Biology subjects

John, E.

Publications and source records attributed to John, E..

14 recordsLinked to original sources

bioRxiv2026

Once in a blue moon: an unexpected evolutionary route to blue floral pigmentation in orchids

Blue flowers are rare in the hyperdiverse orchid family, and the genetic mechanisms enabling their blue delphinidin-based pigmentation remain poorly understood. Within the Australian orchid subtribe Caladeniinae (~350 spp.), repeated transitions from maroon to blue flowers, followed by reversions to maroon, provide a unique opportunity to investigate blue flower evolution. Using phylotranscriptomics, anthocyanin profiling, molecular evolutionary analyses, and gene expression data from 51 species, we reconstructed the genetic changes associated with these transitions. Despite its near-universal role in delphinidin biosynthesis across flowering plants, unexpectedly, we found no evidence for a functional CYP75A-mediated flavonoid 3'5'-hydroxylase (F3'5'H) pathway. Instead, blue-flowered species possess a duplicated CYP75B lineage gene (CYP75B-D) with apparent 5'-hydroxylase activity, a derived D-type dihydroflavonol reductase (DFR), and a distinct anthocyanin biosynthetic pathway co-expression pattern. Phylogenetic analyses suggest that the D-type DFR pre-dated blue flower evolution, representing a permissive evolutionary shift later coupled with the evolution of CYP75B-D. Notably, blue flower evolution coincided with repeated pollinator transitions and major palaeoenvironmental change during the Middle Miocene. Together, these findings reveal an unexpected route to blue floral pigmentation and suggest that its evolution arose through the interaction of molecular innovation, regulatory evolution, and ecological opportunity.

evolutionary biology↗

bioRxiv2026

Major effector loss reveals compensatory pathogenicity networks in a necrotrophic wheat pathogen

Necrotrophic effectors (NEs) are key determinants of virulence in the necrotrophic fungal pathogen Parastagonospora nodorum that causes septoria nodorum blotch of wheat. However, targeted removal of three important NEs SnToxA, SnTox1, and SnTox3 in the mutant{Delta} toxa13 previously revealed a redundancy mechanism is triggered, whereby pathogenicity on wheat is maintained. In this study, we investigated the gene regulatory profile underpinning this phenomenon and discover that virulence is not dependent on a fixed set of dominant effectors but instead arises from a flexible, epistatic compensatory network. Although host transcriptional responses to the P. nodorum wildtype SN15 and{Delta} toxa13 infection remained largely conserved, consistent with an overlapping disease-susceptibility pathway, a significant upregulation of candidate effector genes was observed in{Delta} toxa13. This included the recently characterised NE SnTox267, and several other candidate effectors able to induce necrosis in the non-host Nicotiana benthamiana, each carrying a predicted structural fold conserved across other pathogens. We therefore provide further direct evidence that virulence is maintained in P. nodorum lacking three NEs by an epistatic and compensatory effector network, underpinned by changes in pathogen gene expression. Targeting conserved effector-mediated virulence mechanisms rather than individual host-specific gene-for-gene interactions may provide a more tractable route to host resistance.

molecular biology↗

bioRxiv2026

Development and assessment of tailored illustrations to enhance community understandings of genetics topics

ObjectivesEffective communication about genetics concepts is essential for collaborative anthropological genetics research. However, communication can be challenging because many ideas are abstract and may be especially unfamiliar to communities with limited access to formal education. Indeed, there are no widely adopted models for communicating such information, nor a clear understanding of the social factors that may shape participant engagement. Here, we conducted a qualitative and quantitative, community-driven study to understand how illustrations can be useful to support concept sharing with two Indigenous groups--the Orang Asli of Peninsular Malaysia and the Turkana of Kenya. MethodsWe used a two phase approach to create and evaluate how illustrations can bolster communication about genetics concepts. First, we created images illustrating answers to frequently asked questions about genetics, iteratively updating the illustrations based on participant feedback. Second, we conducted 92 interviews to evaluate the finalized illustrations effectiveness. Finally, we analyzed the interview data using thematic analyses, multivariable modeling, and multiple correspondence analyses to identify patterns in participant understanding and feedback, including age, sex, market integration, and schooling. ResultsParticipants reported high interest in genetics research (92%) and broadly positive perceptions of the illustrations. Familiar, locally-grounded imagery was preferred and associated with greater perceived clarity, while more technical illustrations were more frequently reported as confusing. Quantitative analyses showed strong internal consistency across measures of engagement and understanding, with modest variation by degree of market-integration, schooling, and sex. DiscussionOur findings demonstrate that community-specific visualizations, co-developed through iterative feedback, can effectively support engagement with genetics research in participant communities.

