Biology subjects

King, J.

Publications and source records attributed to King, J..

At least 37 records · Page 2Linked to original sources

bioRxiv2024

Chromosome-scale genome assembly of bread wheat's wild relative Triticum timopheevii

Wheat (Triticum aestivum) is one of the most important food crops with an urgent need for increase in its production to feed the growing world. Triticum timopheevii (2n = 4x = 28) is an allotetraploid wheat wild relative species containing the At and G genomes that has been exploited in many pre-breeding programmes for wheat improvement. In this study, we report the generation of a chromosome-scale reference genome assembly of T. timopheevii accession PI 94760 based on PacBio HiFi reads and chromosome conformation capture (Hi-C). The assembly comprised a total size of 9.35 Gb, featuring a contig N50 of 42.4 Mb, and 166,325 predicted gene models. DNA methylation analysis showed that the G genome had on average more methylated bases than the At genome. The G genome was also more closely related to the S genome of Aegilops speltoides than to the B genome of hexaploid or tetraploid wheat. In summary, the T. timopheevii genome assembly provides a valuable resource for genome-informed discovery of agronomically important genes for food security.

plant biology↗

bioRxiv2023

Methylmercury demethylation and volatilization by animals expressing microbial enzymes.

Methylmercury is a highly toxic pollutant that accumulates in food webs where it is inaccessible to current remediation technologies. We demonstrate that animals can be engineered to express the microbial enzymes, organomercurial lyase (MerB) and mercuric reductase (MerA), to bioremediate methylmercury. MerA and MerB from Escherichia coli were functional in invertebrate (Drosophila melanogaster) and vertebrate (Danio rerio) model systems and converted methylmercury into volatile Hg0. The engineered animals tolerated higher exposures to methylmercury and accumulated less than half as much mercury relative to their wild-type counterparts. The outcomes of this research could be applied to reduce mercury contamination in farmed and recreationally caught fish, for species conservation, and to restore value to organic wastes contaminated with mercury.

synthetic biology↗

bioRxiv2023

Phenology across scales: an intercontinental analysis of leaf-out dates in temperate deciduous tree communities

AimTo quantify the intra-community variability of leaf-out (ICVLo) among dominant trees in temperate deciduous forests, assess its links with specific and phylogenetic diversity, identify its environmental drivers, and deduce its ecological consequences with regard to radiation received and exposure to late frost. LocationEastern North America (ENA) and Europe (EUR). Time period2009-2022 Major taxa studiedTemperate deciduous forest trees. MethodsWe developed an approach to quantify ICVLo through the analysis of RGB images taken from phenological cameras. We related ICVLo to species richness, phylogenetic diversity and environmental conditions. We quantified the intra-community variability of the amount of radiation received and of exposure to late frost. ResultsLeaf-out occurred over a longer time interval in ENA than in EUR. The sensitivity of leaf-out to temperature was identical in both regions (-3.4 days per {degrees}C). The distributions of ICVLo were similar in EUR and ENA forests, despite the latter being more species-rich and phylogenetically diverse. In both regions, cooler conditions and an earlier occurrence of leaf-out resulted in higher ICVLo. ICVLo resulted in a ca. 8% difference of radiation absorption over spring among individual trees. Forest communities in ENA had shorter safety margins as regards the exposure to late frosts, and were actually more frequently exposed to late frosts. Main conclusionsWe conducted the first intercontinental analysis of the variability of leaf-out at the scale of tree communities. North American and European forests showed similar ICVLo, in spite of their differences in terms of species richness and phylogenetic diversity, highlighting the relevance of environmental controls on ICVLo. We quantified two ecological implications of ICVLo (difference in terms of radiation absorption and exposure to late frost), which should be explored in the context of ongoing climate change, which affects trees differently according to their phenological niche.

ecology↗

bioRxiv2023

Pathogen-prey-predator relations of avian raptors during epizootics of highly pathogenic avian influenza virus HPAIV H5N1 (clade 2.3.4.4b) in Germany

