Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “Genomic Structural Variation”

Search indexed PubMed citations on genomics, clinical trials, systematic reviews and public health. Explore titles, authors and supplied subject terms, then open the PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 1,729 records · Page 96Linked to original sources
PubMed2005

Validation of Dwarf8 polymorphisms associated with flowering time in elite European inbred lines of maize (Zea mays L.).

The timing of transition from vegetative growth to flowering is important in nature as well as in agriculture. One of several pathways influencing this transition in plants is the gibberellin (GA) pathway. In maize (Zea mays L.), the Dwarf8 (D8) gene has been identified as an orthologue of the gibberellic acid-insensitive (GAI) gene, a negative regulator of GA response in Arabidopsis. Nine intragenic polymorphisms in D8 have been linked with variation in flowering time of maize. We tested the general applicability of these polymorphisms as functional markers in an independent set of inbred lines. Single nucleotide primer extension (SNuPe) and gel-based indel markers were developed, and a set of 71 elite European inbred lines were phenotyped for flowering time and plant height across four environments. To control for population structure, we genotyped the plant material with 55 simple sequence repeat markers evenly distributed across the genome. When population structure was ignored, six of the nine D8 polymorphisms were significantly associated with flowering time and none with plant height. However, when population structure was taken into consideration, an association with flowering time was only detected in a single environment, whereas an association across environments was identified between a 2-bp indel in the promoter region and plant height. As the number of lines with different haplotypes within subpopulations was a limiting factor in the analysis, D8 alleles would need to be compared in isogenic backgrounds for a reliable estimation of allelic effects.

Analysis of Variance↗
PubMed2005

Mutations and natural genetic variation in the courtship song of Drosophila.

All Drosophila species have a courtship repertoire by which a male stimulates a female to mate with him. In many species, males vibrate their wings to produce courtship song, an element of courtship that plays an important role in female choice. Each species has a unique courtship song, with the major differences among species songs being in timing and/or structure. Analysis of genetic mutations has revealed 17 genes that affect courtship song in Drosophila melanogaster. Most of the genes were first identified as affecting another trait and were subsequently shown to affect song. Quantitative genetic studies have demonstrated a polygenetic additive genetic architecture for many song traits. Few candidate genes, identified through the classical genetic approach, coincide with the regions implicated as affecting natural variation. With many new tools in genetic analysis and the multiple Drosophila genome projects currently underway, the ability to relate mutational and quantitative analyses will improve.

Animals↗
PubMed1990

Structure and polymorphism of human telomere-associated DNA.

We have analyzed the DNA sequences associated with four different human telomeres. Two are members of distinct repeated sequence families which are located mainly but not exclusively at telomeres. Two are unique in the genome, one deriving from the long arm telomere of chromosome 7 and the other from the pseudoautosomal telomere. One telomere-associated repeated sequence has a polymorphic distribution among the chromosome ends, being present at a different combination of ends in different individuals. These data thus identify a new source of human genetic variation and indicate that the canonical features of the organization of telomere-associated DNA are widely conserved in evolution.

Animals↗
PubMed2004

Speculations on the origin of the vertebrate immune system.

As one studies more and more the immune systems of invertebrates their multiplicity and diversity increase. On one hand, the number of different local and systemic innate mechanisms (or cascades of mechanisms) increases with every phylum studied, on the other hand the diversity increases within each system as multiple loci and polymorphisms are discovered. Even somatic variation is not restricted to vertebrates. Yet no immune system similar to that of vertebrates characterized by the usage of RAG enzymes, has been found below jawed vertebrates. The availability of genome projects in early chordates allows understanding better the different causal lines that led to the generation of the vertebrate system with its diverse repertoire of antigen receptors generated somatically. This paper singles out a linkage group in human, gathering genes of the Ig superfamily with structural relationships to the antigen receptor JAM/CTX, nectin, or to some haematopoietic cells CD that have homologues in protochordates such as Branchiostoma and Ciona or in more primitive protostomes. The role of virus receptor for many of these clustered genes products provides perhaps one way of envisaging the recruitment of this family in the adaptive immune system from an ancient form of innate antiviral immunity.

Animals↗
PubMed2002

Complete mitochondrial genomes confirm the distinctiveness of the horse-dog and sheep-dog strains of Echinococcus granulosus.

