Biology subjects

Becher, H.

Publications and source records attributed to Becher, H..

15 recordsLinked to original sources

bioRxiv2025

Chromosome Ageing Occurs at the Primordial Follicle Stage in both Mouse and Human Oocytes

Inherited aneuploidy is one of the most common causes of human genetic disease affecting approximately 20% of all human embryos and is the major cause of non-conception in older women. Inherited aneuploidies typically arise from meiotic chromosome segregation errors and are strongly affected by maternal age. Cohesin, a protein complex that mediates cohesion between sister chromatids, becomes depleted from oocyte chromosomes with age in mice, potentially contributing to the high rate of aneuploidy in older mouse oocytes. However, it remains unclear at which stage of oogenesis ageing affects chromatid cohesion in mice and whether ageing similarly affects cohesin in human oocytes. Here we use fluorescence in situ hybridisation to assess at which stages of oogenesis ageing alters chromatid separation in mice and in humans. We show that chromatid separation increases with age while oocytes remain dormant in primordial follicles in both mice and humans and that this effect of age on chromatid separation is detectable in fertile women of child-bearing age. Furthermore, we show that this age-dependent increase in chromatid separation is accompanied by age-dependent depletion of the acetylated SMC3-marked cohesive subpopulation of cohesin from oocytes at the dormant primordial follicle stage in both mice and humans. These data suggest that ageing impacts on oocyte chromosomes while they remain dormant in primordial follicles, and that this aspect of oocyte chromosome ageing is shared in both mice and humans. Improving our understanding of these pathways may allow strategies to slow or prevent this aspect of oocyte ageing to be developed.

developmental biology↗

bioRxiv2025

High quality genome assemblies of African cattle breeds using PacBio HiFi sequencing

Africa has a uniquely rich cattle diversity of [~]150 breeds comprising the Bos taurus indicus sub-species, Bos taurus taurus, and their crosses. These represent [~]23% of the global cattle population. However, high quality, representative assemblies are limited for African cattle and especially for indicine breeds. Here we built high quality de novo assemblies for five important African indigenous cattle breeds using PacBio HiFi sequencing: Lagune (Bos taurus taurus), Gudali, Iringa Red and Singida White (Bos taurus indicus), and Mpwapwa (Bos taurus taurus x Bos taurus indicus). These new assemblies are the most contiguous and complete African cattle assemblies produced so far, with genome sizes of 3.25 - 3.36Gb, contiguity N50s ranging from 83.59Mb to 97.87Mb and scaffold N50s from 100.30Mb to 113.37Mb. BUSCO genome completeness scores were also higher than 99.68%, indicative of highly contiguous assemblies. These improved and highly contiguous genome assemblies are consequently a valuable resource for future African and global livestock genomic studies.

genomics↗

bioRxiv2025

randPedPCA: Rapid approximation of principal components from large pedigrees

BackgroundPedigrees continue to be extremely important in agriculture and conservation genetics with the pedigrees of modern breeding programmes easily comprising millions of records. The structure of such pedigrees is challenging to visualise. Being directed acyclic graphs, pedigrees can be represented as matrices. Common choices are the numerator relationship matrix, A, and the adjacency matrix T. With these matrices, the structure of pedigrees can then, in principle, be visualised via principal component analysis (PCA). However, the naive PCA of matrices for large pedigrees is challenging due to computational and memory constraints. ResultsWe present the open-access R package randPedPCA for rapid pedigree PCA using sparse matrices and randomised linear algebra. Our rapid pedigree PCA builds on the fact that matrix-vector multiplications with the numerator relationship matrix can be carried out implicitly using the extremely sparse inverse Cholesky factor of the numerator relationship matrix. We demonstrate the utility of randPedPCA using several simulated datasets of pedigrees and SNPs. We then demonstrate the performance of randPedPCA by analysing the pedigree of the UK Labrador Retriever breeding population of almost 1.5 million individuals. ConclusionsThe structure of pedigrees can be efficiently and rapidly visualised using scatter plots of principal component scores. For large pedigrees, this is considerably faster than rendering plots of a pedigree graph.

genetics↗

bioRxiv2024

A model of Hill-Robertson interference caused by purifying selection in a non-recombining genome