Transition of highly pathogenic clade 2.3.4.4b H5 avian influenza virus (HPAIV) from epizootic to enzootic status in Northern European countries was associated with severe losses and even mass mortalities among various wild bird species. Both avian and mammalian raptors hunting infected debilitated birds or scavenging on virus-contaminated avian carcasses contracted HPAIV infection. This precarious pathogen-prey-predator relation further worsened when in 2021 and 2022 outbreaks in Germany overlapped with the hatching season of avian raptor species. Retro- and prospective surveillance revealed avian raptors as important indicators of HPAIV and its genetic diversity on the one hand. On the other hand, their role as victims of HPAIV is stipulated. The first case of an HPAIV H5N1-related death of a white-tailed sea eagle (Haliaeetus albicilla; WTSE) hatch in Germany, 2021, followed by several such cases in 2022, and a low overall seropositivity rate of 5.0-7.9% among WTSE nestlings, raised fears of a serious negative impact on reproduction rates of WTSEs and other birds of prey when HPAIV becomes enzootic in an ecosystem. However, comparably stable breeding success of WTSE in the study area in 2022 and a potentially evolving natural immunity raises hope for a less severe long-term impact. Article impact statementAdapted surveillance measures were developed to assess risks for the conservation of avian raptors due to the panzootic spread of HPAIV.

microbiology↗

bioRxiv2023

Cell Surface β-Lactamase Recruitment: A Facile Selection to Identify Protein-Protein Interactions

Protein-protein interactions are central to many cellular processes, and the identification of novel protein-protein interactions is a critical step in the discovery of protein therapeutics. Simple methods to identify naturally existing or laboratory evolved protein-protein interactions are therefore valuable research tools. We have developed a facile selection that links protein-protein interaction-dependent {beta}-lactamase recruitment on the surface of E. coli with resistance to ampicillin. Bacteria displaying a protein which form a complex with a specific protein-{beta}-lactamase fusion are protected from ampicillin-dependent cell death. In contrast, bacteria that do not recruit {beta}-lactamase to the cell surface are killed by ampicillin. Given its simplicity and tunability, we anticipate this selection will be a valuable addition to the palette of methods for illuminating and interrogating protein-protein interactions.

biochemistry↗

bioRxiv2023

Fluctuations in auxin levels depend upon synchronicity of cell divisions in a one-dimensional model of auxin transport

Auxin is a well-studied plant hormone, the spatial distribution of which remains incompletely understood. Here, we investigate the effects of cell growth and divisions on the dynamics of auxin patterning, using a combination of mathematical modelling and experimental observations. In contrast to most prior work, models are not designed or tuned with the aim to produce a specific auxin pattern. Instead, we use well-established techniques from dynamical systems theory to uncover and classify ranges of auxin patterns as exhaustively as possible, as parameters are varied. Previous work using these techniques has shown how a multitude of stable auxin patterns may coexist, each attainable from a specific ensemble of initial conditions. When a key parameter spans a range of values, these steady patterns form a geometric curve with successive folds, often nicknamed a snaking diagram. As we introduce growth and cell divisions into a one-dimensional model of auxin distribution, we observe new behaviour which can be conveniently explained in terms of this diagram. Cell growth changes the shape of the snaking diagram, corresponding to deformations of auxin patterns. As divisions occur this can lead to abrupt creation or annihilation of auxin peaks. We term this phenomenon snake-jumping. Under rhythmic cell divisions, we show how this can lead to stable oscillations of auxin. However, we also show that this requires a high level of synchronisation between cell divisions. Using 18 hour time-lapse imaging of the auxin reporter DII:Venus in roots of Arabidopsis thaliana, we show auxin fluctuates greatly, both in terms of amplitude and periodicity, consistent with the snake-jumping events observed with non-synchronised cell divisions. Periodic signals downstream the auxin signalling pathway have previously been recorded in plant roots. The present work shows that auxin alone is unlikely to play the role of a pacemaker in this context. Author summaryAuxin is a crucial plant hormone, the function of which underpins almost every known plant development process. The complexity of its transport and signalling mechanisms, alongside the inability to image directly, make mathematical modelling an integral part of research on auxin. One particularly intriguing phenomenon is the experimental observation of oscillations downstream of auxin pathway, which serve as initiator for lateral organ formation. Existing literature, with the aid of modelling, has presented both auxin transport and signalling as potential drivers for these oscillations. In this study, we demonstrate how growth and cell divisions may trigger fluctuations of auxin with significant amplitude, which may lead to regular oscillations in situations where cell divisions are highly synchronised. More physiological conditions including variations in the timing of cell divisions lead to much less temporal regularity in auxin variations. Time-lapse microscope images confirm this lack of regularity of auxin fluctuations in the root apical meristem. Together our findings indicate that auxin changes are unlikely to be strictly periodic in tissues that do not undergo synchronous cell divisions and that other factors may have a robust ability to convert irregular auxin inputs into the periodic outputs underpinning root development.

