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Results for “Genomic Structural Variation”

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PubMed1992

Minisatellite variant repeat (MVR) mapping: analysis of 'null' repeat units at D1S8.

Minisatellite variant repeat mapping by PCR (MVR-PCR) is a new approach to studying variation in human DNA which analyses interspersion patterns of variant repeats within minisatellite arrays. MVR-PCR has been applied to the hypervariable human minisatellite D1S8 which contains two major classes of variant 29bp repeat units designated a-type and t-type. The MVR-PCR assay uses a- or t-type specific primers, together with an amplimer at a fixed site in the DNA flanking the minisatellite, to reveal the interspersion patterns of variant repeats along an allele. Extreme levels of variation are seen both in the internal structures of individual alleles and in the digital code generated from the two superimposed alleles in total genomic DNA. However, occasional repeat units fail to amplify in MVR-PCR, signifying the existence of further repeat sequence variants termed 'null' or O-type repeats. Although not significant in individual identification, correct genotyping of null repeats is important when using MVR digital codes in parentage analysis. We have therefore characterised these null repeats and show that most null repeats share a common variant repeat sequence. We discuss the possible origins of null repeats and their application to paternity testing and the analysis of minisatellite evolution.

Alleles↗
PubMed2026

An integrated human immunoglobulin germline resource linking allele diversity to expressed repertoire structure.

Human immunoglobulin (IG) loci are highly polymorphic, yet existing germline resources remain noisy and incomplete, limiting our ability to link inherited variation to antibody repertoires. Here, we integrate high-fidelity long-read genomic sequencing with matched adaptive immune receptor repertoire sequencing (AIRR-seq) to construct HUSA, a population-scale, evidence-resolved germline resource. Using a conservative allele inference framework, HUSA expands current references more than three-fold, identifying over 1300 alleles while preserving allele-level evidence provenance across genomic and repertoire data. By linking genotype and expressed repertoires within individuals, we show that coding-region similarity predicts the structure of adjacent recombination signal sequences and leader regions, revealing that IG alleles are organized as linked cis-regulatory units associated with differences in recombination context and allele usage. These results define key germline constraints shaping repertoire formation and establish a robust, genotype-aware foundation for the analysis of immune receptor repertoires.

Journal Article↗
PubMed2025

Genomic-based revelation of genetic structure and adaptive characterization of Schizopygopsis malacanthus in the Jinsha River and Yalong River.

BACKGROUND: As a highly specialized class of schizothoracine fishes, Schizopygopsis malacanthus has attracted much attention due to its widespread distribution. To investigate the impact of the Qinghai‒Tibet movement on S. malacanthus, we analyzed the genetic evolutionary history of this species. RESULTS: These results showed that there was a high level of genetic differentiation between Jinsha River (JSR) populations and Yalong River (YLR) populations. The genetic diversity of intra-YLR populations was higher than that of the intra-JSR populations. There was gene exchange of the Suwalong population to the Huoqu and Ganzi populations. Furthermore, both of the JSR and YLR populations exhibited a gradual increase in the genetic differentiation index from low to high altitudes, and the effective population of high-elevation populations has gradually expanded. In high-altitude populations, the selected genes were enriched in DNA repair, light transduction, and energy metabolism, reflecting the genetic basis for their migration to higher altitudes. CONCLUSIONS: S. malacanthus populations had the higher genetic differentiation and genetic diversity in the JSR and its main tributary YLR. Therefore, we should preserve high-elevation natural river sections as much as possible and reserve habitats for their migration and diffusion.

Animals↗
PubMed1993

Sequence analysis of 22 kDa-like alpha-coixin genes and their comparison with homologous zein and kafirin genes reveals highly conserved protein structure and regulatory elements.

