A single-cell transcriptomics atlas for the parasitic nematodeHeligmosomoides bakeri: Extrapolating model organism information to non-model systems

Abstract

AbstractSingle-cell atlases aim to collect the gene expression information for every cell type in an organism but can be challenging to perform in non-model organisms. To try to circumvent the problem of having no verified cell type markers in the parasitic nematodeHeligmosomoides bakerito use for an atlas, we attempted to use orthologs of verified markers from the closely related model organismCaenorhabditis elegans. This resulted in a useful comparison between the two worms for each of the cell types recovered in preliminaryH. bakerisingle-cell RNA-sequencing. ForH. bakerimales and females, robustly recovered cell types include the gametes, embryos, and male intestine, while hypodermis, neurons, muscles, and pharyngeal cells were under-represented cell types. The two worms appear to have a similar hypodermis, cuticle, eggshell, and spermatogenesis process. On the other hand, putative cell identities and cell cycle scores suggest the intestine and muscle cells inH. bakerimay still be cycling and dividing, unlike inC. elegans. Additionally, embryogenesis and early development appear to be quite different between the two worms, with only eight out of 94 confirmed paternal contributions to the embryo inC. elegans(with an ortholog) predicted to also be paternal contributions inH. bakeri. Overall, this new dataset allowed me to move beyond the presence or absence of orthologs to include their tissue specificity and expression level similarities and differences when comparing these two worms to better identify biological processes and traits in a parasitic nematode that are modelled well byC. elegans.