plant biology↗

bioRxiv2023

Modeling and Simulation of Neocortical Micro- and Mesocircuitry. Part II: Physiology and Experimentation

Cortical dynamics underlie many cognitive processes and emerge from complex multi-scale interactions, which are challenging to study in vivo. Large-scale, biophysically detailed models offer a tool which can complement laboratory approaches. We present a model comprising eight somatosensory cortex subregions, 4.2 million morphological and electrically-detailed neurons, and 13.2 billion local and mid-range synapses. In silico tools enabled reproduction and extension of complex laboratory experiments under a single parameterization, providing strong validation. The model reproduced millisecond-precise stimulus-responses, stimulus-encoding under targeted optogenetic activation, and selective propagation of stimulus-evoked activity to downstream areas. The models direct correspondence with biology generated predictions about how multiscale organization shapes activity; for example, how cortical activity is shaped by high-dimensional connectivity motifs in local and mid-range connectivity, and spatial targeting rules by inhibitory subpopulations. The latter was facilitated using a rewired connectome which included specific targeting rules observed for different inhibitory neuron types in electron microscopy. The model also predicted the role of inhibitory interneuron types and different layers in stimulus encoding. Simulation tools and a large subvolume of the model are made available to enable further community-driven improvement, validation and investigation.

neuroscience↗

bioRxiv2023

Conserved Chamber-Specific Polyploidy Maintains Heart Function in Drosophila

Developmentally programmed polyploidy (whole-genome-duplication) of cardiomyocytes is common across evolution. Functions of such polyploidy are essentially unknown. Here, we reveal roles for precise polyploidy levels in cardiac tissue. We highlight a conserved asymmetry in polyploidy level between cardiac chambers in Drosophila larvae and humans. In Drosophila, differential Insulin Receptor (InR) sensitivity leads the heart chamber to reach a higher ploidy/cell size relative to the aorta chamber. Cardiac ploidy-reduced animals exhibit reduced heart chamber size, stroke volume, cardiac output, and acceleration of circulating hemocytes. These Drosophila phenotypes mimic systemic human heart failure. Using human donor hearts, we reveal asymmetry in nuclear volume (ploidy) and insulin signaling between the left ventricle and atrium. Our results identify productive and likely conserved roles for polyploidy in cardiac chambers and suggest precise ploidy levels sculpt many developing tissues. These findings of productive cardiomyocyte polyploidy impact efforts to block developmental polyploidy to improve heart injury recovery.

developmental biology↗

bioRxiv2023

NEK1-Mediated Phosphorylation of YAP1 is key to Prostate Cancer Progression

Understanding how Androgen-dependent PCa cells progress to independence and modify accordingly their transcriptional repertoire is the key to preventing mCRPC progression. We recently identified a novel axis of the Hippo pathway characterized by the sequential kinase cascade induced by androgen deprivation: AR->TLK1B>NEK1>pYAP1-Y407 leading to CRPC adaptation. Phosphorylation of YAP-Y407 increases upon ADT or induction of DNA damage, correlated with the known increase in NEK1 expression/activity, and this is suppressed in the Y407F mutant. Dominant expression of YAP1-Y407F in Hek293 cells reprograms the YAP1-mediated transcriptome to reduced TEAD- and P73-regulated gene expression and mediates sensitivity to MMC. NEK1 haploinsufficient TRAMP mice display reduced YAP1 expression and if castrated fail to progress to overt prostate carcinomas, even while displaying reduced E-CAD expression in hyperplastic ductules. YAP1 overexpression, but not the Y407F mutant, transforms LNCaP cells to androgen independent growth and a mesenchymal morphology. Immunohistochemical examination of Prostate Cancer biopsies revealed that pYAP1-Y407 nuclear signal is low in samples of low-grade cancer but elevated in high GS specimens. We also found that J54, pharmacological inhibitor of the TLK1>NEK1>YAP1 nexus, leading to degradation of YAP1 can suppress the transcriptional reprogramming of LNCaP cells to Androgen-Independent growth and EMT progression even when YAP1-WT is overexpressed.

