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PubMed1996

Two-dimensional RFLP analyses reveal megabase-sized clusters of rRNA gene variants in Arabidopsis thaliana, suggesting local spreading of variants as the mode for gene homogenization during concerted evolution.

Eukaryotic genes encoding the precursor of 18S, 5.8S and 25S ribosomal RNA (rRNA genes or rDNA) are virtually identical within a species, yet they evolve rapidly between species, a phenomenon known as concerted evolution. The mechanisms by which sequence homogenization and fixation of new rRNA gene variants occurs within a genome are not clear. In diploid Arabidopsis thaliana, approximately 1500 rRNA genes are tandemly arrayed at two nucleolus organizer regions, one on chromosome 2 (NOR2), the other on chromosome 4 (NOR4). This paper shows that NOR2 and NOR4 are similar in size, each spanning approximately 3.5-4.0 Mbp. Using two-dimensional mapping techniques involving a combination of pulsed-field and conventional gel electrophoresis, the distributions of four distinct rRNA gene variants at NOR2 and NOR4 have been determined. rRNA genes at NOR4 are homogeneous with respect to a HindIII site occurring once per gene. In contrast, fewer than 10% of the rRNA genes at NOR2 are HindIII-bearing variants. A single intergenic spacer length is found among rRNA genes at NOR2 but three classes of spacer length variants are present at NOR4. The NOR4 variants are not intermingled with one another; instead, they are highly clustered over distances as large as 1.5 Mbp. These data suggest that in the concerted evolution of rRNA genes, homogenization is a consequence of local spreading of new rRNA gene variants.

Arabidopsis↗
PubMed2005

Adaptive evolution after gene duplication in alpha-KT x 14 subfamily from Buthus martensii Karsch.

A series of isoforms of alpha-KT x 14 (short chain potassium channel scorpion toxins) were isolated from the venom of Buthus martensii Karsch by RACE and screening cDNA library methods. These isoforms adding BmKK1--3 and BmSKTx1--2 together shared high homology (more than 97%) with each other. The result of genomic sequence analysis showed that a length 79 bp intron is inserted Ala codes between the first and the second base at the 17th amino acid of signal peptide. The introns of these isoforms also share high homology with those of BmKK2 and BmSKT x 1 reported previously. Sequence analysis of many clones of cDNA and genomic DNA showed that a species population or individual polymorphism of alpha-KT x 14 genes took place in scorpion Buthus martensii Karsch and accelerated evolution played an important role in the forming process of alpha-KT x 14 scorpion toxins subfamily. The result of southern hybridization indicated that alpha-KT x 14 toxin genes existed in scorpion chromosome with multicopies. All findings maybe provided an important evidence for an extensive evolutionary process of the scorpion "pharmacological factory": at the early course of evolution, the ancestor toxic gene duplicated into a series of multicopy genes integrated at the different chromosome; at the late course of evolution, subsequent functional divergence of duplicate genes was generated by mutations, deletions and insertion.

Adaptation, Physiological↗
PubMedDate not supplied

Dynamics and function of intron sequences of the wingless gene during the evolution of the Drosophila genus.

To understand the function and evolution of genes with complex patterns of expression, such as the Drosophila wingless gene, it is essential to know how their transcription is regulated. However, extracting the relevant regulatory information from a genome is still a complex task. We used a combination of comparative genomics and functional approaches to identify putative regulatory sequences in two introns (1 and 3) of the wingless gene and to infer their evolution. Comparison of the sequences obtained from several Drosophila species revealed colinear and well-conserved sequence blocks in both introns. Drosophila willistoni showed a rate of evolution, in both introns, faster than expected from its phylogenetic position. Intron 3 appeared to be composed of two separate modules, one of them lost in the willistoni group. We tested whether sequence conservation in noncoding regions is a reliable indicator of regulatory function and, if this function is conserved, by analyzing D. melanogaster transgenic reporter lines harboring intron 3 sequences from D. melanogaster (Sophophora subgenus) and the species from the Drosophila subgenus presenting the most divergent sequence, D. americana. The analysis indicated that intron 3 contains pupal enhancers conserved during the evolution of the genus, despite the fact that only 30% of the D. melanogaster intron 3 sequences lie in conserved blocks. Additional analysis of D. melanogaster transgenic reporter lines harboring intron 3 sequences from D. willistoni revealed the absence of an abdomen-specific expression pattern, probably due to the above-mentioned loss of a regulatory module in this species.

Animals↗
PubMed1991

Alteration of the RNA polymerase specificity of U3 snRNA genes during evolution and in vitro.