scientific communication and education↗

bioRxiv2026

Divergent Biological Consequences of APOE Isoforms Across Industrialized and Non-Industrial Environments

The apolipoprotein {varepsilon}4 (APOE {varepsilon}4) isoform directly alters cholesterol and immune biology and is associated with an increased risk of neurodegenerative and cardiometabolic disease in industrialized settings; nevertheless, APOE {varepsilon}4--which is ancestral in humans--has persisted over evolutionary time. One potential explanation is that the costs and benefits of APOE {varepsilon}4 were significantly different in the environments in which humans evolved compared to those we experience today. In support, previous work has suggested that living in a high pathogen environment, engaging in high levels of physical activity, or eating a low fat diet can dampen the detrimental effects of APOE {varepsilon}4, and has revealed positive effects for fertility. However, direct tests of whether APOE isoforms are associated with different biological outcomes in non-industrial versus industrialized contexts are lacking. Working with the Turkana of Kenya and the Orang Asli of Peninsular Malaysia--two Indigenous groups in which individuals of shared ancestry span a continuum of subsistence, non-industrial to urban, industrialized lifestyles--we investigated how APOE genotypes impact cholesterol, immunological, and reproductive traits and tested for genotype x environment (GxE) interactions. First, we confirmed established genotype effects across lifestyles, showing that more APOE {varepsilon}4 alleles are associated with higher total cholesterol, higher LDL cholesterol, and lower HDL cholesterol. Second, we tested for lifestyle interactions, finding lifestyle-dependent effects of genotype on innate immune biomarkers in the Orang Asli but not Turkana. Finally, we show that more APOE {varepsilon}4 alleles are correlated with an extended reproductive lifespan, however this effect is relatively weak, is not consistent across populations, and does not correspond with a higher reproductive output. Together, our study provides evidence that industrialized environments can modify the biology of APOE {varepsilon}4; however, we find that APOE {varepsilon}4 is not universally beneficial in non-industrial contexts, highlighting the role of local environmental variation in determining its specific costs and benefits.

evolutionary biology↗

bioRxiv2025

A conserved fungal transcription factor domain drives protein-protein interactions and necrotrophic effector-mediated virulence in Parastagonospora nodorum

The fungal pathogen Parastagonospora nodorum utilises necrotrophic effectors (NEs) to cause chlorosis and necrosis on wheat. NE expression is mediated by an assortment of transcription factors (TF), the most well-characterised of which is PnPf2. Orthologues of PnPf2 regulate virulence in phytopathogenic fungi across the Ascomycete fungal lineage, yet their protein architecture remains functionally uncharacterised. These orthologues are characterised by the archetypal N-terminal Zn2Cys6 zinc-finger DNA-binding domain (DBD), a conserved yet poorly characterised middle-homology region (MHR) and a C-terminal disordered region. We investigated the role of each of the three domains through PnPf2 truncation mutants in situ. This revealed the conserved MHR of PnPf2 is required for the development of disease symptoms on wheat, but also that the C-terminal disordered region in-part modulates NE expression. Domain-interaction analysis through yeast-2-hybrid (Y2H) screening reveals PnPf2 forms a homodimer mediated by the MHR, indicating its importance mediating protein-protein interactions. Using the MHR as a bait in library-scale protein-protein interaction Y2H assays, we identified the COP9-signalosome protein PnCsn6 as a key interaction partner. PnCsn6 is essential for disease symptoms during P. nodorum infection on wheat, including NE expression. Our study presents the first domain-level functional investigation this virulence-regulating TF orthologue, the results of which underpin the essential role of the MHR in driving protein-protein interactions and effector regulation. It also reveals an essential protein-signalling pathway with which PnPf2 directly interacts and shares regulatory control of virulence.

