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PubMed2026

Long-read low-pass sequencing enhances variant detection in a peanut MAGIC population.

Accurate genotyping accelerates crop improvement, yet long-read sequencing remains underused in breeding due to cost. We present a scalable long-read low-pass (LRLP) sequencing framework for high-throughput variant discovery and trait mapping. Using PacBio HiFi reads in an allotetraploid peanut (Arachis hypogaea; AABB, 2n = 4x = 40) MAGIC population, we generated both LRLP and short-read low-pass (SRLP) data. At comparable depths, LRLP achieved substantially greater whole-genome and gene-space coverage than SRLP. Data were analyzed using both a single-reference genome and an 18-parent pangenome graph constructed with KhufuPan, a new tool for graph-based genotyping. Across analytical approaches, LRLP consistently identified more SNPs, indels (2-1,000 bp), and structural variants (>1 kb) than SRLP, improving genotype resolution and selection accuracy, particularly for large structural variants. By reducing cost barriers and increasing variant discovery in complex genomes, LRLP provides a practical path for deploying advanced genomics in under-resourced and orphan crops critical to global food security.

Arachis↗

PubMed2026

Detecting and reconstructing breakage-fusion-bridge cycles from long-read sequencing using BFBArchitect.

MOTIVATION: Focal oncogene amplification is a key driver of tumor progression. Remarkably, the increased pathology depends on the context-whether the amplification is extrachromosomal (ecDNA) or intrachromosomal. EcDNA amplifications promote heterogeneity, therapy resistance, and poor prognosis. Focal intrachromosomal amplifications often arise through breakage-fusion-bridge (BFB) cycles, which produce highly rearranged but stable chromosomes. Distinguishing BFB from ecDNA remains challenging due to overlapping genomic signatures. To address this, we present BFBArchitect, a computational method leveraging long-read Oxford Nanopore data to identify BFB sequences consistent with both copy number and structural variations. RESULTS: We provide a novel combinatorial characterization of BFB, which naturally leads to an integer linear programming (ILP) optimization. The ILP optimization generates a BFB sequence that best explains experimentally observed copy numbers and foldback structural variants. We implement this idea in a tool called BFBArchitect, which achieves near-perfect accuracy in distinguishing BFB from non-BFB structures in extensive simulations as well as on 18 validated tumor samples. Moreover, it generates sequence-level BFB reconstructions that provide mechanistic insights into BFB formation, including repair mechanisms with template switching and other structural variants, and recapture of telomere for stabilization. AVAILABILITY AND IMPLEMENTATION: BFBArchitect is available at https://github.com/AmpliconSuite/BFBArchitect.

Sequence Analysis, DNA↗

PubMed1995

Alpha 3 beta 1 and alpha 6 beta 1 integrins mediate laminin/merosin binding and function as costimulatory molecules for human thymocyte proliferation.

Integrins comprise a superfamily of alpha beta heterodimers that serve as cell signaling as well as adhesion molecules. We demonstrate that the alpha 3 beta 1 and alpha 6 beta 1 integrins are laminin/merosin receptors expressed in human thymocytes. By reverse transcriptase-PCR analysis, we determined that the alpha 3A beta 1, but not the alpha 3B beta 1, cytoplasmic structural variant of alpha 3 beta 1 is expressed in thymocytes. In contrast, both alpha 6A beta 1 and alpha 6B beta 1 cytoplasmic structural variants of alpha 6 beta 1 are expressed. A small percentage (10 to 15%) of human thymocytes bind to immobilized laminin, and even fewer (3 to 5%) bind to merosin, the laminin isoform normally present in the thymus. This binding, however, can be increased to 39 to 41% after activation of thymocytes with Mn2+ (or PMA). Binding to either laminin or merosin is completely inhibited by anti-beta 1 mAb or by a mixture of anti-alpha 3 and anti-alpha 6 mAbs, indicating that both alpha 3 beta 1 and alpha 6 beta 1 participate in thymocyte adhesion to the laminin family of extracellular matrix proteins. The protein kinase C inhibitors, calphostin C and staurosporine, inhibit Mn(2+)-enhanced thymocyte binding, suggesting that protein kinase C activity is crucial for the binding. Furthermore, the data indicate that at least two divalent cation binding sites serve to regulate integrin binding activity. Finally, we show that both immobilized laminin and merosin have costimulatory function for anti-CD3-induced thymocyte proliferation, and both anti-alpha 3 and anti-alpha 6 mAbs can block this proliferative response. The cooperative function of alpha 3 beta 1 and alpha 6 beta 1 evidenced in the laminin/merosin binding and proliferation assays suggests that thymocyte-merosin interactions may play an important role in thymic T cell development.

