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PubMed2004

Relevance of connexin deafness (DFNB1) to human evolution.

The connexins are the subunits of a family of proteins that form gap junctions, allowing ions and small molecules to move between adjacent cells. At least four connexins are expressed in the ear, and, although there are known mutations at >100 loci that can cause deafness, those involving DFNB1, in the interval 13q11-q12 containing the GJB2 and GJB6 genes coding for connexins 26 and 30, are the most frequent cause of recessive deafness in many populations. We have suggested that the combined effects of relaxed selection and linguistic homogamy can explain the high frequency of connexin deafness and may have doubled its incidence in this country during the past 200 years. In this report, we show by computer simulation that assortative mating, in fact, can accelerate dramatically the genetic response to relaxed selection. Along with the effects of gene drift and consanguinity, assortative mating also may have played a key role in the joint evolution and accelerated fixation of genes for speech after they first appeared in Homo sapiens 100,000-150,000 years ago.

Animals↗

PubMed2006

Polymorphism analysis of six selenoprotein genes: support for a selective sweep at the glutathione peroxidase 1 locus (3p21) in Asian populations.

BACKGROUND: There are at least 25 human selenoproteins, each characterized by the incorporation of selenium into the primary sequence as the amino acid selenocysteine. Since many selenoproteins have antioxidant properties, it is plausible that inter-individual differences in selenoprotein expression or activity could influence risk for a range of complex diseases, such as cancer, infectious diseases as well as deleterious responses to oxidative stressors like cigarette smoke. To capture the common genetic variants for 6 important selenoprotein genes (GPX1, GPX2, GPX3, GPX4, TXNRD1, and SEPP1) known to contribute to antioxidant host defenses, a re-sequence analysis was conducted across these genes with particular interest directed at the coding regions, intron-exon borders and flanking untranslated regions (UTR) for each gene in an 102 individual population representative of 4 major ethnic groups found within the United States. RESULTS: For 5 of the genes there was no strong evidence for selection according to the expectations of the neutral equilibrium model of evolution; however, at the GPX1 locus (3p21) there was evidence for positive selection. Strong confirmatory evidence for recent positive selection at the genomic region 3p21 in Asian populations is provided by data from the International HapMap project. CONCLUSION: The SNPs and fine haplotype maps described in this report will be valuable resources for future functional studies, for population specific genetic studies designed to comprehensively explore the role of selenoprotein genetic variants in the etiology of various human diseases, and to define the forces responsible for a recent selective sweep in the vicinity of the GPX1 locus.

Asian People↗

PubMed2005

Intra- and inter-specific variations in the copy number of two types of retrotransposons from the ectomycorrhizal basidiomycete Tricholoma matsutake.

To explore intra- and inter-specific variations of the ectomycorrhizal basidiomycete Tricholoma matsutake that produces the fruit body "matsutake", we carried out real-time PCR analysis based on two types of retrotransposons, one designated marY1, which resembles a retrovirus carrying the long terminal repeat (LTR) and the other marY2N, which resembles mRNA carrying the polyadenylated tail. Calculation based on the average genome size of homobasidiomycetes (34 Mbp) shows that ca. 5.5% of the total genome of T. matsutake isolated from Asia is made up of these retrotransposons, whereas they occupy ca. 1.4% in the isolates from Morocco, ca. 0.8% in isolates from Mexico, and ca. 0.5% in Tricholoma magnivelare, the species which produces "American matsutake". Other Tricholoma spp. that produce fruit bodies similar to those of T. matsutake, such as T. bakamatsutake, T. fulvocastaneum, and T. robustum, carry them in the region less than 0.05% of their total genome. Copy number of LTR of marY1 is consistently and markedly higher than that of the coding regions of marY1 and marY2N. Data suggest that retrotransposons are deeply involved in evolution of the ectomycorrhizal symbiont.

Agaricales↗

PubMed2000

Polymorphism of LMP2, TAP1, LMP7 and TAP2 in Brazilian Amerindians and Caucasoids: implications for the evolution of allelic and haplotypic diversity.

