Biology subjects

Mangelson, H.

Publications and source records attributed to Mangelson, H..

12 recordsLinked to original sources

bioRxiv2026

A chromosome-level assembly of the Fusarium oxysporum biocontrol strain FO12

Fusarium oxysporum FO12 was originally isolated from cork oak (Quercus suber L.) and has been characterised as a highly effective biological control agent of wilt diseases on different crops. FO12 endophytically colonises roots and basal stems of plants, reducing the establishment of the soil-borne pathogen Verticillium dahliae and triggering plant defence-related genes. Here, we report a chromosome-level genome assembly of FO12 using Nanopore and Hi-C data. The 57.60 Mb assembly comprises 14 chromosome-scale scaffolds with centromeres resolved and telomeric repeats detected at 4 of 28 chromosome ends. This high-quality reference genome provides a valuable resource for further research into the use of FO12 in agriculture as a biocontrol agent.

genomics↗

bioRxiv2026

Haplotype-phased genomes of the barley leaf rust pathogen reveal evidence of repeat element expansion and somatic hybridization

Barley leaf rust disease, caused by Puccinia hordei, leads to substantial yield losses and diminished malting quality of barley across temperate growing regions worldwide. To address the paucity of high-resolution genomic resources for this pathogen, we generated haplotype-phased, chromosome-scale assemblies for ten globally distributed isolates using PacBio HiFi and Hi-C sequencing. Phylogenomic analysis revealed seven distinct lineages of P. hordei, including evidence of nuclear exchange, with a shared nuclear haplotype detected between two US lineages. Nuclear genome sizes ranged from [~]140-147Mbp, with the exception of isolate 90ISR03 from Israel ([~]163Mbp), which also harbored a 6.2Mbp supernumerary scaffold in one nucleus exhibiting chromosomal characteristics. Consistent with its larger genome, P. hordei had a higher repeat content ([~]70%) than related cereal rust fungi, driven primarily by the proliferation of LTR retroelements and DNA transposons. Across the global pan-genome of 13 unique nuclear haplotypes, approximately one-third of all protein orthogroups were conserved across all isolates. Only 18% of predicted effector orthogroups were shared between all haplotypes, reflecting the highly dynamic and variable nature of the effector repertoire. The long-term propagation of clonal P. hordei lineages is apparent both within the US and globally, and nuclear exchange is important for generating novel diversity and virulence profiles. The high degree of genome plasticity is evident in extensive structural variation, including large-scale translocations and inversions as well as a putative accessory chromosome. These chromosome-level, haplotype-resolved genomes provide a foundational resource for exploring the evolution, diversity, and avirulence gene repertoire of P. hordei.

genomics↗

bioRxiv2024

Comparative genomics of the sexually transmitted parasite Trichomonas vaginalis reveals relaxed and convergent evolution and genes involved in spillover from birds to humans

Trichomonas vaginalis is the causative agent of the venereal disease trichomoniasis which infects men and women globally and is associated with serious outcomes during pregnancy and cancers of the human reproductive tract. Trichomonads parasitize a range of hosts in addition to humans including birds, livestock, and domesticated animals. Recent genetic analysis of trichomonads recovered from columbid birds has provided evidence that these parasite species undergo frequent host-switching, and that a current epoch spillover event from columbids likely gave rise to T. vaginalis in humans. We undertook a comparative evolutionary genomics study of seven trichomonad species, generating chromosome-scale reference genomes for T. vaginalis and its avian sister species Trichomonas stableri, and assemblies of five other species that infect birds and mammals. Human-infecting trichomonad lineages have undergone recent and convergent genome size expansions compared to their avian sister species, and the major contributor to their increased genome size is increased repeat expansions, especially multicopy gene families and transposable elements, with genetic drift likely a driver due to relaxed selection. Trichomonads have independently host-switched twice from birds to humans, and genes implicated in the transition to the human host include those associated with host tissue adherence and phagocytosis, extracellular vesicles, and CAZyme virulence factors.

microbiology↗

bioRxiv2024

Proxi-RIMS-seq2 applied to native microbiomes uncovers hundreds of known and novel m5C methyltransferase specificities.

