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PubMed2004

[Analysis on the inheritance of inhibition and anti-inhibition of coleoptile purple line in rice and the SSR location of Ai(t) gene].

The ratio of purple line: no-purple line(13:3) was observed in six different F2 populations produced by crossing between parents with purple line and no-purple line in coleoptile. The backcross of XNA//XNA/ 21A150 (XNA, no-purple line and CMS, as the recurrent parent) resulted in a ratio of 1:1 (purple line: no-purple line). Genetic analysis showed that the expression of rice coleoptile purple line was influenced by two genes, inhibiting gene I and anti-inhibiting gene Ai(t). I gene inhibits P gene of C_A_P_ system and Ai(t) inhibits / gene, respectively. The gene pools of Ai(t) ai(t) and ai(t) ai(t) were constructed with BF1 of XNA//XNA/21A150. SSR analysis indicated that Ai(t) gene was linked with the markers of RM335, RM295, RM287 and RM21 and the genetic distance from Ai(t) to these four markers were 2.8 cM, 10.2 cM, 13.9 cM, 26.1 cM, respectively.

Chromosome Mapping↗
PubMed2006

Comparative genomics of Thermus thermophilus: Plasticity of the megaplasmid and its contribution to a thermophilic lifestyle.

The bacterium Thermus thermophilus grows at temperatures up to 85 degrees C and is equipped with thermostable enzymes of biotechnological interest. The recently decoded genomes of two strains of T. thermophilus, HB27 and HB8, each composed of a chromosome and a megaplasmid, must certainly encode specific strategies to encounter the thermophile challenge. Here, a genome comparison was undertaken to distinguish common functions from the flexible gene pool, which gave some clues about the biological traits involved in a thermophile lifestyle. The chromosomes were highly conserved, with about 100 strain-specific genes probably reflecting adaptations to the corresponding biological niche, such as metabolic specialities and distinct cell surface determinates including type IV pili. The two megaplasmids showed an elevated plasticity. Upon comparison and re-examination of their gene content, both megaplasmids seem to be implicated in assisting thermophilic growth: a large portion of their genes are apparently involved in DNA repair functions. About 30 plasmid-encoded genes exhibit sequence and domain composition similarity to a predicted DNA repair system specific for thermophilic Archaea and bacteria. Moreover, the plasmid-encoded carotenoid biosynthesis gene cluster is interlocked with genes involved in UV-induced DNA damage repair. This illustrates the importance of DNA protection and repair at elevated growth temperatures.

Adaptation, Physiological↗
PubMed2006

Selective pressures at a codon-level predict deleterious mutations in human disease genes.

Deleterious mutations affecting biological function of proteins are constantly being rejected by purifying selection from the gene pool. The non-synonymous/synonymous substitution rate ratio (omega) is a measure of selective pressure on amino acid replacement mutations for protein-coding genes. Different methods have been developed in order to predict non-synonymous changes affecting gene function. However, none has considered the estimation of selective constraints acting on protein residues. Here, we have used codon-based maximum likelihood models in order to estimate the selective pressures on the individual amino acid residues of a well-known model protein: p53. We demonstrate that the number of residues under strong purifying selection in p53 is much higher than those that are strictly conserved during the evolution of the species. In agreement with theoretical expectations, residues that have been noted to be of structural relevance, or in direct association with DNA, were among those showing the highest signals of purifying selection. Conversely, those changing according to a neutral, or nearly neutral mode of evolution, were observed to be irrelevant for protein function. Finally, using more than 40 human disease genes, we demonstrate that residues evolving under strong selective pressures (omega<0.1) are significantly associated (p<0.01) with human disease. We hypothesize that non-synonymous change on amino acids showing omega<0.1 will most likely affect protein function. The application of this evolutionary prediction at a genomic scale will provide an a priori hypothesis of the phenotypic effect of non-synonymous coding single nucleotide polymorphisms (SNPs) in the human genome.

Amino Acid Sequence↗
PubMed1992

Heterozygosity for the "DN allele" (G533-greater than A) of the beta-hexosaminidase alpha subunit gene identified by direct DNA sequencing in a family with the B1 variant of GM2-gangliosidosis.