cancer biology↗

bioRxiv2022

Genetic Substrates of Brain Vulnerability and Resilience in APOE2 Mice Transitioning from Midlife to Old Age

Understanding the interplay between genotype, age, and sex has potential to reveal factors that determine the switch between successful and pathological aging. APOE allelic variation modulate brain vulnerability and cognitive resilience during aging and Alzheimer disease (AD). The APOE4 allele confers the most risk and has been extensively studied with respect to the control APOE3 allele. The APOE2 allele has been less studied, and the mechanisms by which it confers cognitive resilience and neuroprotection remain largely unknown. Using mouse models with targeted replacement of the murine APOE gene with the human major APOE2 alleles we sought to identify changes during a critical period of middle to old age transition, in a mouse model of resilience to AD. Age but not female sex was important in modulating learning and memory estimates based on Morris water maze metrics. A small but significant 3% global brain atrophy due to aging was reflected by regional atrophy in the cingulate cortex 24, fornix and hippocampal commissure (>9%). Females had larger regional volumes relative to males for the bed nucleus of stria terminalis, subbrachial nucleus, postsubiculum (~10%), and claustrum (>5%), while males had larger volumes for the orbitofrontal cortex, frontal association cortex, and the longitudinal fasciculus of pons (>9%). Age promoted atrophy in both white (anterior commissure, corpus callosum, etc.), and gray matter, in particular the olfactory cortex, frontal association area 3, thalamus, hippocampus and cerebellum. A negative age by sex interaction was noted for the olfactory areas, piriform cortex, amygdala, ventral hippocampus, entorhinal cortex, and cerebellum, suggesting faster decline in females. Fractional anisotropy indicated an advantage for younger females for the cingulate cortex, insula, dorsal thalamus, ventral hippocampus, amygdala, visual and entorhinal cortex, and cerebellum, but there was faster decline with age. Interestingly white matter tracts were largely spared in females during aging. We used vertex screening to find associations between connectome and traits such as age and sex, and sparse multiple canonical correlation analysis to integrate our analyses over connectomes, traits, and RNA-seq. Brain subgraphs favored in males included the secondary motor cortex and superior cerebellar peduncle, while those for females included hippocampus and primary somatosensory cortex. Age related connectivity loss affected the hippocampus and primary somatosensory cortex. We validated these subgraphs using neural networks, showing increased accuracy for sex prediction from 81.9% when using the whole connectome as a predictor, to 94.28% when using the subgraphs estimated through vertex screening. Transcriptomic analyses revealed the largest fold change (FC) for age related genes was for Cpt1c (log2FC = 7.1), involved in transport of long-chain fatty acids into mitochondria and neuronal oxidative metabolism. Arg1, a critical regulator of innate and adaptive immune responses (log2FC = 4.9) also showed age specific changes. Amongst the sex related genes, the largest FC were observed for Maoa (log2FC = 4.9) involved in the degradation of the neurotransmitters serotonin, epinephrine, norepinephrine, and dopamine, and implicated in response to stress. Four genes were common for age and sex related vulnerability: Myo1e (log2FC = -1.5), Creld2 (log2FC = 1.4), Ptprt (log2FC = 2.9), and Pex1 (log2FC = 3.6). We tested whether blood gene expression help track phenotype changes with age and sex. Genes with the highest weight after connectome filtering included Ankzfp1 with a role in maintaining mitochondrial integrity under stress, as well as Pex1, Cep250, Nat14, Arg1, and Rangrf. Connectome filtered genes pointed to pathways relate to stress response, transport, and metabolic processes. Our modeling approaches using sparse canonical correlation analysis help relate quantitative traits to vulnerable brain networks, and blood markers for biological processes. Our study shows the APOE2 impact on neurocognition, brain networks, and biological pathways during a critical middle to old age transition in an animal model of resilience. Identifying changes in vulnerable brain and gene networks and markers of resilience may help reveal targets for therapies that support successful aging.