Methylation patterns in bacteria can be used to study Restriction-Modification (RM) or other defense systems with novel properties. While m4C and m6A methylation is well characterized mainly through PacBio sequencing, the landscape of m5C methylation is under-characterized. To bridge this gap, we performed RIMS-seq2 on microbiomes composed of resolved assemblies of distinct genomes through proximity ligation. This high-throughput approach enables the identification of m5C methylated motifs and links them to cognate methyltransferases directly on native microbiomes without the need to isolate bacterial strains. Methylation patterns can also be identified on viral DNA and compared to host DNA, strengthening evidence for virus-host interaction. Applied to three different microbiomes, the method unveils over 1900 motifs that were deposited in REBASE. The motifs include a novel 8-base recognition site (CATm5CGATG) that was experimentally validated by characterizing its cognate methyltransferase. Our findings suggest that microbiomes harbor arrays of untapped m5C methyltransferase specificities, providing insights to bacterial biology and biotechnological applications.

genomics↗

bioRxiv2024

Highly accurate metagenome-assembled genomes from human gut microbiota using long-read assembly, binning, and consolidation methods

Long-read metagenomic sequencing is a powerful approach for cataloging the microbial diversity present in complex microbiomes, including the human gut microbiome. We performed a deep-sequencing experiment using PacBio HiFi reads to obtain metagenome-assembled genomes (MAGs) from a pooled human gut microbiome. We performed long-read metagenome assembly using two methods (hifiasm-meta, metMDBG), used improved bioinformatic and proximity ligation binning strategies to cluster contigs and identify MAGs, and developed a novel framework to compare and consolidate MAGs (pb-MAG-mirror). We found proximity ligation binning yielded more MAGs than bioinformatic binning, but our novel comparison framework resulted in higher MAG yields than either binning strategy individually. In total, from 255 Gbp of total HiFi data we produced 595 total MAGs (including 175 high-quality MAGs) using hifiasm-meta, and 547 total MAGs (including 277 high-quality MAGs) with metaMDBG. Hifiasm-meta assembled almost twice as many strain-level MAGs as metaMDBG (246 vs. 156), but both assembly methods produced up to five strains for a species. Approximately 85% of the MAGs were assigned to known species, but we recovered >35 high-quality MAGs that represent uncultured diversity. Based on strict similarity scores, we found 125 MAGs were unequivocally shared across the assembly methods at the strain level, representing [~]22% of the total MAGs recovered per method. Finally, we detected more total viral sequences in the metaMDBG assembly versus the hifiasm-meta assembly ([~]6,700 vs. [~]4,500). Overall, we find the use of HiFi sequencing, improved metagenome assembly methods, and complementary binning strategies is highly effective for rapidly cataloging microbial genomes in complex microbiomes.

microbiology↗

bioRxiv2023

Patterns of genomic variation reveal a single evolutionary origin of the wild allotetraploid Mimulus sookensis

Polyploidy occurs across the tree of life and is especially common in plants. Because newly formed cytotypes are often incompatible with their progenitors, polyploidy is also said to trigger "instantaneous" speciation. If a polyploid can self-fertilize or reproduce asexually, it is even possible for one individual to produce an entirely new lineage. How often this extreme scenario occurs is unclear, with most studies of wild polyploids reporting multiple origins. Here, we explore the evolutionary history of the wild allotetraploid Mimulus sookensis, which was formed through hybridization between self-compatible, diploid species in the Mimulus guttatus complex. We generate a chromosome-scale reference assembly for M. sookensis and define its distinct subgenomes. Despite previous reports suggesting multiple origins of this highly selfing polyploid, we discover patterns of population genomic variation that provide unambiguous support for a single origin, which we estimate occurred [~]71,000 years ago. One M. sookensis subgenome is clearly derived from the selfer M. nasutus, which, based on organellar variation, also appears to be the maternal progenitor. The ancestor of the other subgenome is less certain, but it shares variation with both M. decorus and M. guttatus, two outcrossing diploids that overlap broadly with M. sookensis. Whatever its precise ancestry, this study establishes M. sookensis as an example of instantaneous speciation, likely facilitated by the polyploids predisposition to self-fertilize. With a reference genome for M. sookensis now available and its origin clarified, this wild tetraploid is poised to become a model for understanding the genetic and evolutionary mechanisms of polyploid persistence.

