antigens (VSAs). These genes have been classed into two groups. In the first group a permanently silent basic gene copy is duplicated and the expression-linked copy (ELC) transposed to an expression site located at a chromosome end. The process is a gene conversion which changes a variable stretch of the preceding ELC. Genes belonging to the second group do not give rise to an additional copy when expressed by a still unknown mechanism. We report here that the gene for antigenic type AnTat 1.6 is located in a telomeric DNA region and is expressed without being duplicated. In clone AnTat 1.6 and the ensuing ones, the ELC of the preceding VSA (AnTat 1.3) is conserved, but in a inactive conformation. Moreover, the AnTat 1.6 gene is lost from the genome of the AnTat 1.6-derived variants, in which the duplication-linked mechanism of gene activation occurs: the gene appears to be replaced by the incoming ELC. These observations show that a trypanosome surface antigen repertoire may evolve by loss and gain of VSA genes, depending on the alternation of the different recombinational mechanism involved in antigenic variation.

Antigens, Surface↗

PubMed2000

A segmental gene duplication generated differentially expressed myb-homologous genes in maize.

The myb-homologous p1 gene regulates the synthesis of flavonoid pigments in maize kernel pericarp and cob; these floral organs are greatly modified in size and shape compared with their counterparts in teosinte, the progenitor of maize. To elucidate the molecular evolution of the p1 gene in relation to its expression and possible functions in maize and teosinte, we have isolated a second maize gene (p2) that is highly homologous with the p1 gene, and a related gene (p2-t) from Zea mays subsp parviglumis. We present evidence that the maize p1 and p2 genes were generated by duplication of an ancestral p gene (p(pre)) and its downstream sequences; the duplicated 3' flanking sequences were inserted upstream of the p(pre) gene, thereby changing its transcription pattern. This model accounts for the structural organization and the observed differential expression of the p1 and p2 genes: p1 transcripts accumulate in kernel pericarp, cob, tassel glumes, and silk, whereas p2 transcripts are found in developing anther and silk. The duplication is estimated to have occurred 2.75 million years ago; subsequently, multiple retroelements have been inserted between the p1 and p2 genes. Our results demonstrate the evolution of a single gene into a compound locus containing two component genes with different tissue specificities. Expression of the p1 gene in the kernel pericarp may have provided a selective advantage during the evolution of maize kernel morphology.

Amino Acid Sequence↗

PubMed1999

Gene duplications in early metazoan evolution.

Major increases in complexity during animal evolution occurred at the transition from a unicellular protozoan to a multicellular metazoan, the evolution of Bilateria from diploblasts (possibly the Cambrian explosion) and during early vertebrate evolution. A role for gene duplication in the third event has been widely discussed. Here I examine the possible role of gene duplications and domain shuffling in the first two events. There is evidence for a wave of gene duplications and shuffling which may have paved the way for multicellularity; there are also examples of gene duplications that may have facilitated the transition from diploblasts to Bilateria.

Animals↗

PubMed1994

Gene duplications and the origins of vertebrate development.

All vertebrates possess anatomical features not seen in their closest living relatives, the protochordates (tunicates and amphioxus). Some of these features depend on developmental processes or cellular behaviours that are again unique to vertebrates. We are interested in the genetic changes that may have permitted the origin of these innovations. Gene duplication, followed by functional divergence of new genes, may be one class of mutation that permits major evolutionary change. Here we examine the hypothesis that gene duplication events occurred close to the origin and early radiation of the vertebrates. Genome size comparisons are compatible with the occurrence of duplications close to vertebrate origins; more precise insight comes from cloning and phylogenetic analysis of gene families from amphioxus, tunicates and vertebrates. Comparisons of Hox gene clusters, other homeobox gene families, Wnt genes and insulin-related genes all indicate that there was a major phase of gene duplication close to vertebrate origins, after divergence from the amphioxus lineage; we suggest there was probably a second phase of duplication close to jawed vertebrate origins. From amphioxus and vertebrate homeobox gene expression patterns, we suggest that there are multiple routes by which new genes arising from gene duplication acquire new functions and permit the evolution of developmental innovations.

Amino Acid Sequence↗

PubMed2004

A scale of functional divergence for yeast duplicated genes revealed from analysis of the protein-protein interaction network.