neuroscience↗

bioRxiv2022

Amino acid availability acts as a metabolic rheostat to determine the magnitude of ILC2 responses

Group 2 innate lymphoid cells (ILC2) are functionally poised, tissue-resident lymphocytes that respond rapidly to damage and infection at mucosal barrier sites. ILC2 reside within complex microenvironments where they are subject to cues from the diet, commensal microbiota and invading pathogens - most notably helminths. Emerging evidence suggests ILC2 are acutely sensitive not only to canonical activating signals, but also perturbations in nutrient and metabolite availability. In the context of helminth infection, we identify amino acid availability as a nutritional cue in regulating ILC2 responses. ILC2 were found to be uniquely pre-primed to import amino acids via the large neutral amino acid transporters Slc7a5 and Slc7a8. Cell-intrinsic deletion of these transporters impaired ILC2 expansion, but not cytokine production, in part via tuning of mTOR activation. These findings implicate the import of amino acids as a metabolic requisite for optimal ILC2 responses, and further highlight nutritional cues as critical regulators of innate immune responses within mucosal barrier tissues.

immunology↗

bioRxiv2022

Cold-passaged isolates and bat-swine influenza A chimeric viruses as modified live-attenuated vaccines against influenza A viruses in pigs

Swine influenza A virus (swIAV) infections in pig populations cause considerable morbidity and economic losses. Frequent reverse zoonotic incursions of human IAV boost reassortment opportunities with authentic porcine and avian-like IAV in swine herds potentially enhancing zoonotic and even pre-pandemic potential. Vaccination using adjuvanted inactivated full virus vaccines is frequently used in attempting control of swIAV infections. Accelerated antigenic drift of swIAV in large swine holdings and interference of maternal antibodies with vaccine in piglets can compromise these efforts. Potentially more efficacious modified live-attenuated vaccines (MLVs) bear the risk of reversion of MLV to virulence. Here we evaluated new MLV candidates based on cold-passaged swIAV or on reassortment-incompetent bat-IAV-swIAV chimeric viruses. Serial cold-passaging of various swIAV subtypes did not yield unambiguously temperature-sensitive mutants although safety studies in mice and pigs suggested some degree of attenuation. Chimeric bat-swIAV expressing the hemagglutinin and neuraminidase of an avian-like H1N1, in contrast, proved to be safe in mice and pigs, and a single nasal inoculation induced protective immunity against homologous challenge in pigs. Reassortant-incompetent chimeric bat-swIAV vaccines could aid in reducing the amount of swIAV circulating in pig populations, thereby increasing animal welfare, limiting economic losses and lowering the risk of zoonotic swIAV transmission.

microbiology↗

bioRxiv2022

Identification of Fusarium Head Blight resistance in Triticum timopheevii accessions and characterisation of wheat-T. timopheevii introgression lines for enhanced resistance.

A diverse panel of wheat wild relative species was screened for resistance to Fusarium head blight (FHB) by spray inoculation. The great majority of species and accessions were susceptible or highly susceptible to FHB. Accessions of Triticum timopheevii (P95-99.1-1), Agropyron desertorum (9439957) and Elymus vaillantianus (531552) were highly resistant to FHB while additional accessions of T. timopheevii were found to be susceptible to FHB. A combination of spray and point inoculation assessments over two consecutive seasons indicated that the resistance in accession P95-99.1-1 was due to enhanced resistance to initial infection of the fungus (type 1 resistance), and not to reduction in spread (type 2 resistance). A panel of wheat-T. timopheevii (accession P95-99.1-1) introgression lines was screened for FHB resistance over two consecutive seasons using spray inoculation. Most introgression lines were similar in susceptibility to FHB as the wheat recipient (Paragon) but substitution of the terminal portion of chromosome 3BS of wheat with a similar-sized portion of 3G of T. timopheevii significantly enhanced FHB resistance in the wheat background.