Unlike other members of the genus, Echinococcus granulosus is known to exhibit considerable levels of variation in biology, physiology and molecular genetics. Indeed, some of the taxa regarded as 'genotypes' within E. granulosus might be sufficiently distinct as to merit specific status. Here, complete mitochondrial genomes are presented of 2 genotypes of E. granulosus (G1-sheep-dog strain: G4-horse-dog strain) and of another taeniid cestode, Taenia crassiceps. These genomes are characterized and compared with those of Echinococcus multilocularis and Hymenolepis diminuta. Genomes of all the species are very similar in structure, length and base-composition. Pairwise comparisons of concatenated protein-coding genes indicate that the G1 and G4 genotypes of E. granulosus are almost as distant from each other as each is from a distinct species, E. multilocularis. Sequences for the variable genes atp6 and nad3 were obtained from additional genotypes of E. granulosus, from E. vogeli and E. oligarthrus. Again, pairwise comparisons showed the distinctiveness of the G1 and G4 genotypes. Phylogenetic analyses of concatenated atp6, nad1 (partial) and cox1 (partial) genes from E. multilocularis, E. vogeli, E. oligarthrus, 5 genotypes of E. granulosus, and using T. crassiceps as an outgroup, yielded the same results. We conclude that the sheep-dog and horse-dog strains of E. granulosus should be regarded as distinct at the specific level.

Amino Acid Sequence↗
PubMed1999

DNA fingerprinting reveals polygyny in the subterranean rodent Ctenomys talarum.

DNA fingerprinting was used to characterize patterns of paternity in two populations of Ctenomys talarum from Buenos Aires Province, Argentina. The multilocus probe PV47-2 was used to detect variation in genomic DNA extracted from 12 females, their 32 offspring, and 14 putative sires. For 11 out of 12 litters examined, a single male capable of providing all nonmaternal bands was identified. Within each study population, individual males sired more than one litter, suggesting that C. talarum is polygynous. No evidence of multiple paternity of litters was found. High band-sharing values among females suggest that further research is needed to assess the population genetic structure of this species.

Animals↗
PubMed2001

Multiple maternal origins and weak phylogeographic structure in domestic goats.

Domestic animals have played a key role in human history. Despite their importance, however, the origins of most domestic species remain poorly understood. We assessed the phylogenetic history and population structure of domestic goats by sequencing a hypervariable segment (481 bp) of the mtDNA control region from 406 goats representing 88 breeds distributed across the Old World. Phylogeographic analysis revealed three highly divergent goat lineages (estimated divergence >200,000 years ago), with one lineage occurring only in eastern and southern Asia. A remarkably similar pattern exists in cattle, sheep, and pigs. These results, combined with recent archaeological findings, suggest that goats and other farm animals have multiple maternal origins with a possible center of origin in Asia, as well as in the Fertile Crescent. The pattern of goat mtDNA diversity suggests that all three lineages have undergone population expansions, but that the expansion was relatively recent for two of the lineages (including the Asian lineage). Goat populations are surprisingly less genetically structured than cattle populations. In goats only approximately 10% of the mtDNA variation is partitioned among continents. In cattle the amount is >/=50%. This weak structuring suggests extensive intercontinental transportation of goats and has intriguing implications about the importance of goats in historical human migrations and commerce.

Animals↗
PubMed2005

Assessing the odd secondary structural properties of nuclear small subunit ribosomal RNA sequences (18S) of the twisted-wing parasites (Insecta: Strepsiptera).