A new approach to modeling the effects of Hill-Robertson interference on levels of adaptation and patterns of variability in a non-recombining genome or genomic region is described. The model assumes a set of L diallelic sites subject to reversible mutations between beneficial and deleterious alleles, with the same selection coefficient at each site. The assumption of reversibility allows the system to reach a stable statistical equilibrium with respect to the frequencies of deleterious mutations, in contrast to many previous models that assume irreversible mutations to deleterious alleles. The model is therefore appropriate for understanding the long-term properties of non-recombining genomes such as Y chromosomes, and is applicable to haploid genomes or to diploid genomes when there is intermediate dominance with respect to the effects of mutations on fitness. Approximations are derived for the equilibrium frequencies of deleterious mutations, the effective population size that controls the fixation probabilities of mutations at sites under selection, the nucleotide site diversity at neutral sites located within the non-recombining region, and the site frequency spectrum for segregating neutral variants. The approximations take into account the effects of linkage disequilibrium on the genetic variance at sites under selection. Comparisons with published and new computer simulation results show that the approximations are sufficiently accurate to be useful, and can provide insights into a wider range of parameter sets than is accessible by simulation. The relevance of the findings to data on non-recombining genome regions is discussed.

evolutionary biology↗

bioRxiv2024

Selection efficacy differs between lifestages in thehaploid-diploid Marchantia polymorpha subsp. ruderalis

Ploidy has profound effects on evolution. Perhaps the most compelling effect is related to dominance: In cells with more than one genome copy, the effects of non-dominant deleterious variants are masked to some extent, leading to a reduction in the efficacy of selection. This, in turn, leads to increased levels of nucleotide diversity, and it may also affect nucleotide substitution rates. To test this predicted association between ploidy and the efficacy of selection, we studied genome scale per-gene patterns of genetic diversity and divergence in the genome of the haploid-diploid bryophyte Marchantia. We treated lifestage gene expression bias as a continuous covariate and accounted for genomic autocorrelation patterns using smoothing splines in a general additive regression model (GAM) framework. Consistent with a lower efficacy of purifying selection, we found increased levels of sequence diversity, Wattersons{theta} , and net divergence at non-degenerate sites in genes with diploid-biased gene expression. These genes also showed reduced levels of codon usage bias. In addition, we found chromosome 5 to be an outlier with overall decreased levels of diversity, the site-frequency spectrum skewed towards common alleles, and increased linkage disequilibrium. In this study, we show the utility of generalized additive models in population genomics, and we present evidence for a ploidy associated difference in the efficacy of selection. We discuss parallels to the evolution of (diploid) sex chromosomes and why the patterns observed are unlikely to be mediated by masking.

evolutionary biology↗

bioRxiv2024

Nuclear RNA forms an interconnected network of transcription-dependent and tunable microgels

Living cells are organised through active, non-equilibrium processes, yet the physical principles governing their material states remain unclear. The cell nucleus has been described as either fluid-like or solid-like, but these behaviours have not been reconciled within a single framework. Here we show that nascent RNA and the multivalent RNA-binding protein SAF-A assemble into a nucleus-spanning microgel network maintained near the sol-gel transition. This active network exhibits scale- and time-dependent viscoelasticity and naturally reconciles solid-like and fluid-like responses. By integrating super-resolution imaging with mechanistic polymer modelling, we identify RNA production and degradation as control parameters that tune network connectivity. The model predicts enhanced susceptibility to modest perturbations near criticality, which we confirm experimentally by shifting the system between sol-like and gel-like regimes. Measurements of molecular transport, combined with simulations, reveal size-dependent diffusion and transient trapping within gel pores, establishing direct physical consequences of the near-critical state. Our results identify RNA metabolism as an energy-driven regulator of nuclear material properties and position the nucleus as a living example of an active microgel poised near criticality.

molecular biology↗

bioRxiv2023

Mutational scanning reveals oncogenic CTNNB1 mutations have diverse effects on signalling and clinical traits

