Biology subjects

Coombes, B.

Publications and source records attributed to Coombes, B..

9 recordsLinked to original sources

bioRxiv2025

Phage intervention improves colitis and response to corticosteroids by attenuating virulence of Crohn's disease-associated bacteria

Adherent-invasive Escherichia coli (AIEC) exhibit proinflammatory properties and have been implicated in the pathogenesis of Crohns disease (CD), a form of inflammatory bowel disease (IBD). Antibiotic use in CD lacks specificity and may worsen microbiome disruption, prompting interest in bacteriophages (phages) for targeted microbiome editing. Here, we identified HER259, a phage active against the clinical AIEC strain NRG857c. Using gnotobiotic models of AIEC-driven colitis, we show that HER259 attenuates AIEC virulence, including suppression of the FimH adhesin through inversion of the fimS promoter to its off orientation. Withdrawal of HER259 treatment leads to reversion of the fimS promoter and reactivated colitis in mice. HER259 phage also enhances the therapeutic effect of sub-therapeutic budesonide, independent of microbial drug metabolism. These findings support targeted phage therapy as an adjunct treatment approach in IBD, demonstrating modulation of bacterial virulence and improved response to conventional treatments which may reduce drug-related side effects. One Sentence SummaryBacteriophage HER259 improves colitis severity mediated by Crohns disease Escherichia coli NRG857c, and increases efficacy of budesonide.

microbiology↗

bioRxiv2025

Engineered spermidine-secreting Saccharomyces boulardii ameliorate colitis and colon cancer in mice

Experimental studies suggest that the probiotic yeast Saccharomyces boulardii can mitigate the symptoms of inflammatory bowel disease. However, these results are equivocal and S boulardii probiotic therapy has not gained widespread acceptance in clinical practice. To assess whether the therapeutic properties of S boulardii might be improved upon, we engineered S boulardii to overproduce and secrete spermidine, a pro-regenerative natural metabolite. We employed CRISPR gene deletion and transposon-mediated gene integration to manipulate expression of key enzymes in the polyamine synthetic and transport pathways. We tested the engineered yeast by oral gavage of mice treated with azoxymethane and dextran sulfate sodium to induce chronic colitis and colon cancer. We demonstrate that oral delivery of spermidine-secreting S boulardii in mice populates the gastrointestinal tract with viable spermidine-secreting S boulardii cells and raises free spermidine levels in the gastrointestinal tract. Strikingly, spermidine-secreting S boulardii strains were significantly more effective than wild-type S boulardii in reducing dextran sulfate sodium-induced colitis as well as colitis-associated colon cancer in mice. These results suggest that in situ spermidine secretion by engineered synthetic biotic yeast strains may be an effective and low-cost therapy to mitigate inflammatory bowel disease and colon cancer.

cancer biology↗

bioRxiv2024

De novo annotation of the wheat pangenome reveals complexity and diversity of the hexaploid wheat pan-transcriptome

Wheat is the most widely cultivated crop in the world with over 215 million hectares grown annually. However, to meet the demands of a growing global population, breeders face the challenge of increasing wheat production by approximately 60% within the next 40 years. The 10+ Wheat Genomes Project recently sequenced and assembled to chromosome level the genomes of nine wheat cultivars to develop our understanding of genetic diversity and selection within the pan-genome of wheat. Here, we provide a wheat pan-transcriptome with de novo annotation and differential expression analysis for these wheat cultivars, across multiple different tissues and whole seedlings sampled at dusk/dawn. Analysis of these de novo annotations facilitated the discovery of genes absent from the Chinese Spring reference, identified genes specific to particular cultivars and defined the core and dispensable genomes. Expression analysis across cultivars and tissues revealed conservation in expression between a large core set of homeologous genes, but also widespread changes in subgenome homeolog expression bias between cultivars. Co-expression network analysis revealed the impact of divergence of sub-genome homeolog expression and identified cultivar-specific expression profiles. In a case study utilising both the newly constructed wheat pan-genome and pan-transcriptome we demonstrate prevalent variation in the prolamin superfamily and immune-reactive proteins across the pan-cultivars.In summary, this work provides both a valuable resource for the wider wheat community and reveals diversity in gene content and expression patterns between global wheat cultivars.