Base Sequence↗

PubMed2002

Genome restructuring in rye affects the expression, organization and disposition of homologous rDNA loci.

The standard rye cultivar 'Imperial' and a structural variant carrying an intact 1R chromosome and two telocentric 1R chromosomes (short and long arms) were used to investigate expression patterns of homologous rDNA loci, and the influence of chromosome structural change on their interphase organisation and relative disposition. Sequential silver staining and in situ hybridization with the rDNA probe pTa71, established a correspondence between the expression and organization patterns of rDNA domains in metaphase and interphase cells. In most cells of the cultivar Imperial, nucleolar organizer region (NOR) silver staining on metaphase chromosomes with equivalent numbers of rDNA genes revealed a size heteromorphism between homologous rDNA loci, resulting from their differential expression. NOR heteromorphism in the structural variant line was significantly reduced. The preferential activity of one NOR over its homologue was found to be random within cells and independent of parental origin. Nucleotypic modifications mediated by changes in the 1R chromosome structure include increased proximity between homologous rDNA loci in interphase, and an increase in the frequency of cells with intra-nucleolar ribosomal condensed chromatin. These results seem to indicate a 'sequence recognition' process for the regulation of homologous loci.

Cell Cycle↗

PubMed2006

The human Y chromosome: a masculine chromosome.

Once considered to be a genetic wasteland of no scientific interest beyond sex determination, the human Y chromosome has made a significant comeback in the past few decades and is currently implicated in multiple diseases, including spermatogenic failure - absent or very low levels of sperm production. The Y chromosome contains over one hundred testis-specific transcripts, and several deletions have been described that remove some of these transcripts, thereby causing spermatogenic failure. Screening for such deletions in infertile men is now a standard part of clinical evaluation. Many other Y-chromosome structural variants, some of which affect gene copy number, have been reported recently, and future research will be necessary to address the phenotypic effect of these structural variants.

Animals↗

PubMed2026

Two cases of mosaic germline SVA insertions in SMARCB1: implications for rhabdoid tumour predisposition diagnosis.

Rhabdoid tumour predisposition syndrome (RTPS) is a highly penetrant cancer predisposition syndrome caused by germline variants in SMARCB1 or less frequently in SMARCA4. Genetic testing for this syndrome involves sequence and deletion/duplication analysis of these two genes. Standard clinical testing is limited in detecting structural variants. Here we describe two patients who tested negative on standard clinical germline panel testing for RTPS but were each found to have a mosaic germline insertion of an SVA (SINE-VNTR-Alu) element in the SMARCB1 gene by more advanced comprehensive genomic analysis. These two cases demonstrate the importance of structural variants and broader genomic sequencing for individuals suspected of having an underlying germline cancer predisposition syndrome, such as RTPS.

Journal Article↗

PubMed2001

Genomic organization of the CC chemokine mip-3alpha/CCL20/larc/exodus/SCYA20, showing gene structure, splice variants, and chromosome localization.

We describe the genomic organization of a recently identified CC chemokine, MIP3alpha/CCL20 (HGMW-approved symbol SCYA20). The MIP-3alpha/CCL20 gene was cloned and sequenced, revealing a four exon, three intron structure, and was localized by FISH analysis to 2q35-q36. Two distinct cDNAs were identified, encoding two forms of MIP-3alpha/CCL20, Ala MIP-3alpha/CCL20 and Ser MIP-3alpha/CCL20, that differ by one amino acid at the predicted signal peptide cleavage site. Examination of the sequence around the boundary of intron 1 and exon 2 showed that use of alternative splice acceptor sites could give rise to Ala MIP-3alpha/CCL20 or Ser MIP-3alpha/CCL20. Both forms of MIP-3alpha/CCL20 were chemically synthesized and tested for biological activity. Both flu antigen plus IL-2-activated CD4(+) and CD8(+) T lymphoblasts and cord blood-derived dendritic cells responded to Ser and Ala MIP-3alpha/CCL20. T lymphocytes exposed only to IL-2 responded inconsistently, while no response was detected in naive T lymphocytes, monocytes, or neutrophils. The biological activity of Ser MIP-3alpha/CCL20 and Ala MIP-3alpha/CCL20 and the tissue-specific preference of different splice acceptor sites are not yet known.

