Biology subjects

Glanzmann, B.

Publications and source records attributed to Glanzmann, B..

5 recordsLinked to original sources

bioRxiv2026

Benchmarking sequence performance on the DNBSEQ-T7 using Genome in a Bottle reference genomes

Advances in sequencing technologies have improved the accuracy, throughput, and completeness of human genome characterization, enabling more reliable detection of genetic variation. Well-characterized reference genomes are critical for benchmarking sequencing platforms and bioinformatics analysis pipelines. Here, we present whole genome sequencing datasets generated for the Ashkenazi Jewish trio reference samples from the Genome in a Bottle Consortium. Libraries were prepared using three distinct MGI-based workflows: PCR-free library preparation, FastFS DNA library preparation, and Universal DNA library preparation. Sequencing was performed on the MGI DNBSEQ-T7 platform, generating a minimum of 400 million paired-end reads per sample, corresponding to 30X mean genome coverage. Raw reads were processed using a standardized GATK bioinformatics workflow. Sequencing performance and variant detection accuracy were evaluated using the Genome in a Bottle high-confidence benchmark variant sets. All workflows demonstrated high sequencing quality and concordance with GIAB benchmark truth sets, with PCR-free libraries showing the strongest indel calling performance and lowest Mendelian violation rates across the Ashkenazi trio. This dataset provides a resource for benchmarking DNBSEQ-T7 sequencing and bioinformatics workflows, and for evaluating the impact of library preparation strategies on whole genome variant detection performance.

bioinformatics↗

bioRxiv2026

Chromosome-level genome assembly of Helichrysum odoratissimum, a medicinal plant from Southern Africa

Helichrysum odoratissimum, a plant species native to Southern Africa, holds deep cultural significance and is widely used in traditional medicine. It is valued for its antimicrobial and anti-inflammatory properties and is cultivated and traded in South Africa due to its growing commercial relevance to the pharmaceutical and cosmetic industries. Despite its ecological and economic importance, genomic resources for this species remain limited. Here, we report a high-quality chromosome-level genome assembly for H. odoratissimum to facilitate investigations into its genetic basis of bioactivity, environmental adaptation, and taxonomic relationships. High-molecular-weight DNA extracted from leaf tissue was sequenced using Oxford Nanopore Technologies (ONT) long-read sequencing, and Hi-C proximity ligation data were generated to enable chromosome-scale scaffolding. The final assembly spans 2.4 Gb, with a scaffold N50 of 354 Mb, and was anchored and oriented into seven chromosomes, with 2,935 smaller scaffolds remaining unplaced. Assembly quality and completeness were evaluated using QUAST and BUSCO, and chromosomal structure was validated using Hi-C contact maps. This genome provides a foundational resource for functional genomics, conservation planning, molecular breeding, and the discovery of bioactive compounds underpinning the medicinal and commercial value of H. odoratissimum.

genomics↗

bioRxiv2023

A highly divergent mitochondrial genome in extant Cape buffalo from Addo Elephant National Park, South Africa

The reduced cost of next-generation sequencing (NGS) has allowed researchers to generate nuclear and mitochondrial genome data to gain deeper insights into the phylogeography, evolutionary history, and biology of non-model species. While the Cape buffalo (Syncerus caffer caffer) has been well-studied across its range with traditional genetic markers over the last 25 years, researchers are building on this knowledge by generating whole genome, population-level data sets to improve understanding of the genetic composition and evolutionary history of the species. Using publicly available NGS data, we assembled 40 Cape buffalo mitochondrial genomes (mitogenomes) from four protected areas in South Africa, expanding the geographical range and almost doubling the number of mitogenomes available for this species. Coverage of the mitogenomes ranged from 154-1,036X. Haplotype and nucleotide diversity for Kruger National Park (n = 15) and Mokala National Park (n = 5) were similar to diversity levels in southern and eastern Africa. Hluhluwe-iMfolozi Park (n = 15) had low levels of genetic diversity, with only four haplotypes detected, reflecting its past bottleneck. Addo Elephant National Park (n = 5) had the highest nucleotide diversity of all populations across Africa, which was unexpected, as it is known from previous studies to have low nuclear diversity. This diversity was driven by a highly divergent mitogenome from one sample, which was subsequently identified in another sample via Sanger sequencing of the cytochrome b gene. Using a fossil-calibrated phylogenetic analysis, we estimated that this lineage diverged from all other Cape buffalo lineages approximately 2.51 million years ago. We discuss several potential sources of this mitogenome but propose that it most likely originated through introgressive hybridisation with an extinct buffalo species, either S. acoelotus or S. antiquus. We conclude by discussing the conservation consequences of this finding for the Addo Elephant National Park population, proposing careful genetic management to prevent inbreeding depression while maintaining this highly unique diversity.

genetics↗

bioRxiv2021

Establishment of a Patient-Derived, Magnetic Levitation-Based, 3D Spheroid Granuloma Model for Human Tuberculosis.

Tuberculous granulomas that develop in response to Mycobacterium tuberculosis (M.tb) infection are highly dynamic entities shaped by the host immune response and disease kinetics. Within this microenvironment, immune cell recruitment, polarization and activation is driven not only by co-existing cell types and multi-cellular interactions, but also by M.tb-mediated changes involving metabolic heterogeneity, epigenetic reprogramming and rewiring of the transcriptional landscape of host cells. There is an increased appreciation of the in vivo complexity, versatility and heterogeneity of the cellular compartment that constitutes the tuberculosis (TB) granuloma, and the difficulty in translating findings from animal models to human disease. Here we describe a novel biomimetic in vitro 3-dimentional (3D) human lung granuloma model, resembling early "innate" and "adaptive" stages of the TB granuloma spectrum, and present results of histological architecture, host transcriptional characterization, mycobacteriological features, cytokine profiles and spatial distribution of key immune cells. A range of manipulations of immune cell populations in these granulomas will allow the study of host/pathogen pathways involved in the outcome of infection, as well as pharmacological interventions. IMPORTANCETuberculosis is a highly infectious disease, with granulomas as its hallmark. Granulomas play an important role in the control of M.tb infection and as such are crucial indicators for our understanding of host resistance to TB. Correlates of risk and protection to M.tb are still elusive, and the granuloma provides the perfect environment in which to study the immune response to infection and broaden our understanding thereof; however, human granulomas are difficult to obtain, and animal models are costly and do not always faithfully mimic human immunity. In fact, most TB research is conducted in vitro on immortalized or primary immune cells and cultured in 2D on flat, rigid plastic, which does not reflect in vivo characteristics. We have therefore conceived a 3D, human in vitro granuloma model which allows researchers to study features of granuloma-forming diseases, in an 3D structural environment resembling in vivo granuloma architecture and cellular orientation.

immunology↗

bioRxiv2020

Human Whole Genome Sequencing in South Africa

The advent and evolution of next generation sequencing has considerably impacted genomic research. Until recently, South African researchers were unable to access affordable platforms capable of human whole genome sequencing locally and DNA samples had to be exported. Here we report the whole genome sequences of the first six human DNA samples sequenced and analysed at the South African Medical Research Council Genomics Centre. We demonstrate that the data obtained is of high quality, with an average sequencing depth of 36.41, and that the output is comparable to data generated internationally on a similar platform. The Genomics Centre creates an environment where African researchers are able to access world class facilities, increasing local capacity to sequence whole genomes as well as store and analyse the data.Competing Interest StatementThe authors have declared no competing interest.View Full Text

genomics↗