A new patient having clinical, pathologic and biochemical features of the exceedingly rate B1 variant of GM2-gangliosidosis is described. This patient, of northern European (non-Ashkenazi) ancestry, is the first affected child of this ethnic background available for molecular genetic analysis; thus, she represented an opportunity to identify a new mutation associated with this phenotype or, conversely, to further characterize the DN allele of the hexosaminidase alpha gene (G533-greater than A) as a more widely distributed mutation not previously observed in this gene pool. As a means of rapid analysis, we report a strategy for PCR amplification and direct DNA sequencing of exon 5 of the hexosaminidase alpha gene, the most frequent site of mutations in this condition. With this technique, the father of the affected child was determined to be heterozygous for the DN allele, while the mother was found to have only the normal sequence in this region. This observation further extends the known geographic and ethnic distribution of this mutation, and suggests the likelihood that the DN allele has been derived by multiple independent mutational events.

Alleles↗
PubMed2002

Rapid spread of immigrant genomes into inbred populations.

When local populations are genetically differentiated from one another and partially inbred, as typically occurs in subdivided populations, immigrant genomes are predicted to be at a frequency-dependent fitness advantage due to heterosis (hybrid vigour) in their descendants. We tested this prediction with pedigreed laboratory populations of the butterfly Bicyclus anynana and report here on a rapid increase over five generations in the contribution of an initially rare immigrant genome to the local population gene pool. The replicated experimental design, including immigrant controls, demonstrates that the mechanism underlying immigrant genome spread is heterosis, and that the advantage to the immigrant genes is sustained over several generations. Our result suggests that effective migration rates may often be much higher than the numbers of individual migrants assumed by classical population genetics models, with implications for the persistence and evolution of metapopulations.

Animals↗
PubMed2001

Toward integration of comparative genetic, physical, diversity, and cytomolecular maps for grasses and grains, using the sorghum genome as a foundation.

The small genome of sorghum (Sorghum bicolor L. Moench.) provides an important template for study of closely related large-genome crops such as maize (Zea mays) and sugarcane (Saccharum spp.), and is a logical complement to distantly related rice (Oryza sativa) as a "grass genome model." Using a high-density RFLP map as a framework, a robust physical map of sorghum is being assembled by integrating hybridization and fingerprint data with comparative data from related taxa such as rice and using new methods to resolve genomic duplications into locus-specific groups. By taking advantage of allelic variation revealed by heterologous probes, the positions of corresponding loci on the wheat (Triticum aestivum), rice, maize, sugarcane, and Arabidopsis genomes are being interpolated on the sorghum physical map. Bacterial artificial chromosomes for the small genome of rice are shown to close several gaps in the sorghum contigs; the emerging rice physical map and assembled sequence will further accelerate progress. An important motivation for developing genomic tools is to relate molecular level variation to phenotypic diversity. "Diversity maps," which depict the levels and patterns of variation in different gene pools, shed light on relationships of allelic diversity with chromosome organization, and suggest possible locations of genomic regions that are under selection due to major gene effects (some of which may be revealed by quantitative trait locus mapping). Both physical maps and diversity maps suggest interesting features that may be integrally related to the chromosomal context of DNA-progress in cytology promises to provide a means to elucidate such relationships. We seek to provide a detailed picture of the structure, function, and evolution of the genome of sorghum and its relatives, together with molecular tools such as locus-specific sequence-tagged site DNA markers and bacterial artificial chromosome contigs that will have enduring value for many aspects of genome analysis.

DNA Fingerprinting↗
PubMed2005

Micro-geographical variation among male populations of the sandfly, Lutzomyia (Nyssomyia) intermedia, from an endemic area of American cutaneous leishmaniasis in the state of Rio de Janeiro, Brazil.

The genetic relationships among male Lutzomyia (Nyssomyia) intermedia (Lutz & Neiva) (Diptera: Psychodidae) from three populations from the same endemic area of American cutaneous leishmaniasis (ACL) in the state of Rio de Janeiro, Brazil, were compared. The sandflies were collected in three ecologically different habitats: domestic, extra-domestic and sylvatic over a total range of 800 m. Three molecular markers were employed to assess population variation. Based on MLEE markers, it could not be concluded that the three populations do not belong to the same gene pool (F(st) = 0.005). No within-population departure from Hardy-Weinberg equilibrium was detected (P < 0.05) and they presented the same level of gene variation. The number of migrants (Nm) indicated that at least 50 individuals per generation migrated between the three habitats. RAPD-PCR markers revealed that, except for the primer five, all were polymorphic. Phenetic analysis of the genotypes showed the presence of two principal clusters corresponding to: (1) domestic plus extra-domestic and (2) sylvatic. Unique genotypes were observed in each population. The sylvatic population was the most polymorphic, showing the largest number of genotypes and low level of similarity between them. Three mtDNA gene markers were studied by SSCP analysis. The most frequent haplotype for each marker ranged in frequency from 60 to 87% and individuals with unique haplotypes varied from 1 to 5%. Interestingly, the SSCP analysis showed a low level of polymorphism within populations. The disagreement between the different molecular markers observed and the hypothesis that L. intermedia could be participating in the transmission cycle of Leishmania (Viannia) braziliensis in environments ranging from the interior of human dwellings to the forest, are discussed.