molecular biology↗

bioRxiv2025

Fair-weather friends: Unequal partnerships between Parastagonospora nodorum and Pyrenophora tritici-repentis define disease dynamics in wheat

Parastagonospora nodorum and Pyrenophora tritici-repentis are the causal agents of septoria nodorum blotch and tan spot of wheat, respectively. Though these fungal phytopathogens have been found to frequently cohabitate the same leaf, their interaction dynamics in the manifestation of disease remain poorly understood due to limitations in species-specific detection methods. We developed a digital PCR based model targeting conserved regions of the -tubulin gene, enabling biomass quantification of both pathogens during infection. Field surveys revealed up to two in three symptomatic infections involved both pathogens, with co-infected plants showing significantly higher individual pathogen biomass than single-species infections. Host plants in the field with moderate resistance to both pathogens were found to be significantly more necrotic under co-infection, with individual pathogen biomass up to twice that observed value for single infections. However, like fair-weather friends the partnership between these two pathogens seems to be conditional.When P. tritici-repentisestablished first, secondary P. nodorumcolonisationled to a breakdown of host resistance. Conversely, when P. nodorum established on the host first, it suppressed P. tritici-repentis colonisation regardless of host resistance. To our knowledge this is the first description of asymmetric priority effects overcoming host resistance in a plant pathosystem. Resistance breeding strategies evaluating single pathogen challenges may inadvertently select for cultivars vulnerable to sequential co-infection, necessitating integrated disease complex approaches for durable resistance development.

microbiology↗

bioRxiv2023

Reconstructing oral cavity tumor evolution through brush biopsy

Oral premalignant lesions (OPLs) with genomic alterations have a heightened risk of evolving into oral squamous cell carcinoma (OSCC). Currently, genomic data are obtained through invasive tissue biopsy. Brush biopsy has been utilized for diagnosing dysplasia but its effectiveness in reflecting the complete genomic landscape of OPLs remains uncertain. This study investigates the potential of brush biopsy samples in accurately reconstructing the genomic profile of OPLs. We analyzed single nucleotide variants (SNVs), copy number aberrations (CNAs), and subclonal structures in paired tissue and brush biopsy samples from a patient with both OPL and OSCC lesions. The results showed that brush biopsy can effectively reflect about 90% of SNVs and similar CNA profiles as those found in tissue biopsies. It was specific, as normal oral epithelium didnt share these genomic alterations. Interestingly, brush biopsy revealed shared SNVs and CNAs between the distinct OPL and OSCC lesions, indicating a common ancestral origin. Subclonal reconstruction confirmed this shared ancestry, followed by divergent evolution of the lesions. These findings highlight the potential of brush biopsies in accurately representing the genomic profile of OPL and OSCC, proving useful in understanding tumor evolution.

genomics↗

bioRxiv2023

The Velvet transcription factor PnVeA regulates necrotrophic effectors and secondary metabolism in the wheat pathogen Parastagonospora nodorum

The fungus Parastagonospora nodorum causes septoria nodorum blotch on wheat. The role of the fungal Velvet-family transcription factor VeA in P. nodorum development and virulence was investigated here. Deletion of the P. nodorum VeA ortholog, PnVeA, resulted in growth abnormalities including pigmentation, abolished asexual sporulation and highly reduced virulence on wheat. Comparative RNA-Seq and RT-PCR analyses revealed that the deletion of PnVeA also decoupled the expression of major necrotrophic effector genes. In addition, the deletion of PnVeA resulted in an up-regulation of four predicted secondary metabolite (SM) gene clusters. Using liquid-chromatography mass-spectrometry, it was observed that one of the SM gene clusters led to an accumulation of the mycotoxin alternariol. PnVeA is essential for asexual sporulation, full virulence, secondary metabolism and necrotrophic effector regulation.