CTNNB1, the gene encoding {beta}-catenin, is a frequent target for oncogenic mutations activating the canonical Wnt signalling pathway, typically via missense mutations within a degron hotspot motif in exon 3. Here, we combine saturation genome editing with a fluorescent reporter assay to quantify signalling phenotypes for all 342 missense mutations in the mutation hotspot, including 74 recurrent mutations reported in over 6000 tumours. Our data define the genetic requirements for {beta}-catenin degron function and reveal diverse levels of signal activation among known driver mutations. Tumorigenesis in different human tissues involves selection for CTNNB1 mutations spanning distinct ranges of effect size. In hepatocellular carcinoma, mutations that activate {beta}-catenin relatively weakly are associated with worse prognosis compared to stronger activating mutations, despite greater immune cell infiltration in the tumour microenvironment. Our work therefore provides a resource to understand mutational diversity within a pan-cancer mutation hotspot, with potential implications for targeted therapy.

cancer biology↗

bioRxiv2021

Measuring the invisible - The sequences causal of genome size differences in eyebrights (Euphrasia) revealed by k-mers

Genome size variation within plant (and other) taxa may be due to presence/absence variation in low-copy sequences or copy number variation in genomic repeats of various frequency classes. However, identifying the sequences underpinning genome size variation has been challenging because genome assemblies commonly contain collapsed representations of repetitive sequences and because genome skimming studies miss low-copy number sequences. Here, we take a novel approach based on k-mers, short sub-sequences of equal length k, generated from whole genome sequencing data of diploid eyebrights (Euphrasia), a group of plants which have considerable genome size variation within a ploidy level. We compare k-mer inventories within and between closely related species, and quantify the contribution of different copy number classes to genome size differences. We further assign high-copy number k-mers to specific repeat types as retrieved from the RepeatExplorer2 pipeline. We find complex patterns of k-mer differences between samples. While all copy number classes contributed to genome size variation, the largest contribution came from repeats with 1000-10,000 genomic copies including the 45S rDNA satellite DNA and, unexpectedly, a repeat associated with an Angela transposable element. We also find size differences in the low-copy number class, likely indicating differences in gene space between our samples. In this study, we demonstrate that it is possible to pinpoint the sequences causing genome size variation within species without use of a reference genome. Such sequences can serve as targets for future cytogenetic studies. We also show that studies of genome size variation should go beyond repeats and consider the whole genome. To allow future work with other taxonomic groups, we share our analysis pipeline, which is straightforward to run, relying largely on standard GNU command line tools.

evolutionary biology↗

bioRxiv2021

The nature of intraspecific genome size variation in taxonomically complex eyebrights

O_LIGenome size (GS) is a key trait related to morphology, life history, and evolvability. Although GS is, by definition, affected by presence/absence variants (PAVs), which are ubiquitous in population sequencing studies, GS is often treated as an intrinsic property of a species. Here, we studied intra- and interspecific GS variation in taxonomically complex British eyebrights (Euphrasia). C_LIO_LIWe generated GS data for 192 individuals of diploid and tetraploid Euphrasia and analysed GS variation in relation to ploidy, taxonomy, population affiliation, and geography. We further compared the genomic repeat content of 30 samples. C_LIO_LIWe found considerable genuine intraspecific GS variation, and observed isolation-by-distance for GS in outcrossing diploids. Tetraploid Euphrasia showed contrasting patterns, with GS increasing with latitude in outcrossing Euphrasia arctica, but little GS variation in the highly selfing Euphrasia micrantha. Interspecific differences in GS genomic repeat percentages were small. C_LIO_LIWe show the utility of treating GS as the outcome of polygenic variation. Like other types of genetic variation, such as single nucleotide polymorphisms, GS variation may be increased through hybridisation and population subdivision. In addition to selection on associated traits, GS is predicted to be affected indirectly by selection due to pleiotropy of the underlying PAVs. C_LI

evolutionary biology↗

bioRxiv2020

Molecular phylogenetics and micromorphology of Australasian Stipeae (Poaceae), and the interrelation of whole-genome duplication and evolutionary radiations in this grass tribe

