Biology subjects

Harpum, G.

Publications and source records attributed to Harpum, G..

4 recordsLinked to original sources

bioRxiv2026

3D printing and deep learning enable holistic and dynamic analyses of tens of thousands of parasites infecting hundreds of genotypes

Host-parasite interactions are dynamic systems, where parasites usually outnumber hosts by one or more orders of magnitude. However, our understanding is often limited by the assessment of parts of the host, at arbitrary time points, and/or aggregate parasite responses. Here we combined custom-built 3D-printed hardware and deep-learning-based algorithms to enable holistic (i.e. all infecting individuals on the whole plant), spatio-temporal, and parasite-centric analyses of plant-parasitism by nematodes from timelapse videos of infection over months. In so doing, we tracked the dynamic growth and development of all individual parasites, at the organismal level, for thousands of hosts across hundreds of genotypes of Arabidopsis thaliana. Categorising traits into the static (i.e. in an acquired image at a given time point) and dynamic (i.e. phenotypic changes over time), we revealed a greater extent of host-genetic control of parasite traits, and new physiological limits of the species under these conditions. Using this capability, we identify Quantitative Trait Loci (QTL) in the host plant associated with 18 phenotypic traits in the parasite as a resource for the community. Finally, we leverage the large and diverse dataset to understand fundamental features of the parasite, independent of host genotype, revealing aspects of the life cycle which are pseudo-deterministic as well as local, deleterious interactions between co-infecting parasites. Given that plant-parasitic nematodes cause an estimated $100 billion in agricultural damages per year, these insights are contextualised in a global challenge driven by plant-parasitic nematodes.

pathology↗

bioRxiv2026

Diversity at the HYP1 locus in potato cyst nematodes does not result from developmentally-programmed somatic mutations

Most genetic diversity stems from spontaneous mutations, that is, errors in DNA repair or replication. But for dozens of organisms across the tree of life, mutations at specific loci are not spontaneous but developmentally programmed: effectively, some organisms edit their own DNA sequences. This is perhaps most common among pathogens and parasites, many of which use editing to diversify genes that produce important antigens. Plant-parasitic potato cyst nematodes are damaging agricultural pests that establish a lifelong feeding site inside the root of their host plant. We previously observed extensive diversity of rare alleles at HYP1, the most highly expressed gene that encodes a protein secreted by potato cyst nematodes during parasitism. Importantly, HYP1 alleles differ from each other by complex, in-frame rearrangements of short repeated sequence motifs within a single exon. Combining several lines of evidence, we previously hypothesized that potato cyst nematodes use developmentally-programmed mutations, or editing, to diversify HYP1 alleles in the soma. In the current work, we now test this hypothesis. We employ highly accurate long-read DNA sequencing of a simplified genetic system to identify potential rare edited alleles, we use a transgenic yeast system to describe large de novo mutations at HYP1, and we interpret our findings in light of key population genetic parameters as well as the genetic diversity surrounding HYP1 and across the genome. Significance StatementIn parasites, genetic diversity is valuable fuel for the coevolutionary arms race with their hosts. However, in parasitic nematode worms, low genetic diversity is often observed. Several other parasites and pathogens (e.g., single-celled eukaryotes) generate genetic diversity in an unusual way: they edit the DNA sequence of an important gene in their own genome, instead of waiting for rare spontaneous mutations to occur. This has never been observed in a plant parasite, but we previously described a major parasitism gene (HYP1) in plant-parasitic nematodes with such diverse DNA sequences that it looks like it could perhaps be edited. Now, we generate better data for a simplified genetic system and show that much of the observed HYP1 diversity was actually cryptic DNA sequencing errors. Although there is real genetic diversity at HYP1, it is best explained not by editing but by fundamental evolutionary forces that operate across the genome.

genetics↗

bioRxiv2026

Antagonistic action of a nuclear hormone receptor pair coordinates a switch from lytic to biotrophic effector production in a plant-parasitic nematode

Pathogens secrete overlapping and sequential waves of effectors to manipulate their host, and yet the regulators that conduct the ensemble are poorly understood. Here, we identify the Dorsal Gland Regulator DGR-1 in the beet cyst nematode Heterodera schachtii. DGR-1 controls the expression of 131 putative effectors, acting as a dual-functional switch that "switches off" early stage effectors involved in plant invasion, and "switches on" later stage effectors associated with biotrophic establishment in the host. Interestingly, DGR-1 works antagonistically with the only other known transcriptional regulator of effectors in plant-parasitic nematodes, the Subventral Gland Regulator-1 (SUGR-1), to coordinate this apparent switch from lytic to biotrophic effector production. Together, DGR-1 and SUGR-1 control the expression of nearly one half of all H. schachtii early-stage effectors, and over one fifth of effectors of any kind. The requirement to activate lytic effector functions in the cortex, and biotrophic effector functions in the vascular cylinder, suggests that this transcription factor pair must differentially respond to signals from the host. Consistent with this, we find that diffusates from the roots of A. thaliana Casparian strip mutant myb36/sgn3, which are enriched in molecules ordinarily restricted to the vascular cylinder, upregulate dgr-1, but not sugr-1, compared to Col-0. Taken together, these data indicate that H. schachtii responds to compartmentalised host-derived signals to appropriately regulate spatiotemporal effector expression during infection. Given that misregulating DGR-1 results in delayed development of parasitic nematodes in Arabidopsis and Mustard, strategies which impair effector regulation as a whole may hold promise for crop protection against these agriculturally important pathogens.

pathology↗

bioRxiv2026

Better late than never: the impact of hatching time on Heterodera schachtii parasitism

Plant-parasitic nematodes are a diverse, polyphyletic group of plant pathogens which can infect most plant tissues and all major crops. Amongst the most damaging clades are the cyst nematodes, which can remain dormant in the soil for decades as infection-competent, developmentally arrested, second-stage juveniles in eggs. Hatching is stimulated by a variety of factors. However, the impact of hatching factor responsiveness on nematode morphology, physiology, gene expression, and infection biology has not been explored. We examined the impact of hatching time on the beet cyst nematode, Heterodera schachtii. We found that late hatchers invaded host roots and established feeding sites in greater numbers than early hatchers. We demonstrate variation in baseline parasitism gene expression and in responsiveness of genes to effectostimulins, small, plant-derived molecules which upregulate parasitism genes. Three quarters of effectostimulin-induced transcriptional changes were also modulated, either positively or negatively, by hatching time. While there were no observable morphological differences between early and late hatching nematodes on the day of their emergence from the egg, the late hatchers displayed signs of faster utilisation of internal energy reserves after 7 days at 4{degrees}C, as evidenced by less body area attributed to fat, than early hatchers. Finally, we found no evidence of substantive genetic differences between early and late hatchers, they were representative of a single population, despite the observed differences in infection, gene expression, and physiology. Taken together, non-genetic differences likely drive late hatchers to more rapidly utilise their internal energy reserves, to be more responsive to host-derived signals, and to be ultimately more infective than their early hatching counterparts.

molecular biology↗