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PubMed2002

Genome sequencing of a 239-kb region of rice chromosome 10L reveals a high frequency of gene duplication and a large chloroplast DNA insertion.

In this study we describe a 239-kb region on the long arm of rice chromosome 10 that contains a high density (71%) of locally duplicated genes, including 24 copies of a glutathione S-transferase gene. Intriguingly, embedded within this cluster is a large insertion (approximately 33 kb) of rice (Oryza sativa) chloroplast DNA that is derived from two separate regions of the chloroplast genome. We used DNA fiber-based fluorescence in situ hybridization (fiber-FISH) analyses of O. sativa spp. japonica nuclei to confirm that the insertion of organellar DNA was not a cloning artifact. The sequence of the chloroplast insertion is nearly identical (99.7% identity) to the corresponding regions in the published rice chloroplast genome sequence, suggesting that the transfer event occurred recently. PCR amplification and sequence analysis in two subspecies of rice, O. sativa spp. japonica and spp. indica, indicates that the transfer event predated the divergence of these two subspecies. The chloroplast insertion is flanked by a 2.1-kb perfect direct repeat that is unique to this location in the rice genome.

Base Sequence↗

PubMed1996

Duplication of an amphioxus myogenic bHLH gene is independent of vertebrate myogenic bHLH gene duplication.

Gene duplication is thought to be a major genetic change that may have permitted the evolution of vertebrates from invertebrates. The myogenic genes encode basic helix-loop-helix (bHLH) transcriptional factors essential for the formation of skeletal muscle. The invertebrate genome contains only a single myogenic bHLH gene, whereas the vertebrate genome contains four (MyoD, Myf-5, myogenin and MRF4). Since the tunicate genome contains a single myogenic bHLH gene, its duplication might have occurred some time during chordate evolution. To determine whether the duplication of the myogenic bHLH gene occurred prior to, or after the divergence of vertebrates from the cephalochordate lineage, we amplified target fragments from the amphioxus, Branchiostoma floridae, by means of PCR. Sequence analysis and genomic Southern analysis revealed that the amphioxus genome contains two myogenic bHLH genes (BMD1 and BMD2). A comparison of the amino acid sequences in the bHLH domain between BMD1, BMD2 and four vertebrate myogenic bHLH gene products, however, showed that neither BMD1 nor BMD2 resembled any of the four genes. These results suggested that the duplication of amphioxus myogenic bHLH gene occurred independently of that leading to the four myogenic bHLH genes in vertebrates.

Amino Acid Sequence↗

PubMed1998

Positive Darwinian selection after gene duplication in primate ribonuclease genes.

Evolutionary mechanisms of origins of new gene function have been a subject of long-standing debate. Here we report a convincing case in which positive Darwinian selection operated at the molecular level during the evolution of novel function by gene duplication. The genes for eosinophil cationic protein (ECP) and eosinophil-derived neurotoxin (EDN) in primates belong to the ribonuclease gene family, and the ECP gene, whose product has an anti-pathogen function not displayed by EDN, was generated by duplication of the EDN gene about 31 million years ago. Using inferred nucleotide sequences of ancestral organisms, we showed that the rate of nonsynonymous nucleotide substitution was significantly higher than that of synonymous substitution for the ECP gene. This strongly suggests that positive Darwinian selection operated in the early stage of evolution of the ECP gene. It was also found that the number of arginine residues increased substantially in a short period of evolutionary time after gene duplication, and these amino acid changes probably produced the novel anti-pathogen function of ECP.

Amino Acid Sequence↗

PubMed1999

Ancient gene duplication and differential gene flow in plastid lineages: the GroEL/Cpn60 example.