microbiology↗

bioRxiv2022

Chromatin-immunoprecipitation reveals the PnPf2 transcriptional network controlling effector-mediated virulence in a fungal pathogen of wheat

The regulation of virulence in plant-pathogenic fungi has emerged as a key area of importance underlying host infections. Recent work has highlighted the role of transcription factors (TFs) that mediate the expression of virulence-associated genes. A prominent example is Pf2, a member of the Zn2Cys6 family of fungal TFs, where orthologues regulate the expression of genes linked to parasitism in several plant-pathogen lineages. These include PnPf2 which controls effector-gene expression in Parastagonospora nodorum, thereby determining the outcome of effector-triggered susceptibility on its host, wheat. PnPf2 is a promising target for disease suppression but the genomic targets, or whether other are regulators involved, remain unknown. This study used chromatin immunoprecipitation (ChIP-seq) and a mutagenesis analysis to investigate these components. Two distinct binding motifs connected to positive gene-regulation were characterised and genes directly targeted by PnPf2 were identified. These included genes encoding major effectors and other components associated with the P. nodorum pathogenic lifestyle, such as carbohydrate-active enzymes and nutrient assimilators. This supports a direct involvement of PnPf2 in coordinating virulence on wheat. Other TFs were also prominent PnPf2 targets, suggesting it also operates within a transcriptional network. Several TFs were therefore functionally investigated in connection to fungal virulence. Distinct metabolic and developmental roles were evident for the newly characterised PnPro1, PnAda1, PnEbr1 and the carbon-catabolite repressor PnCreA. Overall, the results uphold PnPf2 as the central transcriptional regulator orchestrating genes that contribute to virulence on wheat and provide mechanistic insight into how this occurs. ImportanceFungal pathogens cause large crop losses worldwide and consequently much attention has focused on improving host genetic resistance to diseases. These pathogens use effectors, which require coordinated expression at specific stages of the pathogenic lifecycle, to manipulate the host plant metabolism in favour of infection. However, our understanding of the underlying regulatory network in coordination with other genes involved in fungal pathogenicity is lacking. The Pf2 TF orthologues are key players underpinning virulence and effector gene expression in several fungal phytopathogens, including P. nodorum. This study provided significant insight into the DNA-binding regulatory mechanisms of P. nodorum PnPf2, as well as further evidence that it is central to the coordination of virulence. In the context of crop protection, the Pf2 taxonomic orthologues present opportune targets in major fungal pathogens that can be perturbed to reduce the impact of effector triggered-susceptibility and improve disease resistance.

pathology↗

bioRxiv2021

Transcription factor lineages in plant-pathogenic fungi, connecting diversity with fungal virulence

Plant-pathogenic fungi span diverse taxonomic lineages. Their host-infection strategies are often specialised and require the coordinated regulation of molecular virulence factors. Transcription factors (TFs) are fundamental regulators of gene expression, controlling development and virulence in plant pathogenic fungi. Recent research has established regulatory roles for several taxonomically conserved fungal TFs, but the evolution of specific virulence regulators is not well understood. This study sought to explore the representation of TFs across a taxonomically-diverse range of fungi, with a focus on plant pathogens. A significant trend was observed among the obligate, host-associated pathogens, which possess a reduced overall TF repertoire, alluding to a lack of pressure for maintaining diversity. A novel orthology-based analysis is then presented that refined TF classifications, traditionally based on the nature of the DNA-binding domains. Using this analysis, cases of TF over/underrepresentation across fungal pathogen lineages are systematically highlighted. Specific examples are then explored and discussed that included the TF orthologues of Ste12, Pf2 and EBR1, plus phytotoxic secondary-metabolite cluster regulators, which all presented novel and distinct evolutionary insights. Ultimately, as the examples presented demonstrate, this resource can be interrogated to guide functional studies that seek to characterise virulence-specific regulators and shed light on the factors underpinning plant pathogenicity.