Animals↗
PubMedDate not supplied

Continued high incidence of mutants in a Peruvian population of mice.

A second trapping of wild mice from two sites in a Peruvian river valley confirms the unprecedented high mutant incidence established by a previous trapping. It also shows that the population may be localized. The new mutants are different from those found in the first trapping, and thus indicate a continued source of mutagenic activity either external or within the gene pool of the population. A third study is underway.

Animals↗
PubMed2004

Genetic structure of northwestern Spanish brown trout (Salmo trutta L.) populations, differences between microsatellite and allozyme loci.

Genetic variation in nine wild brown trout (Salmo trutta L.) populations was studied by means of allozyme and microsatellite markers. All brown trout populations were clearly separated into two clusters that represented the Sil and Duero basins. Although both markers revealed a strong genetic differentiation between basins, microsatellite loci resulted much more accurate when population structure at the intrabasin level was analysed. Also pairwise multilocus FST estimates and assignment tests of individual fish to the set of sampled populations demonstrated a much higher efficiency of microsatellites compared to allozymes. The analysis of both markers provides new insights in defining the conservation units at this local area and confirms the existence of a recognized sub-lineage in the Duero basin. The management implications of these findings are discussed and changes in trout release activity are recommended to avoid mixing of trout gene pools mainly in the Sil basin.

Animals↗
PubMed1975

Estimation of race admixture--a new method.

The contribution of a parental population in the gene pool of a hybrid population which arose by hybridization with one or more other populations is estimated here at the population level from the probability of gene identity. The dynamics of accumulation of such admixture is studied incorporating the fluctuations due to finite size of the hybrid population. The method is illustrated with data on admixture in Cherokee Indians.

Alleles↗
PubMed2005

Photosynthesis genes in marine viruses yield proteins during host infection.

Cyanobacteria, and the viruses (phages) that infect them, are significant contributors to the oceanic 'gene pool'. This pool is dynamic, and the transfer of genetic material between hosts and their phages probably influences the genetic and functional diversity of both. For example, photosynthesis genes of cyanobacterial origin have been found in phages that infect Prochlorococcus and Synechococcus, the numerically dominant phototrophs in ocean ecosystems. These genes include psbA, which encodes the photosystem II core reaction centre protein D1, and high-light-inducible (hli) genes. Here we show that phage psbA and hli genes are expressed during infection of Prochlorococcus and are co-transcribed with essential phage capsid genes, and that the amount of phage D1 protein increases steadily over the infective period. We also show that the expression of host photosynthesis genes declines over the course of infection and that replication of the phage genome is a function of photosynthesis. We thus propose that the phage genes are functional in photosynthesis and that they may be increasing phage fitness by supplementing the host production of these proteins.

Bacteriophages↗
PubMed2004

[RAPD- and allozyme analysis of genetic variability of Panax ginseng C.A. Meyer and P. quinquefolius L].

Inter- and intraspecific variation of two ginseng species Panax ginseng and P. quinquefolius was estimated by studying 159 RAPD and 39 allozyme loci. Parameters of polymorphism and genetic diversity were determined and a tree was constructed to characterize the differences between individual plants, samples, and species. Genetic variation in P. ginseng proved to be lower than in P. quinquefolius. Gene diversity in the total P. ginseng sample was comparable with the mean expected heterozygosity of herbaceous plants. This suggests that wild P. ginseng plants in various areas of the currently fragmented natural habitat and cultivated plants of different origin have retained a significant proportion of their gene pool. The mean heterozygosity calculated per polymorphic locus for the RAPD phenotypes is similar to that of the allozyme loci and may be helpful in estimating gene diversity in populations of rare and endangered plant species.

Enzymes↗
PubMed1976

The genetic structure of finland.