Cryptomonads, small biflagellate algae, contain four different genomes. In addition to the nucleus, mitochondrion, and chloroplast is a fourth DNA-containing organelle the nucleomorph. Nucleomorphs result from the successive reduction of the nucleus of an engulfed phototrophic eukaryotic endosymbiont by a secondary eukaryotic host cell. By sequencing the chloroplast genome and the nucleomorph chromosomes, we identified a groEL homologue in the genome of the chloroplast and a related cpn60 in one of the nucleomorph chromosomes. The nucleomorph-encoded Cpn60 and the chloroplast-encoded GroEL correspond in each case to one of the two divergent GroEL homologues in the cyanobacterium Synechocystis sp. PCC6803. The coexistence of divergent groEL/cpn60 genes in different genomes in one cell offers insights into gene transfer from evolving chloroplasts to cell nuclei and convergent gene evolution in chlorophyll a/b versus chlorophyll a/c/phycobilin eukaryotic lineages.

Amino Acid Sequence↗

PubMed2004

Molecular adaptation in plant hemoglobin, a duplicated gene involved in plant-bacteria symbiosis.

The evolutionary history of the hemoglobin gene family in angiosperms is unusual in that it involves two mechanisms known for potentially generating molecular adaptation: gene duplication and among-species interaction. In plants able to achieve symbiosis with nitrogen-fixing bacteria, class 2 hemoglobin is expressed at high concentrations in nodules and appears to be a key factor for the achievement and regulation of the symbiotic exchange. In this study, we make use of codon models of DNA sequence evolution with the goal of determining the nature of the selective forces which have driven the evolution of this gene. Our results suggest that adaptive evolution occurred during the period of time following the duplication event (functional divergence) and that a change in the selective pressures arose in class 2 hemoglobin in relation to the acquisition of a symbiotic function.

Adaptation, Biological↗

PubMed2005

Evolution of alternative splicing after gene duplication.

Alternative splicing and gene duplication are two major sources of proteomic function diversity. Here, we study the evolutionary trend of alternative splicing after gene duplication by analyzing the alternative splicing differences between duplicate genes. We observed that duplicate genes have fewer alternative splice (AS) forms than single-copy genes, and that a negative correlation exists between the mean number of AS forms and the gene family size. Interestingly, we found that the loss of alternative splicing in duplicate genes may occur shortly after the gene duplication. These results support the subfunctionization model of alternative splicing in the early stage after gene duplication. Further analysis of the alternative splicing distribution in human duplicate pairs showed the asymmetric evolution of alternative splicing after gene duplications; i.e., the AS forms between duplicates may differ dramatically. We therefore conclude that alternative splicing and gene duplication may not evolve independently. In the early stage after gene duplication, young duplicates may take over a certain amount of protein function diversity that previously was carried out by the alternative splicing mechanism. In the late stage, the gain and loss of alternative splicing seem to be independent between duplicates.

Alternative Splicing↗

PubMed2002

Codon bias differentiates between the duplicated amylase loci following gene duplication in Drosophila.

We examined the pattern of synonymous substitutions in the duplicated Amylase (Amy) genes (called the Amy1- and Amy3-type genes, respectively) in the Drosophila montium species subgroup. The GC content at the third synonymous codon sites of the Amy1-type genes was higher than that of the Amy3-type genes, while the GC content in the 5'-flanking region was the same in both genes. This suggests that the difference in the GC content at third synonymous sites between the duplicated genes is not due to the temporal or regional changes in mutation bias. We inferred the direction of synonymous substitutions along branches of a phylogeny. In most lineages, there were more synonymous substitutions from G/C (G or C) to A/T (A or T) than from A/T to G/C. However, in one lineage leading to the Amy1-type genes, which is immediately after gene duplication but before speciation of the montium species, synonymous substitutions from A/T to G/C were predominant. According to a simple model of synonymous DNA evolution in which major codons are selectively advantageous within each codon family, we estimated the selection intensity for specific lineages in a phylogeny on the basis of inferred patterns of synonymous substitutions. Our result suggested that the difference in GC content at synonymous sites between the two Amy-type genes was due to the change of selection intensity immediately after gene duplication but before speciation of the montium species.

Amylases↗

PubMed2005

Role of selection in fixation of gene duplications.