molecular biology↗

bioRxiv2021

Variability in an effector gene promoter of a necrotrophic fungal pathogen dictates epistasis and effector-triggered susceptibility in wheat

The fungus Parastagonospora nodorum uses proteinaceous necrotrophic effectors (NEs) to induce tissue necrosis on wheat leaves during infection, leading to the symptoms of septoria nodorum blotch (SNB). The NEs Tox1 and Tox3 induce necrosis on wheat possessing the dominant susceptibility genes Snn1 and Snn3B1/Snn3D1, respectively. We previously observed that Tox1 is epistatic to the expression of Tox3 and a quantitative trait locus (QTL) on chromosome 2A that contributes to SNB resistance/susceptibility. The expression of Tox1 is significantly higher in the Australian strain SN15 compared to the American strain SN4. Inspection of the Tox1 promoter region revealed a 401 bp promoter genetic element in SN4 positioned 267 bp upstream of the start codon that is absent in SN15, called PE401. Analysis of the world-wide P. nodorum population revealed that a high proportion of Northern Hemisphere isolates possess PE401 whereas the opposite was observed in the Southern Hemisphere. The presence of PE401 ablates the epistatic effect of Tox1 on the contribution of the SNB 2A QTL but not Tox3. PE401 was introduced into the Tox1 promoter regulatory region in SN15 to test for direct regulatory roles. Tox1 expression was markedly reduced in the presence of PE401. This suggests a repressor molecule(s) binds PE401 and inhibits Tox1 transcription. Infection assays also demonstrated that P. nodorum which lacks PE401 is more pathogenic on Snn1 wheat varieties than P. nodorum carrying PE401. An infection competition assay between P. nodorum isogenic strains with and without PE401 indicated that the higher Tox1-expressing strain rescued the reduced virulence of the lower Tox1-expressing strain on Snn1 wheat. Our study demonstrated that Tox1 exhibits both selfish and altruistic characteristics. This offers an insight into a NE arms race that is occurring within the P. nodorum population. The importance of PE401 in breeding for SNB resistance in wheat is discussed. Author summaryBreeding for durable resistance to fungal diseases in crops is a continual challenge for crop breeders. Fungal pathogens evolve ways to overcome host resistance by masking themselves through effector evolution and evasion of broad-spectrum defense responses. Association studies on mapping populations infected by isolate mixtures are often used by researchers to seek out novel sources of genetic resistance. Disease resistance quantitative trait loci (QTL) are often minor or inconsistent across environments. This is a particular problem with septoria diseases of cereals such as septoria nodorum blotch (SNB) of wheat caused by Parastagonospora nodorum. The fungus uses a suite of necrotrophic effectors (NEs) to cause SNB. We characterised a genetic element, called PE401, in the promoter of the major NE gene Tox1, which is present in some P. nodorum isolates. PE401 functions as a transcriptional repressor of Tox1 and exerts epistatic control on another major SNB resistance QTL in the host. In the context of crop protection, constant surveillance of the pathogen population for the frequency of PE401 in conjunction with NE diversity will enable agronomists to provide the best advice to growers on which wheat varieties can be tailored to provide optimal SNB resistance to regional pathogen population genotypes.

microbiology↗

bioRxiv2020

Combining genome-wide studies of breast, prostate, ovarian and endometrial cancers maps cross-cancer susceptibility loci and identifies new genetic associations