evolutionary biology↗

bioRxiv2023

A reference assembly for the legume cover crop, hairy vetch (Vicia villosa)

Vicia villosa is an incompletely domesticated annual legume of the Fabaceae family native to Europe and Western Asia. V. villosa is widely used as a cover crop and as a forage due to its ability to withstand harsh winters. A reference-quality genome assembly (Vvill1.0) was prepared from low error rate long sequence reads to improve genetic-based trait selection of this species. The Vvill1.0 assembly includes seven scaffolds corresponding to the seven estimated linkage groups and comprising approximately 68% of the total genome size of 2.03 gigabase pairs (Gbp). This assembly is expected to be a useful resource for genetic improvement of this emerging cover crop species as well as to provide useful insights into plant genome evolution.

genomics↗

bioRxiv2022

A chromosome-level genome resource for studying virulence mechanisms and evolution of the coffee rust pathogen Hemileia vastatrix

Recurrent epidemics of coffee leaf rust, caused by the fungal pathogen Hemileia vastatrix, have constrained the sustainable production of Arabica coffee for over 150 years. The ability of H. vastatrix to overcome resistance in coffee cultivars and evolve new races is inexplicable for a -pathogen that supposedly only utilizes clonal reproduction. Understanding the evolutionary complexity between H. vastatrix and its only known host, including determining how the pathogen evolves virulence so rapidly is crucial for disease management. Achieving such goals relies on the availability of a comprehensive and high-quality genome reference assembly. To date, two reference genomes have been assembled and published for H. vastatrix that, while useful, remain fragmented and do not represent chromosomal scaffolds. Here, we present a complete scaffolded pseudochromosome-level genome resource for H. vastatrix strain 178a (Hv178a). Our initial assembly revealed an unusually high degree of gene duplication (over 50% BUSCO basidiomycota_odb10 genes). Upon inspection, this was predominantly due to a single scaffold that itself showed 91.9% BUSCO Completeness. Taxonomic analysis of predicted BUSCO genes placed this scaffold in Exobasidiomycetes and suggests it is a distinct genome, which we have named Hv178a associated fungal genome (Hv178a AFG). The high depth of coverage and close association with Hv178a raises the prospect of symbiosis, although we cannot completely rule out contamination at this time. The main Ca. 546 Mbp Hv178a genome was primarily (97.7%) localised to 11 pseudochromosomes (51.5 Mb N50), building the foundation for future advanced studies of genome structure and organization.

genomics↗

bioRxiv2021

Differential Expression of α,β, and γ Protocadherin Isoforms During Differentiation, Aging, and Cancer

The cadherin family of cell surface glycoproteins plays a fundamental role in cell-cell recognition, thereby participating in diverse biological process such as embryonic morphogenesis and oncogenic transformation. The subset of clustered protocadherin (PCDH) genes generated from the , {beta}, and {gamma} loci, have been widely studied for their potential role in neuronal cell-cell recognition and neurogenesis, however their broader role in normal embryonic development and cancer has not been examined in detail. We utilized human embryonic stem (hES) cells to model early human development in vitro, comparing PCDH isoform transcription in diverse types of embryonic progenitors with normal adult-derived and cancer counterparts. Embryonic progenitors express genes from the and {beta} cluster at levels comparable to that seen in the CNS, while fetal and adult-derived cells express primarily from the {gamma} cluster. Replicative senescence left fibroblasts with markedly lower expression of all isoforms. We observe that an embryonic pattern of clustered protocadherin gene expression and associated CpG island methylation is commonly associated with cancer cell lines from diverse tissue types. The differential regulation of the , {beta}, and {gamma} loci coincide with alternate regions of DNA accessibility at CTCF binding sites and lamina-associated domains and CPL expression correlated with the expression of LMNA and LMNB1. These observations support a potential role for the differential regulation of genes within the clustered protocadherin locus in selective cell-cell adhesion during embryogenesis, regeneration, cancer and aging.