The Finnish gene pool derives primarily from a relatively homogeneous Finno-Ugric population established during the Iron Age (100 B.C.-800 A.D.) in the southwest and southeast of Finland. Gene flow from Sweden to the southwest coastal areas, dating from prehistoric times, as well as the patterns of settlement and migration throughout Finland during the past 1000 years, appear to have been the major biosocial factors underlying the genetic structure of the contemporary population. Analysis of genetic variation and covariation at nine polymorphic loci in a large random sample of rural Finns, partitioned into either 8 countries or 27 geographic districts, showed that all of the essential features of the genetic structure suggested by the archaeological and historical data could be distinguished. Procedures for obtaining inference on the genetic structure of such a population are reviewed, including coefficients of similarity and (genetic) distance among subpopulations, the relation between linear or planar geographic structure and genetic covariation, and the methods for describing allelic differentiation. Bias resulting from the inappropriate assumption of a simple phylogenetic model can be substantial, expecially for the analysis of isolation by distance; procedures for avoiding misleading inference on the genetic structure are demonstrated.

Demography↗
PubMed1991

Bluetongue virus evolution: sequence analyses of the genomic S1 segments and major core protein VP7.

The S1 segments, encoding the group-specific antigen, VP7, from the five United States prototype BTV serotypes were cloned as full-length entities. The nucleotide and deduced amino acid sequences of segment S1 of BTV-2 were determined and compared with BTV-10, -11, -13, and -17, completing the sequencing of this cognate gene segment from all five US BTV serotypes. Each segment is 1156 bp long and contains an open reading frame encoding the 349-amino acid VP7 protein. Most (greater than 94%) of the amino acids of VP7 among the serotypes are conserved, including the location (position 255) of a single lysine residue. Secondary structure analyses of VP7 predict a putative eight-stranded beta-barrel between amino acid positions 150 and 250, a structure similar to that observed in ssRNA viruses. The S1 genes are flanked by conserved 5' and 3' noncoding regions. Stem-loop structures are predicted at the 3' end of each gene (nucleotide positions 1058-1097). The S1 segments of BTV-2, -10, -11, and -17 have greater than 93% of the nucleotides conserved, while less than 80% of their bases are identical with BTV-13. Analyses of nucleotide mismatches in each codon position of the VP7 open reading frame, transition frequencies, and evolutionary distances show that of the five, BTV-13 is the most distantly related and that BTV-10 and -17 are the most closely related serotypes. Evolutionary distance calculations of segment L2 from BTV-10, -11, and -17 concur with these observations. Comparison of this relationship with hybridization data of segment M3, which codes for VP5, suggests that BTV-17 has evolved by a combination of genetic drift and genomic reassortment. The data also indicate that the five US BTV serotypes are derived from two distinct gene pools. Evolution distances were used to estimate an evolution rate of 2.2 x 10(-3) nucleotide substitution/site/year for BTV segment S1. This rate is similar to the genes of retroviruses and implies an absence of RNA polymerase proofreading activity for dsRNA viruses.

Amino Acid Sequence↗
PubMed2002

Y-chromosome analysis in Egypt suggests a genetic regional continuity in Northeastern Africa.

The geographic location of Egypt, at the interface between North Africa, the Middle East, and southern Europe, prompted us to investigate the genetic diversity of this population and its relationship with neighboring populations. To assess the extent to which the modern Egyptian population reflects this intermediate geographic position, ten Unique Event Polymorphisms (UEPs), mapping to the nonrecombining portion of the Y chromosome, have been typed in 164 Y chromosomes from three North African populations. The analysis of these binary markers, which define 11 Y-chromosome lineages, were used to determine the haplogroup frequencies in Egyptians, Moroccan Arabs, and Moroccan Berbers and thereby define the Y-chromosome background in these regions. Pairwise comparisons with a set of 15 different populations from neighboring European, North African, and Middle Eastern populations and geographic analysis showed the absence of any significant genetic barrier in the eastern part of the Mediterranean area, suggesting that genetic variation and gene flow in this area follow the "isolation-by-distance" model. These results are in sharp contrast with the observation of a strong north-south genetic barrier in the western Mediterranean basin, defined by the Gibraltar Strait. Thus, the Y-chromosome gene pool in the modern Egyptian population reflects a mixture of European, Middle Eastern, and African characteristics, highlighting the importance of ancient and recent migration waves, followed by gene flow, in the region.

Arabs↗
PubMed2004

Environmental genomics, the big picture?