New genes commonly appear through complete or partial duplications of pre-existing genes. Duplications of long DNA segments are constantly produced by rare mutations, may become fixed in a population by selection or random drift, and are subject to divergent evolution of the paralogous sequences after fixation, although gene conversion can impede this process. New data shed some light on each of these processes. Mutations which involve duplications can occur through at least two different mechanisms, backward strand slippage during DNA replication and unequal crossing-over. The background rate of duplication of a complete gene in humans is 10(-9)-10(-10) per generation, although many genes located within hot-spots of large-scale mutation are duplicated much more often. Many gene duplications affect fitness strongly, and are responsible, through gene dosage effects, for a number of genetic diseases. However, high levels of intrapopulation polymorphism caused by presence or absence of long, gene-containing DNA segments imply that some duplications are not under strong selection. The polymorphism to fixation ratios appear to be approximately the same for gene duplications and for presumably selectively neutral nucleotide substitutions, which, according to the McDonald-Kreitman test, is consistent with selective neutrality of duplications. However, this pattern can also be due to negative selection against most of segregating duplications and positive selection for at least some duplications which become fixed. Patterns in post-fixation evolution of duplicated genes do not easily reveal the causes of fixations. Many gene duplications which became fixed recently in a variety of organisms were positively selected because the increased expression of the corresponding genes was beneficial. The effects of gene dosage provide a unified framework for studying all phases of the life history of a gene duplication. Application of well-known methods of evolutionary genetics to accumulating data on new, polymorphic, and fixed duplication will enhance our understanding of the role of natural selection in the evolution by gene duplication.

Animals↗

PubMed1988

Concerted gene duplications in the two keratin gene families.

Evolutionary trees were derived from the keratin protein sequences using the Phylogeny Analysis Using Parsimony (PAUP) set of programs. Three major unexpected conclusions were derived from the analysis: The smallest keratin protein subunit, K#19 (Moll et al. 1982), is not the most primitive one, but has evolved to fulfill a highly specialized function, presumably to redress the unbalanced synthesis of keratin subunits. Second, the ancestors of keratins expressed in the early embryonic stages, K#8 and K#18, were the first to diverge from the ancestors of all the other keratins. The branches leading to these two keratins are relatively short, indicating a comparatively strong selection against changes in the sequences of these two proteins. Third, the two keratin families show extraordinary parallelism in their patterns of gene duplications. In both families the genes expressed in embryos diverged first, later bursts of gene duplications created the subfamilies expressed in various differentiated cells, and relatively recent gene duplications gave rise to the hair keratin genes and separated the basal cell-specific keratin from those expressed under hyperproliferative conditions. The parallelism of gene duplications in the two keratin gene families implies a mechanism in which duplications in one family influence duplication events in the other family.

Animals↗

PubMed1996

Evidence that mouse Bmp8a (Op2) and Bmp8b are duplicated genes that play a role in spermatogenesis and placental development.

We have identified two highly conserved mouse genes encoding bone morphogenetic protein 8A (BMP8A/OP2) and 8B (BMP8B). The two loci are tightly linked on chromosome 4, suggesting that they arose through a recent gene duplication. Contrary to previous reports, neither gene is expressed in the early postimplantation mouse embryo (7.5-10.5 days post coitum) as judged by a variety of sensitive techniques. By contrast, high levels of Bmp8b RNA are found in the decidual cells of the uterus, and both genes are expressed in the trophoblast cells of the labyrinthine region of the placenta and in the inner root sheath of hair follicles of early postnatal skin. In addition, both Bmp8a and Bmp8b are expressed in the testis during specific stages of spermatogenesis, with the highest levels of RNA in stage 6-8 round spermatids after 3 weeks of age. Bmp8a and 8b are, therefore, the first members of the transforming growth factor beta (TGF beta)-related gene family to be found expressed in the germ cells of the testis, rather than in the somatic Sertoli cells. These results suggest that Bmp8a and 8b are not required for development of the embryo proper but regulate aspects of cell proliferation, survival and/or differentiation during spermatogenesis and placentation.

