Biology subjects

Oakeshott, J. G.

Publications and source records attributed to Oakeshott, J. G..

4 recordsLinked to original sources

bioRxiv2026

Rapid thermal adaptation in coral photosymbionts draws on standing variation and recombination

Bleaching tolerance in corals depends in part on the thermal tolerance of their microalgal symbionts. Laboratory evolution has increased the thermal tolerance of the symbiont Cladocopium proliferum in ~120 generations, but the genetic basis of that response was unknown. We compared single nucleotide polymorphisms in transcriptomes of three heat-evolved C. proliferum strains and one wild-type (unselected) strain from the same progenitor. We found 15,640 polymorphic loci, but no variant was both private to a strain and consistent across its replicates, which indicates that new mutations contributed little to the response in expressed sequences. Instead, allele frequencies at 350 loci differed significantly between strains, and linkage patterns indicated recombination had occurred within scaffolds both before and after the strains were separated. Selection and recombination of variation already present in the progenitor therefore underpinned the rapid thermal adaptation. Experimental evolution for reef restoration should start from genetically diverse cultures rather than single cell isolates.

evolutionary biology↗

bioRxiv2025

Structural and Evolutionary Constraints of Organophosphate Resistance in Dipteran Carboxylesterases

Enzymatic detoxification of organophosphate (OP) insecticides can confer resistance in some insects, yet the precise molecular basis of this trait, and how it has evolved, remains poorly understood. In certain dipteran species, a G[->]D mutation in the oxyanion hole of -carboxylesterases (CBEs) enhances OP hydrolysis, yet this adaptation is not widespread despite the presence of orthologous CBEs in other insect species that are also exposed to OPs. The extent, and molecular basis, of evolutionary contingency and epistasis in this catalytic OP resistance has not been explored, and how further mutations might optimize OP detoxification in the future is not clear. Here, we systematically compare OP hydrolysis and analyse structures of CBE orthologs across several dipteran species, revealing that the success of the G137D mutation is sequence context-dependent. We employed laboratory-directed evolution to enhance OP turnover over 1000-fold vs. the wild-type enzyme and tested these variants in transgenic Drosophila melanogaster, demonstrating that improved catalytic rates do not directly translate to increased resistance. By highlighting the trade-off between organophosphate affinity and turnover, this work further clarifies the complex evolutionary trajectories determining why a particular resistance mechanism may evolve in some species but not others. SignificanceThis study reveals the intricate evolutionary path to insecticide resistance in insects, highlighting why a potent resistance mutation is effective in some species but not others. We show that the mutations success is contingent on the enzymes pre-existing structural features, highlighting the strong intramolecular epistasis. Using laboratory evolution, we enhanced the enzymes detoxification activity over 1000-fold, yet discovered this did not translate to increased resistance in transgenic flies. This surprising result demonstrates that effective real-world resistance requires a delicate balance between an enzymes ability to bind an insecticide (affinity) and its speed at breaking it down (turnover), providing crucial insights into the constraints governing molecular adaptation.

biochemistry↗

bioRxiv2023

Exhaustive benchmarking of de novo assembly methods for eukaryotic genomes

The assembly of reference-quality, chromosome-resolution genomes for both model and novel eukaryotic organisms is an increasingly achievable task for single research teams. However, the overwhelming abundance of sequencing technologies, assembly algorithms, and post-assembly processing tools currently available means that there is no clear consensus on a best-practice computational protocol for eukaryotic de novo genome assembly. Here, we provide a comprehensive benchmark of 28 state-of-the-art assembly and polishing packages, in various combinations, when assembling two eukaryotic genomes using both next-generation (Illumina HiSeq) and third-generation (Oxford Nanopore and PacBio CLR) sequencing data, at both controlled and open levels of sequencing coverage. Recommendations are made for the most effective tools for each sequencing technology and the best performing combinations of methods, evaluated against common assessment metrics such as contiguity, computational performance, gene completeness, and reference reconstruction, across both organisms and across sequencing coverage depth.

bioinformatics↗

bioRxiv2023

Pyro: A Comprehensive Pipeline for Eukaryotic Genome Assembly

1The assembly of reference-quality, chromosome-level genomes for both model and novel eukaryotic organisms is an increasingly achievable task for single research teams. However, the broad variety of sequencing technologies, assembly algorithms, and post-assembly processing tools currently available means that there is no clear consensus on a best-practice computational protocol for eukaryotic de novo genome assembly. An ever-increasing field of algorithms and packages with unique parameters, setup requirements, and environments makes it difficult for groups to pick up and test new tools, despite potential benefits. Here, we present a comprehensive Snakemake-based pipeline for eukaryotic genome assembly, Pyro, to further assist future de novo assembly and benchmarking projects. Pyro combines 20 assembly and eight polishing packages, comprising 30 different assembly approaches and up to 48 different polishing approaches in combination. These are available across Illumina short-read, Nanopore and PacBio CLR long-read technologies in one container, complete with data preparation, quality metric calculation and result reporting. We demonstrate Pyro effectiveness by running Pyro on publicly available Illumina, Nanopore and PacBio CLR read sets for Arabidopsis thaliana, producing 12 candidate assembly options with minimal initial input or configuration, each with extremely high contiguity and completeness. Pyro is highly customizable to expert needs, while also providing an accessible suggested set of tools for more casual users based on simple inputs. Pyro is available as a Singularity container suitable for execution on any Unix-compatible OS, and is freely available on GitHub (https://github.com/genomeassembler/pyro). This pipeline provides a one-stop solution for a variety of de novo eukaryotic genome assembly needs, and will also assist in the assessment of new tools as a convenient benchmark-generating platform.

bioinformatics↗