In the class II region of the major histocompatibility complex (MHC), four genes implicated in processing of MHC class I-presented antigens have been described. Two of these (TAP1 and TAP2) code for endoplasmic reticulum membrane transporter proteins and the other two (LMP2 and LMP7) for proteasome subunits. These genes are polymorphic, although much less so than classical MHC class I and II genes. There is controversy concerning the possible functional implications of this variation. Population genetics is one of the means of investigating the evolutionary and functional significance of genetic polymorphisms; however, few populations have been analysed with respect to TAP and LMP diversity. We present here the polymorphism of TAP1, TAP2, LMP2 and LMP7 genes in the Kaingang and Guarani Amerindian tribes, and in the Caucasoid population of the Brazilian State of Paraná. Allele frequencies found in the Caucasoids were close to those described for similar populations. Amerindians had a somewhat more restricted polymorphism, and allele and haplotype frequencies differed greatly between the two tribes. Overall linkage disequilibrium (LD) between the four genes was low in the Caucasoids, but high in the Amerindians, for which significant LD was seen for all informative pairs of loci. Comparing results of this and previous studies we observed that, whenever significant LD occurs in non-Amerindians, it tends to be similar in the different ethnic groups. While this might be interpreted as evidence of co-evolution of genes in the TAP-LMP region, the high haplotypic diversity in all populations and low LD in non-Amerindians indicate absence of co-evolution of the different genes. Distributions of allele and genotype frequencies are consistent with the hypothesis of selective neutrality. We conclude that genetic polymorphism of the human TAP and LMP genes and haplotypes is of little, if any, functional significance.

ATP Binding Cassette Transporter, Subfamily B, Mem↗

PubMed2006

Evolution of virulence in picornaviruses.

The Picornaviridae encompass many positive-strand RNA viruses, all of which share a generally similar genome design and capsid structure, but which induce quite diverse diseases in humans and other animals. Picornavirus strains of the same serotype have been shown to express different virulence (or pathogenic) phenotypes when studied in animal models, demonstrating that key elements of pathogenesis reside in the viral genome. However, the genetics that determine the virulence phenotype of any picornavirus are poorly understood. Picornaviruses do not have virulence genes per se, but the design ofthe capsid andhow it interacts with the virus receptor expressed on the host cell surface, specific sequences within the nontranslated regions of the viral genome, as well as coding sequences that result in different protein sequences may all have a part in determining the virulence phenotype. Virulence may be better understood as a continuum from an apparent inability to induce disease to the ability to cause severe pathogenic changes. Ultimately, the ability of a picornavirus to induce disease depends upon viral genetics and how they are modulated by the host environment.

Animals↗

PubMed2000

Genomic characterization of the lysophosphatidic acid receptor gene, lp(A2)/Edg4, and identification of a frameshift mutation in a previously characterized cDNA.

To understand the regulation, evolution, and genetics of lp(A2)/Edg4, a second lysophosphatidic acid receptor gene, we characterized its complete cDNA sequence, genomic structure, and chromosomal location. The full-length mouse transcript sequence was determined using rapid amplification of cDNA ends. Southern blot and restriction fragment length polymorphism segregation analyses revealed that the mouse gene was present as a single copy and located at the middle of Chromosome 8 near the mutations for myodystrophy (myd) and "kidney-anemia-testes" (kat). This region is syntenic with human chromosome 19p12, where the human genomic clone containing the lp(A2) gene (EDG4) was mapped. Sequence analysis of genomic clones demonstrated that both mouse and human transcripts were encoded by three exons, with an intron separating the coding region for transmembrane domain VI. Reverse transcriptase-PCR demonstrated that the three exons were spliced in all mouse tissues shown to express the transcript. Finally, in a comparison of all human lp(A2) sequences present in the database, we identified several sequence variants in multiple tumors. One such variant (a G deletion) in the initially characterized Edg4 cDNA clone (derived from an ovarian tumor) results in a frameshift mutation near the 3' end of the coding region. In addition to increasing our understanding of the mechanisms underlying lysophosphatidic acid signaling and lysophospholipid receptor gene evolution, these results have important implications regarding the genomic targeting and oncogenic potential of lp(A2).