We present evidence that the genes encoding U3 snRNA in plants are transcribed by RNA polymerase III (pol III) and not by RNA polymerase II (pol II) as in vertebrates or lower eukaryotes. The U3 gene is the only known example of a gene transcribed by different polymerases in different organisms. It is possible to convert the plant U3 gene into a functional pol II-transcribed gene by manipulating the spacing between the promoter elements and inserting a pol II-specific termination signal. Pol II-transcribed U3 RNA, containing the 5'-terminal cap different from that present in the wild-type counterpart, is packaged in transfected protoplasts into U3 snRNP precipitable with anti-fibrillarin antibodies. These findings provide further evidence for the common ancestry of the pol II and pol III transcription systems, and indicate that promoter diversification in some genes has occurred relatively recently.

Base Sequence↗
PubMed2004

DEAD-box RNA helicases in Arabidopsis thaliana: establishing a link between quantitative expression, gene structure and evolution of a family of genes.

The model genome of Arabidopsis thaliana contains a DEAD-box RNA helicase family (RH) of 58 members, i.e. almost twice as many as in the animal or yeast genomes. Transcript profiling using real-time quantitative polymerase chain reaction (PCR) has been obtained for 20 AtRHs from nine different organs. Two AtRHs exhibited plant-specific profiles associated with photosynthetic and sink organs. The other 18 AtRHs had the same transcript profile, and the levels of transcription of these 'housekeeping'AtRHs were under strict quantitative control over a large range of values. Transcript levels may be very different between the most recently duplicated genes. The master regulatory element in the definition of the transcript level is the simultaneous presence of a TATA-box and an intron in the 5' untranslated region (UTR). There is a positive and highly significant correlation between the size of the 5' UTR intron and the transcription level, as long as a characteristic TATA-box is present. Our work on the housekeeping AtRHs suggests a scenario for the evolution of duplicated genes, leading to both highly and poorly transcribed genes in the same terminal branch of the phylogenetic tree. The general evolutionary drive of the AtRH family, after duplication of a highly transcribed ancestral AtRH, was towards an alteration of the transcriptional activity of the divergent duplicates through successive events of suppression of the TATA-box and/or the 5' UTR intron.

Journal Article↗
PubMed2004

Characterization and evolution of major histocompatibility complex class II genes in the aye-aye, Daubentonia madagascariensis.

Major histocompatibility complex genes (Mhc-DQB and Mhc-DRB) were sequenced in seven aye-ayes (Daubentonia madagascariecsis), which is an endemic and endangered species in Madagascar. An aye-aye from a north-eastern population showed genetic relatedness to individuals of a north-western population and had a somewhat different repertoire from another north-eastern individual. These observations suggest that the extent of genetic variation in Mhc genes is not excessively small in the aye-aye in spite of recent rapid destruction of their habitat by human activities. In light of Mhc gene evolution, trans-species and allelic polymorphisms can be estimated to have been retained for more than 50 Ma (million years) based on the time scale of lemur evolution.

Animals↗
PubMed2000

Gene family evolution and homology: genomics meets phylogenetics.

With the advent of high-throughput DNA sequencing and whole-genome analysis, it has become clear that the coding portions of the genome are organized hierarchically in gene families and superfamilies. Because the hierarchy of genes, like that of living organisms, reflects an ancient and continuing process of gene duplication and divergence, many of the conceptual and analytical tools used in phylogenetic systematics can and should be used in comparative genomics. Phylogenetic principles and techniques for assessing homology, inferring relationships among genes, and reconstructing evolutionary events provide a powerful way to interpret the ever increasing body of sequence data. In this review, we outline the application of phylogenetic approaches to comparative genomics, beginning with the inference of phylogeny and the assessment of gene orthology and paralogy. We also show how the phylogenetic approach makes possible novel kinds of comparative analysis, including detection of domain shuffling and lateral gene transfer, reconstruction of the evolutionary diversification of gene families, tracing of evolutionary change in protein function at the amino acid level, and prediction of structure-function relationships. A marriage of the principles of phylogenetic systematics with the copious data generated by genomics promises unprecedented insights into the nature of biological organization and the historical processes that created it.

Animals↗
PubMed1990

Gene conversion, linkage, and the evolution of repeated genes dispersed among multiple chromosomes.