Several genomic and cDNA clones encoding the 22 kDa-like alpha-coixin, the alpha-prolamin of Coix seeds, were isolated and sequenced. Three contiguous 22 kDa-like alpha-coixin genes designated alpha-3A, alpha-3B and alpha-3C were found in the 15 kb alpha-3 genomic clone. The alpha-3A and alpha-3C genes presented in-frame stop codons at position +652. The two genes with truncated ORFs are flanking the alpha-3B gene, suggesting that the three alpha-coixin genes may have arisen by tandem duplication and that the stop codon was introduced before the duplication. Comparison of the deduced amino acid sequences of alpha-coixin clones with the published sequences of 22 kDa alpha-zein and 22 kDa-like alpha-kafirin revealed a highly conserved protein structure. The protein consists of an N-terminus, containing the signal peptide, followed by ten highly conserved tandem repeats of 15-20 amino acids flanked by polyglutamines, and a short C-terminus. The difference between the 22 kDa-like alpha-prolamins and the 19 kDa alpha-zein lies in the fact that the 19 kDa protein is exactly one repeat motif shorter than the 22 kDa proteins. Several putative regulatory sequences common to the zein and kafirin genes were identified within both the 5' and 3' flanking regions of alpha-3B. Nucleotide sequences that match the consensus TATA, CATC and the ca. -300 prolamin box are present at conserved positions in alpha-3B relative to zein and kafirin genes. Two putative Opaque-2 boxes are present in alpha-3B that occupies approximately the same positions as those identified for the 22 kDa alpha-zein and alpha-kafirin genes. Southern hybridization, using a fragment of a maize Opaque-2 cDNA clone as a probe, confirmed the presence of Opaque-2 homologous sequences in the Coix and sorghum genomes. The overall results suggest that the structural and regulatory genes involved in the expression of the 22 kDa-like alpha-prolamin genes of Coix, sorghum and maize, originated from a common ancestor, and that variations were introduced in the structural and regulatory sequences after species separation.

Amino Acid Sequence↗
PubMed1995

The structure of hepatitis B envelope and molecular variants of hepatitis B virus.

Accumulated evidence in recent years has shown that the variation of hepatitis B virus (HBV) genomes may have profound implications for our understanding of hepatitis B pathogenesis and prevention. Attention has focused on areas of the outer envelope coded by the S gene which are involved in the induction of a protective neutralising antibody response, and mutations which directly affect the production of C gene products, one of which is considered as a target for immune T cells involved in virus clearance. This review highlights recent experimental data which emphasizes the role of such mutations in the establishment and maintenance of chronic HBV infections and focuses attention on the significance of HBV variants with respect to the expanding use of HBV vaccines for mass immunization.

Amino Acid Sequence↗
PubMed1998

Human ARHGDIG, a GDP-dissociation inhibitor for Rho proteins: genomic structure, sequence, expression analysis, and mapping to chromosome 16p13.3.

GDP-dissociation inhibitors (GDIs) play a primary role in modulating the activity of GTPases. We recently reported the identification of a new GDI for the Rho-related GTPases named RhoGDIgamma. This gene is now designated ARHGDIG by HUGO. Here, in a detailed analysis of tissue expression of ARHGDIG, we observe high levels in the entire brain, with regional variations. The mRNA is also present at high levels in kidney and pancreas and at moderate levels in spinal cord, stomach, and pituitary gland. In other tissues examined, the mRNA levels are very low (lung, trachea, small intestine, colon, placenta) or undetectable. RT-PCR analysis of total RNA isolated from exocrine pancreas and islets shows that the gene is expressed in both tissues. We also report the genomic structure of ARHGDIG. The gene spans over 4 kb and is organized into six exons and five introns. The upstream region lacks a canonical TATA box and contains several putative binding sites for ubiquitous and tissue-specific factors active in central nervous system development. Using FISH, we have mapped the gene to chromosome band 16p13.3. This band is rich in deletion mutants of genes involved in several human diseases, notably polycystic kidney disease, alpha-thalassemia, tuberous sclerosis, mental retardation, and cancer. The promoter structure and the chromosomal location of RhoGDIgamma suggest its importance and underscore the need for further investigation into its biology.