The enormous sequencing capabilities of our times might be reaching the point of overflowing the possibilities to analyse data and allow for a feedback on where to focus the available resources. We have now a foreseeable future in which most bacterial species will have an annotated genome. However, we know also that most prokaryotic diversity would not be included there. On the one hand, there is the problem of many groups not being easily amenable to culture and hence not represented in culture-centred microbial taxonomy. On the other hand, the gene pools present in one species can be orders of magnitude larger than the genome of one strain (selected for genome sequencing). Contrasting with eukaryotic genomes, the repertoire of genes present in one prokaryotic cell genome does not correlate stringently with its taxonomic identity. Hence gene catalogues from one environment might provide more meaningful information than the classical species catalogues. Metagenomics or microbial environmental genomics provide a different tool that gravitates around the habitat rather than the species. Such a tool could be just the right way to complement "organismal genomics". Its potential to advance our understanding of microbial ecology and prokaryotic diversity and evolution is discussed.

Ecology↗
PubMed1983

Surnames in Sardinia. I. Fit of frequency distributions for neutral alleles and genetic population structure.

Distributions of surnames were examined using data from about 40 000 individuals from consanguineous marriages (1930-59) in the island of Sardinia. They fit the Karlin-McGregor (1967) distribution for neutral alleles. The logarithmic distribution by Fisher (1943) and the Karlin-McGregor (1967) distribution give practically indistinguishable fits to these data. The two parameters underlying the Fisher distribution, alpha and nu, are fully interdependent, given the sample size N. From the latter and from the number of surnames S, they can be easily and satisfactorily estimated. The quantity nu measures immigration to the area and can be taken as a measure of the richness of the gene pool, being closely related to the quantity theta = Nemu (Ne = effective population size, mu = mutation rate) after the necessary corrections have been taken care of. Surnames behave like genes transmitted by the male line. Differences of female and male migrations require correction for comparison with data from autosomal gene frequencies but there seem to be no important differences between female and male migration in this area, as judged by analysis of pedigrees of consanguineous marriages. It is probable that the migration estimates obtained in this material are lower than real ones, mostly because of a bias characteristic of the particular source of surnames here employed. The distribution of surnames from areas which have very recently undergone economic development is not at equilibrium and is not fitted as well as that of areas which have had less important recent changes. As might be expected, the disturbance is particularly marked in the class most sensitive to effects of recent increases in migration, that of rarest surnames (represented by only one individual). In fact in this material it is noticeable only in this class and correction can be made for it. At equilibrium of migration and drift, the number of surnames in a population sample of given size can give a complete description of the population structure for that sample, in the same sense that the number of alleles is a sufficient statistic for the study of neutral evolution. The study of surnames, given their nature of 'neutral' alleles, the large number of alleles and the ease with which large numbers of individual data can be collected, can be a valuable help in the study of genetic population structure.

Alleles↗
PubMed2006

Comparative and functional genomics of Listeria spp.

The genus Listeria comprises a group of non-sporulating, Gram-positive, soil bacteria belonging to the low G+C group of microorganisms. The genus consists of only six species, L. monocytogenes, L. ivanovii, L. seeligeri, L. innocua, L. welshimeri, and L. grayi.L. monocytogenes and L. ivanovii are the only known pathogens of this group. Comparative whole-genome sequencing of representative strains comprising the entire genus is currently being performed and nearing completion. In the genus Listeria, genome reduction has led to the generation of non-pathogenic species from pathogenic progenitor strains. Indeed, many of the regions absent in the non-pathogenic species represent commonly deleted genes. Speciation and diversity of strains has been achieved by horizontal gene transfer of DNA encoding novel genes probably required for niche specific survival. The sequencing of several listerial genomes has also been accompanied by studies using global strategies involving whole-genome transcriptional profiling and proteomics to examine the adaptative changes of L. monocytogenes to growth in different environments and to catalogue the genes mediating these responses. We review this data and present information on the expression profile of L. monocytogenes EGD-e inside the vacuolar and the cytosolic environments of the host cell using whole-genome microarray analysis. Of the 484 genes regulated during intracellular growth 41 genes are species-specific, being absent from the genome of the non-pathogenic L. innocua CLIP 11262 strain. There were 25 genes that are strain-specific i.e. absent from the genome of the L. monocytogenes F2365 serotype 4b strain suggesting heterogeneity in the gene pool required for intracellular survival of L. monocytogenes in host cells.

Chromosomes, Bacterial↗