We report a meta-analysis of breast, prostate, ovarian, and endometrial cancer genome-wide association data (effective sample size: 237,483 cases/317,006 controls). This identified 465 independent lead variants (P<5x10-8) across 192 genomic regions. Four lead variants were >1Mb from previously identified risk loci for the four cancers and an additional 23 lead variant-cancer associations were novel for one of the cancers. Bayesian models supported pleiotropic effects involving at least two cancers at 222/465 lead variants in 118/192 regions. Gene-level association analysis identified 13 shared susceptibility genes (P<2.6x10-6) in 13 regions not previously implicated in any of the four cancers and not uncovered by our variant-level meta-analysis. Several lead variants had opposite effects across cancers, including a cluster of such variants in the TP53 pathway. Fifty-four lead variants were associated with blood cell traits and suggested genetic overlaps with clonal hematopoiesis. Our study highlights the remarkable pervasiveness of pleiotropy across hormone-related cancers, further illuminating their shared genetic and mechanistic origins at variant- and gene-level resolution.

genetics↗

bioRxiv2018

Identification of Novel Common Breast Cancer Risk Variants in Latinas at the 6q25 Locus

Background: Breast cancer is a partially heritable trait and over 180 common genetic variants have been associated with breast cancer in genome wide association studies (GWAS). We have previously performed breast cancer GWAS in Latinas and identified a strongly protective single nucleotide polymorphism (SNP) at 6q25 with the protective minor allele originating from Indigenous American ancestry. Here we report on additional GWAS and replication in Latinas.\n\nMethods: We performed GWAS in 2385 cases and 7342 controls who were either U.S. Latinas or Mexican women. We replicated 2412 cases and 1620 controls of U.S Latina, Mexican, and Colombian women. In addition, we replicated the top novel variants in study of African American and African women and in one study of Chinese women. In each dataset we used logistic regression models to test the association between SNPs and breast cancer risk and corrected for genetic ancestry using either principal components or genetic ancestry inferred from ancestry informative markers using a model based approach.\n\nResults: We identified 3 SNPs (p=1.9x10-8 - 2.8x10-8) at 6q25 locus not in linkage disequilibrium (LD) with variants previously reported at this locus. These SNPs were in high LD with each other, with the top SNP, rs3778609, associated with breast cancer with an odds ratio (OR) and 95% confidence interval (95% CI) of 0.75 (0.68-0.83). In a replication in women of Latin American origin, we also observed a consistent effect (OR: 0.88; 95% CI: 0.78-0.99; p=0.037). Since the minor allele was common in East Asians and African American but not European ancestry populations, we replicated in a meta-analysis of those populations and also observed a consistent effect (OR 0.94; 95% CI: 0.91 - 0.97; p=0.013).\n\nConclusion: The effect size of this variant is relatively large compared to other common variants associated with breast cancer and adds to evidence about the importance of the 6q25 locus for breast cancer susceptibility. Our finding also highlights the utility of performing additional searches for genetic variants for breast cancer in non-European populations.

genetics↗

bioRxiv2018

The Virtual Metabolic Human database: integrating human and gut microbiome metabolism with nutrition and disease

A multitude of factors contribute to complex diseases and can be measured with \"omics\" methods. Databases facilitate data interpretation for underlying mechanisms. Here, we describe the Virtual Metabolic Human (VMH, http://vmh.life) database encapsulating current knowledge of human metabolism within five interlinked resources \"Human metabolism\", \"Gut microbiome\", \"Disease\", \"Nutrition\", and \"ReconMaps\". The VMH captures 5,180 unique metabolites, 17,730 unique reactions, 3,288 human genes, 255 Mendelian diseases, 818 microbes, 632,685 microbial genes, and 8,790 food items. The VMHs unique features are i) the hosting the metabolic reconstructions of human and gut microbes amenable for metabolic modeling; ii) seven human metabolic maps for data visualization; iii) a nutrition designer; iv) a user-friendly webpage and application-programming interface to access its content; and v) user feedback option for community engagement. We demonstrate with four examples the VMHs utility. The VMH represents a novel, interdisciplinary database for data interpretation and hypothesis generation to the biomedical community.

systems biology↗