Alternative Splicing↗

PubMed2006

Hierarchical gene expression profiles of HUVEC stimulated by different lipid A structures obtained from Porphyromonas gingivalis and Escherichia coli.

The ability of lipid A structural variants to elicit unique endothelial cell gene expression was examined by measuring global gene expression profiles in human umbilical cord vein endothelial cells (HUVEC) using Affymetrix full genome chips. Two lipid A structural variants obtained from Porphyromonas gingivalis designated PgLPS(1435/1449) and PgLPS(1690) as well as LPS obtained from Escherichia coli wild type and an E. coli msbB mutant (missing myristic acid in the lipid A) were examined. Each of these lipid A structures has been shown to interact with TLR4; however, PgLPS(1435/1449) and E. coli msbB LPS have been shown to be TLR4 antagonists while PgLPS(1690) and wild-type E. coli LPS are TLR4 agonists. It was found that PgLPS(1435/1449) and PgLPS(1690) as well as E. coli msbB LPS activated a subset of those genes significantly transcribed in response to E. coli wild-type LPS. Furthermore, the subset of genes expressed in response to the different lipid A structural forms were those most significantly activated by wild-type E. coli LPS demonstrating a hierarchy in TLR4-dependent endothelial cell gene activation. A unique gene expression profile for the weak TLR4 agonist PgLPS(1690) was observed and represents a TLR4 hierarchy in endothelial cell gene activation.

Cell Line↗

PubMed2026

Graph-based pan-genome reveals structural and functional diversity across oil palm domestication gradients.

BACKGROUND: Oil palm (Elaeis guineensis Jacq.), the world's most land-efficient oil crop, underpins global vegetable oil supply yet faces mounting constraints from limited expansion, climate stress, and disease pressure. These challenges highlight the urgent need for genomic resources that capture species-wide diversity to support sustainable improvement. While recent reference assemblies have advanced trait discovery, single linear genomes fail to represent the full spectrum of structural and gene-content variation, limiting resolution of agronomic alleles. RESULTS: Here, we constructed a graph-based pan-genome from 30 diverse oil palm assemblies representing wild, semi-domesticated, and commercial accessions. We characterized structural variants, gene presence-absence variation, and copy-number gains, with focusing on functional stratification and resistance gene dynamics. The graph-based pan-genome revealed extensive structural and gene-content variation, including a large conserved core, complemented by shell and unique fractions enriched or biased toward regulatory, stress-responsive, and defense-related functions. Structural variation and duplication-derived copy-number gains contributed substantially to gene-content diversity, with semi-domesticated accessions exhibiting the greatest variability. Resistance gene repertoires showed contrasting patterns: receptor-like kinases remained comparatively stable, whereas the CNL subclass of NLR genes contributed disproportionately to shell-genome variation and duplication-associated turnover. CONCLUSIONS: This graph-based pan-genome provides a curated multi-assembly reference and comparative framework for oil palm genomics. By capturing structural variants, gene-content variations, copy-number gains, and resistance gene dynamics across domestication gradients, it establishes a foundation for future pan-GWAS analysis, functional genomics, and molecular breeding strategies aimed at improving resilience and productivity in this globally important crop.

Arecaceae↗

PubMed1977

Chromosomes 1 in 14 ovarian cancers. Heterochromatin variants and structural changes.

Structurally rearranged chromosomes 1 were found in 9 out of 14 ovarian carcinomas and may also have been present in three others. In the remaining two, pericentric inversions involving the heterochromatic regions of chromosomes 1 were seen, and were also identified in one of the chromosomes 1 in the patient's normal cells (lymphocytes). Altogether, heterochromatin variants (variation in size and/or the presence of a pericentric inversion) were seen in the tumour cells of eight cases, and one or both types of variation were identified in the normal cells of six of these. The possibility of an association between the presence of chromosome 1 heterochromatin variants as a constitutional anomaly, a liability to ovarian (and perhaps other forms of) cancer and structural changes involving the chromosomes 1 in the tumour cells is considered.

Adult↗

PubMed2005

Inter-individual variation in brain phenylalanine concentration in patients with PKU is not caused by genetic variation in the 4F2hc/LAT1 complex.