We report the entire sequence (2864 nts) and secondary structure of the nuclear small subunit ribosomal RNA (SSU rRNA) gene (18S) from the twisted-wing parasite Caenocholax fenyesi texensis Kathirithamby & Johnston (Strepsiptera: Myrmecolacidae). The majority of the base pairings in this structural model map on to the SSU rRNA secondary and tertiary helices that were previously predicted with comparative analysis. These regions of the core rRNA were unambiguously aligned across all Arthropoda. In contrast, many of the variable regions, as previously characterized in other insect taxa, had very large insertions in C. f. texensis. The helical base pairs in these regions were predicted with a comparative analysis of a multiple sequence alignment (that contains C. f. texensis and 174 published arthropod 18S rRNA sequences, including eleven strepsipterans) and thermodynamic-based algorithms. Analysis of our structural alignment revealed four unusual insertions in the core rRNA structure that are unique to animal 18S rRNA and in general agreement with previously proposed insertion sites for strepsipterans. One curious result is the presence of a large insertion within a hairpin loop of a highly conserved pseudoknot helix in variable region 4. Despite the extraordinary variability in sequence length and composition, this insertion contains the conserved sequences 5'-AUUGGCUUAAA-3' and 5'-GAC-3' that immediately flank a putative helix at the 5'- and 3'-ends, respectively. The longer sequence has the potential to form a nine base pair helix with a sequence in the variable region 2, consistent with a recent study proposing this tertiary interaction. Our analysis of a larger set of arthropod 18S rRNA sequences has revealed possible errors in some of the previously published strepsipteran 18S rRNA sequences. Thus we find no support for the previously recovered heterogeneity in the 18S molecules of strepsipterans. Our findings lend insight to the evolution of RNA structure and function and the impact large insertions pose on genome size. We also provide a novel alignment template that will improve the phylogenetic placement of the Strepsiptera among other insect taxa.

Animals↗
PubMed2026

A Mobile Glycosylation Locus Modulates Cell Wall Architecture in Lactobacillus crispatus.

Lactobacillus crispatus dominance in the vaginal microbiome is associated with beneficial health outcomes, yet strain-level variation and its implications remain poorly understood. Here, we resolve the genomic context of three glycosyltransferase gene fragments (GT1-3) previously linked with dysbiotic states. Long-read resequencing revealed that GT1-3 are part of a ~18.7 kb Wzx/Wzy-dependent cell wall polysaccharide (CWPS) locus, containing several IS256-family transposases. Serial propagation in vitro produced isolates with 4.1 kb excised via a composite transposon encompassing the GT3, UDP-galactopyranose mutase, flippase, and hypothetical protein, demonstrating structural plasticity. Transmission electron microscopy showed a ~20%-25% thinner peptidoglycan layer in the derived strains, while FT-IR and monosaccharide analysis indicated no gross changes. Molecular dynamics simulations suggest that GT3 contributes to the structural stability of the glycosyltransferase complex, without compromising catalytic function. Together, these findings establish the CWPS locus as a mobile, structurally plastic element that directly influences cell wall architecture in L. crispatus.

Lactobacillus crispatus↗
PubMed2004

Selection of functional mutations in the U5-IR stem and loop regions of the Rous sarcoma virus genome.

BACKGROUND: The 5' end of the Rous sarcoma virus (RSV) RNA around the primer-binding site forms a series of RNA secondary stem/loop structures (U5-IR stem, TpsiC interaction region, U5-leader stem) that are required for efficient initiation of reverse transcription. The U5-IR stem and loop also encode the U5 integrase (IN) recognition sequence at the level of DNA such that this region has overlapping biological functions in reverse transcription and integration. RESULTS: We have investigated the ability of RSV to tolerate mutations in and around the U5 IR stem and loop. Through the use of viral libraries with blocks of random sequence, we have screened for functional mutants in vivo, growing the virus libraries in turkey embryo fibroblasts. The library representing the U5-IR stem rapidly selects for clones that maintain the structure of the stem, and is subsequently overtaken by wild type sequence. In contrast, in the library representing the U5-IR loop, wild type sequence is found after five rounds of infection but it does not dominate the virus pool, indicating that the mutant sequences identified are able to replicate at or near wild type levels. CONCLUSION: These results indicate that the region of the RNA genome in U5 adjacent to the PBS tolerates much sequence variation even though it is required for multiple biological functions in replication. The in vivo selection method utilized in this study was capable of detecting complex patterns of selection as well as identifying biologically relevant viral mutants.

Avian Sarcoma Viruses↗
PubMed2005

[Bioinformatic analysis of the 14-3-3 gene family in rice].