The mainly Australian grass genus Austrostipa with ca. 64 species represents a remarkable example of an evolutionary radiation. To investigate aspects of diversification, macro- and micromorphological variation in this genus we conducted a molecular phylogenetic and scanning electron microscopy (SEM) analysis including representatives from all of its accepted subgenera. Plastid DNA variation within Austrostipa was low and only few lineages were resolved. Nuclear ITS and Acc1 yielded comparable groupings of taxa and resolved subgenera Arbuscula, Petaurista, Bambusina in a common clade and as monophyletic. In summary, we suggest recognizing nine subgenera in Austrostipa. Because of its taxonomic significance in Stipeae, we studied the lemma epidermal structure in 34 representatives of Austrostipa. In most species, the lemma epidermal pattern (LEP) was relatively uniform (maize-like LEP), but in six species it was more similar to that of Stipa s.str., Neotrinia, Ptilagrostis and Orthoraphium. The species representing subgenera Lobatae, Petaurista, Bambusina and A. muelleri from subg. Tuberculatae were well-separated from all the other species included in the analysis. Two different sequence copies of Acc1 were found in polyploid Austrostipa and Anemanthele. Each of the copy types formed a single clade. This was also true of the sampled species of Stipa s.str., but their clades were strongly separated from those of Austrostipa and Anemanthele. This underlines the statement of Tzvelev (1977) that most if not all contemporary Stipeae are of hybrid origin and demonstrates it for the first time unambiguously on the molecular level. Chromosome number variation is surveyed and reviewed for the whole tribe Stipeae and interpreted in a molecular phylogenetic framework. The rather coherent picture of chromosome number variation underlines the phylogenetic and evolutionary significance of this character. The closest extant relatives of Austrostipa and Anemanthele are in the clade of Achnatherum s.str., Celtica, Oloptum and Stipellula. These genera are most abundant in Central and Eastern Asia, which makes a colonization of Australian and New Zealand from this region more likely, perhaps via long-distance dispersal, than colonization of Australia from southern South America via Antarctica as previously invoked. Supporting Information may be found online in the Supporting Information section at the end of the article.

plant biology↗

bioRxiv2020

Maintenance of species differences in closely related tetraploid parasitic Euphrasia (Orobanchaceae) on an isolated island

Polyploidy is pervasive in angiosperm evolution and plays important roles in adaptation and speciation. However, polyploid groups are understudied due to complex sequence homology, challenging genome assembly, and taxonomic complexity. Here we study adaptive divergence in taxonomically complex eyebrights (Euphrasia), where recent divergence, phenotypic plasticity and hybridisation blur species boundaries. We focus on three closely-related tetraploid species with contrasting ecological preferences, and which are sympatric on Fair Isle, a small isolated island in the British Isles. Using a common garden experiment, we show a genetic component to the morphological differences present between these species. Using whole genome sequencing and a novel k-mer approach, we demonstrate an allopolyploid origin, with sub-genome divergence of approximately 5%. Using ~2 million SNPs we show sub-genome homology across species consistent with a common origin, with very low sequence divergence characteristic of recent speciation. This genetic variation is broadly structured by species, with clear divergence of Fair Isle heathland E. micrantha, while grassland E. arctica and coastal E. foulaensis are more closely related. Overall, we show tetraploid Euphrasia is an allopolyploid system characterised by postglacial species divergence, where adaptation to novel environments may be conferred by old variants rearranged into new genetic lineages.

evolutionary biology↗

bioRxiv2019

Genome-wide association study identifies 32 novel breast cancer susceptibility loci from overall and subtype-specific analyses

Breast cancer susceptibility variants frequently show heterogeneity in associations by tumor subtype. To identify novel loci, we performed a genome-wide association study (GWAS) including 133,384 breast cancer cases and 113,789 controls, plus 18,908 BRCA1 mutation carriers (9,414 with breast cancer) of European ancestry, using both standard and novel methodologies that account for underlying tumor heterogeneity by estrogen receptor (ER), progesterone receptor (PR), and human epidermal growth factor receptor 2 (HER2) status and tumor grade. We identified 32 novel susceptibility loci (P<5.0x10-8), 15 of which showed evidence for associations with at least one tumor feature (false discovery rate <0.05). Five loci showed associations (P<0.05) in opposite directions between luminal- and non-luminal subtypes. In-silico analyses showed these five loci contained cell-specific enhancers that differed between normal luminal and basal mammary cells. The genetic correlations between five intrinsic-like subtypes ranged from 0.35 to 0.80. The proportion of genome-wide chip heritability explained by all known susceptibility loci was 37.6% for triple-negative and 54.2% for luminal A-like disease. These findings provide an improved understanding of genetic predisposition to breast cancer subtypes and will inform the development of subtype-specific polygenic risk scores.

