Biology subjects

Wood, P.

Publications and source records attributed to Wood, P..

4 recordsLinked to original sources

bioRxiv2026

Genomic signals of local adaptation in UK black alder populations (Alnus glutinosa)

Black alder (Alnus glutinosa) is a native tree species in the British Isles, which it colonised after the last glaciation from continental refugia. It is now a widespread pioneer species, thriving on wetlands and riverbanks. We present whole genome sequence data for 324 alder seedlings grown from seed collected from 44 populations across the UK. Among these we found two triploids and one sample with trisomy at chromosome five. Removing these, we found little population genetic structure apart from diverging northern populations with lower diversity. Using Latent-Factor Mixed Models (LFMM) analyses we identified 1,364 loci whose allele frequencies were significantly associated with environmental variables. Of these loci, 93% were associated with the number of snow days. In contrast, the greatest total genomic signal (variance in SNP effect sizes of 7.38 million SNP loci) was observed for mean temperature of the wettest quarter and annual number of frost days. Estimates of maladaptation using 1.49 million SNPs, predicted that northern populations are worst adapted to present and future worst-case climates. Our results suggest that similarity of source-site temperature variables should be prioritised when choosing seed sources for new planting, and northern populations could benefit from assisted gene flow from the south.

plant biology↗

bioRxiv2024

Genomic biosurveillance of the kiwifruit pathogen Pseudomonas syringae pv. actinidiae biovar 3 reveals adaptation to selective pressures in New Zealand orchards

In the late 2000s, a pandemic of Pseudomonas syringae pv. actinidiae biovar 3 (Psa3) devastated kiwifruit orchards growing susceptible yellow-fleshed cultivars. New Zealands kiwifruit industry has since recovered, following the deployment of the tolerant cultivar Zesy002. However, little is known about the extent to which the Psa population is evolving since its arrival. Over 500 Psa3 isolates from New Zealand kiwifruit orchards were sequenced between 2010 and 2022, from commercial monocultures and diverse germplasm collections. While effector loss was previously observed on Psa-resistant germplasm vines, effector loss appears to be rare in commercial orchards, where the dominant cultivars lack Psa resistance. However, a new Psa3 variant, which has lost the effector hopF1c, has arisen. The loss of hopF1c appears to have been mediated by the movement of integrative conjugative elements introducing copper resistance into this population. Following this variants identification, in planta pathogenicity and competitive fitness assays were performed to better understand the risk and likelihood of its spread. While hopF1c loss variants had similar in planta growth to wild-type Psa3, a lab-generated {Delta}hopF1c strain could outcompete wild-type on select hosts. Further surveillance was conducted in commercial orchards where these variants were originally isolated, with 6.6% of surveyed isolates identified as hopF1c loss variants. These findings suggest that the spread of these variants is currently limited, and they are unlikely to cause more severe symptoms than the current population. Ongoing genome biosurveillance of New Zealands Psa3 population is recommended to enable early detection and management of variants of interest.

genomics↗

bioRxiv2023

In the murine and bovine maternal mammary gland signal transducer and activator of transcription 3 is activated in clusters of epithelial cells around the day of birth

Signal Transducers and Activators of Transcription (STATs) regulate mammary gland development. Here we investigate the expression of pSTAT3 in the murine and bovine mammary gland around the day of birth. We identify polarisation of mammary alveoli towards either a low- or high-proportion of pSTAT3 positive alveolar epithelial cells. We present localised colocation analysis applicable to other mammary studies where identification, quantification and interrogation of significant, spatially congregated events is required. We demonstrate that pSTAT3-positive events are multifocally clustered in a non-random and statistically significant fashion. This finding represents a new facet of mammary STAT3 biology meriting further functional investigation.

cell biology↗

bioRxiv2018

One Health genomic surveillance of Escherichia coli demonstrates distinct lineages and mobile genetic elements in isolates from humans versus livestock

Livestock have been proposed as a reservoir for drug-resistant Escherichia coli that infect humans. We isolated and sequenced 431 E. coli (including 155 ESBL-producing isolates) from cross-sectional surveys of livestock farms and retail meat in the East of England. These were compared with the genomes of 1517 E. coli associated with bloodstream infection in the United Kingdom. Phylogenetic core genome comparisons demonstrated that livestock and patient isolates were genetically distinct, indicating that E. coli causing serious human infection do not directly originate from livestock. By contrast, we observed highly related isolates from the same animal species on different farms. Analysis of accessory (variable) genomes identified a virulence cassette associated previously with cystitis and neonatal meningitis that was only present in isolates from humans. Screening all 1948 isolates for accessory genes encoding antibiotic resistance revealed 41 different genes present in variable proportions of humans and livestock isolates. We identified a low prevalence of shared antimicrobial resistance genes between livestock and humans based on analysis of mobile genetic elements and long-read sequencing. We conclude that in this setting, there was limited evidence to support the suggestion that antimicrobial resistant pathogens that cause serious infection in humans originate from livestock.\n\nImportanceThe increasing prevalence of E. coli bloodstream infections is a serious public health problem. We used genomic epidemiology in a One Health study conducted in the East of England to examine putative sources of E. coli associated with serious human disease. E. coli from 1517 patients with bloodstream infection were compared with 431 isolates from livestock farms and meat. Livestock-associated and bloodstream isolates were genetically distinct populations based on core genome and accessory genome analyses. Identical antimicrobial resistance genes were found in livestock and human isolates, but there was little overlap in the mobile elements carrying these genes. In addition, a virulence cassette found in humans isolates was not identified in any livestock-associated isolate. Our findings do not support the idea that E. coli causing invasive disease or their resistance genes are commonly acquired from livestock.

genomics↗