Base Sequence↗
PubMed1993

Structure of the intergenic spacer region from the ribosomal RNA gene family of white spruce (Picea glauca).

Five genomic clones containing ribosomal DNA repeats from the gymnosperm white spruce (Picea glauca) have been isolated and characterized by restriction enzyme analysis. No nucleotide variation or length variation was detected within the region encoding the ribosomal RNAs. Four clones which contained the intergenic spacer (IGS) region from different rDNA repeats were further characterized to reveal the sub-repeat structure within the IGS. The sub-repeats were unusually long, ranging from 540 to 990 bp but in all other respects the structure of the IGS was very similar to the organization of the IGS from wheat, Drosophila and Xenopus.

DNA, Ribosomal↗
PubMed2026

Scaling up orphan crop research: genebank genetics highlight geographic structure in cultivated cowpea from 10 617 global accessions.

Vigna unguiculata (L.) Walp. is a dryland legume crop, providing essential food and nutritional security for millions of people across the semi-arid tropics, in Africa, Asia and Latin America. However, as a typical 'orphan crop', cowpea has long remained underrepresented in global genomic research to support crop improvement. Here, we conducted the largest genetic diversity analysis of cowpea to date, comprising 10 617 accessions sourced from seven international collections. Using genotyping-by-sequencing, we characterised the global patterns of genetic diversity, assessed redundancy within and across collections, and examined the geographic structure of the cowpea global allele pool. Our results revealed nine distinct genetic groups with clear geographic associations and fine-scale population differentiation, reflecting dispersal history, regional adaptation and the influence of modern breeding. Duplication across collections was detected, highlighting the need for improved curation and integration of germplasm resources. Landraces from sub-Saharan Africa do not fully capture the genetic diversity present in several other geographic regions, indicating the existence of abundant and untapped genetic resources worldwide. These findings not only provide insights into the genetic structure and evolutionary history of cowpea but also offer a valuable foundation for harnessing global germplasm diversity to enhance breeding potential and accelerate crop improvement.

Vigna↗
PubMed2025

Proteomic comparison of epidemic Australian Bordetella pertussis biofilm cells.

Bordetella pertussis causes whooping cough, a severe respiratory infectious disease. Studies have compared the currently dominant single nucleotide polymorphism (SNP) cluster I (pertussis toxin promoter allele, ptxP3) and previously dominant SNP cluster II (ptxP1) strains as planktonic cells. Since biofilm formation is linked with B. pertussis pathogenesis in vivo, this study compared the biofilm formation capabilities of representative strains of cluster I and cluster II. Confocal laser scanning microscopy found that the cluster I strain had a denser biofilm structure compared to the cluster II strain. Differences in protein abundance of the biofilm cells were then compared using tandem mass tagging and high-resolution multiple reaction monitoring. In total, 1,453 proteins were identified, of which 40 proteins had significant differential abundance between the two strains in biofilm conditions. Of particular interest was a large increase in the abundance of energy metabolism proteins (cytochrome proteins PetABC and BP3650) in the cluster I strain. When the abundance of these proteins was compared between six additional strains from each cluster, it was found that the protein abundance varied between all strains. These findings suggest that there are large levels of individual proteomic diversity between B. pertussis strains in biofilm conditions despite the highly conserved genome of the species. Overall, this study revealed visual differences in biofilm structure between B. pertussis strains and highlighted strain-specific variation in protein abundance that dominates potential cluster-specific changes that may be linked with the dominance of cluster I strains.IMPORTANCEBordetella pertussis causes whooping cough. The currently circulating cluster I strains have taken over previously dominant cluster II strains. It is important to understand the reasons behind this evolution to develop new strategies against the pathogen. Recent studies have shown that B. pertussis can form biofilms during infection. This study compared the biofilm formation capabilities of a cluster I and a cluster II strain and identified visual differences in the biofilms. The protein abundance between these strains grown in biofilms was compared, and proteins identified with varied abundance were measured with additional strains from each cluster. It was found that despite the highly conserved genetics of the species, there was varied protein abundance between the additional strains. This study highlights that strain-specific variation in protein abundance during biofilm conditions may dominate the cluster-specific changes that may be linked to the dominance of cluster I strains.