Using two-step HMM (hidden markov model) scan strategy,eight 14-3-3-like proteins were identified by searching the Oryza sativa L. ssp. japonica protein database. From them four genes were newly detected in this study. We confined the genes expressing in Nipponbare by EST search. Expression analysis also showed each gene expressed diversely within any individual,this tends suggested specific function of particular gene. Alignment of amino acid sequences suggested that there could be isoform function of the specific residues. The analyses of gene structure and chromosome location indicated that rice genome contains both epsilon and no-epsilon forms of 14-3-3 proteins. In addition,we analyzed the evolution of the rice 14-3-3 protein family.

14-3-3 Proteins↗
PubMed2006

A Survey of the Brassica rapa genome by BAC-end sequence analysis and comparison with Arabidopsis thaliana.

Brassica rapa ssp. pekinensis (Chinese cabbage) is an economically important crop and a model plant for studies on polyploidization and phenotypic evolution. To gain an insight into the structure of the B. rapa genome we analyzed 12,017 BAC-end sequences for the presence of transposable elements (TEs), SSRs, centromeric satellite repeats and genes, and similarity to the closely related genome of Arabidopsis thaliana. TEs were estimated to occupy 14% of the genome, with 12.3% of the genome represented by retrotransposons. It was estimated that the B. rapa genome contains 43,000 genes, 1.6 times greater than the genome of A. thaliana. A number of centromeric satellite sequences, representing variations of a 176-bp consensus sequence, were identified. This sequence has undergone rapid evolution within the B. rapa genome and has diverged among the related species of Brassicaceae. A study of SSRs demonstrated a non-random distribution with a greater abundance within predicted intergenic regions. Our results provide an initial characterization of the genome of B. rapa and provide the basis for detailed analysis through whole-genome sequencing.

Arabidopsis↗
PubMed1992

Alterations in potential sites for glycosylation predominate during evolution of the simian immunodeficiency virus envelope gene in macaques.

Genetic diversity is a hallmark of the human immunodeficiency virus (HIV) genome, but the role of distinct HIV variants in the development of AIDS is unclear. Envelope (env) is the most highly variable gene in HIV as well as in other retroviruses. We have previously demonstrated that variation in simian immunodeficiency virus (SIV) env is primarily localized in two regions (V1 and V4) during progression to simian AIDS. To determine whether there is a common genotype that evolves as AIDS develops, a total of 160 SIV env genes isolated directly from the tissue DNAs of four macaques infected with cloned virus were compared. Common amino acid sequence changes were identified within V1, V4, and, in the late stages of disease, near V3. At several positions, the same amino acid change was seen frequently in the variant genomes from all four animals. As AIDS developed, the majority of viruses evolved an extended sequence in V1 that was rich in serine and threonine residues and shared similarity with proteins modified by O-linked glycosylation. Several of the predominant common sequence changes in V1 and V4 created new sites for N-linked glycosylation. Thus, common features of the SIV variants that evolve during progression to AIDS are motifs that potentially allow for structural and functional changes in the env protein as a result of carbohydrate addition.

Amino Acid Sequence↗
PubMed1981

Molecular cloning of foot and mouth disease virus genome and nucleotide sequences in the structural protein genes.

Foot and mouth disease virus (FMDV), of the family Picornaviridae, consists of a single-stranded RNA (approximately 8,000 nucleotides), the translation of which is initiated on the 3' side of a 150-nucleotide poly(C) tract and yields a single polyprotein which is processed by host cell proteases into four primary products (Fig. 1). One or more virus-specified proteases further cleave these into the final products, the capsid proteins (VP1-4) being derived from the precursor p88 (for review see ref. 5). There are seven serotypes of the virus and as it has been shown that the immunizing activity of FMDV particles is associated primarily with VP1 (refs 6, 7), it seems likely that antigenic variation in FMDV is a result of changes in the structure of this protein. To further our understanding of this variation and as a first step in the possible development of FMDV vaccines from genetically manipulated microorganisms, we report here the construction and analysis of recombinant plasmids containing cDNA copies of the RNA. Comparison of the deduced amino acid sequence with the known polypeptide sequences shows that the NH2-termini of VP2 and VP3 are conserved between the A and O serotypes whereas that of VP1 (the immunizing antigen) varies by as much as 42% between serotypes.

Amino Acid Sequence↗
PubMed2000

A case for evolutionary genomics and the comprehensive examination of sequence biodiversity.