Animals↗

PubMed1998

Transposons in filamentous fungi--facts and perspectives.

Transposons are ubiquitous genetic elements discovered so far in all investigated prokaryotes and eukaryotes. In remarkable contrast to all other genes, transposable elements are able to move to new locations within their host genomes. Transposition of transposons into coding sequences and their initiation of chromosome rearrangements have tremendous impact on gene expression and genome evolution. While transposons have long been known in bacteria, plants, and animals, only in recent years has there been a significant increase in the number of transposable elements discovered in filamentous fungi. Like those of other eukaryotes, each fungal transposable element is either of class or of class II. While class I elements transpose by a RNA intermediate and employ reverse transcriptases, class II elements transpose directly at the DNA level. We present structural and functional features for such transposons that have been identified so far in filamentous fungi. Emphasis is given to specific advantages or unique features when fungal systems are used to study transposable elements, e.g., the evolutionary impact of transposons in coenocytic organisms and possible experimental approaches toward horizontal gene transfer. Finally, we focus on the potential of transposons for tagging and identifying fungal genes.

Animals↗

PubMed1997

Sequence similarities of a subgroup of CXC chemokines related to murine LIX: implications for the interpretation of evolutionary relationships among chemokines.

The murine CXC chemokine LIX has distinctive sequence features that suggest it is a novel chemokine. Among known human chemokines, ENA-78 and GCP-2 are the two most closely related to LIX. We have recently cloned the human GCP-2 gene. Phylogenetic analysis shows that the LIX coding region is more distant from both human GCP-2 and ENA-78 than is porcine AMCF-II, the chemokine with greatest sequence similarity to LIX. Human GCP-2 and ENA-78 have very high nucleotide similarity in non-coding as well as coding sequences, which suggests that these genes are the result of an evolutionarily recent gene duplication event. If this duplication occurred during primate evolution, then non-primate species may have only a single chemokine corresponding to this pair of human genes. This example shows that a one-to-one genetic correspondence does not necessarily exist between all the chemokine genes in two different species. These observations may have important implications for other chemokines that belong to clusters of closely related genes.

Amino Acid Sequence↗

PubMed2025

A chromosome-level genome assembly of Coffea arabica L. var. 'Kona Typica'.

Coffea arabica L. var. 'Kona Typica' is renowned for its premium cup quality, but its vulnerability to pests and diseases limits production. To accelerate cultivar improvement, we generated a chromosome-level genome assembly of 'Kona Typica' using PacBio HiFi sequencing and Hi-C scaffolding technology. The final assembly spans 1.13 Gb, with a scaffold N50 of 50.50 Mb, organized into 22 chromosomes. BUSCO assessment indicated a high completeness at 99.1%. We annotated 65,458 protein-coding genes and identified 1,073,545 interspersed repeats, accounting for 65.16% of the genome. Analysis of transposon insertion ages revealed that most long terminal repeat retrotransposons proliferated after the polyploidization event. This high-quality genome assembly of 'Kona Typica' provides a valuable resource for exploring coffee genomic evolution and genetic mechanisms of complex traits, facilitating genomics studies and the development of improved coffee cultivars with enhanced disease resistance and quality traits.

Coffea↗

PubMed2005

The statistical analysis of spatially clustered genes under the maximum gap criterion.

Statistical validation of gene clusters is imperative for many important applications in comparative genomics which depend on the identification of genomic regions that are historically and/or functionally related. We develop the first rigorous statistical treatment of max-gap clusters, a cluster definition frequently used in empirical studies. We present exact expressions for the probability of observing an individual cluster of a set of marked genes in one genome, as well as upper and lower bounds on the probability of observing a cluster of h homologs in a pairwise whole-genome comparison. We demonstrate the utility of our approach by applying it to a whole-genome comparison of E. coli and B. subtilis. Code for statistical tests is available at.