It remains a question why some patients with phenylketonuria (PKU) have high IQ and low brain phenylalanine (Phe) concentrations in spite of high blood Phe levels. One possible explanation for the low brain Phe concentrations in these patients would be a reduced transport of Phe across the blood-brain barrier. The 4F2hc/LAT1 complex has been suggested to be the most important molecular component responsible for this transport. To test the hypothesis that structural variant(s) in the genes encoding 4F2hc and LAT1 might result in a complex with reduced affinity for Phe, we have screened the two genes for sequence variants in a group of 13 PKU patients with a low ratio of brain to blood Phe concentrations. Several common sequence variants were identified, but none of these is predicted to affect the resulting protein product. Our data suggest that individual vulnerability to Phe in patients with PKU is not due to structural variants in the 4F2hc/LAT1 complex.

Adult↗

PubMed2003

Detection and consequences of recombinant protein isoforms: implications for biological potency.

Various types of structural variants have been observed in recombinant DNA - derived products. These isoforms include variations in post translational carbohydrate modifications where variations in site occupancy or unoccupied sites may occur. In addition, varying degrees of C-terminal processing and N-terminal substitutions have been observed. Isoforms may also be generated during processing and can include aggregated and/or chemically modified forms of the protein. Sophisticated analytical techniques exist for the identification and characterization of these structural variants. Several strategies have been used to isolate or enrich the isoform before molecular characterization. However, the effect these structural variations have on the biological activity of the product is less well understood. This may, in part, be due to the specificity and variability of the bioassay employed. This presentation describes the isolation and characterization of specific molecular isoforms for a monoclonal antibody product as well as an assessment of effects on biological activity.

Animals↗

PubMed2002

Structure of the core part of the lipopolysaccharides from Proteus penneri strains 7, 8, 14, 15, and 21.

The core-lipid A region of the lipopolysaccharides from Proteus penneri strains 7, 8, 14, 15, and 21 was studied using NMR spectroscopy, ESI MS, and chemical analysis after alkaline deacylation, deamination, and mild-acid hydrolysis of the lipopolysaccharides. The following general structure of the major core oligosaccharides is proposed: [abstract: see text] where all sugars are in the pyranose form and have the D configuration unless otherwise stated, Hep and DDHep=L-glycero- and D-glycero-D-manno-heptose, respectively, K=H, and Q=H in strain 8 or alpha-Glc in strains 7, 14, 15, and 21. In addition, several minor structural variants are present, including those lacking Ara4N in strains 7 and 15 and having the alpha-GlcN residue N-acylated to a various degree with glycine in strains 7, 8, 14, and 21. In strain 14, there are also core oligosaccharides with K=amide of beta-D-GalpA with putrescine, spermidine, or 4-azaheptane-1,7-diamine; remarkably, these structural variants lack either the PEtN group or the alpha-Hep-(1-->2)-alpha-DDHep disaccharide fragment at alpha-D-GalpA. While structural features of the inner core part are shared by Proteus strains studied earlier, the outermost Q-(1-->4)-alpha-GalNAc-(1-->2)-alpha-DDHep-(1-->6)-alpha-GlcN oligosaccharide unit has not been hitherto reported.

Carbohydrate Conformation↗

PubMed1993

Rapid identification of beta-globin structural mutations by sequencing the mRNA from peripheral blood reticulocytes.

A simple and rapid method for the molecular detection of beta-globin structural mutations is described using a reverse transcription-polymerase chain reaction of reticulocyte mRNA and direct sequencing of the product. The amplified segment (employing a sense primer 5'-ATTTGCTTCTGACACAACTGT-3', located at position + 1 with respect to the Cap site and an antisense primer 5'-TCCAGATGCTCAAGGCCCTTC-3', located at position + 1772 with respect to the Cap site) encompasses the cDNA sequence including the three globin exons. Employing this method we were able to characterize two hemoglobin structural variants: Hb S (beta 6 (A3) Glu-Val: GAG-GTG) and Hb Porto Alegre (beta 9 (A6) Ser-Cys: TCT-TGT). The approach described in this paper should be very useful to detect hemoglobin structural variants because the RNA extraction is simple, rapid and does not require cesium chloride, guanidinium and proteinase K. In addition, the direct sequencing of the RT-PCR product permits the screening of the entire globin genes with only two reactions.

Base Sequence↗

PubMed1990

Locus assignment of human alpha globin mutations by selective amplification and direct sequencing.

We describe a simple approach for molecular characterization and locus assignment of structural mutants by direct sequencing of enzymatically amplified DNA selective to alpha 1 and alpha 2 globin gene regions. Nucleotide substitution of two structural variants (Stanleyville II alpha 2(78Lys) and J Mexico alpha 2(54Glu) were determined and their encoding loci were specified. The amplified segment encompasses sequences upstream of the CAAT box to downstream of the Poly(A) addition signal. Hence all of the alpha globin structural variants and most of the nondeletion alpha thalassaemic mutants should be characterizable by this approach.