plant biology↗

bioRxiv2022

Introgression of the Triticum timopheevii genome into wheat detected by chromosome-specific KASP markers

Triticum timopheevii (2n=28, AtAtGG) is a tetraploid wild relative species with great potential to increase the genetic diversity of hexaploid wheat Triticum aestivum (2n=42, AABBDD) for various important agronomic traits. A breeding scheme that propagated advanced backcrossed populations of wheat-T. timopheevii introgression lines through further backcrossing and self-fertilisation resulted in the generation of 99 introgression lines (ILs) that carried 309 homozygous segments from the At and G subgenomes of T. timopheevii. These introgressions contained 89 and 74 unique segments from the At and G subgenomes, respectively. These overlapping segments covered 98.9% of the T. timopheevii genome that has now been introgressed into bread wheat cv. Paragon including the entirety of all T. timopheevii chromosomes via varying sized segments except for chromosomes 3At, 4G and 6G. Homozygous ILs contained between one and eight of these introgressions with an average of three per introgression line. These homozygous introgressions were detected through the development of a set of 480 chromosome-specific Kompetitive allele specific PCR (KASP) markers that are well-distributed across the wheat genome. Of these, 149 were developed in this study based on single nucleotide polymorphisms (SNPs) discovered through whole genome sequencing of T. timopheevii. A majority of these KASP markers were also found to be T. timopheevii subgenome specific with 182 detecting At subgenome and 275 detecting G subgenome segments. These markers showed that 98% of the At segments had recombined with the A genome of wheat and 74% of the G genome segments had recombined with the B genome of wheat with the rest recombining with the D genome of wheat. These results were validated through multi-colour in situ hybridisation analysis. Together these homozygous wheat-T. timopheevii ILs and chromosome-specific KASP markers provide an invaluable resource to wheat breeders for trait discovery to combat biotic and abiotic stress factors affecting wheat production due to climate change.

plant biology↗

bioRxiv2022

A SARS-CoV-2 Spike Ferritin Nanoparticle Vaccine is Protective and Promotes a Strong Immunological Response in the Cynomolgus Macaque Coronavirus Disease 2019 (COVID-19) Model

The COVID-19 pandemic has had a staggering impact on social, economic, and public health systems worldwide. Vaccine development and mobilization against SARS-CoV-2 (the etiologic agent of COVID-19) has been rapid. However, novel strategies are still necessary to slow the pandemic, and this includes new approaches to vaccine development and/or delivery, which improve vaccination compliance and demonstrate efficacy against emerging variants. Here we report on the immunogenicity and efficacy of a SARS-CoV-2 vaccine comprised of stabilized, pre-fusion Spike protein trimers displayed on a ferritin nanoparticle (SpFN) adjuvanted with either conventional aluminum hydroxide or the Army Liposomal Formulation QS-21 (ALFQ) in a cynomolgus macaque COVID-19 model. Vaccination resulted in robust cell-mediated and humoral responses and a significant reduction of lung lesions following SARS-CoV-2 infection. The strength of the immune response suggests that dose sparing through reduced or single dosing in primates may be possible with this vaccine. Overall, the data support further evaluation of SpFN as a SARS-CoV-2 protein-based vaccine candidate with attention to fractional dosing and schedule optimization.

microbiology↗

bioRxiv2022

The faecal microbiome of the wild European badger Meles meles; a comparison against other wild omnivorous mammals from across the globe