Bacillus subtilis↗

PubMed2003

MCMC genome rearrangement.

MOTIVATION: As more and more genomes have been sequenced, genomic data is rapidly accumulating. Genome-wide mutations are believed more neutral than local mutations such as substitutions, insertions and deletions, therefore phylogenetic investigations based on inversions, transpositions and inverted transpositions are less biased by the hypothesis on neutral evolution. Although efficient algorithms exist for obtaining the inversion distance of two signed permutations, there is no reliable algorithm when both inversions and transpositions are considered. Moreover, different type of mutations happen with different rates, and it is not clear how to weight them in a distance based approach. RESULTS: We introduce a Markov Chain Monte Carlo method to genome rearrangement based on a stochastic model of evolution, which can estimate the number of different evolutionary events needed to sort a signed permutation. The performance of the method was tested on simulated data, and the estimated numbers of different types of mutations were reliable. Human and Drosophila mitochondrial data were also analysed with the new method. The mixing time of the Markov Chain is short both in terms of CPU times and number of proposals. AVAILABILITY: The source code in C is available on request from the author.

Algorithms↗

PubMed1995

A stem-loop "kissing" model for the initiation of recombination and the origin of introns.

Mutations which improve the efficiency of recombination should affect either the proteins which mediate recombination or their substrate, DNA itself. The former mutations would be localized to a few sites. The latter would be dispersed. Studies of hybridization between RNA molecules have suggested that recombination may be initiated by a homology search involving the "kissing" of the tips of stem loops. This predicts that, in the absence of other constraints, mutations which assist the formation of stem loops would be favored. From comparisons of the folding of normal and shuffled DNA sequences, I present evidence for an evolutionary selection pressure to distribute stem loops generally throughout genomes. I propose that this early pressure came into conflict with later local pressures to impose information concerning specific function. The conflict was accommodated by permitting sections of DNA concerned with a specific function to evolve in dispersed segments. Traces of the conflict seem to be present in some modern intron-containing genes. Thus, introns may have allowed the interspersing of selectively advantageous stem loops in coding regions of DNA.

Algorithms↗

PubMed2003

Phylogenetic analysis of the mammalian Hoxc8 non-coding region.

The non-coding intergenic regions of Hox genes are remarkably conserved among mammals. To determine the usefulness of this sequence for phylogenetic comparisons, we sequenced an 800-bp fragment of the Hoxc9-Hoxc8 intergenic region from several species belonging to different mammalian clades. Results obtained from the phylogenetic analysis are congruent with currently accepted mammalian phylogeny. Additionally, we found a TC mini satellite repeat polymorphism unique to felines. This polymorphism may serve as a useful marker to differentiate between mammalian species or as a genetic marker in feline matings. This study demonstrates usefulness of a comparative approach employing non-coding regions of Hox gene complexes.

Animals↗

PubMed2006

Hox genes, homology and axis formation--the application of morphological concepts to evolutionary developmental biology.

This article focuses on the interphyletic comparison of gene expression patterns. By means of the hypothesis of the inversion of the dorsoventral axis during the evolution of the Bilateria, it is demonstrated, that evolutionary developmental biologists use similarities in spatial and temporal gene expression patterns as evidence for the formulation of hypotheses of homology concerning either developing structures or body regions. The molecular genetic and morphogenetic evidence used is discussed within the framework of a cladistic-phylogenetic analysis based on the phylogenetic tree of the Bilateria. I argue that similarity of spatial and temporal gene expression patterns is not a sufficient criterion for homology inference. Therefore, gene expression patterns should be coded as characters. Their homology should be tested in concert with other characters. Furthermore, it is demonstrated, that spatial and temporal similar gene expression patterns, indicating similar molecular genetic mechanisms, were interpreted as an analytical criterion of homology, offering the possibility to identify similar structures. In contrast to this, the evolutionary developmental biologists have not developed a causal-analytically extended concept of shape, from which a causal-analytical concept of homology could be deduced. Instead, the homology concept from evolutionary morphology is used.

Animals↗

PubMed1995

Hox genes and the evolution of vertebrate axial morphology.