The evolution of the probabilities of genetic identity within and between the loci of a multigene family dispersed among multiple chromosomes is investigated. Unbiased gene conversion, equal crossing over, random genetic drift, and mutation to new alleles are incorporated. Generations are discrete and nonoverlapping; the diploid, monoecious population mates at random. The linkage map is arbitrary, but the same for every chromosome; the dependence of the probabilities of identity on the location on each chromosome is formulated exactly. The greatest of the rates of gene conversion, random drift, and mutation is epsilon much less than 1. Under the assumption of loose linkage (i.e., all the crossover rates greatly exceed epsilon, though they may still be much less than 1/2), explicit approximations are obtained for the equilibrium values of the probabilities of identity and of the linkage of disequilibria. The probabilities of identity are of order one [i.e., O(1)] and do not depend on location; the linkage disequilibria are of O(epsilon) and, within each chromosome, depend on location through the crossover rates. It is demonstrated also that the ultimate rate and pattern of convergence to equilibrium are close to that of a much simpler, location-independent model. If intrachromosomal conversion is absent, the above results hold even without the assumption of loose linkage. In all cases, the relative errors are of O(epsilon). Even if the conversion rate between genes on nonhomologous chromosomes is considerably less than between genes on the same chromosome or homologous chromosomes, the probabilities of identity between the former genes are still almost as high as those between the latter, and the rate of convergence is still not much less than with equal conversion rates. If the crossover rates are much less than 1/2, then most of the linkage disequilibrium is due to intrachromosomal conversion. If linkage is loose, the reduction of the linkage disequilibria to O(epsilon) requires only O(-ln epsilon) generations.

Alleles↗
PubMed2005

Host-parasite interactions and the evolution of gene expression.

Interactions between hosts and parasites provide an ongoing source of selection that promotes the evolution of a variety of features in the interacting species. Here, we use a genetically explicit mathematical model to explore how patterns of gene expression evolve at genetic loci responsible for host resistance and parasite infection. Our results reveal the striking yet intuitive conclusion that gene expression should evolve along very different trajectories in the two interacting species. Specifically, host resistance loci should frequently evolve to co-express alleles, whereas parasite infection loci should evolve to express only a single allele. This result arises because hosts that co-express resistance alleles are able to recognize and clear a greater diversity of parasite genotypes. By the same token, parasites that co-express antigen or elicitor alleles are more likely to be recognized and cleared by the host, and this favours the expression of only a single allele. Our model provides testable predictions that can help interpret accumulating data on expression levels for genes relevant to host-parasite interactions.

Biological Evolution↗
PubMed1995

Transcriptional noise and the evolution of gene number.

Several proposals are made to explain the apparent increase in complexity of certain lineages during evolution. The proposals (not made in this order) are: (1) that gene number is a valid measure of biological complexity; (2) that gene number has not increased continuously during evolution, but has risen in discrete steps; (3) that two of the biggest steps occurred at the transition from prokaryotes to eukaryotes and the transition from invertebrates to vertebrates; (4) that these steps were made possible by 'systemic' changes in the way that genetic information is managed in the genome; (5) that the ability to silence inappropriate promoters is the primary limitation on gene number; (6) that the invention of nucleosomes (and perhaps the nuclear membrane) facilitated the evolution of eukaryotes from prokaryotic ancestors; (7) that the spread of low density methylation throughout the genome facilitated the evolution of vertebrates from invertebrate ancestors.

Animals↗
PubMed1992

Two common polymorphisms in the APO A-IV coding gene: their evolution and linkage disequilibrium.

Human apolipoprotein A-IV (APO A-IV) exhibits a common protein polymorphism detectable by isoelectric focusing (IEF) due to a single base substitution at codon 360 which replaces the frequently occurring glutamine residue (allele 1) with histidine (allele 2). Recently, sequence analysis of the APO A-IV coding region has revealed another common nucleotide substitution at codon 347 which converts the commonly present threonine residue (allele A) into serine (allele T). In order to investigate the extent of genetic variation at codon 347, we screened DNA samples from 192 unrelated individuals using a polymerase chain reaction based assay. The frequencies of the two alleles, A-IV*A and A-IV*T, were 0.81 and 0.19, respectively, with average heterozygosity 0.31. Genetic screening of the corresponding 192 plasma samples by IEF gave frequencies of 0.922 and 0.078 for the A-IV*1 and A-IV*2 alleles, respectively, at codon 360 with average heterozygosity 0.14. Genotype data at the two polymorphic sites were used to assign unequivocal haplotypes to all the 384 chromosomes. Of the expected four haplotypes (A1, T1, A2, and T2) only three were observed and their frequencies were 0.732 for A1, 0.190 for T1 and 0.078 for A2, with average heterozygosity 0.42. Although our data indicate significant linkage disequilibrium between the two sites (chi 21 = 7.65, P < 0.006, standardized disequilibrium constant phi = -0.14) the degree of nonrandom association varied between alleles at the two sites. Based upon allele frequency data and variable linkage disequilibrium between alleles, we propose that the A2 and T1 haplotypes may have evolved from the parental A1 haplotype by two independent mutations.