Bordetella pertussis↗
PubMed2026

A Cis-Regulatory Duplication in a Hox Hotspot Implicated in Mimetic Convergence in the Bumble Bee Bombus flavifrons.

Several species of North American bumble bees spanning the Pacific Coastal and Rocky Mountain regions converge onto distinct mimetic abdominal colour forms for each region by switching abdominal coloration from black to red. Previous genome-wide association studies (GWAS) of red and black transitions in two mimics (Bombus melanopygus and Bombus vancouverensis) revealed that black forms were generated by independently deleting a portion of the same cis-regulatory region near the Hox gene Abdominal-B (Abd-B). Here, we test the genetic basis of these mimetic colour forms in a third co-mimic, Bombus flavifrons, that has continuous variation in red and black that is shifted posteriorly one segment compared to its co-mimics. Using genome-wide association of red and black forms, we identified a structural variant <&#x2009;50&#x2009;bp away from the deletions in B. melanopygus and B. vancouverensis that was strongly associated with the colour phenotype. Sequencing across mimicry zones and closely related taxa revealed that all red forms of B. flavifrons and monomorphic red close relative Bombus centralis have a 319&#x2009;bp tandem duplication at this locus that has extensive modification to the duplicated copy. Black forms of B. flavifrons from the Cascades also have this duplication but without the modifications, while black forms in the western Rockies mostly lack this duplication, similar to ancestral black forms. This suggests independent mechanisms may regulate the black phenotypes in different populations and that ancestral sorting of variation and/or adaptive introgression generated these phenotypes. This study strengthens support for this Abd-B cis-regulatory region being a hotspot for regulating abdominal coloration in bumble bees, and features the role of regulatory region duplication in creating novel phenotypes.

Animals↗
PubMed1994

The relationship between DNA structural variation and activities of P elements in P and Q strains of Drosophila melanogaster.

To characterize the relationship between P element activities and their structures, we cloned P elements from genomic libraries of three isogenic P and Q strains derived from natural populations in Japan. These P elements were mapped with BamHI, AvaII and PstI and were classified by their size. The majority of P elements cloned were classified as either complete or relatively small P elements rather than medium size. The numbers of full length (2.9 kb) P elements per haploid genome of NP280 (P), AK194 (weak P) and WY113 (Q) were at least four, five and one, respectively. However, the 2.9 kb P element of WY113 was thought to be defective since this strain has no transposase activity. In our previous work, we demonstrated that the ORF 3-deleted P element is essential for P cytotype determination in WY113. A similar P element also exists in NP280, and this may have an important role for P cytotype determination in this strain. Two and one copies of the KP element, a deletion derivative of the P element, were found in NP280 and AK194, respectively. One of four complete P elements in NP280 was fully sequenced, and the base sequence was completely identical to that of p pi 25.1 originally derived from the U.S.A. This result is consistent with the notion that these P elements have a relatively recent origin in Drosophila melanogaster.

Animals↗
PubMed1997

How Escherichia coli can bias the results of molecular cloning: preferential selection of defective genomes of hepatitis C virus during the cloning procedure.