BACKGROUND: Studying the evolution of the function of duplicated genes usually implies an estimation of the extent of functional conservation/divergence between duplicates from comparison of actual sequences. This only reveals the possible molecular function of genes without taking into account their cellular function(s). We took into consideration this latter dimension of gene function to approach the functional evolution of duplicated genes by analyzing the protein-protein interaction network in which their products are involved. For this, we derived a functional classification of the proteins using PRODISTIN, a bioinformatics method allowing comparison of protein function. Our work focused on the duplicated yeast genes, remnants of an ancient whole-genome duplication. RESULTS: Starting from 4,143 interactions, we analyzed 41 duplicated protein pairs with the PRODISTIN method. We showed that duplicated pairs behaved differently in the classification with respect to their interactors. The different observed behaviors allowed us to propose a functional scale of conservation/divergence for the duplicated genes, based on interaction data. By comparing our results to the functional information carried by GO annotations and sequence comparisons, we showed that the interaction network analysis reveals functional subtleties, which are not discernible by other means. Finally, we interpreted our results in terms of evolutionary scenarios. CONCLUSIONS: Our analysis might provide a new way to analyse the functional evolution of duplicated genes and constitutes the first attempt of protein function evolutionary comparisons based on protein-protein interactions.

Computational Biology↗

PubMed1999

The evolution of trichromatic color vision by opsin gene duplication in New World and Old World primates.

Trichromacy in all Old World primates is dependent on separate X-linked MW and LW opsin genes that are organized into a head-to-tail tandem array flanked on the upstream side by a locus control region (LCR). The 5' regions of these two genes show homology for only the first 236 bp, although within this region, the differences are conserved in humans, chimpanzees, and two species of cercopithecoid monkeys. In contrast, most New World primates have only a single polymorphic X-linked opsin gene; all males are dichromats and trichromacy is achieved only in those females that possess a different form of this gene on each X chromosome. By sequencing the upstream region of this gene in a New World monkey, the marmoset, we have been able to demonstrate the presence of an LCR in an equivalent position to that in Old World primates. Moreover, the marmoset sequence shows extensive homology from the coding region to the LCR with the upstream sequence of the human LW gene, a distance of >3 kb, whereas homology with the human MW gene is again limited to the first 236 bp, indicating that the divergent MW sequence identifies the site of insertion of the duplicated gene. This is further supported by the presence of an incomplete Alu element on the upstream side of this insertion point in the MW gene of both humans and a cercopithecoid monkey, with additional Alu elements present further upstream. Therefore, these Alu elements may have been involved in the initial gene duplication and may also be responsible for the high frequency of gene loss and gene duplication within the opsin gene array. Full trichromacy is present in one species of New World monkey, the howler monkey, in which separate MW and LW genes are again present. In contrast to the separate genes in humans, however, the upstream sequences of the two howler genes show homology with the marmoset for at least 600 bp, which is well beyond the point of divergence of the human MW and LW genes, and each sequence is associated with a different LCR, indicating that the duplication in the howler monkey involved the entire upstream region. [The sequence data described in this paper have been submitted to GenBank under accession nos. AF155218, AF156715, and AF156716.]

Animals↗

PubMed1998

Evidence of independent gene duplications during the evolution of archaeal and eukaryotic family B DNA polymerases.

Eukaryotes and archaea both possess multiple genes coding for family B DNA polymerases. In animals and fungi, three family B DNA polymerases, alpha, delta, and epsilon, are responsible for replication of nuclear DNA. We used a PCR-based approach to amplify and sequence phylogenetically conserved regions of these three DNA polymerases from Giardia intestinalis and Trichomonas vaginalis, representatives of early-diverging eukaryotic lineages. Phylogenetic analysis of eukaryotic and archaeal paralogs suggests that the gene duplications that gave rise to the three replicative paralogs occurred before the divergence of the earliest eukaryotic lineages, and that all eukaryotes are likely to possess these paralogs. One eukaryotic paralog, epsilon, consistently branches within archaeal sequences to the exclusion of other eukaryotic paralogs, suggesting that an epsilon-like family B DNA polymerase was ancestral to both archaea and eukaryotes. Because crenarchaeote and euryarchaeote paralogs do not form monophyletic groups in phylogenetic analysis, it is possible that archaeal family B paralogs themselves evolved by a series of gene duplications independent of the gene duplications that gave rise to eukaryotic paralogs.

Amino Acid Sequence↗

PubMed1992

Partial gene duplication as a cause of human disease.

Tandem duplication of large regions of DNA, including duplication of whole genes, provides a substrate for genetic evolution. Tandem duplication of smaller regions involving parts of genes is now recognized as a contributor to the mutation spectrum that results in genetic disease. In this review, more than 30 unrelated partial gene duplications that have been implicated in the genesis of human genetic disease are presented and the pathogenic effects and frequency of such duplications are summarized. The mechanisms of duplication formation are analyzed with special emphasis on the molecular details of the nucleotide sequences at the duplication junctions. Evidence to date suggests that duplication may arise from either homologous (Alu-Alu) recombination or nonhomologous recombination, the latter possibly mediated by topoisomerases. For the dystrophin gene, in which most duplications have been identified, these recombination events are intrachromosomal, suggesting that unequal sister chromatid exchange is the major mechanism.

Biological Evolution↗