Apolipoproteins A↗
PubMed1988

Reversal of genetic homeostasis in laboratory populations of Drosophila melanogaster under long-term selection for geotaxis and estimates of gene correlates: evolution of behavior-genetic systems.

Among Drosophila melanogaster, divergently selected for geotaxis intermittently over 600 generations (28 years), about 80,000 animals have been analyzed behavior-genetically. Each major chromosome pair from two lines was isogenized on an unselected isogenic background. Measurement of their behavioral effects revealed the relative magnitudes II greater than III greater than X for the negatively geotactic (high) line and X greater than III greater than II for the positively geotactic (low) line. When reversing selection for the now phenotypically stable high and low lines and then repeatedly relaxing the reversals, a new genetic homeostasis in the low line was indicated by the return of the reversed-line average scores towards the low extreme; that is, the low line has attained a stable equilibrium for positive geotaxis, an uncharacteristic behavior and an effect not seen before 1979. This change suggests the recent evolution of a new coadaptation among genes. Although not as conclusive, a similar genetic interpretation is suggested for the high line.

Animals↗
PubMed2004

[The evolution of plant disease resistance gene].

The evolution of plant disease resistance genes has shaped in some kinds of common forms. The duplication of plant progenitor disease resistance gene creates disease resistance gene loci. The intragenic and extragenic recombination results in variation. Recombination also is involved in generation novel resistance specificities. In addition, the leucine-rich repeats (LRRs) involved in recognitional specificity are subject to adaptive selection. Insertion of transposable elements into several resistance gene loci result in further evolution of resistance genes. With the evolution of plant disease resistance genes, the R genes (resistance genes)-mediated response shows diversification which represents different stages in the oscillating evolution between plants and their pathogens.

Adaptation, Physiological↗
PubMed2005

Patterns of evolution of genes disrupted in expression in Drosophila species hybrids.

Divergence between species in regulatory pathways may contribute to hybrid incompatibilities such as sterility. Consistent with this idea, genes involved in male fertility often evolve faster than most other genes both in amino acid sequence and in expression. Previously, we identified a panel of male-specific genes under-expressed in sterile male hybrids of Drosophila simulans and D. mauritiana relative to pure species, and we showed that this under-expression is associated with infertility. In a preliminary effort to assess the generalities in the patterns of evolution of these genes, I examined patterns of mRNA expression in three of these genes in sterile F 1 hybrid males of D. pseudoobscura and D. persimilis . F 1 hybrid males bearing D. persimilis X chromosomes under-expressed all these genes relative to the parental species, while hybrids bearing D. pseudoobscura X chromosomes under-expressed two of these three genes. Interestingly, the third gene, CG5762 , has undergone extensive amino acid evolution within the D. pseudoobscura species group, possibly driven by positive natural selection. We conclude that some of the same genes exhibit disruptions in expression within each of the two species groups, which could suggest commonalities in the regulatory architecture of sterility in these groups. Alternative explanations are also considered.

Animals↗
PubMedDate not supplied

Modularity and dissociation in the evolution of gene expression territories in development.

Modularity is a salient feature of development and crucial to its evolution. This paper extends modularity to include the concept of gene expression territory, as established for sea urchin embryos. Territories provide a mechanism for partitioning of the cells of a rapidly developing embryo into functional units of a feeding larva. Territories exhibit the characteristics of modules. The paper asks if the embryo and the nonfeeding larva of the direct-developing sea urchin Heliocidaris erythrogramma are organized into gene expression territories, and if its territories correspond to the canonical territories of the pluteus. An analysis of cell lineage and gene expression data for H. erythrogramma shows that skeletogenic cell, coelomic, and vegetal plate gene expression territories are conserved, although they arise from cell lineages distinct from those of the pluteus, and the overall morphology of the larva differs from that of a pluteus. The ectoderm, as in indirect developers, is divided into territories. However, the oral ectodermal territory characteristic of the pluteus is absent in H. erythrogramma. Oral ectoderm is restored in hybrids of H. erythrogramma eggs fertilized by Heliocidaris tuberculata sperm. This indicates that embryonic modules evolve by changes in expression of dominant regulatory genes within territories and that entire modules can be eliminated in evolution of embryos.

Animals↗