genomics↗

bioRxiv2023

Introgressions lead to reference bias in wheat RNA-Seq analysis

RNA-Seq is a fundamental technique in genomics, yet reference bias, where transcripts derived from non-reference alleles are quantified less accurately, can undermine the accuracy of RNA-Seq quantification and thus the conclusions made downstream. Reference bias in RNA-Seq analysis has yet to be explored in complex polyploid genomes despite evidence that they are often a complex mosaic of wild relative introgressions, which introduce blocks of highly divergent genes. Here we use hexaploid wheat as a model complex polyploid, using both simulated and experimental data to show that RNA-Seq alignment in wheat suffers from widespread reference bias which is largely driven by divergent introgressed genes. This leads to underestimation of gene expression and incorrect assessment of homoeologue expression balance. By incorporating gene models from ten wheat genome assemblies into a pantranscriptome reference, we present a novel method to reduce reference bias, which can be readily scaled to capture more variation as new genome and transcriptome data becomes available.

genomics↗

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

Exotic alleles contribute to heat tolerance in wheat under field conditions

Global warming is one of the most significant threats to food security. With temperatures predicted to rise and extreme weather events becoming more common we must safeguard food production by developing crop varieties that are more tolerant to heat stress without compromising yield under favourable conditions. By evaluating 149 spring wheat lines in the field under yield potential and heat stressed conditions, we demonstrate how strategic integration of exotic material significantly increases yield under heat stress compared to elite lines, with no significant yield penalty under favourable conditions. Genome-wide association analysis revealed three marker trait associations, which together increase yield under heat stress by over 50% compared to lines without the advantageous alleles and was associated with approximately 2{degrees}C lower canopy temperature. We identified an Aegilops tauschii introgression underlying the most significant of these associations. By comparing overlapping recombination of this introgressed segment between lines, we identified a 1.49Mbp region of the introgression responsible for this association that increases yield under heat stress by 32.4%. The genes within this region were extracted from diverse Ae. tauschii genomes, revealing a novel Ae. tauschii MAPK gene, a SOC1 orthologue and a pair of type-B two-component response regulators. Incorporating these exotic alleles into breeding programmes could serve as a pre-emptive strategy to produce high yielding wheat cultivars that are resilient to the effects of future climate uncertainty with no yield penalty under favourable conditions.

plant biology↗

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

A novel approach to develop wheat chromosome-specific KASP markers for detecting Amblyopyrum muticum segments in doubled haploid introgression lines

Many wild relative species are being used in pre-breeding programmes to increase the genetic diversity of wheat. Genotyping tools such as single nucleotide polymorphism (SNP)-based arrays and molecular markers have been widely used to characterise wheat-wild relative introgression lines. However, due to the polyploid nature of the recipient wheat genome, it is difficult to develop SNP-based KASP markers that are codominant to track the introgressions from the wild species. Previous attempts to develop KASP markers have involved both exome- and PCR-amplicon-based sequencing of the wild species. But chromosome-specific KASPs assays have been hindered by homoeologous SNPs within the wheat genome. This study involved whole genome sequencing of the diploid wheat wild relative Amblyopyrum muticum and development of a SNP discovery pipeline that generated [~]38,000 SNPs in single-copy wheat genome sequences. New assays were designed to increase the density of Am. muticum polymorphic KASP markers. With a goal of one marker per 60 Mbp, 335 new KASP assays were validated as functional. Together with assays validated in previous studies, 498 well distributed chromosome-specific markers were used to recharacterize previously genotyped wheat-Am. muticum doubled haploid (DH) introgression lines. The chromosome specific nature of the KASP markers allowed clarification of which wheat chromosomes were involved with recombination events or substituted with Am. muticum chromosomes and the higher density of markers allowed detection of new small introgressions in these DH lines. Key MessageA novel methodology to generate chromosome-specific SNPs between wheat and its wild relative Amblyopyrum muticum and their use in the development of KASP markers to genotype wheat-Am. muticum introgression lines.

genetics↗

bioRxiv2020

Uncovering candidate genes involved in photosynthetic capacity using unexplored genetic variation in Spring Wheat

To feed an ever-increasing population we must leverage advances in genomics and phenotyping to harness the variation in wheat breeding populations for traits like photosynthetic capacity which remains unoptimized. Here we survey a diverse set of wheat germplasm containing elite, introgression and synthetic derivative lines uncovering previously uncharacterised variation. We demonstrate how strategic integration of exotic material alleviates the D genome genetic bottleneck in wheat, increasing SNP rate by 62% largely due to Ae. tauschii synthetic wheat donors. Across the panel, 67% of the Ae. tauschii donor genome is represented as introgressions in elite backgrounds. We show how observed genetic variation together with hyperspectral reflectance data can be used to identify candidate genes for traits relating to photosynthetic capacity using association analysis. This demonstrates the value of genomic methods in uncovering hidden variation in wheat and how that variation can assist breeding efforts and increase our understanding of complex traits.

plant biology↗