Comparative analysis is one of the most powerful methods available for understanding the diverse and complex systems found in biology, but it is often limited by a lack of comprehensive taxonomic sampling. Despite the recent development of powerful genome technologies capable of producing sequence data in large quantities (witness the recently completed first draft of the human genome), there has been relatively little change in how evolutionary studies are conducted. The application of genomic methods to evolutionary biology is a challenge, in part because gene segments from different organisms are manipulated separately, requiring individual purification, cloning, and sequencing. We suggest that a feasible approach to collecting genome-scale data sets for evolutionary biology (i.e., evolutionary genomics) may consist of combination of DNA samples prior to cloning and sequencing, followed by computational reconstruction of the original sequences. This approach will allow the full benefit of automated protocols developed by genome projects to be realized; taxon sampling levels can easily increase to thousands for targeted genomes and genomic regions. Sequence diversity at this level will dramatically improve the quality and accuracy of phylogenetic inference, as well as the accuracy and resolution of comparative evolutionary studies. In particular, it will be possible to make accurate estimates of normal evolution in the context of constant structural and functional constraints (i.e., site-specific substitution probabilities), along with accurate estimates of changes in evolutionary patterns, including pairwise coevolution between sites, adaptive bursts, and changes in selective constraints. These estimates can then be used to understand and predict the effects of protein structure and function on sequence evolution and to predict unknown details of protein structure, function, and functional divergence. In order to demonstrate the practicality of these ideas and the potential benefit for functional genomic analysis, we describe a pilot project we are conducting to simultaneously sequence large numbers of vertebrate mitochondrial genomes.

Animals↗
PubMed1978

The isolation of defective variants of simian virus 40 whose genomes contain sequences derived from adenovirus 2 DNA.

A new set of hybrid viruses has been isolated whose closed circular genomes 5 to 6 kB in size, contain DNA sequences derived in part from adenoviruses 2 and in part from SV40. The structure of these genomes is complex, but in the simplest case, analyses by restriction endonuclease digestion and hybridization indicate that the adenovirus 2 DNA is present as a continuous block, of maximum size 2.8 kB. Different hybrids contain sequences derived from different segments of the adenovirus 2 genome.

Adenoviridae↗
PubMed2000

Genomic structure of the human tetratricopeptide repeat-containing gene, TTC4, from chromosome region 1p31 and mutation analysis in breast cancers.

Loss of heterozygosity (LOH) in 1p31 is a frequent genetic alteration in breast tumors indicating the site of a tumor suppressor gene. We recently isolated a new member of the human tetratricopeptide repeat-containing family of genes, TTC4, which maps to this region. Other members of this gene family have been implicated in tumorigenesis suggesting that TTC4 may represent a breast cancer tumor suppressor gene. We now report the exon/intron structure of TTC4 and single strand conformation polymorphism (SSCP) analysis of DNA from 20 sporadic breast tumors. Although polymorphic variations were identified no mutations affecting the open reading frame of TTC4 were detected. Since the overall region of chromosome 1p31 which undergoes LOH can be relatively large, excluding involvement of newly isolated genes from this region in breast cancer tumorigenesis is an important process for the successful identification of the critical gene. Understanding the structure of TTC4 now makes mutation analysis possible for other cancers and diseases that map to this region.

Breast Neoplasms↗
PubMed2006

Genetic variability of fragmented stands of pedunculate oak (Quercus robur) in Finland.

The genetic structure of 33 natural Quercus robur stands in Finland was studied using 13 allozyme loci to analyze the effects of fragmentation in a wind-pollinated tree species. The present fragmented and discontinuous distribution of oak is a result of both short-term human impact and long-term climatic and geological change, including post-glacial land uplift. In accordance with general expectations, genetic diversity in small populations was lower than that in large populations, and differentiation among small populations was higher than that among large populations. Heterozygote deficiency was more pronounced in large populations, which is proposed to be a Wahlund effect created by either spatial sub-structuring or the existence of synchronized flowering lineages. Also genetic differentiation was higher and diversity lower in Finland than the estimates reported for Central Europe. There were differences in the genetic structure on sites of different geological age. We suggest that on most geologically old sites drift has a prominent effect whereas on younger sites also founder effects may be important.

Age Factors↗