Amino Acid Sequence↗

PubMed1974

Gene duplication and fixed heterozygosity for alcohol dehydrogenase in the diploid plant Clarkia franciscana.

All individuals of the diploid plant Clarkia franciscana, an annual species native to California, have duplicated genes for the dimeric enzyme alcohol dehydrogenase. Since each gene specifies a polypeptide with a distinct charge, the species has a fixed heterozygous phenotype consisting of three isozyme variants. The enzyme is coded by a single gene in closely related species. Clarkia franciscana is highly self-pollinated and monomorphic at all but one of its loci that have been examined. Consequently, the duplication provides enzyme variability in the absence of genetic variability.

Alcohol Oxidoreductases↗

PubMed1981

Mouse alcohol dehydrogenase isozymes: products of closely localized duplicate genes exhibiting divergent kinetic properties.

Electrophoretic variants for the stomach isozyme (ADH-C2) and liver isozyme (ADH-A2) of alcohol dehydrogenase in strains of Mus musculus have been used in genetic analyses to demonstrate close linkage between the structural genes (Ahd-3 and Adh-1, respectively) encoding these enzymes. No recombinants were observed between these loci among 126 backcross animals, which places them less than 0.8 centimorgans apart. Previous studies have positioned Adh-3, and a temporal locus (ADh-3t), on chromosome 3 (Holmes, "79; Holmes et al., "80). Kinetic analyses on partially purified preparations of these isozymes have demonstrated widely divergent catalytic properties and inhibitor specificities. The liver isozyme exhibited Michaelis constants that were nearly 3 orders of magnitude lower than the stomach isozyme for various alcohol and aldehyde substrates. Moreover, aminopropyl pyrazole strongly inhibited ADH-A2 (Ki=1.2M), whereas ADH-C2 was insensitive to inhibition under the conditions used. It is proposed that Adh-1 and Adh-3 are products of a recent gene duplication event during mammalian evolution and that considerable divergence in the active sites of these enzymes and the "temporal" genes controlling loci expression in differentiated tissues has subsequently occurred.

Alcohol Dehydrogenase↗

PubMed1987

Orosomucoid (ORM) typing by isoelectric focusing: evidence for gene duplication of ORM1 and genetic polymorphism of ORM2.

It has been demonstrated that the genetic polymorphism of human serum orosomucoid (ORM) is controlled by polymorphic ORM1 and monomorphic ORM2 loci. In this study a Japanese family was encountered in which several members had puzzling electrophoretic patterns consisting of four bands. The ORM patterns were due to the products of a duplicated ORM1 locus haplotype (ORM1 2.1) or the products of new variant alleles at the ORM2 locus. The ORM1 2.1 haplotype is very common in the Japanese population, occurring at an allele frequency of 0.16. The increased occurrence of ORM12-1 and the heterogeneity in band intensity among ORM12-1 phenotypes could be explained in terms of a duplicated gene ORM1 2.1. The ORM2 locus proved to be polymorphic, with six alleles in the Japanese population.

Alleles↗

PubMed1989

New dimeric inhibitor of heterologous alpha-amylases encoded by a duplicated gene in the short arm of chromosome 3B of wheat (Triticum aestivum L.).

A new wheat dimeric alpha-amylase inhibitor, designated WDAI-3, has been characterized. WDAI-3 is a homodimeric protein active against alpha-amylase from human saliva and from the insect Tenebrio molitor, but inactive against that from pig pancreas or against trypsin. Its N-terminal amino acid sequence is closer to those of the wheat dimeric inhibitors 0.19 and 0.53 (89-91% identical positions in 44 residues) than to that of the monomeric 0.28 inhibitor (69% identical positions). Iha-B1-2, the gene encoding the new inhibitor, is located in the short arm of chromosome 3B, where it is part of an intrachromosomal gene duplication that also codes for the 0.53 inhibitor.

