Biology subjects

Winter, M. R.

Publications and source records attributed to Winter, M. R..

4 recordsLinked to original sources

bioRxiv2024

The molecular arsenal of the key coastal bioturbator Hediste diversicolor faced with changing oceans

The importance of infaunal bioturbators for the functioning of marine ecosystems cannot be overstated. Inhabitants of estuarine and coastal habitats are expected to show resilience to fluctuations in seawater temperature and pH, which adds complexity to our understanding of the effects of global change drivers. Further, stress responses may be propagated through chemical cues within and across species, which may amplify the costs of life and alter species interactions. Research into the molecular mechanisms underlying this resilience has been limited by a lack of annotated genomes and associated molecular tools. In this study, we present the first chromosome-level, annotated draft genome of the marine ragworm Hediste diversicolor, specifically mapping genes important for chemical communication, sensing and pH homeostasis. Using these resources, we then evaluate the transcriptomic and behavioural responses of two distinct populations -- one field-sampled from Portugal (Ria Formosa) and one laboratory-acclimated and -bred from the United Kingdom (Humber) -- to changes in seawater pH, temperature, and odour cues from a low pH-stressed predator. Both populations displayed adaptive responses to future oceanic conditions, with targeted acid-base regulation in the Ria Formosa population experiment, and broader changes in metabolism and growth genes in the Humber population experiment. Chemical cues from stressed fish predators induced genes related to Schreckstoff biosynthesis in ragworms. Additionally, under future ocean conditions including increased temperature, the Humber population exhibited signs of cellular stress and damage. Our findings using the new annotated genome offer novel insights into the molecular arsenal of acid-base regulation which aids in predicting the impacts of an increasingly acidified and unstable ocean, and to transfer this knowledge to investigate these mechanisms in species with less tolerance.

genomics↗

bioRxiv2024

Who Grows There? A Course-based Undergraduate Research Experience to explore the human microbiome through 16S DNA metabarcoding

We describe a two week Course-based Undergraduate Research Experience (CURE) to introduce students to next-generation DNA sequencing, molecular biology methods and a bioinformatic workflow. The CURE is designed to take students with little to no technical and bioinformatic experience through key steps of the protocol through scaffolded laboratory and computational practicals. Our students extract and amplify human microbiome DNA using 16S ribosomal RNA specific primers, then construct a sequencing library for Oxford Nanopore based sequencing. They taxonomically assign the sequencing reads, and determine the ecological community composition using relevant software packages. Our students were able to successfully prepare sequencing libraries and analyse the data to produce relevant figures, demonstrating they met the learning objectives of the CURE. Students identified that they had developed higher level learning as defined by Blooms taxonomy, and that their confidence in practical work significantly increased as a result of doing the CURE. We share recommendations for implementation of the CURE in undergraduate curricula, and adaptations of the methods for use in schools outreach. Our CURE successfully provides training for students in genetic analysis in an enjoyable and relatively time and cost efficient manner, preparing them for future research or careers in modern molecular biology techniques.

scientific communication and education↗

bioRxiv2023

Phased chromosome-scale genome assembly of an asexual, allopolyploid root-knot nematode reveals complex subgenomic structure

We present the chromosome-scale genome of the allopolyploid root-knot nematode Meloidogyne javanica. We show that the M. javanica genome is predominantly allotetraploid, comprising two subgenomes, A and B, that most likely originated from hybridisation of two ancestral parental species. The assembly is annotated using full-length non-chimeric transcripts, comparison to reference databases, and ab initio prediction techniques, and the subgenomes are phased using ancestral k-mer spectral analysis. Subgenome B appears to show greater fission of chromosomal contigs, and while there is substantial synteny between subgenomes, we also identify regions lacking synteny that may have diverged in the ancestral genomes prior to or following hybridisation. Indels are common both between alleles within a subgenome, and between the A and B subgenomes, suggesting the M. javanica genome exists in a dynamic hypo-tetraploidy where copy number can vary along the chromosome. This annotated and phased genome assembly forms a significant resource for understanding the origins and genetics of these globally important plant pathogens. Author SummaryRoot-knot nematodes represent one of the most significant crop parasites globally. Despite their agricultural importance, only rudimentary genomic resources have been published to date, leaving a gap in the understanding of genetic mechanisms driving genome evolution and crop virulence. Here, we have used modern genomic and bioinformatic approaches to create a chromosome-scale reference genome to investigate the origins and genomic constitution of the root-knot nematode species Meloidogyne javanica. This species reproduces by ameiotic parthenogenesis and has an allopolyploid genome and is among the most damaging plant parasitic nematodes with a large and evolving plant host range. Utilising modern long-range DNA sequencing and bioinformatics approaches, we successfully phased the genome into its constituent subgenomes, a first for this agriculturally important clade. While we find the genomic landscape is mostly syntenic between subgenomes, we identified regions of minimal similarity, and highlight structural divergence between subgenomes. We demonstrate that this species was originally tetraploid, but insertions and deletions have been the major force in generating diversity, resulting in a hypo-tetraploid genome with local variations in ploidy.

genomics↗

bioRxiv2023

Testing for the fitness benefits of natural transformation during community-embedded evolution

Natural transformation is a process where bacteria actively take up DNA from the environment and recombine it into their genome or reconvert it into extra-chromosomal genetic elements. The evolutionary benefits of transformation are still under debate. One main explanation is that foreign allele and gene uptake facilitates natural selection by increasing genetic variation, analogous to meiotic sex. However, previous experimental evolution studies comparing fitness gains of evolved transforming- and isogenic non-transforming strains have yielded mixed support for the "sex hypothesis." Previous studies testing the sex hypothesis for natural transformation have largely ignored species interactions, which theory predicts provide conditions favourable to sex. To test for the adaptive benefits of bacterial transformation, the naturally transformable wildtype Acinetobacter baylyi and a transformation-deficient {Delta}comA mutant were evolved for five weeks. To provide strong and potentially fluctuating selection, A. baylyi was embedded in a community of five other bacterial species. DNA from a pool of different Acinetobacter strains was provided as a substrate for transformation. No effect of transformation ability on the fitness of evolved populations was found, with fitness increasing non-significantly in most treatments. Populations showed fitness improvement in their respective environments, with no apparent costs of adaptation to competing species. Despite the absence of fitness effects of transformation, wildtype populations evolved variable transformation frequencies that were slightly greater than their ancestor which potentially could be caused by genetic drift.

microbiology↗