A common form of evolutionary variation between vertebrate taxa is the different numbers of segments that contribute to various regions of the anterior-posterior axis; cervical vertebrae, thoracic vertebrae, etc. The term 'transposition' is used to describe this phenomenon. Genetic experiments with homeotic genes in mice have demonstrated that Hox genes are in part responsible for the specification of segmental identity along the anterior-posterior axis, and it has been proposed that an axial Hox code determines the morphology of individual vertebrae (Kessel, M. and Gruss, P. (1990) Science 249, 347-379). This paper presents a comparative study of the developmental patterns of homeobox gene expression and developmental morphology between animals that have homologous regulatory genes but different morphologies. The axial expression boundaries of 23 Hox genes were examined in the paraxial mesoderm of chick, and 16 in mouse embryos by in situ hybridization and immunolocalization techniques. Hox gene anterior expression boundaries were found to be transposed in concert with morphological boundaries. This data contributes a mechanistic level to the assumed homology of these regions in vertebrates. The recognition of mechanistic homology supports the historical homology of basic patterning mechanisms between all organisms that share these genes.

Animals↗

PubMed2001

Genetic differentiation of oak populations within the Quercus robur/Quercus petraea complex in Central and Eastern Europe.

Genetic structure of 25 indigenous populations of sessile and pedunculate oaks (Quercus petraea and Q. robur), originating from three geographical regions: Slovakia, Bulgaria and the Republic Mari-El (Russia), was investigated using isozyme markers. Mean number of alleles per locus ranged between 1.8 and 2.6 in Q. robur populations and from 2.0 to 3.0 in Q. petraea populations; slightly higher expected heterozygosity values were found in Q. robur compared to Q. petraea. One locus, coding for a substrate-nonspecific dehydrogenase, differentiated the two species. The interspecific component of gene diversity was 46.7% at this locus, compared to 0.4-7.8% at the remaining loci.

Alleles↗

PubMed2006

How do genes make teeth to order through development?

This introduction to new patterning theories for the vertebrate dentition outlines the historical concepts to explain graded sequences in tooth shape in mammals (incisors, canines, premolars, molars) which change in evolution in a linked manner, constant for each region. The classic developmental models for shape regulation, known as the 'regional field' and 'dental clone' models, were inspired by the human dentition, where it is known that the last tooth in each series is the one commonly absent. The mouse, as a valuable experimental model, has provided data to test these models and more recently, based on spatial-temporal gene expression data, the 'dental homeobox code' was proposed to specify regions and regulate tooth shape. We have attempted to combine these hypotheses in a new model of the combinatorial homeobox gene expression pattern with the clone and field theories in one of 'co-operative genetic interaction'. This also explains the genetic absence of teeth in humans ascribed to point mutations in mesenchymally expressed genes, which affect tooth number in each series.

Animals↗

PubMed2006

Progress and challenges in studies of the evolution of development.

Plant evolutionary developmental genetics (EDG) has made considerable progress over the last decade. This is in part due to the accumulation of large amounts of sequence data that have provided robust organismal phylogenies and, increasingly, broad assessments of molecular evolution. Attempts to use primary sequence data to identify genes that have changed function in evolutionary time have not been as successful as initially hoped. The coding sequences of most genes, which are more amenable to statistical analysis than are regulatory sequences, are generally under purifying selection, as would be expected if much evolutionary change is the result of changes in cis-regulatory sequences. Sequence-based analysis of the regulatory sequences themselves remains difficult. Comparative studies of gene expression have been useful to identify genes whose developmental role may have changed in evolutionary time and will be critical to the future development of EDG. Such studies can be used to test hypotheses of gene function. Transformation experiments are often illuminating, but can be hard to interpret, particularly if genes from multiple species are all placed into a single heterologous system such as Arabidopsis. The ideal experiment would be a gene swap or promoter swap between two species, but this awaits development of good transformation systems. The immediate need for EDG is studies of gene expression on a massive scale, far broader than any studies undertaken to date.

Botany↗