Africa↗

PubMed1967

Degradation of streptococcal cell wall antigens in vivo.

Specific chemical modification of group A polysaccharide antigen to the A-variant structure was demonstrated in the lymphoid organs of mice by autoradiography by use of radioantibodies specific for these structures. Both antigenic moieties persisted and were still discerned 10 weeks after injection of the group A cell wall. In rabbit skin, the group A specificity was altered after a prolonged period. Unlike the situation for the mouse, polysaccharide A was not converted to A-variant structure, but another specificity common to both polysaccharides persisted at the site of injection. Mucopeptide, separated from the polysaccharide of group A cell walls, was eliminated from the site of injection in rabbit skin between 4 and 8 hr after injection. Group D streptococcal cell walls were also rapidly eliminated from tissue, and were no longer detectable 8 hr after injection into rabbit skin or 24 hr after injection into mice. The rapid degradation of these structures was correlated with their susceptibility to lysozyme in vitro and was in contrast to the prolonged persistence of group A cell walls, which were completely resistant to egg white lysozyme. This persistence in tissue correlated with the capacity of group A cell wall fragments to induce a chronic inflammatory process, whereas the isolated mucopeptide or group D cell walls produced only an acute necrotoxic reaction.

Animals↗

PubMed2000

Diversity and phylogeny of gephyrin: tissue-specific splice variants, gene structure, and sequence similarities to molybdenum cofactor-synthesizing and cytoskeleton-associated proteins.

Gephyrin is essential for both the postsynaptic localization of inhibitory neurotransmitter receptors in the central nervous system and the biosynthesis of the molybdenum cofactor (Moco) in different peripheral organs. Several alternatively spliced gephyrin transcripts have been identified in rat brain that differ in their 5' coding regions. Here, we describe gephyrin splice variants that are differentially expressed in non-neuronal tissues and different regions of the adult mouse brain. Analysis of the murine gephyrin gene indicates a highly mosaic organization, with eight of its 29 exons corresponding to the alternatively spliced regions identified by cDNA sequencing. The N- and C-terminal domains of gephyrin encoded by exons 3-7 and 16-29, respectively, display sequence similarities to bacterial, invertebrate, and plant proteins involved in Moco biosynthesis, whereas the central exons 8, 13, and 14 encode motifs that may mediate oligomerization and tubulin binding. Our data are consistent with gephyrin having evolved from a Moco biosynthetic protein by insertion of protein interaction sequences.

Alternative Splicing↗

PubMed1993

Structural studies on the bacterial lyase-resistant tetrasaccharides derived from the antithrombin III-binding site of porcine intestinal heparin.

Three discrete tetrasaccharide structures which are resistant to Flavobacterium heparinase and heparitinases I and II were isolated from porcine intestinal heparin after exhaustive digestion with a mixture of all the above enzymes, and the tri-, tetra-, and penta-sulfated structures were determined by negative ion mode fast atom bombardment mass spectrometry and 500-MHz 1H NMR analysis as delta 4,5GlcA beta 1-4GlcNAc (6-sulfate)alpha 1-4GlcA beta 1-4GlcN(N,3-disulfate), delta 4,5 GlcA beta 1-4GlcNAc(6-sulfate)alpha 1-4GlcA beta 1-4GlcN (N,3,6-trisulfate), and delta 4,5GlcA beta 1-4GlcN (N,6-disulfate)alpha 1-4GlcA beta 1-4GlcN(N,3,6-trisulfate). The three components share the 3-O-sulfated reducing GlcN and the 6-O-sulfated internal GlcN, indicating that they are structural variants derived from the nonreducing portion of the minimal pentasaccharide sequence required for binding to antithrombin III. Isolation of the pentasulfated component has never been reported. Their unexpected resistance to heparitinases I and II indicates that 3-O-sulfation of the reducing GlcN contributes to the resistant nature of these tetrasaccharides to the enzymes. The present study demonstrates that the nonreducing trisaccharide portion of the structural variants of the antithrombin III-binding pentasaccharide sequence can be isolated in tetrasaccharides resistant to heparinase/heparitinases I and II, while the rest of the repeating region is degraded into disaccharide units. The lyase treatment is applicable to evaluation of heparin/heparan sulfate preparations in terms of the presence or absence of the specific structure containing the 3-O-sulfated GlcN representing biosynthetic precursors, intermediates or final products of the binding site.

Animals↗