Amino Acid Sequence↗

PubMed1999

The effect of gene duplication on homology.

Genes related by gene duplication within an organism's evolutionary lineage are termed paralogues; genes related by speciation are orthologues. It is generally agreed that orthologous genes must be compared when using DNA sequences to reconstruct the evolutionary history of organisms. There is an important exception: information from paralogous genes can reveal the root position of a phylogenetic tree. The duplicated rDNA genes of arrow worms provide an example. Gene duplication is also relevant when comparing gene expression between taxa; for example, when trying to identify homologous roles of genes. When gene duplication occurred after lineage divergence, single orthologues no longer exist, and comparison is complicated. This is a particular problem when comparing roles of vertebrate and invertebrate genes. Amphioxus and ascidian genes can be useful in such situations, since they diverged before extensive gene duplication in the vertebrate lineage. Using Otx and Pax as examples, I show how examination of amphioxus or ascidian genes reveals patterns of gene divergence after duplication, assisting the identification of homologous gene functions. Given the problems of comparing duplicated genes between species, the time is ripe for the introduction of additional terminology to elaborate on the concepts of paralogy and orthology.

Animals↗

PubMed1993

Pattern of nucleotide substitutions in growth hormone-prolactin gene family: a paradigm for evolution by gene duplication.

The growth hormone-prolactin gene family in mammals is an interesting example of evolution by gene duplication. Divergence among members of duplicated gene families and among species was examined by using reported gene sequences of growth hormone, prolactin and their receptors. Sequence divergence among species was found to show a general tendency in which a generation-time effect is pronounced for synonymous substitutions but not so for nonsynonymous substitutions. Divergence among duplicated genes is characterized by the relatively high rate of nonsynonymous substitutions, i.e., the rate is close to that of synonymous ones. In view of the stage- and tissue-specific expression of duplicated genes, some of the amino acid substitutions among duplicated genes is likely to be caused by positive Darwinian selection.

Amino Acid Sequence↗

PubMed2001

Birth and death of duplicated genes in completely sequenced eukaryotes.

Gene and genome duplications are commonly regarded as being of major evolutionary significance. But how often does gene duplication occur? And, once duplicated, what are the fates of duplicated genes? How do they contribute to evolution? In a recent article, Lynch and Conery analyze divergence between duplicate genes from six eukaryotic genomes. They estimate the rate of gene duplication, the rate of gene loss after duplication and the strength of selection experienced by duplicate genes. They conclude that although the rate of gene duplications is high, so is the rate of gene loss, and they argue that gene duplications could be a major factor in speciation.

Animals↗

PubMed2005

Ancient gene duplications and the root(s) of the tree of life.

Tracing organismal histories on the timescale of the tree of life remains one of the challenging tasks in evolutionary biology. The hotly debated questions include the evolutionary relationship between the three domains of life (e.g., which of the three domains are sister domains, are the domains para-, poly-, or monophyletic) and the location of the root within the universal tree of life. For the latter, many different points of view have been considered but so far no consensus has been reached. The only widely accepted rationale to root the universal tree of life is to use anciently duplicated paralogous genes that are present in all three domains of life. To date only few anciently duplicated gene families useful for phylogenetic reconstruction have been identified. Here we present results from a systematic search for ancient gene duplications using twelve representative, completely sequenced, archaeal and bacterial genomes. Phylogenetic analyses of identified cases show that the majority of datasets support a root between Archaea and Bacteria; however, some datasets support alternative hypotheses, and all of them suffer from a lack of strong phylogenetic signal. The results are discussed with respect to the impact of horizontal gene transfer on the ability to reconstruct organismal evolution. The exchange of genetic information between divergent organisms gives rise to mosaic genomes, where different genes in a genome have different histories. Simulations show that even low rates of horizontal gene transfer dramatically complicate the reconstruction of organismal evolution, and that the different most recent common molecular ancestors likely existed at different times and in different lineages.

Carbamoyl-Phosphate Synthase (Ammonia)↗