developmental biology↗

bioRxiv2020

Hi-C deconvolution of a textile-dye degrader microbiome reveals novel taxonomic landscapes and link phenotypic potential to individual genomes

Microbial biodiversity is represented by genomic landscapes populating dissimilar environments on earth. These genomic landscapes usually contain microbial functional signatures connected with the community phenotypes. Here we assess the genomic microbiodiversity landscape of a river associated microbiome enriched with 200 mg.mL-1 of anthraquinone Deep-Blue 35 (); we subjected to nutritional selection a composite sample from four different sites from a local river basin (Morelos, Mexico). This paper explores the resultant textile-dye microbiome, and infer links between predicted biodegradative functions and the individual genome fractions. By using a proximity-ligation deconvolution method, we deconvoluted 97 genome composites, with 80% of this been potentially novel species associated with the textile-dye environment. The main determinants of taxonomic composition were the genera Methanobacterium, Clostridium, and Cupriavidus constituting 50, 22, and 11 % of the total population profile respectively; also we observe an extended distribution of novel taxa without clear taxonomic standing. Removal of 50% chemical oxygen demand (COD) with 23% decolorization was observed after 30 days after dye enrichment. By metagenome wide analysis we postulate that sequence elements related to catalase-peroxidase, polyphenol oxidase, and laccase enzymes may be causally associated with the textile-dye degradation phenotype under our study conditions. This study prompts rapid genomic screening in order to select statistically represented functional features, reducing costs, and experimental efforts. As well as predicting phenotypes within complex communities under environmental pressures.

microbiology↗

bioRxiv2020

Advancing pre-clinical species genetic utility through a high-quality assembly of the cynomolgus monkey (Macaca fascicularis) genome

The cynomolgus macaque is a non-human primate model, heavily used in biomedical research, but with outdated genomic resources. Here we have used the latest long-read sequencing technologies in order to assemble a fully phased, chromosome-level assembly for the cynomolgus macaque. We have built a hybrid assembly with PacBio, 10x Genomics, and HiC technologies, resulting in a diploid assembly that spans a length of 5.1 Gb with a total of 16,741 contigs (N50 of 0.86Mb) contained in 370 scaffolds (N50 of 138 Mb) positioned on 42 chromosomes (21 homologous pairs). This assembly is highly homologous to former assemblies and identifies novel inversions and provides higher confidence in the genetic architecture of the cynomolgus macaque genome. A demographic estimation is also able to capture the recent genetic bottleneck in the Mauritius population, from which the sequenced individual originates. We offer this resource as an enablement for genetic tools to be built around this important model for biomedical research.

genomics↗

bioRxiv2019

The Genome of the Zebra Mussel, Dreissena polymorpha: A Resource for Invasive Species Research

The zebra mussel, Dreissena polymorpha, continues to spread from its native range in Eurasia to Europe and North America, causing billions of dollars in damage and dramatically altering invaded aquatic ecosystems. Despite these impacts, there are few genomic resources for Dreissena or related bivalves, with nearly 450 million years of divergence between zebra mussels and its closest sequenced relative. Although the D. polymorpha genome is highly repetitive, we have used a combination of long-read sequencing and Hi-C-based scaffolding to generate the highest quality molluscan assembly to date. Through comparative analysis and transcriptomics experiments we have gained insights into processes that likely control the invasive success of zebra mussels, including shell formation, synthesis of byssal threads, and thermal tolerance. We identified multiple intact Steamer-Like Elements, a retrotransposon that has been linked to transmissible cancer in marine clams. We also found that D. polymorpha have an unusual 67 kb mitochondrial genome containing numerous tandem repeats, making it the largest observed in Eumetazoa. Together these findings create a rich resource for invasive species research and control efforts.

genomics↗