genetics↗

bioRxiv2019

Mitochondrial sequences or Numts - By-catch differs between sequencing methods

Nuclear inserts derived from mitochondrial DNA (Numts) encode valuable information. Being mostly non-functional, and accumulating mutations more slowly than mitochondrial sequence, they act like molecular fossils - they preserve information on the ancestral sequences of the mitochondrial DNA. In addition, changes to the Numt sequence since their insertion into the nuclear genome carry information about the nuclear phylogeny. These attributes cannot be reliably exploited if Numt sequence is confused with the mitochondrial genome (mtDNA). The analysis of mtDNA would be similarly compromised by any confusion, for example producing misleading results in DNA barcoding that used mtDNA sequence. We propose a method to distinguish Numts from mtDNA, without the need for comprehensive assembly of the nuclear genome or the physical separation of organelles and nuclei. It exploits the different biases of long and short-read sequencing. We find that short-read data yield mainly mtDNA sequences, whereas long-read sequencing strongly enriches for Numt sequences. We demonstrate the method using genome-skimming (coverage < 1x) data obtained on Illumina short-read and PacBio long-read technology from DNA extracted from six grasshopper individuals. The mitochondrial genome sequences were assembled from the short-read data despite the presence of Numts. The PacBio data contained a much higher proportion of Numt reads (over 16-fold), making us caution against the use of long-read methods for studies using mitochondrial loci. We obtained two estimates of the genomic proportion of Numts. Finally, we introduce \"tangle plots\", a way of visualising Numt structural rearrangements and comparing them between samples.

evolutionary biology↗

bioRxiv2019

Patterns of genetic variability in genomic regions with low rates of recombination

Surveys of DNA sequence variation have shown that the level of genetic variability in a genomic region is often strongly positively correlated with its rate of crossing over (CO) [1-3]. This pattern is caused by selection acting on linked sites, which reduces genetic variability and can also cause the frequency distribution of segregating variants to contain more rare variants than expected without selection (skew). These effects of selection may involve the spread of beneficial mutations (selective sweeps, SSWs), the elimination of deleterious mutations (background selection, BGS) or both together, and are expected to be stronger with lower rates of crossing over [1-3]. However, in a recent study of human populations, the skew was reduced in the lowest CO regions compared with regions with somewhat higher CO rates [4]. A similar pattern is seen in the population genomic studies of Drosophila simulans described here. We propose an explanation for this paradoxical observation, and validate it using computer simulations. This explanation is based on the finding that partially recessive, linked deleterious mutations can increase rather than reduce neutral variability when the product of the effective population size (Ne) and the selection coefficient against homozygous carriers of mutations (s) is [≤] 1, i.e. there is associative overdominance (AOD) rather than BGS [5]. We show that AOD can operate in a genomic region with a low rate of CO, opening up a new perspective on how selection affects patterns of variability at linked sites.

evolutionary biology↗

bioRxiv2019

Common breast cancer risk loci predispose to distinct tumor subtypes

BackgroundGenome-wide association studies (GWAS) have identified multiple common breast cancer susceptibility variants. Many of these variants have differential associations by estrogen receptor (ER), but how these variants relate with other tumor features and intrinsic molecular subtypes is unclear. MethodsAmong 106,571 invasive breast cancer cases and 95,762 controls of European ancestry with data on 173 breast cancer variants identified in previous GWAS, we used novel two-stage polytomous logistic regression models to evaluate variants in relation to multiple tumor features (ER, progesterone receptor (PR), human epidermal growth factor receptor 2 (HER2) and grade) adjusting for each other, and to intrinsic-like subtypes. ResultsEighty-five of 173 variants were associated with at least one tumor feature (false discovery rate <5%), most commonly ER and grade, followed by PR and HER2. Models for intrinsic-like subtypes found nearly all of these variants (83 of 85) associated at P<0.05 with risk for at least one luminal-like subtype, and approximately half (41 of 85) of the variants were associated with risk of at least one non-luminal subtype, including 32 variants associated with triple-negative (TN) disease. Ten variants were associated with risk of all subtypes in different magnitude. Five variants were associated with risk of luminal A-like and TN subtypes in opposite directions. ConclusionThis report demonstrates a high level of complexity in the etiology heterogeneity of breast cancer susceptibility variants and can inform investigations of subtype-specific risk prediction.

genetics↗