Here we investigate the faecal microbiome of wild European badgers Meles meles using samples collected at post-mortem as part of the All Wales Badger Found Dead study based on sequencing the V3-V4 region of the 16S rRNA gene. This is the first published characterisation of the badger microbiome. We initially undertook a sex-matched age comparison between the adult and cub microbiomes. Analysis used the QIIME 2 pipeline utilising DADA2 and the Silva database for taxonomy assignment. Fusobacteria appeared to be more abundant in the microbiomes of the cubs than the adults although no significant difference was seen in alpha or beta diversity between the adult and cub badger microbiomes. Comparisons were also made against other wild, omnivorous, mammals faecal microbiomes using publicly available data. Significant differences were seen in both alpha and beta diversity between the microbiomes from different species. As a wildlife species of interest to the disease bovine tuberculosis, knowledge of the faecal microbiome could assist in identification of infected badgers. Our work here suggests that if comparisons were made between the faeces of bTB infected and non-infected badgers, its possible age may not have a significant impact on the microbiome.

microbiology↗

bioRxiv2021

Whole genome sequencing uncovers the structural and transcriptomic landscape of hexaploid wheat/Am. muticum introgression lines

Wheat is a globally vital crop, but its limited genetic variation creates a challenge for breeders aiming to maintain or accelerate agricultural improvements over time. Introducing novel genes and alleles from wheats wild relatives into the wheat breeding pool via introgression lines is an important component of overcoming this low variation but is constrained by poor genomic resolution and limited understanding of the genomic impact of introgression breeding programmes. By sequencing 17 hexaploid wheat/Ambylopyrum muticum introgression lines and the parent lines, we have precisely pinpointed the borders of introgressed segments, most of which occur within genes. We report a genome assembly and annotation of Am. muticum that has facilitated the identification of Am. muticum resistance genes commonly introgressed in lines resistant to stripe rust. Our analysis has identified an abundance of structural disruption and homoeologous pairing across the introgression lines, likely caused by the suppressed Ph1 locus. mRNAseq analysis of six of these introgression lines revealed that novel introgressed genes are rarely expressed and those that directly replace a wheat orthologue have a tendency towards downregulation, with no discernible compensation in the expression of homoeologous copies. This study explores the genomic impact of introgression breeding and provides a schematic that can be followed to characterise introgression lines and identify segments and candidate genes underlying the phenotype. This will facilitate more effective utilisation of introgression pre-breeding material in wheat breeding programmes.

genomics↗

bioRxiv2021

Disentangling the role of poultry farms and wild birds in the spread of highly pathogenic avian influenza virus H5N8 in Europe

Recent outbreaks of highly pathogenic avian influenza H5N8 virus in Europe have caused severe damage to animal health, wildlife conservation and livestock economic sustainability. While epidemiological and phylogenetic studies have generated important clues about the virus spread in Europe, they remained opaque to the specific role of poultry farms and wild birds. Using a phylodynamic framework, we inferred the H5N8 virus transmission dynamics among poultry farms and wild birds in four severely affected countries and investigated drivers of spread between farms across borders during the 2016-17 epidemic. Based on existing genetic data, we showed that the virus was likely introduced into poultry farms during the autumn, in line with the timing of arrival of migratory wild birds. Then, transmission was mainly driven by farm-to-farm transmission in Germany, Hungary and Poland, suggesting that better understanding of how infected farms are connected in those countries would greatly help control efforts. In contrast, the epidemic was dominated by wild bird-to-farm transmission in Czech Republic, meaning that more sustainable prevention strategies should be developed to reduce virus exposure from wild birds. We inferred effective reproduction number Re estimates among poultry farms and wild birds. We expect those estimates being useful to parameterize predictive models of virus spread aiming at optimising control strategies. None of the investigated predictors related to live poultry trade, poultry census and geographic proximity were identified as supportive predictors of the viral spread between farms across borders, suggesting that other drivers should be considered in future studies. Significance statementIn winter 2016-17, Europe was severely hit by an unprecedented epidemic of highly pathogenic avian influenza (HPAI) H5N8 virus, causing significant impact on animal health, wildlife conservation and livestock economic sustainability. By applying phylodynamic tools to H5N8 sequence data collected from poultry farms and wild birds during the epidemic, we quantified how effectively the first infections were detected, how fast the virus spread, how many infections were missed and how many transmission events occurred at the wildlife-domestic interface. Also, we investigated predictors of the virus spread between farms across borders. These results are crucial to better understand the virus transmission dynamics, with the view to inform policy decision-making and reduce the impact of future epidemics of HPAI viruses.

ecology↗