Cloned PCR products containing hepatitis C virus (HCV) genomic fragments have been used for analyses of HCV genomic heterogeneity and protein expression. These studies assume that the clones derived are representative of the entire virus population and that subsets are not inadvertently selected. The aim of the present study was to express HCV structural proteins. However, we found that there was a strong cloning selection for defective genomes and that most clones generated initially were incapable of expressing the HCV proteins. The HCV structural region (C-E1-E2-p7) was directly amplified by long reverse transcription-PCR from the plasma of an HCV-infected patient or from a control plasmid containing a viable full-length cDNA of HCV derived from the same patient but cloned in a different vector. The PCR products were cloned into a mammalian expression vector, amplified in Escherichia coli, and tested for their ability to produce HCV structural proteins. Twenty randomly picked clones derived from the HCV-infected patient all contained nucleotide mutations leading to absence or truncation of the expected HCV products. Of 25 clones derived from the control plasmid, only 8% were fully functional for polyprotein synthesis. The insertion of extra nucleotides in the region just upstream of the start codon of the HCV insert led to a statistically significant increase in the number of fully functional clones derived from the patient (42%) and from the control plasmid (72-92%). Nonrandom selection of clones during the cloning procedure has enormous implications for the study of viral heterogeneity, because it can produce a false spectrum of genomic diversity. It can also be an impediment to the construction of infectious viral clones.

Animals↗
PubMed2026

Utilization of long-read sequencing for the detection of structural rearrangements with AgileStructure.

MOTIVATION: Changes in genome organisation contribute to genetic disease when they disrupt gene function or regulation. Structural rearrangements may interrupt coding sequence or alter expression through promoter loss or gain, chromatin changes, copy-number variation, or disruption of short-range regulatory elements. Although short-read sequencing excels at detecting small variants, it performs poorly at resolving breakpoints of large rearrangements, especially in repetitive or low-complexity regions. Long-read sequencing overcomes these limitations, but analytical tools have not kept pace, making accurate identification and annotation of large structural variants challenging. RESULTS: We developed AgileStructure, a desktop application for locating and annotating large&#x2011;scale genomic rearrangements using aligned long&#x2011;read data. The software enables user&#x2011;guided exploration of breakpoint&#x2011;spanning reads, supporting accurate interpretation of complex events and filling a key gap in current structural variant analysis workflows. AVAILABILITY AND IMPLEMENTATION: Source code, binaries, user guide, and example aligned read data, are available on GitHub: https://github.com/msjimc/AgileStructure. An archived version is also available on Zenodo at https://doi.org/10.5281/zenodo.18610110.

Software↗
PubMed1995

Genetic variability in mitochondrial DNA of the screwworm, Cochliomyia hominivorax (Diptera: Calliphoridae), from Brazil.

Restriction fragment length polymorphism (RFLP) analysis of mitochondrial DNA (mtDNA) was used to examine genetic variation and population structure of screwworm flies in four populations from São Paulo State, Brazil. The total DNA of 405 individuals was digested with 15 restriction endonucleases and probed with five cloned HindIII fragments representing the entire mitochondrial genome of Cochliomyia hominivorax. The survey revealed that four enzymes (HaeIII, HindIII, MspI, and PvuII) were suitable to detect mtDNA variation among all populations. Based on the fragment patterns obtained for these four enzymes, a total of 15 haplotypes in combination was detected. Heteroplasmic individuals for the PvuII pattern were obtained in one of the populations. The estimated average for nucleotide sequence divergence (delta) was 0.92%. The cladogram of the geographical distribution among the observed haplotypes suggests that the sampled screwworms probably belong to a single evolutionary lineage with populations interconnected by reduced gene flow.

Animals↗
PubMed1985

An invertible element of DNA controls phase variation of type 1 fimbriae of Escherichia coli.

The expression of type 1 fimbriae (pili) of Escherichia coli is turned on and off at the transcriptional level at a high frequency (10(-3) per cell per generation) in a process termed phase variation. Using Southern blot and DNA sequence analysis, we have detected a genomic rearrangement in the switch region immediately upstream of the fimbrial structural gene. This rearrangement involves an invertible 314-base-pair segment of DNA whose alternating orientation apparently results in the on-and-off activation of a promoter that determines the state of fimbrial expression.

Base Sequence↗